James Ford

All Publications

• Multiomic analysis of familial adenomatous polyposis reveals molecular pathways associated with early tumorigenesis. Nature cancer Esplin, E. D., Hanson, C., Wu, S., Horning, A. M., Barapour, N., Nevins, S. A., Jiang, L., Contrepois, K., Lee, H., Guha, T. K., Hu, Z., Laquindanum, R., Mills, M. A., Chaib, H., Chiu, R., Jian, R., Chan, J., Ellenberger, M., Becker, W. R., Bahmani, B., Khan, A., Michael, B., Weimer, A. K., Esplin, D. G., Shen, J., Lancaster, S., Monte, E., Karathanos, T. V., Ladabaum, U., Longacre, T. A., Kundaje, A., Curtis, C., Greenleaf, W. J., Ford, J. M., Snyder, M. P. 2024

  Abstract

  Familial adenomatous polyposis (FAP) is a genetic disease causing hundreds of premalignant polyps in affected persons and is an ideal model to study transitions of early precancer states to colorectal cancer (CRC). We performed deep multiomic profiling of 93 samples, including normal mucosa, benign polyps and dysplastic polyps, from six persons with FAP. Transcriptomic, proteomic, metabolomic and lipidomic analyses revealed a dynamic choreography of thousands of molecular and cellular events that occur during precancerous transitions toward cancer formation. These involve processes such as cell proliferation, immune response, metabolic alterations (including amino acids and lipids), hormones and extracellular matrix proteins. Interestingly, activation of the arachidonic acid pathway was found to occur early in hyperplasia; this pathway is targeted by aspirin and other nonsteroidal anti-inflammatory drugs, a preventative treatment under investigation in persons with FAP. Overall, our results reveal key genomic, cellular and molecular events during the earliest steps in CRC formation and potential mechanisms of pharmaceutical prophylaxis.

  View details for DOI 10.1038/s43018-024-00831-z

  View details for PubMedID 39478120

  View details for PubMedCentralID 2706149

• Global loss of promoter-enhancer connectivity and rebalancing of gene expression during early colorectal cancer carcinogenesis. Nature cancer Zhu, Y., Lee, H., White, S., Weimer, A. K., Monte, E., Horning, A., Nevins, S. A., Esplin, E. D., Paul, K., Krieger, G., Shipony, Z., Chiu, R., Laquindanum, R., Karathanos, T. V., Chua, M. W., Mills, M., Ladabaum, U., Longacre, T., Shen, J., Jaimovich, A., Lipson, D., Kundaje, A., Greenleaf, W. J., Curtis, C., Ford, J. M., Snyder, M. P. 2024

  Abstract

  Although three-dimensional (3D) genome architecture is crucial for gene regulation, its role in disease remains elusive. We traced the evolution and malignant transformation of colorectal cancer (CRC) by generating high-resolution chromatin conformation maps of 33 colon samples spanning different stages of early neoplastic growth in persons with familial adenomatous polyposis (FAP). Our analysis revealed a substantial progressive loss of genome-wide cis-regulatory connectivity at early malignancy stages, correlating with nonlinear gene regulation effects. Genes with high promoter-enhancer (P-E) connectivity in unaffected mucosa were not linked to elevated baseline expression but tended to be upregulated in advanced stages. Inhibiting highly connected promoters preferentially represses gene expression in CRC cells compared to normal colonic epithelial cells. Our results suggest a two-phase model whereby neoplastic transformation reduces P-E connectivity from a redundant state to a rate-limiting one for transcriptional levels, highlighting the intricate interplay between 3D genome architecture and gene regulation during early CRC progression.

  View details for DOI 10.1038/s43018-024-00823-z

  View details for PubMedID 39478119

  View details for PubMedCentralID 7541718

• Germline CDH1 Variants and Lifetime Cancer Risk. JAMA Ryan, C. E., Fasaye, G. A., Gallanis, A. F., Gamble, L. A., McClelland, P. H., Duemler, A., Samaranayake, S. G., Blakely, A. M., Drogan, C. M., Kingham, K., Patel, D., Rodgers-Fouche, L., Siegel, A., Kupfer, S. S., Ford, J. M., Chung, D. C., Dowty, J. G., Sampson, J., Davis, J. L. 2024

  Abstract

  Approximately 1% to 3% of gastric cancers and 5% of lobular breast cancers are hereditary. Loss of function CDH1 gene variants are the most common gene variants associated with hereditary diffuse gastric cancer and lobular breast cancer. Previously, the lifetime risk of gastric cancer was estimated to be approximately 25% to 83% and for breast cancer it was estimated to be approximately 39% to 55% in individuals with loss of function CDH1 gene variants.To describe gastric and breast cancer risk estimates for individuals with CDH1 variants.Multicenter, retrospective cohort and modeling study of 213 families from North America with a CDH1 pathogenic or likely pathogenic (P/LP) variant in 1 or more family members conducted between January 2021 and August 2022.Hazard ratios (HRs), defined as risk in variant carriers relative to noncarriers, were estimated for each cancer type and used to calculate cumulative risks and risks per decade of life up to age 80 years.A total of 7323 individuals from 213 families were studied, including 883 with a CDH1 P/LP variant (median proband age, 53 years [IQR, 42-62]; 4% Asian; 4% Hispanic; 85% non-Hispanic White; 50% female). In individuals with a CDH1 P/LP variant, the prevalence of gastric cancer was 13.9% (123/883) and the prevalence of breast cancer among female carriers was 26.3% (144/547). The estimated HR for advanced gastric cancer was 33.5 (95% CI, 9.8-112) at age 30 years and 3.5 (95% CI, 0.4-30.3) at age 70 years. The lifetime cumulative risk of advanced gastric cancer in male and female carriers was 10.3% (95% CI, 6%-23.6%) and 6.5% (95% CI, 3.8%-15.1%), respectively. Gastric cancer risk estimates based on family history indicated that a carrier with 3 affected first-degree relatives had a penetrance of approximately 38% (95% CI, 25%-64%). The HR for breast cancer among female carriers was 5.7 (95% CI, 2.5-13.2) at age 30 years and 3.9 (95% CI, 1.1-13.7) at age 70 years. The lifetime cumulative risk of breast cancer among female carriers was 36.8% (95% CI, 25.7%-62.9%).Among families from North America with germline CDH1 P/LP variants, the cumulative risk of gastric cancer was 7% to 10%, which was lower than previously described, and the cumulative risk of breast cancer among female carriers was 37%, which was similar to prior estimates. These findings inform current management of individuals with germline CDH1 variants.

  View details for DOI 10.1001/jama.2024.10852

  View details for PubMedID 38873722

• Identifying homologous recombination deficiency in breast cancer: genomic instability score distributions differ among breast cancer subtypes. Breast cancer research and treatment Lenz, L., Neff, C., Solimeno, C., Cogan, E. S., Abramson, V. G., Boughey, J. C., Falkson, C., Goetz, M. P., Ford, J. M., Gradishar, W. J., Jankowitz, R. C., Kaklamani, V. G., Marcom, P. K., Richardson, A. L., Storniolo, A. M., Tung, N. M., Vinayak, S., Hodgson, D. R., Lai, Z., Dearden, S., Hennessy, B. T., Mayer, E. L., Mills, G. B., Slavin, T. P., Gutin, A., Connolly, R. M., Telli, M. L., Stearns, V., Lanchbury, J. S., Timms, K. M. 2023

  Abstract

  A 3-biomarker homologous recombination deficiency (HRD) score is a key component of a currently FDA-approved companion diagnostic assay to identify HRD in patients with ovarian cancer using a threshold score of ≥ 42, though recent studies have explored the utility of a lower threshold (GIS ≥ 33). The present study evaluated whether the ovarian cancer thresholds may also be appropriate for major breast cancer subtypes by comparing the genomic instability score (GIS) distributions of BRCA1/2-deficient estrogen receptor-positive breast cancer (ER + BC) and triple-negative breast cancer (TNBC) to the GIS distribution of BRCA1/2-deficient ovarian cancer.Ovarian cancer and breast cancer (ER + BC and TNBC) tumors from ten study cohorts were sequenced to identify pathogenic BRCA1/2 mutations, and GIS was calculated using a previously described algorithm. Pathologic complete response (pCR) to platinum therapy was evaluated in a subset of TNBC samples. For TNBC, a threshold was set and threshold validity was assessed relative to clinical outcomes.A total of 560 ovarian cancer, 805 ER + BC, and 443 TNBC tumors were included. Compared to ovarian cancer, the GIS distribution of BRCA1/2-deficient samples was shifted lower for ER + BC (p = 0.015), but not TNBC (p = 0.35). In the subset of TNBC samples, univariable logistic regression models revealed that GIS status using thresholds of ≥ 42 and ≥ 33 were significant predictors of response to platinum therapy.This study demonstrated that the GIS thresholds used for ovarian cancer may also be appropriate for TNBC, but not ER + BC. GIS thresholds in TNBC were validated using clinical response data to platinum therapy.

  View details for DOI 10.1007/s10549-023-07046-3

  View details for PubMedID 37589839

• The New NCI Precision Medicine Trials. Clinical cancer research : an official journal of the American Association for Cancer Research Harris, L. N., Blanke, C. D., Erba, H. P., Ford, J. M., Gray, R. J., LeBlanc, M. L., Hu-Lieskovan, S., Litzow, M. R., Luger, S. M., Meric-Bernstam, F., O'Dwyer, P. J., Othus, M. K., Politi, K., Shepherd, L. E., Allegra, C. J., Chen, H. X., Ivy, S. P., Korde, L. A., Little, R. F., McShane, L. M., Moscow, J. A., Patton, D. R., Thurin, M., Yee, L. M., Doroshow, J. H. 2023

  Abstract

  Basket, umbrella, and platform trial designs (master protocols) have emerged over the last decade to study precision medicine approaches in oncology. First generation trials like NCI-MATCH have proven the principle that studying targeted therapies on a large scale is feasible both from the laboratory and clinical perspectives. However, single agent targeted therapies have shown limited ability to control metastatic disease, despite careful matching of drug to target. As such, newer approaches employing combinations of targeted therapy, or targeted therapy with standard therapies, need to be considered. The NCI has recently embarked on three 2nd generation precision medicine trials to address this need: ComboMATCH, iMATCH, and myeloMATCH. The design of these trials and necessary infrastructure are discussed in the following perspective.

  View details for DOI 10.1158/1078-0432.CCR-23-0917

  View details for PubMedID 37531248

• Clinical implications of conflicting variant interpretations in the cancer genetics clinic. Genetics in medicine : official journal of the American College of Medical Genetics Zukin, E., Culver, J. O., Liu, Y., Yang, Y., Ricker, C. N., Hodan, R., Sturgeon, D., Kingham, K., Chun, N. M., Rowe-Teeter, C., Singh, K., Zell, J. A., Ladabaum, U., McDonnell, K. J., Ford, J. M., Parmigiani, G., Braun, D., Kurian, A. W., Gruber, S. B., Idos, G. E. 2023: 100837

  Abstract

  To describe the clinical impact of commercial laboratories issuing conflicting classifications of genetic variants.Results from 2,000 patients undergoing a multi-gene hereditary cancer panel by a single laboratory were analyzed. Clinically significant discrepancies between the lab provided test reports and other major commercial laboratories were identified, including differences between pathogenic/likely pathogenic (P/LP) and variant of uncertain significance (VUS) classifications, via review of ClinVar archives. For patients carrying a VUS, clinical documentation was assessed for evidence of provider awareness of the conflict.50/975 (5.1%) patients with non-negative results carried a variant with a clinically significant conflict, 19 with a P/LP variant reported in APC or MUTYH, and 31 with a VUS reported in CDKN2A, CHEK2, MLH1, MSH2, MUTYH, RAD51C, or TP53. Only 10/28 (36%) patients with a VUS with a clinically significant conflict had a documented discussion by a provider about the conflict. Discrepant counseling strategies were utilized for different patients with the same variant. Among patients with a CDKN2A variant or a monoallelic MUTYH variant, providers were significantly more likely to make recommendations based on the laboratory-reported classification.Our findings highlight the frequency of variant interpretation discrepancies and importance of clinician awareness. Guidance is needed on managing patients with discrepant variants to support accurate risk assessment.

  View details for DOI 10.1016/j.gim.2023.100837

  View details for PubMedID 37057674

• Antitumour activity of neratinib in patients with HER2-mutant advanced biliary tract cancers. Nature communications Harding, J. J., Piha-Paul, S. A., Shah, R. H., Murphy, J. J., Cleary, J. M., Shapiro, G. I., Quinn, D. I., Brana, I., Moreno, V., Borad, M., Loi, S., Spanggaard, I., Park, H., Ford, J. M., Arnedos, M., Stemmer, S. M., de la Fouchardiere, C., Fountzilas, C., Zhang, J., DiPrimeo, D., Savin, C., Duygu Selcuklu, S., Berger, M. F., Eli, L. D., Meric-Bernstam, F., Jhaveri, K., Solit, D. B., Abou-Alfa, G. K. 2023; 14 (1): 630

  Abstract

  HER2 mutations are infrequent genomic events in biliary tract cancers (BTCs). Neratinib, an irreversible, pan-HER, oral tyrosine kinase inhibitor, interferes with constitutive receptor kinase activation and has activity in HER2-mutant tumours. SUMMIT is an open-label, single-arm, multi-cohort, phase 2, 'basket' trial of neratinib in patients with solid tumours harbouring oncogenic HER2 somatic mutations (ClinicalTrials.gov: NCT01953926). The primary objective of the BTC cohort, which is now complete, is first objective response rate (ORR) to neratinib 240mg orally daily. Secondary objectives include confirmed ORR, clinical benefit rate, progression-free survival, duration of response, overall survival, safety and tolerability. Genomic analyses were exploratory. Among 25 treatment-refractory patients (11 cholangiocarcinoma, 10 gallbladder, 4 ampullary cancers), the ORR is 16% (95% CI 4.5-36.1%). The most common HER2 mutations are S310F (n=11; 48%) and V777L (n=4; 17%). Outcomes appear worse for ampullary tumours or those with co-occurring oncogenic TP53 and CDKN2A alterations. Loss of amplified HER2 S310F and acquisition of multiple previously undetected oncogenic co-mutations are identified at progression in one responder. Diarrhoea is the most common adverse event, with any-grade diarrhoea in 14 patients (56%). Although neratinib demonstrates antitumour activity in patients with refractory BTC harbouring HER2 mutations, the primary endpoint was not met and combinations may be explored.

  View details for DOI 10.1038/s41467-023-36399-y

  View details for PubMedID 36746967

• Therapeutic Implications of Oncogenic Missense HER2 (ERBB2) Mutations in Gastric Adenocarcinoma. JCO precision oncology King, D. A., Weiel, J. J., Reyes, R., Mills, M., Itchon, A., Fisher, G. A., Ford, J. M., Suarez, C. J. 2023; 7: e2200093

  View details for DOI 10.1200/PO.22.00093

  View details for PubMedID 36787506

• National Cancer Institute Combination Therapy Platform Trial with Molecular Analysis for Therapy Choice (ComboMATCH). Clinical cancer research : an official journal of the American Association for Cancer Research Meric-Bernstam, F., Ford, J. M., O'Dwyer, P. J., Shapiro, G. I., McShane, L. M., Freidlin, B., O'Cearbhaill, R. E., George, S., Glade Bender, J., Lyman, G. H., Tricoli, J. V., Patton, D., Hamilton, S. R., Gray, R. J., Hawkins, D. S., Ramineni, B., Flaherty, K. T., Grivas, P., Yap, T. A., Berlin, J., Doroshow, J. H., Harris, L. N., Moscow, J. A. 2023

  Abstract

  Over the past decade, multiple trials, including the precision medicine trial NCI-MATCH (National Cancer Institute-Molecular Analysis for Therapy Choice, EAY131, NCT02465060) have sought to determine if treating cancer based on specific genomic alterations is effective, irrespective of the cancer histology. Although many therapies are now approved for the treatment of cancers harboring specific genomic alterations, most patients do not respond to therapies targeting a single alteration. Further, when antitumor responses do occur, they are often not durable due to the development of drug resistance. Therefore, there is a great need to identify rational combination therapies that may be more effective. To address this need, the National Cancer Institute (NCI) and National Clinical Trials Network have developed NCI-ComboMATCH, the successor to NCI-MATCH. Like the original trial, NCI-ComboMATCH is a signal-seeking study. The goal of ComboMATCH is to overcome drug resistance to single-agent therapy and/or utilize novel synergies to increase efficacy by developing genomically-directed combination therapies, supported by strong preclinical in vivo evidence. While NCI-MATCH was mainly comprised of multiple single-arm studies, NCI-ComboMATCH tests combination therapy, evaluating both combination of targeted agents as well as combinations of targeted therapy with chemotherapy. While NCI-MATCH was histology agnostic with selected tumor exclusions, ComboMATCH has histology-specific and histology-agnostic arms. While NCI-MATCH consisted of single arm studies, ComboMATCH utilizes single-arm as well as randomized designs. NCI-MATCH had a separate, parallel Pediatric MATCH trial, whereas ComboMATCH will include children within the same trial. We present rationale, scientific principles, study design and logistics supporting the ComboMATCH study.

  View details for DOI 10.1158/1078-0432.CCR-22-3334

  View details for PubMedID 36662819

• A phase II study of talazoparib monotherapy in patients with wild-type BRCA1 and BRCA2 with a mutation in other homologous recombination genes. Nature cancer Gruber, J. J., Afghahi, A., Timms, K., DeWees, A., Gross, W., Aushev, V. N., Wu, H., Balcioglu, M., Sethi, H., Scott, D., Foran, J., McMillan, A., Ford, J. M., Telli, M. L. 2022

  Abstract

  Talazoparib, a PARP inhibitor, is active in germline BRCA1 and BRCA2 (gBRCA1/2)-mutant advanced breast cancer, but its activity beyond gBRCA1/2 is poorly understood. We conducted Talazoparib Beyond BRCA ( NCT02401347 ), an open-label phase II trial, to evaluate talazoparib in patients with pretreated advanced HER2-negative breast cancer (n=13) or other solid tumors (n=7) with mutations in homologous recombination (HR) pathway genes other than BRCA1 and BRCA2. In patients with breast cancer, four patients had a Response Evaluation Criteria in Solid Tumors (RECIST) partial response (overall response rate,31%), and three additional patients had stable disease of ≥6 months (clinical benefit rate, 54%). All patients with germline mutations in PALB2 (gPALB2; encoding partner and localizer of BRCA2) had treatment-associated tumor regression. Tumor or plasma circulating tumor DNA (ctDNA) HR deficiency (HRD) scores were correlated with treatment outcomes and were increased in all gPALB2 tumors. In addition, a gPALB2-associated mutational signature was associated with tumor response. Thus, talazoparib has been demonstrated to have efficacy in patients with advanced breast cancer who have gPALB2 mutations, showing activity in the context of HR pathway gene mutations beyond gBRCA1/2.

  View details for DOI 10.1038/s43018-022-00439-1

  View details for PubMedID 36253484

• Overall survival in the OlympiA phase III trial of adjuvant olaparib in patients with germline pathogenic variants in BRCA1/2 and high-risk, early breast cancer. Annals of oncology : official journal of the European Society for Medical Oncology Geyer, C. E., Garber, J. E., Gelber, R. D., Yothers, G., Taboada, M., Ross, L., Rastogi, P., Cui, K., Arahmani, A., Aktan, G., Armstrong, A. C., Arnedos, M., Balmaña, J., Bergh, J., Bliss, J., Delaloge, S., Domchek, S. M., Eisen, A., Elsafy, F., Fein, L. E., Fielding, A., Ford, J. M., Friedman, S., Gelmon, K. A., Gianni, L., Gnant, M., Hollingsworth, S. J., Im, S. A., Jager, A., Jóhannsson, Ó. Þ., Lakhani, S. R., Janni, W., Linderholm, B., Liu, T. W., Loman, N., Korde, L., Loibl, S., Lucas, P. C., Marmé, F., Martinez de Dueñas, E., McConnell, R., Phillips, K. A., Piccart, M., Rossi, G., Schmutzler, R., Senkus, E., Shao, Z., Sharma, P., Singer, C. F., Španić, T., Stickeler, E., Toi, M., Traina, T. A., Viale, G., Zoppoli, G., Park, Y. H., Yerushalmi, R., Yang, H., Pang, D., Jung, K. H., Mailliez, A., Fan, Z., Tennevet, I., Zhang, J., Nagy, T., Sonke, G. S., Sun, Q., Parton, M., Colleoni, M. A., Schmidt, M., Brufsky, A. M., Razaq, W., Kaufman, B., Cameron, D., Campbell, C., Tutt, A. N. 2022

  Abstract

  The randomized, double-blind OlympiA trial compared 1 year of the oral poly(adenosine diphosphate-ribose) polymerase inhibitor, olaparib, to matching placebo as adjuvant therapy for patients with pathogenic or likely pathogenic variants in germline BRCA1 or BRCA2 (gBRCA1/2pv) and high-risk, human epidermal growth factor receptor 2-negative, early breast cancer (EBC). The first pre-specified interim analysis (IA) previously demonstrated statistically significant improvement in invasive disease-free survival (IDFS) and distant disease-free survival (DDFS). The olaparib group had fewer deaths than the placebo group, but the difference did not reach statistical significance for overall survival (OS). We now report the pre-specified second IA of OS with updates of IDFS, DDFS, and safety.One thousand eight hundred and thirty-six patients were randomly assigned to olaparib or placebo following (neo)adjuvant chemotherapy, surgery, and radiation therapy if indicated. Endocrine therapy was given concurrently with study medication for hormone receptor-positive cancers. Statistical significance for OS at this IA required P < 0.015.With a median follow-up of 3.5 years, the second IA of OS demonstrated significant improvement in the olaparib group relative to the placebo group [hazard ratio 0.68; 98.5% confidence interval (CI) 0.47-0.97; P = 0.009]. Four-year OS was 89.8% in the olaparib group and 86.4% in the placebo group (Δ 3.4%, 95% CI -0.1% to 6.8%). Four-year IDFS for the olaparib group versus placebo group was 82.7% versus 75.4% (Δ 7.3%, 95% CI 3.0% to 11.5%) and 4-year DDFS was 86.5% versus 79.1% (Δ 7.4%, 95% CI 3.6% to 11.3%), respectively. Subset analyses for OS, IDFS, and DDFS demonstrated benefit across major subgroups. No new safety signals were identified including no new cases of acute myeloid leukemia or myelodysplastic syndrome.With 3.5 years of median follow-up, OlympiA demonstrates statistically significant improvement in OS with adjuvant olaparib compared with placebo for gBRCA1/2pv-associated EBC and maintained improvements in the previously reported, statistically significant endpoints of IDFS and DDFS with no new safety signals.

  View details for DOI 10.1016/j.annonc.2022.09.159

  View details for PubMedID 36228963

• Circulating tumor DNA monitoring for early recurrence detection in epithelial ovarian cancer. Gynecologic oncology Hou, J. Y., Chapman, J. S., Kalashnikova, E., Pierson, W., Smith-McCune, K., Pineda, G., Vattakalam, R. M., Ross, A., Mills, M., Suarez, C. J., Davis, T., Edwards, R., Boisen, M., Sawyer, S., Wu, H., Dashner, S., Aushev, V. N., George, G. V., Malhotra, M., Zimmermann, B., Sethi, H., ElNaggar, A. C., Aleshin, A., Ford, J. M. 2022

  Abstract

  OBJECTIVE: Epithelial ovarian cancer (EOC) is the most lethal gynecologic malignancy. We examined the utility of circulating tumor DNA (ctDNA) as a prognostic biomarker for EOC by assessing its relationship with patient outcome and CA-125, pre-surgically and during post-treatment surveillance.METHODS: Plasma samples were collected from patients with stage I-IV EOC. Cohort A included patients with pre-surgical samples (N = 44, median follow-up: 2.7 years), cohort B and C included: patients with serially collected post-surgically (N = 12) and, during surveillance (N = 13), respectively (median follow-up: 2 years). Plasma samples were analyzed using a tumor-informed, personalized multiplex-PCR NGS assay; ctDNA status and CA-125 levels were correlated with clinical features and outcomes.RESULTS: Genomic profiling was performed on the entire cohort and was consistent with that seen in TCGA. In cohort A, ctDNA-positivity was observed in 73% (32/44) of presurgical samples and was higher in high nuclear grade disease. In cohort B and C, ctDNA was only detected in patients who relapsed (100% sensitivity and specificity) and preceded radiological findings by an average of 10 months. The presence of ctDNA at a single timepoint after completion of surgery +/- adjuvant chemotherapy and serially during surveillance was a strong predictor of relapse (HR:17.6, p = 0.001 and p < 0.0001, respectively), while CA-125 positivity was not (p = 0.113 and p = 0.056).CONCLUSIONS: The presence of ctDNA post-surgically is highly prognostic of reduced recurrence-free survival. CtDNA outperformed CA-125 in identifying patients at highest risk of recurrence. These results suggest that monitoring ctDNA could be beneficial in clinical decision-making for EOC patients.

  View details for DOI 10.1016/j.ygyno.2022.09.004

  View details for PubMedID 36117009

• Somatic tumor mutations in moderate risk cancer genes: Targets for germline confirmatory testing. Cancer genetics Llorin, H., Graf, M., Chun, N., Ford, J. 2022; 268-269: 22-27

  Abstract

  BACKGROUND: Recent changes in oncology practice guidelines indicate that mutations in cancer susceptibility genes identified on tumor genomic profiling (TGP) should prompt confirmatory germline testing. Our study aimed to determine the proportion of patients with TGP-identified mutations in moderate risk breast and ovarian cancer genes who previously would not have been considered for germline testing.METHODS: From January 2013 to September 2020, 7468 adult Stanford Health Care patients underwent TGP on solid tumor samples and 166 had TGP-identified mutations in moderate risk breast and ovarian cancer susceptibility genes (ATM, BRIP1, CHEK2, PALB2, RAD51C and RAD51D). Retrospective chart reviews were performed on 160 patients. Cases were analyzed to determine eligibility for germline testing using established NCCN criteria, and somatic and germline results were compared where both were available.RESULTS: Nearly half (45.3% [73/160]) of patients would not have been eligible for germline testing if not for a TGP-identified mutation in a moderate risk breast or ovarian cancer gene. Of the 64 cases that underwent germline testing, about half (51.5% [33/64]) had results that confirmed germline origin of the TGP finding. High rates of germline confirmation were found in PALB2 (100% [5/5]), ATM (40% [14/35]), CHEK2 (61.5% [8/13]), and BRIP1 (57.1% [4/7]).CONCLUSION: Our study shows that the presence of TGP-identified mutations in moderate risk breast and ovarian cancer genes increases eligibility for germline testing beyond those that would be eligible based largely on personal and family history criteria alone. Additionally, results of germline testing in these newly eligible cases supports that this expanded eligibility captures individuals with hereditary cancer syndromes that would not have otherwise been identified.

  View details for DOI 10.1016/j.cancergen.2022.09.001

  View details for PubMedID 36116289

• Enhancing Repair of Oxidative DNA Damage with Small-Molecule Activators of MTH1. ACS chemical biology Lee, Y., Onishi, Y., McPherson, L., Kietrys, A. M., Hebenbrock, M., Jun, Y. W., Das, I., Adimoolam, S., Ji, D., Mohsen, M. G., Ford, J. M., Kool, E. T. 2022

  Abstract

  Impaired DNA repair activity has been shown to greatly increase rates of cancer clinically. It has been hypothesized that upregulating repair activity in susceptible individuals may be a useful strategy for inhibiting tumorigenesis. Here, we report that selected tyrosine kinase (TK) inhibitors including nilotinib, employed clinically in the treatment of chronic myeloid leukemia, are activators of the repair enzyme Human MutT Homolog 1 (MTH1). MTH1 cleanses the oxidatively damaged cellular nucleotide pool by hydrolyzing the oxidized nucleotide 8-oxo-2'-deoxyguanosine (8-oxo-dG)TP, which is a highly mutagenic lesion when incorporated into DNA. Structural optimization of analogues of TK inhibitors resulted in compounds such as SU0448, which induces 1000 ± 100% activation of MTH1 at 10 muM and 410 ± 60% at 5 muM. The compounds are found to increase the activity of the endogenous enzyme, and at least one (SU0448) decreases levels of 8-oxo-dG in cellular DNA. The results suggest the possibility of using MTH1 activators to decrease the frequency of mutagenic nucleotides entering DNA, which may be a promising strategy to suppress tumorigenesis in individuals with elevated cancer risks.

  View details for DOI 10.1021/acschembio.2c00038

  View details for PubMedID 35830623

• The Gastric Cancer Registry: A Genomic Translational Resource for Multidisciplinary Research in Gastric Cancer. Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology Almeda, A. F., Grimes, S. M., Lee, H., Greer, S., Shin, G., McNamara, M., Hooker, A. C., Arce, M. M., Kubit, M., Schauer, M. C., Van Hummelen, P., Ma, C., Mills, M. A., Huang, R. J., Hwang, J. H., Amieva, M. R., Han, S. S., Ford, J. M., Ji, H. P. 2022

  Abstract

  Gastric cancer (GC) is a leading cause of cancer morbidity and mortality. Developing information systems which integrate clinical and genomic data may accelerate discoveries to improve cancer prevention, detection, and treatment. To support translational research in GC, we developed the GC Registry (GCR), a North American repository of clinical and cancer genomics data.Participants self-enrolled online. Entry criteria into the GCR included the following: (1) diagnosis of GC, (2) history of GC in a first- or second-degree relative, or (3) known germline mutation in the gene CDH1. Participants provided demographic and clinical information through a detailed survey. Some participants provided specimens of saliva and tumor samples. Tumor samples underwent exome sequencing, whole genome sequencing and transcriptome sequencing.From 2011-2021, 567 individuals registered and returned the clinical questionnaire. For this cohort 65% had a personal history of GC, 36% reported a family history of GC and 14% had a germline CDH1 mutation. 89 GC patients provided tumor samples. For the initial study, 41 tumors were sequenced using next generation sequencing. The data was analyzed for cancer mutations, copy number variations, gene expression, microbiome, neoantigens, immune infiltrates, and other features. We developed a searchable, web-based interface (the GCR Genome Explorer) to enable researchers access to these datasets.The GCR is a unique, North American GC registry which integrates clinical and genomic annotation.Available for researchers through an open access, web-based explorer, the GCR Genome Explorer will accelerate collaborative GC research across the United States and world.

  View details for DOI 10.1158/1055-9965.EPI-22-0308

  View details for PubMedID 35771165

• Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer. Nature genetics Becker, W. R., Nevins, S. A., Chen, D. C., Chiu, R., Horning, A. M., Guha, T. K., Laquindanum, R., Mills, M., Chaib, H., Ladabaum, U., Longacre, T., Shen, J., Esplin, E. D., Kundaje, A., Ford, J. M., Curtis, C., Snyder, M. P., Greenleaf, W. J. 2022

  Abstract

  To chart cell composition and cell state changes that occur during the transformation of healthy colon to precancerous adenomas to colorectal cancer (CRC), we generated single-cell chromatin accessibility profiles and single-cell transcriptomes from 1,000 to 10,000 cells per sample for 48 polyps, 27 normal tissues and 6 CRCs collected from patients with or without germline APC mutations. A large fraction of polyp and CRC cells exhibit a stem-like phenotype, and we define a continuum of epigenetic and transcriptional changes occurring in these stem-like cells as they progress from homeostasis to CRC. Advanced polyps contain increasing numbers of stem-like cells, regulatory T cells and a subtype of pre-cancer-associated fibroblasts. In the cancerous state, we observe T cell exhaustion, RUNX1-regulated cancer-associated fibroblasts and increasing accessibility associated with HNF4A motifs in epithelia. DNA methylation changes in sporadic CRC are strongly anti-correlated with accessibility changes along this continuum, further identifying regulatory markers for molecular staging of polyps.

  View details for DOI 10.1038/s41588-022-01088-x

  View details for PubMedID 35726067

• Personalised Risk Prediction in Hereditary Breast and Ovarian Cancer: A Protocol for a Multi-Centre Randomised Controlled Trial. Cancers Archer, S., Fennell, N., Colvin, E., Laquindanum, R., Mills, M., Dennis, R., Stutzin Donoso, F., Gold, R., Fan, A., Downes, K., Ford, J., Antoniou, A. C., Kurian, A. W., Evans, D. G., Tischkowitz, M. 2022; 14 (11)

  Abstract

  Women who test positive for an inherited pathogenic/likely pathogenic gene variant in BRCA1, BRCA2, PALB2, CHEK2 and ATM are at an increased risk of developing certain types of cancer-specifically breast (all) and epithelial ovarian cancer (only BRCA1, BRCA2, PALB2). Women receive broad cancer risk figures that are not personalised (e.g., 44-63% lifetime risk of breast cancer for those with PALB2). Broad, non-personalised risk estimates may be problematic for women when they are considering how to manage their risk. Multifactorial-risk-prediction tools have the potential to deliver personalised risk estimates. These may be useful in the patient's decision-making process and impact uptake of risk-management options. This randomised control trial (registration number to follow), based in genetic centres in the UK and US, will randomise participants on a 1:1 basis to either receive conventional cancer risk estimates, as per routine clinical practice, or to receive a personalised risk estimate. This personalised risk estimate will be calculated using the CanRisk risk prediction tool, which combines the patient's genetic result, family history and polygenic risk score (PRS), along with hormonal and lifestyle factors. Women's decision-making around risk management will be monitored using questionnaires, completed at baseline (pre-appointment) and follow-up (one, three and twelve months after receiving their risk assessment). The primary outcome for this study is the type and timing of risk management options (surveillance, chemoprevention, surgery) taken up over the course of the study (i.e., 12 months). The type of risk-management options planned to be taken up in the future (i.e., beyond the end of the study) and the potential impact of personalised risk estimates on women's psychosocial health will be collected as secondary-outcome measures. This study will also assess the acceptability, feasibility and cost-effectiveness of using personalised risk estimates in clinical care.

  View details for DOI 10.3390/cancers14112716

  View details for PubMedID 35681696

• A Novel Framework for the Next Generation of Precision Oncology Targets. JAMA oncology Chen, C. T., Ford, J. M. 2022

  View details for DOI 10.1001/jamaoncol.2022.0760

  View details for PubMedID 35587343

• Somatic tumor testing implications for Lynch syndrome germline genetic testing. Cancer genetics Barrus, K., Purington, N., Chun, N., Ladabaum, U., Ford, J. M. 2022; 264-265: 16-22

  Abstract

  Clinicians involved in cancer treatment often utilize somatic tumor sequencing to help tailor chemotherapy and immunotherapy. However, somatic tumor sequencing can also identify patients at risk for germline pathogenic variants causing cancer predisposition syndromes like Lynch syndrome. The extent to which clinicians realize this implication of tumor sequencing is currently unclear. We performed a retrospective chart review of Stanford Health Care patients who had somatic variant(s) in the Lynch syndrome genes or microsatellite instability identified on tumor sequencing to determine the proportion of patients who were referred to genetics. Among 6,556 patients who had tumor testing, 90 (1.37%) had findings compatible with Lynch syndrome. Of the 62 patients who had not already seen genetics, 47/62 (75.8%) were not referred to genetics for germline testing. Additionally, 26/47 (55.3%) of these individuals had a tumor type within the Lynch syndrome spectrum. Of the 10 patients who did elect germline testing after tumor sequencing, 3/10 were positive for Lynch syndrome. Our study highlights the need for specific guidelines to inform clinician referral practices on germline follow-up of somatic tumor testing and demonstrates the importance of continued research on the relationship between somatic tumor variants and germline variants to inform such guidelines.

  View details for DOI 10.1016/j.cancergen.2022.02.010

  View details for PubMedID 35286930

• Hereditary diffuse gastric cancer: updated clinical practice guidelines LANCET ONCOLOGY Blair, V. R., McLeod, M., Carneiro, F., Coit, D. G., D'Addario, J. L., Dieren, J., Harris, K. L., Hoogerbrugge, N., Oliveira, C., van der Post, R. S., Arnold, J., Benusiglio, P. R., Bisseling, T. M., Boussioutas, A., Cats, A., Charlton, A., Schreiber, K., Davis, J. L., di Pietro, M., Fitzgerald, R. C., Ford, J. M., Gamet, K., Gullo, I., Hardwick, R. H., Huntsman, D. G., Kaurah, P., Kupfer, S. S., Latchford, A., Mansfield, P. F., Nakajima, T., Parry, S., Rossaak, J., Sugimura, H., Svrcek, M., Tischkowitz, M., Ushijima, T., Yamada, H., Yang, H., Claydon, A., Figueiredo, J., Paringatai, K., Seruca, R., Bougen-Zhukov, N., Brew, T., Busija, S., Carneiro, P., DeGregorio, L., Fisher, H., Gardner, E., Godwin, T. D., Holm, K. N., Humar, B., Lintott, C. J., Monroe, E. C., Muller, M. D., Norero, E., Nouri, Y., Paredes, J., Sanches, J. M., Schulpen, E., Ribeiro, A. S., Sporle, A., Whitworth, J., Zhang, L., Reeve, A. E., Guilford, P. 2020; 21 (8): E386–E397

  View details for Web of Science ID 000555457500006

• The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution. Cell Rozenblatt-Rosen, O., Regev, A., Oberdoerffer, P., Nawy, T., Hupalowska, A., Rood, J. E., Ashenberg, O., Cerami, E., Coffey, R. J., Demir, E., Ding, L., Esplin, E. D., Ford, J. M., Goecks, J., Ghosh, S., Gray, J. W., Guinney, J., Hanlon, S. E., Hughes, S. K., Hwang, E. S., Iacobuzio-Donahue, C. A., Jane-Valbuena, J., Johnson, B. E., Lau, K. S., Lively, T., Mazzilli, S. A., Pe'er, D., Santagata, S., Shalek, A. K., Schapiro, D., Snyder, M. P., Sorger, P. K., Spira, A. E., Srivastava, S., Tan, K., West, R. B., Williams, E. H., Human Tumor Atlas Network, Aberle, D., Achilefu, S. I., Ademuyiwa, F. O., Adey, A. C., Aft, R. L., Agarwal, R., Aguilar, R. A., Alikarami, F., Allaj, V., Amos, C., Anders, R. A., Angelo, M. R., Anton, K., Ashenberg, O., Aster, J. C., Babur, O., Bahmani, A., Balsubramani, A., Barrett, D., Beane, J., Bender, D. E., Bernt, K., Berry, L., Betts, C. B., Bletz, J., Blise, K., Boire, A., Boland, G., Borowsky, A., Bosse, K., Bott, M., Boyden, E., Brooks, J., Bueno, R., Burlingame, E. A., Cai, Q., Campbell, J., Caravan, W., Cerami, E., Chaib, H., Chan, J. M., Chang, Y. H., Chatterjee, D., Chaudhary, O., Chen, A. A., Chen, B., Chen, C., Chen, C., Chen, F., Chen, Y., Chheda, M. G., Chin, K., Chiu, R., Chu, S., Chuaqui, R., Chun, J., Cisneros, L., Coffey, R. J., Colditz, G. A., Cole, K., Collins, N., Contrepois, K., Coussens, L. M., Creason, A. L., Crichton, D., Curtis, C., Davidsen, T., Davies, S. R., de Bruijn, I., Dellostritto, L., De Marzo, A., Demir, E., DeNardo, D. G., Diep, D., Ding, L., Diskin, S., Doan, X., Drewes, J., Dubinett, S., Dyer, M., Egger, J., Eng, J., Engelhardt, B., Erwin, G., Esplin, E. D., Esserman, L., Felmeister, A., Feiler, H. S., Fields, R. C., Fisher, S., Flaherty, K., Flournoy, J., Ford, J. M., Fortunato, A., Frangieh, A., Frye, J. L., Fulton, R. S., Galipeau, D., Gan, S., Gao, J., Gao, L., Gao, P., Gao, V. R., Geiger, T., George, A., Getz, G., Ghosh, S., Giannakis, M., Gibbs, D. L., Gillanders, W. E., Goecks, J., Goedegebuure, S. P., Gould, A., Gowers, K., Gray, J. W., Greenleaf, W., Gresham, J., Guerriero, J. L., Guha, T. K., Guimaraes, A. R., Guinney, J., Gutman, D., Hacohen, N., Hanlon, S., Hansen, C. R., Harismendy, O., Harris, K. A., Hata, A., Hayashi, A., Heiser, C., Helvie, K., Herndon, J. M., Hirst, G., Hodi, F., Hollmann, T., Horning, A., Hsieh, J. J., Hughes, S., Huh, W. J., Hunger, S., Hwang, S. E., Iacobuzio-Donahue, C. A., Ijaz, H., Izar, B., Jacobson, C. A., Janes, S., Jane-Valbuena, J., Jayasinghe, R. G., Jiang, L., Johnson, B. E., Johnson, B., Ju, T., Kadara, H., Kaestner, K., Kagan, J., Kalinke, L., Keith, R., Khan, A., Kibbe, W., Kim, A. H., Kim, E., Kim, J., Kolodzie, A., Kopytra, M., Kotler, E., Krueger, R., Krysan, K., Kundaje, A., Ladabaum, U., Lake, B. B., Lam, H., Laquindanum, R., Lau, K. S., Laughney, A. M., Lee, H., Lenburg, M., Leonard, C., Leshchiner, I., Levy, R., Li, J., Lian, C. G., Lim, K., Lin, J., Lin, Y., Liu, Q., Liu, R., Lively, T., Longabaugh, W. J., Longacre, T., Ma, C. X., Macedonia, M. C., Madison, T., Maher, C. A., Maitra, A., Makinen, N., Makowski, D., Maley, C., Maliga, Z., Mallo, D., Maris, J., Markham, N., Marks, J., Martinez, D., Mashl, R. J., Masilionais, I., Mason, J., Massague, J., Massion, P., Mattar, M., Mazurchuk, R., Mazutis, L., Mazzilli, S. A., McKinley, E. T., McMichael, J. F., Merrick, D., Meyerson, M., Miessner, J. R., Mills, G. B., Mills, M., Mondal, S. B., Mori, M., Mori, Y., Moses, E., Mosse, Y., Muhlich, J. L., Murphy, G. F., Navin, N. E., Nawy, T., Nederlof, M., Ness, R., Nevins, S., Nikolov, M., Nirmal, A. J., Nolan, G., Novikov, E., Oberdoerffer, P., O'Connell, B., Offin, M., Oh, S. T., Olson, A., Ooms, A., Ossandon, M., Owzar, K., Parmar, S., Patel, T., Patti, G. J., Pe'er, D., Pe'er, I., Peng, T., Persson, D., Petty, M., Pfister, H., Polyak, K., Pourfarhangi, K., Puram, S. V., Qiu, Q., Quintanal-Villalonga, A., Raj, A., Ramirez-Solano, M., Rashid, R., Reeb, A. N., Regev, A., Reid, M., Resnick, A., Reynolds, S. M., Riesterer, J. L., Rodig, S., Roland, J. T., Rosenfield, S., Rotem, A., Roy, S., Rozenblatt-Rosen, O., Rudin, C. M., Ryser, M. D., Santagata, S., Santi-Vicini, M., Sato, K., Schapiro, D., Schrag, D., Schultz, N., Sears, C. L., Sears, R. C., Sen, S., Sen, T., Shalek, A., Sheng, J., Sheng, Q., Shoghi, K. I., Shrubsole, M. J., Shyr, Y., Sibley, A. B., Siex, K., Simmons, A. J., Singer, D. S., Sivagnanam, S., Slyper, M., Snyder, M. P., Sokolov, A., Song, S., Sorger, P. K., Southard-Smith, A., Spira, A., Srivastava, S., Stein, J., Storm, P., Stover, E., Strand, S. H., Su, T., Sudar, D., Sullivan, R., Surrey, L., Suva, M., Tan, K., Terekhanova, N. V., Ternes, L., Thammavong, L., Thibault, G., Thomas, G. V., Thorsson, V., Todres, E., Tran, L., Tyler, M., Uzun, Y., Vachani, A., Van Allen, E., Vandekar, S., Veis, D. J., Vigneau, S., Vossough, A., Waanders, A., Wagle, N., Wang, L., Wendl, M. C., West, R., Williams, E. H., Wu, C., Wu, H., Wu, H., Wyczalkowski, M. A., Xie, Y., Yang, X., Yapp, C., Yu, W., Yuan, Y., Zhang, D., Zhang, K., Zhang, M., Zhang, N., Zhang, Y., Zhao, Y., Zhou, D. C., Zhou, Z., Zhu, H., Zhu, Q., Zhu, X., Zhu, Y., Zhuang, X. 2020; 181 (2): 236–49

  Abstract

  Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.

  View details for DOI 10.1016/j.cell.2020.03.053

  View details for PubMedID 32302568

• Germline Testing for Patients With BRCA1/2 Mutations on Somatic Tumor Testing JNCI CANCER SPECTRUM Vlessis, K., Purington, N., Chun, N., Haraldsdottir, S., Ford, J. M. 2020; 4 (1): pkz095

  Abstract

  The National Comprehensive Cancer Network (NCCN) recommends germline testing for pathogenic BRCA1/2 mutations identified by somatic tumor sequencing. The aim of this study was to explore whether patients at Stanford with somatic BRCA1/2 mutations were recommended germline testing in accordance with NCCN guidelines.We retrospectively collected all Stanford patients with BRCA1/2 mutations found by tumor sequencing. Medical records were reviewed for each patient to identify those recommended germline testing. A multivariable logistic regression model was fit associating baseline characteristics with whether or not a recommendation was made.Of 164 participants, 51 (31.1%) had no recommendation for germline testing. Of the 97 available germline-testing results, 54 (55.7%) were positive for pathogenic BRCA1/2 mutations. After adjusting for possible confounders, patients with genitourinary cancer (odds ratio [OR] = 0.03, 95% confidence interval [CI] = 0.00 to 0.03; P = .003), lung cancer (OR = 0.04, 95% CI = 0.01 to 0.21; P < .001), sarcoma (OR = 0.02, 95% CI = 0.00 to 0.14; P < .001), skin cancer (OR = 0.01, 95% CI = 0.98 to 1.03; P = .002), or "other" diagnoses (OR = 0.01, 95% CI = 0.00 to 0.16; P < .001) were statistically significantly less likely to be recommended germline testing compared with patients with breast or gynecological cancers.Our study highlights the importance of provider education outside of the oncologic specialties typically associated with BRCA-related cancers and continued exploration of referrals to genetics for germline testing on the basis of somatic findings.

  View details for DOI 10.1093/jncics/pkz095

  View details for Web of Science ID 000523291600017

  View details for PubMedID 32259017

  View details for PubMedCentralID PMC7043298

• One Step Further Toward Defining the Exceptional Cancer Responder. Journal of the National Cancer Institute Ford, J. M., Mitchell, B. S. 2020

  View details for DOI 10.1093/jnci/djaa062

  View details for PubMedID 32339239

• Prevalence of Lynch syndrome in women with mismatch repair-deficient ovarian cancer. Cancer medicine Hodan, R. n., Kingham, K. n., Cotter, K. n., Folkins, A. K., Kurian, A. W., Ford, J. M., Longacre, T. n. 2020

  Abstract

  There are limited data on the prevalence of Lynch syndrome (LS) in women with primary ovarian cancer with mismatch repair deficiency (MMR-D) by immunohistochemistry (IHC).Three hundred and eight cases of primary ovarian, fallopian, and peritoneal cancer between January 2012 and December 2019 were evaluated for MMR-D by IHC. The incidence of LS in this cohort was evaluated.MMR-D by IHC was identified in 16 of 308 (5.2%) (95% CI: 3.2%-8.3%) primary ovarian-related cancers. Most cases with MMR-D were endometrioid (n = 11, 68.7%); (95% CI: 44.2%-86.1%). MSH2/MSH6 protein loss was detected in eight cases (50.0%); (95% CI: 28.0%-72.0%) and MLH1/PMS2 protein loss was detected in four cases (25.0%); (95% CI: 9.7%-50.0%). MSH6 protein loss was detected in two cases (12.5%); (95% CI: 2.2%-37.3%) and PMS2 protein loss was detected in two cases (12.5%); (95% CI: 2.2%-37.3%). All four cases with MLH1/PMS2 protein loss had MLH1 promotor hypermethylation. All 12 women with ovarian cancer suggestive of LS underwent germline testing and 8 (66.6%); (95% CI: 38.8%-86.5%) were confirmed to have LS.Most ovarian cancers with somatic MMR-D were confirmed to have LS in this cohort. Germline testing for LS in addition to BRCA1/2 for all women with an epithelial ovarian cancer would be efficient and would approach 100% sensitivity for identifying Lynch syndrome. Utilization of a multigene panel should also be considered, given the additional non-Lynch germline mutation identified in this cohort.

  View details for DOI 10.1002/cam4.3688

  View details for PubMedID 33369189

• Mutation Rates in Cancer Susceptibility Genes in Patients With Breast Cancer With Multiple Primary Cancers. JCO precision oncology Maxwell, K. N., Wenz, B. M., Kulkarni, A., Wubbenhorst, B., D'Andrea, K., Weathers, B., Goodman, N., Vijai, J., Lilyquist, J., Hart, S. N., Slavin, T. P., Schrader, K. A., Ravichandran, V., Thomas, T., Hu, C., Robson, M. E., Peterlongo, P., Bonanni, B., Ford, J. M., Garber, J. E., Neuhausen, S. L., Shah, P. D., Bradbury, A. R., DeMichele, A. M., Offit, K., Weitzel, J. N., Couch, F. J., Domchek, S. M., Nathanson, K. L. 2020; 4

  Abstract

  PURPOSE: Women with breast cancer have a 4%-16% lifetime risk of a second primary cancer. Whether mutations in genes other than BRCA1/2 are enriched in patients with breast and another primary cancer over those with a single breast cancer (S-BC) is unknown.PATIENTS AND METHODS: We identified pathogenic germline mutations in 17 cancer susceptibility genes in patients with BRCA1/2-negative breast cancer in 2 different cohorts: cohort 1, high-risk breast cancer program (multiple primary breast cancer [MP-BC], n = 551; S-BC, n = 449) and cohort 2, familial breast cancer research study (MP-BC, n = 340; S-BC, n = 1,464). Mutation rates in these 2 cohorts were compared with a control data set (Exome Aggregation Consortium [ExAC]).RESULTS: Overall, pathogenic mutation rates for autosomal, dominantly inherited genes were higher in patients with MP-BC versus S-BC in both cohorts (8.5% v 4.9% [P = .02] and 7.1% v 4.2% [P = .03]). There were differences in individual gene mutation rates between cohorts. In both cohorts, younger age at first breast cancer was associated with higher mutation rates; the age of non-breast cancers was unrelated to mutation rate. TP53 and MSH6 mutations were significantly enriched in patients with MP-BC but not S-BC, whereas ATM and PALB2 mutations were significantly enriched in both groups compared with ExAC.CONCLUSION: Mutation rates are at least 7% in all patients with BRCA1/2 mutation-negative MP-BC, regardless of age at diagnosis of breast cancer, with mutation rates up to 25% in patients with a first breast cancer diagnosed at age < 30 years. Our results suggest that all patients with breast cancer with a second primary cancer, regardless of age of onset, should undergo multigene panel testing.

  View details for DOI 10.1200/PO.19.00301

  View details for PubMedID 32954205

• NCI-MATCH EAY131-Z1I: Phase II study of AZD1775, a wee-1 kinase inhibitor, in patients with tumors containing BRCA1 and BRCA2 mutations Kummar, S., Li, S., Reiss, K., Ford, J. M., Mitchell, E. P., Zwiebel, J. A., Takebe, N., Gray, R. J., McShane, L. M., Rubinstein, L. V., Patton, D., Williams, P., Hamilton, S. R., Brufsky, A., Conley, B. A., Arteaga, C. L., Harris, L. N., O'Dwyer, P. J., Chen, A. P., Flaherty, K. T. AMER ASSOC CANCER RESEARCH. 2019

  View details for DOI 10.1158/1538-7445.AM2019-CT138

  View details for Web of Science ID 000488129900123

• HAT1 Coordinates Histone Production and Acetylation via H4 Promoter Binding. Molecular cell Gruber, J. J., Geller, B., Lipchik, A. M., Chen, J., Salahudeen, A. A., Ram, A. N., Ford, J. M., Kuo, C. J., Snyder, M. P. 2019

  Abstract

  The energetic costs of duplicating chromatin are large and therefore likely depend on nutrient sensing checkpoints and metabolic inputs. By studying chromatin modifiers regulated by epithelial growth factor, we identified histone acetyltransferase 1 (HAT1) as an induced gene that enhances proliferation through coordinating histone production, acetylation, and glucose metabolism. In addition to its canonical role as a cytoplasmic histone H4 acetyltransferase, we isolated a HAT1-containing complex bound specifically at promoters of H4 genes. HAT1-dependent transcription of H4 genes required an acetate-sensitive promoter element. HAT1 expression was critical for S-phase progression and maintenance of H3 lysine 9 acetylation at proliferation-associated genes, including histone genes. Therefore, these data describe a feedforward circuit whereby HAT1 captures acetyl groups on nascent histones and drives H4 production by chromatin binding to support chromatin replication and acetylation. These findings have important implications for human disease, since high HAT1 levels associate with poor outcomes across multiple cancer types.

  View details for DOI 10.1016/j.molcel.2019.05.034

  View details for PubMedID 31278053

• High-Resolution Bisulfite-Sequencing of Peripheral Blood DNA Methylation in Early-Onset and Familial Risk Breast Cancer Patients. Clinical cancer research : an official journal of the American Association for Cancer Research Chen, J. n., Haanpää, M. K., Gruber, J. J., Jäger, N. n., Ford, J. M., Snyder, M. P. 2019

  Abstract

  Understanding and explaining hereditary predisposition to cancer has focused on the genetic etiology of the disease. However, mutations in known genes associated with breast cancer, such as BRCA1 and BRCA2, account for less than 25% of familial cases of breast cancer. Recently, specific epigenetic modifications at BRCA1 have been shown to promote hereditary breast cancer, but the broader potential for epigenetic contribution to hereditary breast cancer is not yet well understood.We examined DNA methylation through deep bisulfite sequencing of CpG islands and known promoter or regulatory regions in peripheral blood DNA from 99 familial or early-onset breast or ovarian cancer patients, 6 unaffected BRCA-mutation carriers, and 49 unaffected controls.In 9% of patients, we observed altered methylation in the promoter regions of genes known to be involved in cancer including hypermethylation at the tumor suppressor PTEN and hypomethylation at the proto-oncogene TEX14 These alterations occur in the form of allelic methylation that span up to hundreds of base-pairs in length.Our observations suggest a broader role for DNA methylation in early-onset, familial risk breast cancer. Further studies are warranted to clarify these mechanisms and the benefits of DNA methylation screening for early risk prediction of familial cancers.

  View details for DOI 10.1158/1078-0432.CCR-18-2423

  View details for PubMedID 31175093

• Association of Tumor Infiltrating Lymphocytes with Homologous Recombination Deficiency and BRCA1/2 Status in Patients with Early Triple-Negative Breast Cancer: A Pooled Analysis. Clinical cancer research : an official journal of the American Association for Cancer Research Telli, M. L., Chu, C. n., Badve, S. S., Vinayak, S. n., Silver, D. P., Isakoff, S. J., Kaklamani, V. n., Gradishar, W. n., Stearns, V. n., Connolly, R. M., Ford, J. M., Gruber, J. J., Adams, S. n., Garber, J. n., Tung, N. n., Neff, C. n., Bernhisel, R. n., Timms, K. M., Richardson, A. L. 2019

  Abstract

  Patients with triple-negative breast cancer (TNBC) with homologous recombination deficient tumors achieve significantly higher pathologic complete response (pCR) rates when treated with neoadjuvant platinum-based therapy. Tumor infiltrating lymphocytes (TILs) are prognostic and predictive of chemotherapy benefit in early stage TNBC. The relationship between TILs, BRCA1/2 mutation status and Homologous Recombination Deficiency (HRD) status in TNBC remains unclear.We performed a pooled analysis of 5 phase II studies that included patients with TNBC treated with neoadjuvant platinum-based chemotherapy to evaluate the association of TILs with HRD status (Myriad Genetics) and tumor BRCA1/2 mutation status. Further, the relationship between pathologic response assessed using the residual cancer burden (RCB) index and HRD status with adjustment for TILs was evaluated.Among 161 patients, stromal TIL (sTIL) density was not significantly associated with HRD status (p=0.107) or tumor BRCA1/2 mutation status (p=0.391). In multivariate analyses, sTIL density (OR 1.23, 95% CI 0.94-1.61, p=0.139) was not associated with pCR, but was associated with RCB 0/I status (OR 1.62, 95% CI 1.20-2.28, p=0.001). HRD was significantly associated with both pCR (OR 12.09, 95% CI 4.11-44.29, p= 7.82 x10-7) and RCB 0/I (OR 10.22, 95% CI 4.11-28.75, p= 1.09 x10-7) in these models.In patients with TNBC treated with neoadjuvant platinum-based therapy, TIL density was not significantly associated with either tumor BRCA1/2 mutation status or HRD status. In this pooled analysis, HRD and sTIL density were independently associated with treatment response, with HRD status being the strongest predictor.

  View details for DOI 10.1158/1078-0432.CCR-19-0664

  View details for PubMedID 31796517

• Genomics in medicine: a novel elective rotation for internal medicine residents. Postgraduate medical journal Geng, L. N., Kohler, J. N., Levonian, P. n., Bernstein, J. A., Ford, J. M., Ahuja, N. n., Witteles, R. n., Hom, J. n., Wheeler, M. n. 2019

  Abstract

  It is well recognised that medical training globally and at all levels lacks sufficient incorporation of genetics and genomics education to keep up with the rapid advances and growing application of genomics to clinical care. However, the best strategy to implement these desired changes into postgraduate medical training and engage learners is still unclear. We developed a novel elective rotation in 'Genomic Medicine and Undiagnosed Diseases' for categorical Internal Medicine Residents to address this educational gap and serve as an adaptable model for training that can be applied broadly across different specialties and at other institutions. Key curriculum goals achieved include increased understanding about genetic testing modalities and tools available for diagnosis and risk analysis, the role of genetics-trained allied health professionals, and indications and limitations of genetic and genomic testing in both rare and common conditions.

  View details for DOI 10.1136/postgradmedj-2018-136355

  View details for PubMedID 31439813

• Chromatin Remodeling in Response to BRCA2-Crisis. Cell reports Gruber, J. J., Chen, J. n., Geller, B. n., Jäger, N. n., Lipchik, A. M., Wang, G. n., Kurian, A. W., Ford, J. M., Snyder, M. P. 2019; 28 (8): 2182–93.e6

  Abstract

  Individuals with a single functional copy of the BRCA2 tumor suppressor have elevated risks for breast, ovarian, and other solid tumor malignancies. The exact mechanisms of carcinogenesis due to BRCA2 haploinsufficiency remain unclear, but one possibility is that at-risk cells are subject to acute periods of decreased BRCA2 availability and function ("BRCA2-crisis"), which may contribute to disease. Here, we establish an in vitro model for BRCA2-crisis that demonstrates chromatin remodeling and activation of an NF-κB survival pathway in response to transient BRCA2 depletion. Mechanistically, we identify BRCA2 chromatin binding, histone acetylation, and associated transcriptional activity as critical determinants of the epigenetic response to BRCA2-crisis. These chromatin alterations are reflected in transcriptional profiles of pre-malignant tissues from BRCA2 carriers and, therefore, may reflect natural steps in human disease. By modeling BRCA2-crisis in vitro, we have derived insights into pre-neoplastic molecular alterations that may enhance the development of preventative therapies.

  View details for DOI 10.1016/j.celrep.2019.07.057

  View details for PubMedID 31433991

• Increased MTH1-specific 8-oxodGTPase activity is a hallmark of cancer in colon, lung and pancreatic tissue. DNA repair McPherson, L. A., Troccoli, C. I., Ji, D. n., Bowles, A. E., Gardiner, M. L., Mohsen, M. G., Nagathihalli, N. S., Nguyen, D. M., Robbins, D. J., Merchant, N. B., Kool, E. T., Rai, P. n., Ford, J. M. 2019: 102644

  Abstract

  Cellular homeostasis is dependent on a balance between DNA damage and DNA repair mechanisms. Cells are constantly assaulted by both exogenous and endogenous stimuli leading to high levels of reactive oxygen species (ROS) that cause oxidation of the nucleotide dGTP to 8-oxodGTP. If this base is incorporated into DNA and goes unrepaired, it can result in G > T transversions, leading to genomic DNA damage. MutT Homolog 1 (MTH1) is a nucleoside diphosphate X (Nudix) pyrophosphatase that can remove 8-oxodGTP from the nucleotide pool before it is incorporated into DNA by hydrolyzing it into 8-oxodGMP. MTH1 expression has been shown to be elevated in many cancer cells and is thought to be a survival mechanism by which a cancer cell can stave off the effects of high ROS that can result in cell senescence or death. It has recently become a target of interest in cancer because it is thought that inhibiting MTH1 can increase genotoxic damage and cytotoxicity. Determining the role of MTH1 in normal and cancer cells is confounded by an inability to reliably and directly measure its native enzymatic activity. We have used the chimeric ATP-releasing guanine-oxidized (ARGO) probe that combines 8-oxodGTP and ATP to measure MTH1 enzymatic activity in colorectal cancer (CRC), non-small cell lung cancer (NSCLC) and pancreatic ductal adenocarcinoma (PDAC) along with patient-matched normal tissue. MTH1 8-oxodGTPase activity is significantly increased in tumors across all three tissue types, indicating that MTH1 is a marker of cancer. MTH1 activity measured by ARGO assay was compared to mRNA and protein expression measured by RT-qPCR and Western blot in the CRC tissue pairs, revealing a positive correlation between ARGO assay and Western blot, but little correlation with RT-qPCR in these samples. The adoption of the ARGO assay will help in establishing the level of MTH1 activity in model systems and in assessing the effects of MTH1 modulation in the treatment of cancer.

  View details for DOI 10.1016/j.dnarep.2019.102644

  View details for PubMedID 31311767

• Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations. BMC medical genomics Lal, A. n., Ramazzotti, D. n., Weng, Z. n., Liu, K. n., Ford, J. M., Sidow, A. n. 2019; 12 (1): 84

  Abstract

  Germline mutations in the BRCA1 and BRCA2 genes predispose carriers to breast and ovarian cancer, and there remains a need to identify the specific genomic mechanisms by which cancer evolves in these patients. Here we present a systematic genomic analysis of breast tumors with BRCA1 and BRCA2 mutations.We analyzed genomic data from breast tumors, with a focus on comparing tumors with BRCA1/BRCA2 gene mutations with common classes of sporadic breast tumors.We identify differences between BRCA-mutated and sporadic breast tumors in patterns of point mutation, DNA methylation and structural variation. We show that structural variation disproportionately affects tumor suppressor genes and identify specific driver gene candidates that are enriched for structural variation.Compared to sporadic tumors, BRCA-mutated breast tumors show signals of reduced DNA methylation, more ancestral cell divisions, and elevated rates of structural variation that tend to disrupt highly expressed protein-coding genes and known tumor suppressors. Our analysis suggests that BRCA-mutated tumors are more aggressive than sporadic breast cancers because loss of the BRCA pathway causes multiple processes of mutagenesis and gene dysregulation.

  View details for DOI 10.1186/s12920-019-0545-0

  View details for PubMedID 31182087

• Tumor Molecular Profiling Aids in Determining Tissue of Origin and Therapy for Metastatic Adenocarcinoma in a Patient With Multiple Primary Malignancies JCO PRECISION ONCOLOGY Costa, H. A., Reyes, R., Mills, M., Zehnder, J. L., Sledge, G., Curtis, C., Ford, J. M., Suarez, C. J. 2018; 2

  View details for DOI 10.1200/PO.18.00177

  View details for Web of Science ID 000462187500001

• Strategies For Clinical Implementation: Precision Oncology At Three Distinct Institutions HEALTH AFFAIRS Nadauld, L. D., Ford, J. M., Pritchard, D., Brown, T. 2018; 37 (5): 751–56

  View details for DOI 10.1377/hlthaff.2017.1575

  View details for Web of Science ID 000463856100011

• Precision oncology in advanced cancer patients improves overall survival with lower weekly healthcare costs. Oncotarget Haslem, D. S., Chakravarty, I., Fulde, G., Gilbert, H., Tudor, B. P., Lin, K., Ford, J. M., Nadauld, L. D. 2018; 9 (15): 12316–22

  Abstract

  The impact of precision oncology on guiding treatment decisions of late-stage cancer patients was previously studied in a retrospective analysis. However, the overall survival and costs were not previously evaluated. We report the overall survival and healthcare costs associated with precision oncology in these patients with advanced cancer. Building on a matched cohort study of 44 patients with metastatic cancer who received all of their care within a single institution, we evaluated the overall survival and healthcare costs for each patient. We analyzed the outcomes of 22 patients who received genomic testing and targeted therapy (precision oncology) between July 1, 2013 and January 31, 2015, and compared to 22 historically controlled patients (control) who received standard chemotherapy (N = 17) or best supportive care (N = 5). The median overall survival was 51.7 weeks for the targeted treatment group and 25.8 weeks for the control group (P = 0.008) when matching on age, gender, histological diagnosis and previous treatment lines. Average costs over the entire period were $2,720 per week for the targeted treatment group and $3,453 per week for the control group, (P = 0.036). A separate analysis of 1,814 patients with late-stage cancer diagnoses found that those who received a targeted cancer treatment (N = 93) had 6.9% lower costs in the last 3 months of life compared with those who did not. These findings suggest that precision oncology may improve overall survival for refractory cancer patients while lowering average per-week healthcare costs, resource utilization and end-of-life costs.

  View details for PubMedID 29552312

• Homologous recombination deficiency (HRD) status predicts response to standard neoadjuvant chemotherapy in patients with triple-negative or BRCA1/2 mutation-associated breast cancer. Breast cancer research and treatment Telli, M. L., Hellyer, J. n., Audeh, W. n., Jensen, K. C., Bose, S. n., Timms, K. M., Gutin, A. n., Abkevich, V. n., Peterson, R. N., Neff, C. n., Hughes, E. n., Sangale, Z. n., Jones, J. n., Hartman, A. R., Chang, P. J., Vinayak, S. n., Wenstrup, R. n., Ford, J. M. 2018; 168 (3): 625–30

  Abstract

  Defects in the homologous recombination (HR) DNA repair pathway sensitize tumors to therapeutics that target this pathway. A significant proportion of triple-negative breast cancers (TNBC) carry HR defects. The HRD assay is highly associated with sensitivity to neoadjuvant platinum-based chemotherapy in TNBC. Standard chemotherapy consists of some combination of an anthracycline, cyclophosphamide, and taxane. This study assesses the association of HR deficiency status with response to standard neoadjuvant chemotherapy in TNBC or BRCA1/2 mutation-associated breast cancer.Tumor samples were retrospectively obtained from 45 TNBC patients and 2 BRCA1/2 mutant, hormone receptor-positive/HER2-negative breast cancer patients who received anthracycline- and/or taxane-based neoadjuvant chemotherapy at Stanford University or Cedars-Sinai Medical Centers. The HRD score and tumor BRCA1/2 mutation status were determined from baseline tumor biopsies. HR deficient tumors were those with a HRD score of ≥ 42 or a tumor BRCA1/2 mutation. Response was categorized by the residual cancer burden (RCB) index.HR deficient patients were more likely to achieve a pathologic complete response (pCR) compared with non-deficient patients (OR 13.06, CI 1.52-11.241, p = 0.0028). Among BRCA1/2 mutation wild-type patients, HR deficient patients were more likely to achieve a pCR (OR 16, 95% CI 1.65-160.41, p = 0.0041) compared with HR non-deficient patients. Further, HRD scores were highly concordant pre- and post-therapy (Spearman correlation > 99%).HR deficiency status is significantly associated with response to standard neoadjuvant chemotherapy in TNBC. This observation is consistent with the mechanisms of action of doxorubicin and cyclophosphamide as DNA damaging agents.

  View details for PubMedID 29275435

• Totally Unexpected: Nonsyndromic CDH1 Mutations and Hereditary Diffuse Gastric Cancer Syndrome. JCO precision oncology Ford, J. M. 2017; 1: 1-2

  View details for DOI 10.1200/PO.17.00006

  View details for PubMedID 35172477

• IDH2 Mutation in a Patient with Metastatic Colon Cancer NEW ENGLAND JOURNAL OF MEDICINE Zhang, B. M., Zehnder, J. L., Suarez, C. J. 2017; 376 (20): 1991-1992

  View details for DOI 10.1056/NEJMc1701072

  View details for PubMedID 28514606

• Poly (ADP-ribose) polymerase inhibitor, an effective radiosensitizer in lung and pancreatic cancers ONCOTARGET Hastak, K., Bhutra, S., Parry, R., Ford, J. M. 2017; 8 (16): 26344-26355

  Abstract

  The development of stereotactic body radiation therapy (SBRT) has revolutionized radiation therapy for lung cancers and is an emerging treatment option for pancreatic cancers. However, there are many questions on how to optimize its use in chemoradiotherapy. The most relevant addition to radiotherapy regimens are inhibitors of DNA repair and DNA damage response pathways. One such class of agents are inhibitors of poly (ADP-ribose) polymerase (PARP). In this study we examined the effects of the PARP inhibitor LT626 in combination with ionizing radiation in lung and pancreatic cancers. Our study demonstrated that combination treatment with LT626 and radiation effectively inhibited growth in lung and pancreatic cancer cell lines, better than individual treatment alone. Combination treatment also increased expression of γH2AX and 53BP1 foci and upregulated expression of phosphorylated ATM, ATR and their respective kinases. Using in vivo lung cancer xenograft models we demonstrated that LT626 functioned as an effective radiosensitizer during fractionated radiation treatment, leading to significant decrease in tumor burden and doubling the median survival compared to control group. Overall our in vitro and in vivo studies showed that PARP inhibitor LT626 acted synergistically with radiation in lung and pancreatic cancers.

  View details for DOI 10.18632/oncotarget.15464

  View details for PubMedID 28412751

• Tumor BRCA1 Reversion Mutation Arising During Neoadjuvant Platinum-Based Chemotherapy in Triple-Negative Breast Cancer Is Associated with Therapy Resistance. Clinical cancer research : an official journal of the American Association for Cancer Research Afghahi, A., Timms, K. M., Vinayak, S., Jensen, K. C., Kurian, A. W., Carlson, R. W., Chang, P., Schackmann, E. A., Hartman, A., Ford, J. M., Telli, M. L. 2017

  Abstract

  In germline BRCA1 or BRCA2 (BRCA1/2) mutation carriers, restoration of tumor BRCA1/2 function by a secondary mutation is recognized as a mechanism of resistance to platinum and PARP inhibitors, primarily in ovarian cancer. We evaluated this mechanism of resistance in newly diagnosed BRCA1/2-mutant breast cancer patients with poor response to neoadjuvant platinum-based therapy.PrECOG 0105 was a phase II neoadjuvant study of gemcitabine, carboplatin and iniparib in patients with stage I-IIIA triple-negative or BRCA1/2 mutation-associated breast cancer (n=80). All patients underwent comprehensive BRCA1/2 genotyping. For mutation carriers with moderate or extensive residual disease after neoadjuvant therapy, BRCA1/2 status was re-sequenced in the residual surgical breast tumor tissue.Nineteen patients had a deleterious germline BRCA1/2 mutation and 4 had moderate residual disease at surgery. BRCA1/2 sequencing of residual tissue was performed on three patients. These patients had BRCA1 1479delAG, 3374insGA and W1712X mutations, respectively, with loss of heterozygosity at these loci in the pre-treatment tumors. In the first case, a new BRCA1 mutation was detected in the residual disease. This resulted in a 14 amino acid deletion and restoration of the BRCA1 reading frame. A local relapse biopsy four months later revealed the identical reversion mutation, and the patient subsequently died of metastatic breast cancer.We report a BRCA1 reversion mutation in a newly diagnosed triple-negative breast cancer patient that developed over 18 weeks of platinum-based neoadjuvant therapy. This was associated with poor therapy response, early relapse and death.

  View details for DOI 10.1158/1078-0432.CCR-16-2174

  View details for PubMedID 28087643

• Racial/ethnic differences in multiple-gene sequencing results for hereditary cancer risk. Genetics in medicine : official journal of the American College of Medical Genetics Caswell-Jin, J. L., Gupta, T. n., Hall, E. n., Petrovchich, I. M., Mills, M. A., Kingham, K. E., Koff, R. n., Chun, N. M., Levonian, P. n., Lebensohn, A. P., Ford, J. M., Kurian, A. W. 2017

  Abstract

  PurposeWe examined racial/ethnic differences in the usage and results of germ-line multiple-gene sequencing (MGS) panels to evaluate hereditary cancer risk.MethodsWe collected genetic testing results and clinical information from 1,483 patients who underwent MGS at Stanford University between 1 January 2013 and 31 December 2015.ResultsAsians and Hispanics presented for MGS at younger ages than whites (48 and 47 vs. 55; P = 5E-16 and 5E-14). Across all panels, the rate of pathogenic variants (15%) did not differ significantly between racial groups. Rates by gene did differ: in particular, a higher percentage of whites than nonwhites carried pathogenic CHEK2 variants (3.8% vs. 1.0%; P = 0.002). The rate of a variant of uncertain significance (VUS) result was higher in nonwhites than whites (36% vs. 27%; P = 2E-4). The probability of a VUS increased with increasing number of genes tested; this effect was more pronounced for nonwhites than for whites (1.1% absolute difference in VUS rates testing BRCA1/2 vs. 8% testing 13 genes vs. 14% testing 28 genes), worsening the disparity.ConclusionIn this diverse cohort undergoing MGS testing, pathogenic variant rates were similar between racial/ethnic groups. By contrast, VUS results were more frequent among nonwhites, with potential significance for the impact of MGS testing by race/ethnicity.GENETICS in MEDICINE advance online publication, 27 July 2017; doi:10.1038/gim.2017.96.

  View details for PubMedID 28749474

• Precision Oncology: A New Forum for an Emerging Field JCO PRECISION ONCOLOGY Ford, J. M. 2017; 1

  View details for DOI 10.1200/PO.16.00048

  View details for Web of Science ID 000462058200014

• A Retrospective Analysis of Precision Medicine Outcomes in Patients With Advanced Cancer Reveals Improved Progression-Free Survival Without Increased Health Care Costs. Journal of oncology practice Haslem, D. S., Van Norman, S. B., Fulde, G., Knighton, A. J., Belnap, T., Butler, A. M., Rhagunath, S., Newman, D., Gilbert, H., Tudor, B. P., Lin, K., Stone, G. R., Loughmiller, D. L., Mishra, P. J., Srivastava, R., Ford, J. M., Nadauld, L. D. 2016

  Abstract

  The advent of genomic diagnostic technologies such as next-generation sequencing has recently enabled the use of genomic information to guide targeted treatment in patients with cancer, an approach known as precision medicine. However, clinical outcomes, including survival and the cost of health care associated with precision cancer medicine, have been challenging to measure and remain largely unreported.We conducted a matched cohort study of 72 patients with metastatic cancer of diverse subtypes in the setting of a large, integrated health care delivery system. We analyzed the outcomes of 36 patients who received genomic testing and targeted therapy (precision cancer medicine) between July 1, 2013, and January 31, 2015, compared with 36 historical control patients who received standard chemotherapy (n = 29) or best supportive care (n = 7).The average progression-free survival was 22.9 weeks for the precision medicine group and 12.0 weeks for the control group (P = .002) with a hazard ratio of 0.47 (95% CI, 0.29 to 0.75) when matching on age, sex, histologic diagnosis, and previous lines of treatment. In a subset analysis of patients who received all care within the Intermountain Healthcare system (n = 44), per patient charges per week were $4,665 in the precision treatment group and $5,000 in the control group (P = .126).These findings suggest that precision cancer medicine may improve survival for patients with refractory cancer without increasing health care costs. Although the results of this study warrant further validation, this precision medicine approach may be a viable option for patients with advanced cancer.

  View details for PubMedID 27601506

• Precision genomic medicine improves clinical outcomes in advanced cancer patients Nadauld, L. D., Van Norman, B., Fulde, G., Newman, D., Butler, A., Tudor, B., Gilbert, H., Lin, K., Stone, G., Konde, A., Petrovchich, I., Ford, J. M., Haslem, D. AMER ASSOC CANCER RESEARCH. 2016

  View details for DOI 10.1158/1557-3265.PMSCLINGEN15-PR07

  View details for Web of Science ID 000369082700022

• American Society of Clinical Oncology Policy Statement Update: Genetic and Genomic Testing for Cancer Susceptibility. Journal of clinical oncology Robson, M. E., Bradbury, A. R., Arun, B., Domchek, S. M., Ford, J. M., Hampel, H. L., Lipkin, S. M., Syngal, S., Wollins, D. S., Lindor, N. M. 2015; 33 (31): 3660-3667

  Abstract

  The American Society of Clinical Oncology (ASCO) has long affirmed that the recognition and management of individuals with an inherited susceptibility to cancer are core elements of oncology care. ASCO released its first statement on genetic testing in 1996 and updated that statement in 2003 and 2010 in response to developments in the field. In 2014, the Cancer Prevention and Ethics Committees of ASCO commissioned another update to reflect the impact of advances in this area on oncology practice. In particular, there was an interest in addressing the opportunities and challenges arising from the application of massively parallel sequencing-also known as next-generation sequencing-to cancer susceptibility testing. This technology introduces a new level of complexity into the practice of cancer risk assessment and management, requiring renewed effort on the part of ASCO to ensure that those providing care to patients with cancer receive the necessary education to use this new technology in the most effective, beneficial manner. The purpose of this statement is to explore the challenges of new and emerging technologies in cancer genetics and provide recommendations to ensure their optimal deployment in oncology practice. Specifically, the statement makes recommendations in the following areas: germline implications of somatic mutation profiling, multigene panel testing for cancer susceptibility, quality assurance in genetic testing, education of oncology professionals, and access to cancer genetic services.

  View details for DOI 10.1200/JCO.2015.63.0996

  View details for PubMedID 26324357

• Clinical Actionability of Multigene Panel Testing for Hereditary Breast and Ovarian Cancer Risk Assessment JAMA ONCOLOGY Desmond, A., Kurian, A., Gabree, M., Mills, M. A., Anderson, M. J., Kobayashi, Y., Horick, N., Yang, S., Shannon, K. M., Tung, N., Ford, J., Lincoln, S. E., Ellisen, L. 2015; 1 (7): 943-951

  Abstract

  The practice of genetic testing for hereditary breast and/or ovarian cancer (HBOC) is rapidly evolving owing to the recent introduction of multigene panels. While these tests may identify 40% to 50% more individuals with hereditary cancer gene mutations than does testing for BRCA1/2 alone, whether finding such mutations will alter clinical management is unknown.To define the potential clinical effect of multigene panel testing for HBOC in a clinically representative cohort.Observational study of patients seen between 2001 and 2014 in 3 large academic medical centers. We prospectively enrolled 1046 individuals who were appropriate candidates for HBOC evaluation and who lacked BRCA1/2 mutations.We carried out multigene panel testing on all participants, then determined the clinical actionability, if any, of finding non-BRCA1/2 mutations in these and additional comparable individuals.We evaluated the likelihood of (1) a posttest management change and (2) an indication for additional familial testing, considering gene-specific consensus management guidelines, gene-associated cancer risks, and personal and family history.Among 1046 study participants, 40 BRCA1/2-negative patients (3.8%; 95% CI, 2.8%-5.2%) harbored deleterious mutations, most commonly in moderate-risk breast and ovarian cancer genes (CHEK2, ATM, and PALB2) and Lynch syndrome genes. Among these and an additional 23 mutation-positive individuals enrolled from our clinics, most of the mutations (92%) were consistent with the spectrum of cancer(s) observed in the patient or family, suggesting that these results are clinically significant. Among all 63 mutation-positive patients, additional disease-specific screening and/or prevention measures beyond those based on personal and family history alone would be considered for most (33 [52%] of 63; 95% CI, 40.3%-64.2%). Furthermore, additional familial testing would be considered for those with first-degree relatives (42 [72%] of 58; 95% CI, 59.8%-82.2%) based on potential management changes for mutation-positive relatives. This clinical effect was not restricted to a few of the tested genes because most identified genes could change clinical management for some patients.In a clinically representative cohort, multigene panel testing for HBOC risk assessment yielded findings likely to change clinical management for substantially more patients than does BRCA1/2 testing alone. Multigene testing in this setting is likely to alter near-term cancer risk assessment and management recommendations for mutation-affected individuals across a broad spectrum of cancer predisposition genes.

  View details for DOI 10.1001/jamaoncol.2015.2690

  View details for Web of Science ID 000383675900013

• American Gastroenterological Association Technical Review on the Diagnosis and Management of Lynch Syndrome. Gastroenterology Ladabaum, U., Ford, J. M., Martel, M., Barkun, A. N. 2015; 149 (3): 783-813 e20

  View details for DOI 10.1053/j.gastro.2015.07.037

  View details for PubMedID 26226576

• Phase II Study of Gemcitabine, Carboplatin, and Iniparib As Neoadjuvant Therapy for Triple-Negative and BRCA1/2 Mutation-Associated Breast Cancer With Assessment of a Tumor-Based Measure of Genomic Instability: PrECOG 0105. Journal of clinical oncology Telli, M. L., Jensen, K. C., Vinayak, S., Kurian, A. W., Lipson, J. A., Flaherty, P. J., Timms, K., Abkevich, V., Schackmann, E. A., Wapnir, I. L., Carlson, R. W., Chang, P., Sparano, J. A., Head, B., Goldstein, L. J., Haley, B., Dakhil, S. R., Reid, J. E., Hartman, A., Manola, J., Ford, J. M. 2015; 33 (17): 1895-1901

  Abstract

  This study was designed to assess efficacy, safety, and predictors of response to iniparib in combination with gemcitabine and carboplatin in early-stage triple-negative and BRCA1/2 mutation-associated breast cancer.This single-arm phase II study enrolled patients with stage I to IIIA (T ≥ 1 cm) estrogen receptor-negative (≤ 5%), progesterone receptor-negative (≤ 5%), and human epidermal growth factor receptor 2-negative or BRCA1/2 mutation-associated breast cancer. Neoadjuvant gemcitabine (1,000 mg/m(2) intravenously [IV] on days 1 and 8), carboplatin (area under curve of 2 IV on days 1 and 8), and iniparib (5.6 mg/kg IV on days 1, 4, 8, and 11) were administered every 21 days for four cycles, until the protocol was amended to six cycles. The primary end point was pathologic complete response (no invasive carcinoma in breast or axilla). All patients underwent comprehensive BRCA1/2 genotyping, and homologous recombination deficiency was assessed by loss of heterozygosity (HRD-LOH) in pretreatment core breast biopsies.Among 80 patients, median age was 48 years; 19 patients (24%) had germline BRCA1 or BRCA2 mutations; clinical stage was I (13%), IIA (36%), IIB (36%), and IIIA (15%). Overall pathologic complete response rate in the intent-to-treat population (n = 80) was 36% (90% CI, 27 to 46). Mean HRD-LOH scores were higher in responders compared with nonresponders (P = .02) and remained significant when BRCA1/2 germline mutations carriers were excluded (P = .021).Preoperative combination of gemcitabine, carboplatin, and iniparib is active in the treatment of early-stage triple-negative and BRCA1/2 mutation-associated breast cancer. The HRD-LOH assay was able to identify patients with sporadic triple-negative breast cancer lacking a BRCA1/2 mutation, but with an elevated HRD-LOH score, who achieved a favorable pathologic response. Confirmatory controlled trials are warranted.

  View details for DOI 10.1200/JCO.2014.57.0085

  View details for PubMedID 25847929

• Hereditary diffuse gastric cancer: updated clinical guidelines with an emphasis on germline CDH1 mutation carriers JOURNAL OF MEDICAL GENETICS van der Post, R. S., Vogelaar, I. P., Carneiro, F., Guilford, P., Huntsman, D., Hoogerbrugge, N., Caldas, C., Schreiber, K. E., Hardwick, R. H., Ausems, M. G., Bardram, L., Benusiglio, P. R., Bisseling, T. M., Blair, V., Bleiker, E., Boussioutas, A., Cats, A., Coit, D., DeGregorio, L., Figueiredo, J., Ford, J. M., Heijkoop, E., Hermens, R., Humar, B., Kaurah, P., Keller, G., Lai, J., Ligtenberg, M. J., O'Donovan, M., Oliveira, C., Pinheiro, H., Ragunath, K., Rasenberg, E., Richardson, S., Roviello, F., Schackert, H., Seruca, R., Taylor, A., ter Huurne, A., Tischkowitz, M., Joe, S. T., van Dijck, B., van Grieken, N. C., van Hillegersberg, R., van Sandick, J. W., Vehof, R., Van Krieken, J. H., Fitzgerald, R. C. 2015; 52 (6): 361-374

  Abstract

  Germline CDH1 mutations confer a high lifetime risk of developing diffuse gastric (DGC) and lobular breast cancer (LBC). A multidisciplinary workshop was organised to discuss genetic testing, surgery, surveillance strategies, pathology reporting and the patient's perspective on multiple aspects, including diet post gastrectomy. The updated guidelines include revised CDH1 testing criteria (taking into account first-degree and second-degree relatives): (1) families with two or more patients with gastric cancer at any age, one confirmed DGC; (2) individuals with DGC before the age of 40 and (3) families with diagnoses of both DGC and LBC (one diagnosis before the age of 50). Additionally, CDH1 testing could be considered in patients with bilateral or familial LBC before the age of 50, patients with DGC and cleft lip/palate, and those with precursor lesions for signet ring cell carcinoma. Given the high mortality associated with invasive disease, prophylactic total gastrectomy at a centre of expertise is advised for individuals with pathogenic CDH1 mutations. Breast cancer surveillance with annual breast MRI starting at age 30 for women with a CDH1 mutation is recommended. Standardised endoscopic surveillance in experienced centres is recommended for those opting not to have gastrectomy at the current time, those with CDH1 variants of uncertain significance and those that fulfil hereditary DGC criteria without germline CDH1 mutations. Expert histopathological confirmation of (early) signet ring cell carcinoma is recommended. The impact of gastrectomy and mastectomy should not be underestimated; these can have severe consequences on a psychological, physiological and metabolic level. Nutritional problems should be carefully monitored.

  View details for DOI 10.1136/jmedgenet-2015-103094

  View details for Web of Science ID 000354952300001

  View details for PubMedCentralID PMC4453626

• Multigene Panel Testing in Oncology Practice: How Should We Respond? JAMA oncology Kurian, A. W., Ford, J. M. 2015; 1 (3): 277-278

  View details for DOI 10.1001/jamaoncol.2015.28

  View details for PubMedID 26181167

• Genomic Complexity Profiling Reveals That HORMAD1 Overexpression Contributes to Homologous Recombination Deficiency in Triple-Negative Breast Cancers CANCER DISCOVERY Watkins, J., Weekes, D., Shah, V., Gazinska, P., Joshi, S., Sidhu, B., Gillett, C., Pinder, S., Vanoli, F., Jasin, M., Mayrhofer, M., Isaksson, A., Cheang, M. C., Mirza, H., Frankum, J., Lord, C. J., Ashworth, A., Vinayak, S., Ford, J. M., Telli, M. L., Grigoriadis, A., Tutt, A. N. 2015; 5 (5): 488-505

  Abstract

  Triple-negative breast cancers (TNBCs) are characterised by a wide spectrum of genomic alterations, some of which might be caused by defects in DNA repair processes such as homologous recombination (HR). Despite this understanding, associating particular patterns of genomic instability with response to therapy has been challenging. Here, we show that Allelic-imbalanced Copy Number Aberrations (AiCNA) are more prevalent in TNBCs that respond to platinum-based chemotherapy, thus providing a candidate predictive biomarker for this disease. Furthermore, we show that a high level of AiCNA is linked with elevated expression of a meiosis-associated gene HORMAD1. Elevated HORMAD1 expression suppresses RAD51-dependent HR and drives the use of alternative forms of DNA repair, the generation of AiCNAs as well as sensitising cancer cells to HR targeting therapies. Our data therefore provides a mechanistic association between HORMAD1 expression, a specific pattern of genomic instability and an association with response to platinum-based chemotherapy in TNBC.

  View details for DOI 10.1158/2159-8290.CD-14-1092

  View details for PubMedID 25770156

• Multigene Panel Testing in Oncology Practice: How Should We Respond? JAMA Oncology Kurian, A. W., Ford, J. M. 2015; 1 (3): 277-278

  View details for DOI 10.1001/jamaoncol.2015.28

• Therapeutic Targeting of BRCA1-Mutated Breast Cancers with Agents That Activate DNA Repair CANCER RESEARCH Alli, E., Solow-Cordero, D., Casey, S. C., Ford, J. M. 2014; 74 (21): 6205-6215

  Abstract

  Cancers due to germline mutations in the BRCA1 gene tend to lack targets for approved chemoprevention agents. This study aimed at a targeted chemoprevention strategy for BRCA1-associated malignancies. Mutant BRCA1 limits the base-excision DNA repair activity that addresses oxidative DNA damage, the accumulation of which heightens one's risk for cancer. Therefore, we conducted a high-throughput chemical screen to identify drug candidates that could attenuate the inhibitory effects of mutant BRCA1 on this repair activity, thereby describing a new class of DNA repair-activating chemopreventive agents. In the screen design, such drugs functioned by enhancing base-excision DNA repair of oxidative DNA damage in the presence of mutant BRCA1, with minimal cytotoxicity. We identified at least one new agent that decreased malignant properties associated with tumorigenesis, including anchorage-independent growth and tumor progression. This work offers a preclinical proof-of-concept for a wholly new approach to chemoprevention in carriers of BRCA1 mutations, as a strategy to reduce the prevalence of BRCA1-associated malignancy.

  View details for DOI 10.1158/0008-5472.CAN-14-1716

  View details for Web of Science ID 000344756800026

• Clinical Evaluation of a Multiple-Gene Sequencing Panel for Hereditary Cancer Risk Assessment JOURNAL OF CLINICAL ONCOLOGY Kurian, A. W., Hare, E. E., Mills, M. A., Kingham, K. E., McPherson, L., Whittemore, A. S., McGuire, V., Ladabaum, U., Kobayashi, Y., Lincoln, S. E., Cargill, M., Ford, J. M. 2014; 32 (19): 2001-2009

  Abstract

  Multiple-gene sequencing is entering practice, but its clinical value is unknown. We evaluated the performance of a customized germline-DNA sequencing panel for cancer-risk assessment in a representative clinical sample.Patients referred for clinical BRCA1/2 testing from 2002 to 2012 were invited to donate a research blood sample. Samples were frozen at -80° C, and DNA was extracted from them after 1 to 10 years. The entire coding region, exon-intron boundaries, and all known pathogenic variants in other regions were sequenced for 42 genes that had cancer risk associations. Potentially actionable results were disclosed to participants.In total, 198 women participated in the study: 174 had breast cancer and 57 carried germline BRCA1/2 mutations. BRCA1/2 analysis was fully concordant with prior testing. Sixteen pathogenic variants were identified in ATM, BLM, CDH1, CDKN2A, MUTYH, MLH1, NBN, PRSS1, and SLX4 among 141 women without BRCA1/2 mutations. Fourteen participants carried 15 pathogenic variants, warranting a possible change in care; they were invited for targeted screening recommendations, enabling early detection and removal of a tubular adenoma by colonoscopy. Participants carried an average of 2.1 variants of uncertain significance among 42 genes.Among women testing negative for BRCA1/2 mutations, multiple-gene sequencing identified 16 potentially pathogenic mutations in other genes (11.4%; 95% CI, 7.0% to 17.7%), of which 15 (10.6%; 95% CI, 6.5% to 16.9%) prompted consideration of a change in care, enabling early detection of a precancerous colon polyp. Additional studies are required to quantify the penetrance of identified mutations and determine clinical utility. However, these results suggest that multiple-gene sequencing may benefit appropriately selected patients.

  View details for DOI 10.1200/JCO.2013.53.6607

  View details for Web of Science ID 000337925500007

• Clinical interpretation and implications of whole-genome sequencing. JAMA Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

  Abstract

  Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

  View details for DOI 10.1001/jama.2014.1717

  View details for PubMedID 24618965

• Poly (ADP-ribose) polymerase inhibitor LT-626: Sensitivity correlates with MRE11 mutations and synergizes with platinums and irinotecan in colorectal cancer cells CANCER LETTERS McPherson, L. A., Shen, Y., Ford, J. M. 2014; 343 (2): 217-223

  Abstract

  Some colorectal cancers (CRC) display microsatellite instability (MSI) leading to mutations in genes such as MRE11. The aim of this study was to determine whether MSI or MRE11 mutational status correlates with sensitivity to the PARP inhibitor LT-626 and whether LT-626 synergizes with DNA-damaging chemotherapeutic agents. CRC cells harboring biallelic MRE11 mutations were more sensitive to LT-626 and stable overexpression or knock-down of MRE11 in cell lines correlated with sensitivity. Synergism was evident between LT-626 and cisplatin, oxaliplatin and SN-38 suggesting that PARP inhibitors in combination with DNA damaging agents may be a successful strategy for treatment of CRC.

  View details for DOI 10.1016/j.canlet.2013.10.034

  View details for PubMedID 24215868

• Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. Genome biology Nadauld, L. D., Garcia, S., Natsoulis, G., Bell, J. M., Miotke, L., Hopmans, E. S., Xu, H., Pai, R. K., Palm, C., Regan, J. F., Chen, H., Flaherty, P., Ootani, A., Zhang, N. R., Ford, J. M., Kuo, C. J., Ji, H. P. 2014; 15 (8): 428-?

  Abstract

  Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis.Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of the Fibroblast growth factor receptor 2 (FGFR2) gene, the metastasis notably lacks FGFR2 amplification but rather possesses unique biallelic alterations of Transforming growth factor-beta receptor 2 (TGFBR2), indicating the divergent in vivo evolution of a TGFBR2-mutant metastatic clonal population in this patient. As TGFBR2 mutations have not previously been functionally validated in gastric cancer, we modeled the metastatic potential of TGFBR2 loss in a murine three-dimensional primary gastric organoid culture. The Tgfbr2 shRNA knockdown within Cdh1-/-; Tp53-/- organoids generates invasion in vitro and robust metastatic tumorigenicity in vivo, confirming Tgfbr2 metastasis suppressor activity.We document the metastatic differentiation and genetic heterogeneity of diffuse gastric cancer and reveal the potential metastatic role of TGFBR2 loss-of-function. In support of this study, we apply a murine primary organoid culture method capable of recapitulating in vivo metastatic gastric cancer. Overall, we describe an integrated approach to identify and functionally validate putative cancer drivers involved in metastasis.

  View details for DOI 10.1186/s13059-014-0428-9

  View details for PubMedID 25315765

  View details for PubMedCentralID PMC4145231

• Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer GENOME BIOLOGY Nadauld, L. D., Garcia, S., Natsoulis, G., Bell, J. M., Miotke, L., Hopmans, E. S., Xu, H., Pai, R. K., Palm, C., Regan, J. F., Chen, H., Flaherty, P., Ootani, A., Zhang, N. R., Ford, J. M., Kuo, C. J., Ji, H. P. 2014; 15 (8)

  Abstract

  Gastric cancer is the second-leading cause of global cancer deaths, with metastatic disease representing the primary cause of mortality. To identify candidate drivers involved in oncogenesis and tumor evolution, we conduct an extensive genome sequencing analysis of metastatic progression in a diffuse gastric cancer. This involves a comparison between a primary tumor from a hereditary diffuse gastric cancer syndrome proband and its recurrence as an ovarian metastasis.Both the primary tumor and ovarian metastasis have common biallelic loss-of-function of both the CDH1 and TP53 tumor suppressors, indicating a common genetic origin. While the primary tumor exhibits amplification of the Fibroblast growth factor receptor 2 (FGFR2) gene, the metastasis notably lacks FGFR2 amplification but rather possesses unique biallelic alterations of Transforming growth factor-beta receptor 2 (TGFBR2), indicating the divergent in vivo evolution of a TGFBR2-mutant metastatic clonal population in this patient. As TGFBR2 mutations have not previously been functionally validated in gastric cancer, we modeled the metastatic potential of TGFBR2 loss in a murine three-dimensional primary gastric organoid culture. The Tgfbr2 shRNA knockdown within Cdh1-/-; Tp53-/- organoids generates invasion in vitro and robust metastatic tumorigenicity in vivo, confirming Tgfbr2 metastasis suppressor activity.We document the metastatic differentiation and genetic heterogeneity of diffuse gastric cancer and reveal the potential metastatic role of TGFBR2 loss-of-function. In support of this study, we apply a murine primary organoid culture method capable of recapitulating in vivo metastatic gastric cancer. Overall, we describe an integrated approach to identify and functionally validate putative cancer drivers involved in metastasis.

  View details for DOI 10.1186/s13059-014-0428-9

  View details for Web of Science ID 000346604100009

  View details for PubMedID 25315765

  View details for PubMedCentralID PMC4145231

• Molecular profiling of gastric cancer: toward personalized cancer medicine. Journal of clinical oncology Nadauld, L. D., Ford, J. M. 2013; 31 (7): 838-839

  View details for DOI 10.1200/JCO.2012.47.1714

  View details for PubMedID 23341521

• Lupus Antibody Tops Cancer Cells SCIENCE TRANSLATIONAL MEDICINE Ford, J. M. 2012; 4 (157)

  Abstract

  A lupus causing anti-DNA antibody penetrates living cells and targets DNA repair for therapeutic advantage in human cancer cells.

  View details for DOI 10.1126/scitranslmed.3004955

  View details for PubMedID 23100623

• Lynch Syndrome in Patients With Colorectal Cancer Finding the Needle in the Haystack JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Ladabaum, U., Ford, J. M. 2012; 308 (15): 1581-1583

  View details for Web of Science ID 000309858100025

  View details for PubMedID 23073955

• Long-Term Survivors of Gastric Cancer: A California Population-Based Study JOURNAL OF CLINICAL ONCOLOGY Kunz, P. L., Gubens, M., Fisher, G. A., Ford, J. M., Lichtensztajn, D. Y., Clarke, C. A. 2012; 30 (28): 3507-3515

  Abstract

  In the United States, gastric cancer is rapidly fatal with a 25% 5-year survival. Of the few patients who survive, little is known about their demographic, clinical, and tumor characteristics.Data regarding all cases of gastric and gastroesophageal junction (GEJ) adenocarcinoma diagnosed in California between 1988 and 2005 were obtained from the California Cancer Registry, a member of the National Cancer Institute's Surveillance, Epidemiology, and End Results (SEER) program. A Cox proportional hazards model was constructed to understand the independent relationships of patient demographic, disease, and treatment factors with survival.We identified 47,647 patients diagnosed with gastric or GEJ cancer. Of those, only 9,325 (20%) survived at least 3 years. Variables associated with longer survival were localized stage (hazard ratio [HR], 0.20), surgery with diagnosis in 2002 or later (HR, 0.34), surgery with diagnosis in 2001 or before (0.37), regional stage (HR, 0.53), chemotherapy (HR, 0.56), intestinal histology (HR, 0.74), well- or moderately differentiated tumors (HR, 0.76), radiation (HR, 0.80), Asian/Pacific Islander race (HR, 0.81), treatment at an academic hospital (HR, 0.85), fundus/body/antrum location (HR, 0.90), highest socioeconomic status quintile (HR, 0.91), female sex (HR, 0.92), Hispanic race (HR, 0.92), and hospital size more than 150 beds (HR, 0.94). Kaplan-Meier curves showed longer median disease-specific survival (DSS) in patients with tumors originating in the fundus/body/antrum compared with esophagus/cardia (13.4 v 10.8 months). Intestinal histology had significantly longer median DSS (28.9 months) compared with other (11.0 months) or diffuse (10.1 months) histology.Patients who survive gastric and GEJ cancer more than 3 years after diagnosis have demographic and pathologic characteristics distinct from those who do not survive.

  View details for DOI 10.1200/JCO.2011.35.8028

  View details for PubMedID 22949151

• Genetic Testing by Cancer Site Stomach CANCER JOURNAL Chun, N., Ford, J. M. 2012; 18 (4): 355-363

  Abstract

  Gastric cancer is a global public health concern, ranking as the fourth leading cause of cancer mortality, with a 5-year survival of only 20%. Approximately 10% of gastric cancers appear to have a familial predisposition, and about half of these can be attributed to hereditary germline mutations. We review the genetic syndromes and current standards for genetic counseling, testing, and medical management for screening and treatment of gastric cancer. Recently, germline mutations in the E-cadherin/CDH1 gene have been identified in families with an autosomal dominant inherited predisposition to gastric cancer of the diffuse type. The cumulative lifetime risk of developing gastric cancer in CDH1 mutation carriers is up to 80%, and women from these families also have an increased risk for developing lobular breast cancer. Prophylactic gastrectomies are recommended in unaffected CDH1 mutation carriers, because screening endoscopic examinations and blind biopsies have proven inadequate for surveillance. In addition to this syndrome, gastric cancer risk is elevated in Lynch syndrome associated with germline mutations in DNA mismatch repair genes and microsatellite instability, in hereditary breast and ovarian cancer syndrome due to germline BRCA1 and BRCA2 mutations, in familial adenomatous polyposis caused by germline APC mutations, in Li-Fraumeni syndrome due to germline p53 mutations, in Peutz-Jeghers syndrome associated with germline STK11 mutations, and in juvenile polyposis syndrome associated with germline mutations in the SMAD4 and BMPR1A genes. Guidelines for genetic testing, counseling, and management of individuals with hereditary diffuse gastric cancer are suggested. A raised awareness among the physician and genetic counseling communities regarding these syndromes may allow for increased detection and prevention of gastric cancers in these high-risk individuals.

  View details for DOI 10.1097/PPO.0b013e31826246dc

  View details for PubMedID 22846738

• Breast cancers with compromised DNA repair exhibit selective sensitivity to elesclomol DNA REPAIR Alli, E., Ford, J. M. 2012; 11 (5): 522-524

  Abstract

  The basal-like subtype of breast cancers, including those that contain germline mutations in BRCA1, tend to be triple-negative (i.e. lack expression of estrogen and progesterone receptors and lack overexpression/amplification of the HER2/neu oncogene), which renders them relatively insensitive to existing "targeted" therapy. BRCA1-mutated and basal-like breast cancers harbor compromised ability for repairing oxidative DNA damage by the DNA base-excision repair pathway. We found that this defective repair mechanism predicts sensitivity to elesclomol, an experimental therapeutic that produces elevated levels of oxidative DNA damage. In conclusion, BRCA1-mutated and/or basal-like breast cancers may benefit from treatment regimens that include elesclomol.

  View details for DOI 10.1016/j.dnarep.2012.02.003

  View details for PubMedID 22425348

• Is breast cancer a part of Lynch syndrome? Breast cancer research : BCR Ford, J. M. 2012; 14 (4): 110

  Abstract

  ABSTRACT: A long-standing question is whether breast cancer is an integral part of Lynch syndrome, also known as hereditary non-polyposis colorectal cancer. A recent study by Lotsari and colleagues analyzes molecular features of breast cancers from families with Lynch syndrome, including germline mutation carriers and their non-mutation carrier siblings, and controls with sporadic breast cancer. The study finds microsatellite instability and loss of mismatch DNA repair protein expression in one third and two thirds of Lynch syndrome samples, respectively, but in none of the non-mutation carriers or controls. Overall, the age of diagnosis of breast cancer in Lynch syndrome mutation carriers is no different than that in non-carriers, but diagnosis age was lower in those carriers whose breast tumors exhibited defects in mismatch repair. These results have important implications for genetic counseling and genetic testing of families with breast cancer and other tumors associated with Lynch syndrome, such as colorectal and endometrial cancers.

  View details for DOI 10.1186/bcr3241

  View details for PubMedID 22913763

• Strategies to Identify the Lynch Syndrome Among Patients With Colorectal Cancer A Cost-Effectiveness Analysis ANNALS OF INTERNAL MEDICINE Ladabaum, U., Wang, G., Terdiman, J., Blanco, A., Kuppermann, M., Boland, C. R., Ford, J., Elkin, E., Phillips, K. A. 2011; 155 (2): 69-U50

  Abstract

  Testing has been advocated for all persons with newly diagnosed colorectal cancer to identify families with the Lynch syndrome, an autosomal dominant cancer-predisposition syndrome that is a paradigm for personalized medicine.To estimate the effectiveness and cost-effectiveness of strategies to identify the Lynch syndrome, with attention to sex, age at screening, and differential effects for probands and relatives.Markov model that incorporated risk for colorectal, endometrial, and ovarian cancers.Published literature.All persons with newly diagnosed colorectal cancer and their relatives.Lifetime.Third-party payer.Strategies based on clinical criteria, prediction algorithms, tumor testing, or up-front germline mutation testing, followed by tailored screening and risk-reducing surgery.Life-years, cancer cases and deaths, costs, and incremental cost-effectiveness ratios.The benefit of all strategies accrued primarily to relatives with a mutation associated with the Lynch syndrome, particularly women, whose life expectancy could increase by approximately 4 years with hysterectomy and salpingo-oophorectomy and adherence to colorectal cancer screening recommendations. At current rates of germline testing, screening, and prophylactic surgery, the strategies reduced deaths from colorectal cancer by 7% to 42% and deaths from endometrial and ovarian cancer by 1% to 6%. Among tumor-testing strategies, immunohistochemistry followed by BRAF mutation testing was preferred, with an incremental cost-effectiveness ratio of $36,200 per life-year gained.The number of relatives tested per proband was a critical determinant of both effectiveness and cost-effectiveness, with testing of 3 to 4 relatives required for most strategies to meet a threshold of $50,000 per life-year gained. Immunohistochemistry followed by BRAF mutation testing was preferred in 59% of iterations in probabilistic sensitivity analysis at a threshold of $100,000 per life-year gained. Screening for the Lynch syndrome with immunohistochemistry followed by BRAF mutation testing only up to age 70 years cost $44,000 per incremental life-year gained compared with screening only up to age 60 years, and screening without an upper age limit cost $88,700 per incremental life-year gained compared with screening only up to age 70 years.Other types of cancer, uncertain family pedigrees, and genetic variants of unknown significance were not considered.Widespread colorectal tumor testing to identify families with the Lynch syndrome could yield substantial benefits at acceptable costs, particularly for women with a mutation associated with the Lynch syndrome who begin regular screening and have risk-reducing surgery. The cost-effectiveness of such testing depends on the participation rate among relatives at risk for the Lynch syndrome.National Institutes of Health.

  View details for DOI 10.1059/0003-4819-155-2-201107190-00002

  View details for PubMedID 21768580

• Enhanced sensitivity to cisplatin and gemcitabine in Brca1-deficient murine mammary epithelial cells. BMC pharmacology Alli, E., Sharma, V. B., Hartman, A., Lin, P. S., McPherson, L., Ford, J. M. 2011; 11: 7-?

  Abstract

  Breast cancers due to germline mutations or altered expression of the BRCA1 gene associate with an aggressive clinical course and frequently exhibit a "triple-negative" phenotype, i.e. lack of expression of the estrogen and progesterone hormone receptors and lack of overexpression of the HER2/NEU oncogene, thereby rendering them relatively insensitive to hormonal manipulation and targeted HER2 therapy, respectively. BRCA1 plays a role in multiple DNA repair pathways, and thus, when mutated, results in sensitivity to certain DNA damaging drugs.Here, we used a Brca1 murine mammary epithelial cell (MMEC) model to examine the effect of loss of Brca1 on cellular sensitivity to various chemotherapy drugs. To explore novel therapeutic strategies, we included DNA damaging and non-DNA damaging drugs whose mechanisms are dependent and independent of DNA repair, respectively, and drugs that are used in standard and non-standard lines of therapy for breast cancer. To understand the cellular mechanism, we also determined the role that DNA repair plays in sensitivity to these drugs. We found that cisplatin and gemcitabine had the greatest specific therapeutic benefit to Brca1-deficient MMECs, and that when used in combination produced a synergistic effect. This sensitivity may be attributed in part to defective NER, which is one of the DNA repair pathways normally responsible for repairing DNA adducts produced by cisplatin and is shown in this study to be defective in Brca1-deficient MMECs. Brca1-deficient MMECs were not differentially sensitive to the standard breast cancer chemotherapy drugs doxorubicin, docetaxel or 5-FU.Both cisplatin and gemcitabine should be explored in clinical trials for first line regimens for BRCA1-associated and triple-negative breast cancer.

  View details for DOI 10.1186/1471-2210-11-7

  View details for PubMedID 21771338

• Synergistic Chemosensitivity of Triple-Negative Breast Cancer Cell Lines to Poly(ADP-Ribose) Polymerase Inhibition, Gemcitabine, and Cisplatin CANCER RESEARCH Hastak, K., Alli, E., Ford, J. M. 2010; 70 (20): 7970-7980

  Abstract

  The basal-like subtype of breast cancer is characterized by a triple-negative (TN) phenotype (estrogen receptor, progesterone receptor, and human epidermal growth factor receptor-2/neu negative). TN breast cancers share similar gene expression profiles and DNA repair deficiencies with BRCA1-associated breast cancers. BRCA1-mutant cells exhibit sensitivity to gemcitabine, cisplatin, and poly(ADP-ribose) polymerase (PARP) inhibition; therefore, we hypothesized that TN cancer cells may also exhibit sensitivity to these drugs. In this study, we report that TN breast cancer cells are more sensitive to these drugs compared with non-TN breast cancer cells. Moreover, combination treatments indicated that PARP inhibition by the small-molecule inhibitor PJ34 or siRNA knockdown synergized with gemcitabine and cisplatin in TN cells but not in luminal cancer cells. TN cells exhibited reduced repair of UV-induced cyclobutane pyrimidine dimers after PARP inhibition, suggesting that the synergistic effect of PJ34 and gemcitabine or cisplatin reflected inefficient nucleotide excision repair. Mechanistic investigations revealed that in TN cells, PJ34 reduced the levels of ΔNp63α with a concurrent increase in p73 and its downstream target p21. Thus, the sensitivity to combination treatment seemed to be mediated by sustained DNA damage and inefficient DNA repair triggering p63/p73-mediated apoptosis. Our results suggest a novel therapeutic strategy to treat women with TN breast cancer, an aggressive disease that presently lacks effective treatment options.

  View details for DOI 10.1158/0008-5472.CAN-09-4521

  View details for PubMedID 20798217

• Second Primary Breast Cancer Occurrence According to Hormone Receptor Status JOURNAL OF THE NATIONAL CANCER INSTITUTE Kurian, A. W., McClure, L. A., John, E. M., Horn-Ross, P. L., Ford, J. M., Clarke, C. A. 2009; 101 (15): 1058-1065

  Abstract

  Contralateral second primary breast cancers occur in 4% of female breast cancer survivors. Little is known about differences in risk for second primary breast cancers related to the estrogen and progesterone receptor (hormone receptor [HR]) status of the first tumor.We calculated standardized incidence ratios (SIRs) and 95% confidence intervals (CIs) for contralateral primary breast cancers among 4927 women diagnosed with a first breast cancer between January 1, 1992, and December 31, 2004, using the National Cancer Institute's Surveillance, Epidemiology, and End Results database.For women whose first breast tumors were HR positive, risk of contralateral primary breast cancer was elevated, compared with the general population, adjusted for age, race, and calendar year (SIR = 2.22, 95% CI = 2.15 to 2.29, absolute risk [AR] = 13 cases per 10 000 person-years [PY]), and was not related to the HR status of the second tumor. For women whose first breast tumors were HR negative, the risk of a contralateral primary tumor was statistically significantly higher than that for women whose first tumors were HR positive (SIR = 3.57, 95% CI = 3.38 to 3.78, AR = 18 per 10 000 PY), and it was associated with a much greater likelihood of an HR-negative second tumor (SIR for HR-positive second tumors = 1.94, 95% CI = 1.77 to 2.13, AR = 20 per 10 000 PY; SIR for HR-negative second tumors = 9.81, 95% CI = 9.00 to 10.7, AR = 24 per 10 000 PY). Women who were initially diagnosed with HR-negative tumors when younger than 30 years had greatly elevated risk of HR-negative contralateral tumors, compared with the general population (SIR = 169, 95% CI = 106 to 256, AR = 77 per 10 000 PY). Incidence rates for any contralateral primary cancer following an HR-negative or HR-positive tumor were higher in non-Hispanic blacks, Hispanics, and Asians or Pacific Islanders than in non-Hispanic whites.Risk for contralateral second primary breast cancers varies substantially by HR status of the first tumor, age, and race and/or ethnicity. Women with HR-negative first tumors have nearly a 10-fold elevated risk of developing HR-negative second tumors, compared with the general population. These findings warrant intensive surveillance for second breast cancers in women with HR-negative tumors.

  View details for DOI 10.1093/jnci/djp181

  View details for Web of Science ID 000268812900007

  View details for PubMedID 19590058

  View details for PubMedCentralID PMC2720990

• Defective Repair of Oxidative DNA Damage in Triple-Negative Breast Cancer Confers Sensitivity to Inhibition of Poly(ADP-Ribose) Polymerase CANCER RESEARCH Alli, E., Sharma, V. B., Sunderesakumar, P., Ford, J. M. 2009; 69 (8): 3589-3596

  Abstract

  Subtypes of breast cancer that represent the two major types of epithelial cells in the breast (luminal and basal) carry distinct histopathologic profiles. Breast cancers of the basal-like subtype, which include the majority of hereditary breast cancers due to mutations in the breast cancer susceptibility gene 1 (BRCA1), frequently assume triple-negative status, i.e., they lack expression of estrogen receptor-alpha and progesterone receptor, and lack overexpression or amplification of the HER2/NEU oncogene. Defects in DNA damage response pathways result in genome instability and lead to carcinogenesis, but may also be exploited for therapeutic purposes. We analyzed repair of oxidative DNA damage by the base-excision repair (BER) pathway, which when aberrant leads to genomic instability and breast carcinogenesis, in cell lines that represent the different subtypes of breast cancer and in the presence of BRCA1 deficiency. We found that basal-like and BRCA1-mutated breast cancer cells were defective in BER of oxidative DNA damage, and that this defect conferred sensitivity to inhibition of poly(ADP-ribose) polymerase, a DNA repair enzyme. The defect may be attributed, at least in part, to a novel role for BRCA1 in the BER pathway. Overall, these data offer preventive, prognostic, and therapeutic usefulness.

  View details for DOI 10.1158/0008-5472.CAN-08-4016

  View details for PubMedID 19351835

• Performance of BRCA1/2 mutation prediction models in Asian Americans 43rd Annual Meeting of the American-Society-of-Clinical-Oncology (ASCO) Kurian, A. W., Gong, G. D., Chun, N. M., Mills, M. A., Staton, A. D., Kingham, K. E., Crawford, B. B., Lee, R., Chan, S., Donlon, S. S., Ridge, Y., Panabaker, K., West, D. W., Whittemore, A. S., Ford, J. M. AMER SOC CLINICAL ONCOLOGY. 2008: 4752–58

  Abstract

  There are established differences in breast cancer epidemiology between Asian and white individuals, but little is known about hereditary breast cancer in Asian populations. Although increasing numbers of Asian individuals are clinically tested for BRCA1/2 mutations, it is not known whether computer models that predict mutations work accurately in Asian individuals. We compared the performance in Asian and white individuals of two widely used BRCA1/2 mutation prediction models, BRCAPRO and Myriad II.We evaluated BRCAPRO and Myriad II in 200 Asian individuals and a matched control group of 200 white individuals who were tested for BRCA1/2 mutations at four cancer genetics clinics, by comparing numbers of observed versus predicted mutation carriers and by evaluating area under the receiver operating characteristic curve (AUC) for each model.BRCAPRO and Myriad II accurately predicted the number of white BRCA1/2 mutation carriers (25 observed v 24 predicted by BRCAPRO; 25 predicted by Myriad II, P > or = .69), but underpredicted Asian carriers by two-fold (49 observed v 25 predicted by BRCAPRO; 26 predicted by Myriad II; P < or = 3 x 10(-7)). For BRCAPRO, this racial difference reflects substantial underprediction of Asian BRCA2 mutation carriers (26 observed v 4 predicted; P = 1 x 10(-30)); for Myriad II, separate mutation predictions were not available. For both models, AUCs were nonsignificantly lower in Asian than white individuals, suggesting less accurate discrimination between Asian carriers and noncarriers.Both BRCAPRO and Myriad II underestimated the proportion of BRCA1/2 mutation carriers, and discriminated carriers from noncarriers less well, in Asian compared with white individuals.

  View details for DOI 10.1200/JCO.2008.16.8310

  View details for PubMedID 18779604

• Hereditary diffuse gastric cancer - Implications of genetic testing for screening and prophylactic surgery CANCER Cisco, R. M., Ford, J. M., Norton, J. A. 2008; 113 (7): 1850-1856

  Abstract

  Approximately 10% of patients with gastric cancer show familial clustering, and 3% show autosomal dominance and high penetrance. Hereditary diffuse gastric cancer (HDGC) is an autosomal-dominant, inherited cancer syndrome in which affected individuals develop diffuse-type gastric cancer at a young age. Inactivating mutations in the E-cadherin gene CDH1 have been identified in 30% to 50% of patients. CDH1 mutation carriers have an approximately 70% lifetime risk of developing DGC, and affected women carry an additional 20% to 40% risk of developing lobular breast cancer. Because endoscopic surveillance is ineffective in identifying early HDGC, gene-directed prophylactic total gastrectomy currently is offered for CDH1 mutation carriers. In series of asymptomatic individuals undergoing total gastrectomy for CDH1 mutations, the removed stomachs usually contain small foci of early DGC, making surgery not prophylactic but curative. The authors of this review recommend consideration of total gastrectomy in CDH1 mutation carriers at an age 5 years younger than the youngest family member who developed gastric cancer. Individuals who choose not to undergo prophylactic gastrectomy should be followed with biannual chromoendoscopy, and women with CDH1 mutations also should undergo regular surveillance with magnetic resonance imaging studies of the breast. Because of the emergence of gene-directed gastrectomy for HDGC, today, a previously lethal disease is detected by molecular techniques, allowing curative surgery at an early stage.

  View details for DOI 10.1002/cncr.23650

  View details for PubMedID 18798546

• CDH1 truncating mutations in the E-cadherin gene - An indication for total gastrectomy to treat hereditary diffuse gastric cancer ANNALS OF SURGERY Norton, J. A., Ham, C. M., Van Dam, J., Jeffrey, R. B., Longacre, T. A., Huntsman, D. G., Chun, N., Kurian, A. W., Ford, J. M. 2007; 245 (6): 873-879

  Abstract

  Approximately 1% to 3% of all gastric cancers are associated with families exhibiting an autosomal dominant pattern of susceptibility. E-cadherin (CDH1) truncating mutations have been shown to be present in approximately 30% of families with hereditary diffuse gastric cancer (HDGC) and are associated with a significantly increased risk of gastric cancer and lobular breast cancer.Individuals from a large kindred with HDGC who were identified to have a CDH1 mutation prospectively underwent comprehensive screening with stool occult blood testing, standard upper gastrointestinal endoscopy with random gastric biopsies, high-magnification endoscopy with random gastric biopsies, endoscopic ultrasonography, CT, and PET scans to evaluate the stomach for occult cancer. Subsequently, they each underwent total gastrectomy with D-2 node dissection and Roux-en-Y esophagojejunostomy. The stomach and resected lymph nodes were evaluated pathologically.Six patients were identified as CDH1 carriers from a single family. There were 2 men and 4 women. The mean age was 54 years (range, 51-57 years). No patient had any signs or symptoms of gastric cancer. Exhaustive preoperative stomach evaluation was normal in each case, and the stomach and adjacent lymph nodes appeared normal at surgery. However, each patient (6 of 6, 100%) was found to have multiple foci of T1 invasive diffuse gastric adenocarcinoma (pure signet-ring cell type). No patient had lymph node or distant metastases. Each was staged as T1N0M0. Each patient recovered uneventfully without morbidity or mortality.CDH1 mutations in individuals from families with HDGC are associated with gastric cancer in a highly penetrant fashion. CDH1 mutations are an indication for total gastrectomy in these patients. This mutation will identify patients with cancer before other detectable symptoms or signs of the disease.

  View details for DOI 10.1097/01.sla.0000254370.29893.e4

  View details for PubMedID 17522512

• Predicting and preventing hereditary colorectal cancer JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Ford, J. M., Whittemore, A. S. 2006; 296 (12): 1521-1523

  View details for Web of Science ID 000240770000029

  View details for PubMedID 17003401

• Molecular inversion probe analysis of gene copy alterations reveals distinct categories of colorectal carcinoma CANCER RESEARCH Ji, H., Kumm, J., Zhang, M., Farnam, K., Salari, K., Faham, M., Ford, J. M., Davis, R. W. 2006; 66 (16): 7910-7919

  Abstract

  Genomic instability is a major feature of neoplastic development in colorectal carcinoma and other cancers. Specific genomic instability events, such as deletions in chromosomes and other alterations in gene copy number, have potential utility as biologically relevant prognostic biomarkers. For example, genomic deletions on chromosome arm 18q are an indicator of colorectal carcinoma behavior and potentially useful as a prognostic indicator. Adapting a novel genomic technology called molecular inversion probes which can determine gene copy alterations, such as genomic deletions, we designed a set of probes to interrogate several hundred individual exons of >200 cancer genes with an overall distribution covering all chromosome arms. In addition, >100 probes were designed in close proximity of microsatellite markers on chromosome arm 18q. We analyzed a set of colorectal carcinoma cell lines and primary colorectal tumor samples for gene copy alterations and deletion mutations in exons. Based on clustering analysis, we distinguished the different categories of genomic instability among the colorectal cancer cell lines. Our analysis of primary tumors uncovered several distinct categories of colorectal carcinoma, each with specific patterns of 18q deletions and deletion mutations in specific genes. This finding has potential clinical ramifications given the application of 18q loss of heterozygosity events as a potential indicator for adjuvant treatment in stage II colorectal carcinoma.

  View details for DOI 10.1158/0008-5472.CAN-06-0595

  View details for PubMedID 16912164

• Opposing effects of the UV lesion repair protein XPA and UV bypass polymerase eta on ATR checkpoint signaling EMBO JOURNAL D Bomgarden, R., Lupardus, P. J., Soni, D. V., Yee, M., Ford, J. M., Cimprich, K. A. 2006; 25 (11): 2605-2614

  Abstract

  An essential component of the ATR (ataxia telangiectasia-mutated and Rad3-related)-activating structure is single-stranded DNA. It has been suggested that nucleotide excision repair (NER) can lead to activation of ATR by generating such a signal, and in yeast, DNA damage processing through the NER pathway is necessary for checkpoint activation during G1. We show here that ultraviolet (UV) radiation-induced ATR signaling is compromised in XPA-deficient human cells during S phase, as shown by defects in ATRIP (ATR-interacting protein) translocation to sites of UV damage, UV-induced phosphorylation of Chk1 and UV-induced replication protein A phosphorylation and chromatin binding. However, ATR signaling was not compromised in XPC-, CSB-, XPF- and XPG-deficient cells. These results indicate that damage processing is not necessary for ATR-mediated S-phase checkpoint activation and that the lesion recognition function of XPA may be sufficient. In contrast, XP-V cells deficient in the UV bypass polymerase eta exhibited enhanced ATR signaling. Taken together, these results suggest that lesion bypass and not lesion repair may raise the level of UV damage that can be tolerated before checkpoint activation, and that XPA plays a critical role in this activation.

  View details for DOI 10.1038/sj.emboj.7601123

  View details for PubMedID 16675950

• In vivo recruitment of XPC to UV-induced cyclobutane pyrimidine dimers by the DDB2 gene product JOURNAL OF BIOLOGICAL CHEMISTRY Fitch, M. E., Nakajima, S., Yasui, A., Ford, J. M. 2003; 278 (47): 46906-46910

  Abstract

  The initial step in mammalian nucleotide excision repair (NER) of the major UV-induced photoproducts, cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs), requires lesion recognition. It is believed that the heterodimeric proteins XPC/hHR23B and UV-DDB (UV-damaged DNA binding factor, composed of the p48 and p127 subunits) perform this function in genomic DNA, but their requirement and lesion specificity in vivo remains unknown. Using repair-deficient xeroderma pigmentosum (XP)-A cells that stably express photoproduct-specific photolyases, we determined the binding characteristics of p48 and XPC to either CPDs or 6-4PPs in vivo. p48 localized to UV-irradiated sites that contained either CPDs or 6-4PPs. However, XPC localized only to UV-irradiated sites that contained 6-4PPs, suggesting that XPC does not efficiently recognize CPDs in vivo. XPC did localize to CPDs when p48 was overexpressed in the same cell, signifying that p48 activates the recruitment of XPC to CPDs and may be the initial recognition factor in the NER pathway.

  View details for DOI 10.1074/jbc.M307254200

  View details for PubMedID 12944386

• p53 and regulation of DNA damage recognition during nucleotide excision repair DNA REPAIR Adimoolam, S., Ford, J. M. 2003; 2 (9): 947-954

  Abstract

  In response to a variety of types of DNA damage, the p53 tumor suppressor gene product is activated and regulates a number of downstream cellular processes such as cell cycle arrest, apoptosis and DNA repair. Recent discoveries concerning the regulation of DNA repair processes by p53, such as nucleotide excision repair (NER) and base excision repair (BER) have paved the way for studies to understand the mechanisms governing p53-dependent DNA repair. Although several theories have been proposed, accumulating evidence points to a transcriptional regulatory role for p53 in NER, mediating expression of the global genomic repair (GGR)-specific damage recognition genes, DDB2 and XPC. In BER, a more direct role for p53 has been proposed, potentially acting through protein-protein interactions with BER specific factors. These advances have greatly enhanced our understanding of the role of p53 in DNA repair and this review comprehensively summarizes current opinions on the mechanisms of p53-dependent DNA repair.

  View details for DOI 10.1016/S4568-7864(03)0087-9

  View details for PubMedID 12967652

• The DDB2 nucleotide excision repair gene product p48 enhances global genomic repair in p53 deficient human fibroblasts DNA REPAIR Fitch, M. E., Cross, I. V., Turner, S. J., Adimoolam, S., Lin, C. X., Williams, K. G., Ford, J. A. 2003; 2 (7): 819-826

  Abstract

  The tumor suppressor protein p53 functions in many cellular responses to UV-induced DNA damage, including activating the global nucleotide excision repair (NER) pathway. A potential mechanism for the effect on NER is through the ability of p53 to transcriptionally regulate genes that are directly involved in NER. DDB2 is one such gene that is regulated by p53 at both the basal and UV inducible levels. In order to further understand p53's role in NER, we transfected and selected clones that stably overexpress DDB2 in a human p53 deficient cell line. Global genomic repair (GGR) of cyclobutane pyrimidine dimers was significantly increased in the DDB2 expressing cells in comparison to controls, demonstrating that p53 wt protein itself is not directly required for efficient GGR. The protein product of DDB2, p48, is also post-translationally regulated by proteasomal degradation in response to UV irradiation. The regulation of p48 at both the transcriptional level by p53, and post-translationally by the proteasome suggests that p48 may be a rate limiting component of NER.

  View details for DOI 10.1016/S1568-7864(03)00066-1

  View details for PubMedID 12826282

• p53 responsive nucleotide excision repair gene products p48 and XPC, but not p53, localize to sites of UV-irradiation-induced DNA damage, in vivo CARCINOGENESIS Fitch, M. E., Cross, I. V., Ford, J. M. 2003; 24 (5): 843-850

  Abstract

  The p53 tumor suppressor gene is an important mediator of the cellular response to ultraviolet (UV)-irradiation-induced DNA damage and affects the efficiency of the nucleotide excision repair (NER) pathway. The mechanism by which p53 regulates NER may be through its ability to act as a transcription factor, and/or through direct interactions with damaged DNA or the repair machinery. p53 has been shown to regulate the expression of the DDB2 gene (encoding the p48 protein) and the XPC gene, two important components of the NER pathway involved in DNA damage recognition. In this study, a localized UV-irradiation technique was used to examine the localization of p53, p48 and XPC proteins in relation to sites of UV photoproducts, in vivo. We did not observe any specific co-localization of p53 with sites of UV-induced DNA damage, but did observe rapid co-localization of both p48 and XPC to these sites. p48 bound to UV photoproducts in cells mutant or deficient for either p53, XPC or XPA, and p48 enhanced XPC binding to lesions, suggesting that p48 is a very early recognition factor of DNA damage. We propose that p53 functions to transcriptionally regulate the DDB2 and XPC NER genes, but does not activate the NER pathway through direct interactions with UV-induced damaged DNA or other repair factors.

  View details for DOI 10.1093/carcin/bgg031

  View details for PubMedID 12771027

• p53 and DNA damage-inducible expression of the xeroderma pigmentosum group C gene PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Adimoolam, S., Ford, J. M. 2002; 99 (20): 12985-12990

  Abstract

  The p53 tumor suppressor gene product is a transcription factor involved in cell-cycle regulation, apoptosis, and DNA repair. We and others have shown that p53 is required for efficient nucleotide excision repair (NER) of UV-induced DNA lesions. p53-deficient cells are defective in the repair of UV photoproducts in genomic DNA but proficient for transcription-coupled repair. Therefore, we examined whether p53 regulates the expression of genes required for global genomic repair. In this study, we demonstrate that the mRNA and protein products of the xeroderma pigmentosum group C (XPC) gene are UV-inducible in a time- and dose-dependent manner in human WI38 fibroblasts and HCT116 colorectal cancer cells wild type for p53. However, no significant induction of XPC was observed in p53-deficient counterparts to these cells. Furthermore, regulated expression of wild-type p53 in p53 null Li-Fraumeni syndrome human fibroblasts significantly augmented the expression of XPC protein. Analysis of the human XPC gene sequence revealed a putative p53 response element in the XPC promoter that was capable of mediating sequence-specific DNA binding to p53 in vitro. These results provide strong evidence that the NER gene XPC is a DNA damage-inducible and p53-regulated gene and likely plays a role in the p53-dependent NER pathway.

  View details for DOI 10.1073/pnas.202485699

  View details for PubMedID 12242345

• BRCA1 induces DNA damage recognition factors and enhances nucleotide excision repair NATURE GENETICS Hartman, A. R., Ford, J. M. 2002; 32 (1): 180-184

  Abstract

  Inheritance of a mutation in the gene BRCA1 confers on women a 50-85% lifetime risk of developing breast cancer. Mutations in the TP53 tumor-suppressor gene are found in 70-80% of BRCA1-mutated breast cancer but only 30% of those with wildtype BRCA1 (ref. 3). The p53 protein regulates nucleotide excision repair (NER) through transcriptional regulation of genes involved in the recognition of adducts in genomic DNA. Loss of p53 function results in deficient global genomic repair (GGR), a subset of NER that targets and removes lesions from the whole genome. Here we show that BRCA1 specifically enhances the GGR pathway, independent of p53, and can induce p53-independent expression of the NER genes XPC, DDB2, and GADD45. Defects in the NER pathway in BRCA1-associated breast cancers may be causal in tumor development, suggesting a multistep model of carcinogenesis.

  View details for DOI 10.1038/ng953

  View details for PubMedID 12195423

• Xeroderma pigmentosum p48 gene enhances global genomic repair and suppresses UV-induced mutagenesis MOLECULAR CELL Tang, J. Y., Hwang, B. J., Ford, J. M., Hanawalt, P. C., Chu, G. 2000; 5 (4): 737-744

  Abstract

  UV-damaged DNA-binding activity (UV-DDB) is deficient in some xeroderma pigmentosum group E individuals due to mutation of the p48 gene, but its role in DNA repair has been obscure. We found that UV-DDB is also deficient in cell lines and primary tissues from rodents. Transfection of p48 conferred UV-DDB to hamster cells, and enhanced removal of cyclobutane pyrimidine dimers (CPDs) from genomic DNA and from the nontranscribed strand of an expressed gene. Expression of p48 suppressed UV-induced mutations arising from the nontranscribed strand, but had no effect on cellular UV sensitivity. These results define the role of p48 in DNA repair, demonstrate the importance of CPDs in mutagenesis, and suggest how rodent models can be improved to better reflect cancer susceptibility in humans.

  View details for PubMedID 10882109

• Expression of the p48 xeroderma pigmentosum gene is p53-dependent and is involved in global genomic repair PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Hwang, B. J., Ford, J. M., Hanawalt, P. C., Chu, G. 1999; 96 (2): 424-428

  Abstract

  In human cells, efficient global genomic repair of DNA damage induced by ultraviolet radiation requires the p53 tumor suppressor, but the mechanism has been unclear. The p48 gene is required for expression of an ultraviolet radiation-damaged DNA binding activity and is disrupted by mutations in the subset of xeroderma pigmentosum group E cells that lack this activity. Here, we show that p48 mRNA levels strongly depend on basal p53 expression and increase further after DNA damage in a p53-dependent manner. Furthermore, like p53(-/-) cells, xeroderma pigmentosum group E cells are deficient in global genomic repair. These results identify p48 as the link between p53 and the nucleotide excision repair apparatus.

  View details for PubMedID 9892649

• Expression of wild-type p53 is required for efficient global genomic nucleotide excision repair in UV-irradiated human fibroblasts JOURNAL OF BIOLOGICAL CHEMISTRY Ford, J. M., Hanawalt, P. C. 1997; 272 (44): 28073-28080

  Abstract

  We have shown previously that Li-Fraumeni syndrome fibroblasts homozygous for p53 mutations are deficient in the removal of UV-induced cyclobutane pyrimidine dimers from genomic DNA, but still proficient in the transcription-coupled repair pathway (Ford, J. M., and Hanawalt, P. C. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 8876-8880). We have now utilized monoclonal antibodies specific for cyclobutane pyrimidine dimers or 6-4 photoproducts, respectively, to measure their repair in UV-irradiated human fibroblasts. Cells homozygous for p53 mutations were deficient in the repair of both photoproducts, whereas cells heterozygous for mutant p53 exhibited normal repair of 6-4 photoproducts, but decreased initial rates of removal of cyclobutane pyrimidine dimers, compared with normal cells. The specificity of the effect of wild-type p53 on nucleotide excision repair was demonstrated in a p53 homozygous mutant cell line containing a tetracycline-regulated wild-type p53 gene. Wild-type p53 expression and activity were suppressed in the presence of tetracycline, whereas withdrawal of tetracycline resulted in the induction of p53 expression, cell cycle checkpoint activation, and DNA damage-induced apoptosis. The regulated expression of wild-type p53 resulted in the recovery of normal levels of repair of both cyclobutane pyrimidine dimers and 6-4 photoproducts in genomic DNA, but did not alter the transcription-coupled repair of cyclobutane pyrimidine dimers. Therefore, the wild-type p53 gene product is an important determinant of nucleotide excision repair activity in human cells.

  View details for Web of Science ID A1997YD47300087

  View details for PubMedID 9346961

• LI-FRAUMENI SYNDROME FIBROBLASTS HOMOZYGOUS FOR P53 MUTATIONS ARE DEFICIENT IN GLOBAL DNA-REPAIR BUT EXHIBIT NORMAL TRANSCRIPTION-COUPLED REPAIR AND ENHANCED UV RESISTANCE PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Ford, J. M., Hanawalt, P. C. 1995; 92 (19): 8876-8880

  Abstract

  We investigated whether mutations in the p53 tumor suppressor gene alter UV sensitivity and/or repair of UV-induced DNA damage in primary human skin fibroblasts from patients with Li-Fraumeni syndrome, heterozygous for mutations in one allele of the p53 gene (p53 wt/mut) and sublines expressing only mutant p53 (p53 mut). The p53 mut cells were more resistant than the p53 wt/mut cells to UV cytotoxicity and exhibited less UV-induced apoptosis. DNA repair analysis revealed reduced removal of cyclobutane pyrimidine dimers from overall genomic DNA in vivo in p53 mut cells compared with p53 wt/mut or normal cells. However, p53 mut cells retained the ability to preferentially repair damage in the transcribed strands of expressed genes (transcription-coupled repair). These results suggest that loss of p53 function may lead to greater genomic instability by reducing the efficiency of DNA repair but that cellular resistance to DNA-damaging agents may be enhanced through elimination of apoptosis.

  View details for Web of Science ID A1995RU75900070

  View details for PubMedID 7568035

  View details for PubMedCentralID PMC41070

• Repurposing mebendazole against triple-negative breast cancer CNS metastasis. Journal of neuro-oncology Rodrigues, A. J., Chernikova, S. B., Wang, Y., Trinh, T. T., Solow-Cordero, D. E., Alexandrova, L., Casey, K. M., Alli, E., Aggarwal, A., Quill, T., Koegel, A. K., Feldman, B. J., Ford, J. M., Hayden-Gephart, M. 2024

  Abstract

  PURPOSE: Triple-negative breast cancer (TNBC) often metastasizes to the central nervous system (CNS) and has the highest propensity among breast cancer subtypes to develop leptomeningeal disease (LMD). LMD is a spread of cancer into leptomeningeal space that speeds up the disease progression and severely aggravates the prognosis. LMD has limited treatment options. We sought to test whether the common anti-helminthic drug mebendazole (MBZ) may be effective against murine TNBC LMD.METHODS: A small-molecule screen involving TNBC cell lines identified benzimidazoles as potential therapeutic agents for further study. In vitro migration assays were used to evaluate cell migration capacity and the effect of MBZ. For in vivo testing, CNS metastasis was introduced into BALB/c athymic nude mice through internal carotid artery injections of brain-tropic MDA-MB-231-BR or MCF7-BR cells. Tumor growth and spread was monitored by bioluminescence imaging and immunohistochemistry. MBZ was given orally at 50 and 100mg/kg doses. MBZ bioavailability was assayed by mass spectrometry.RESULTS: Bioinformatic analysis and migration assays revealed higher migratory capacity of TNBC compared to other breast cancer subtypes. MBZ effectively slowed down migration of TNBC cell line MDA-MB-231 and its brain tropic derivative MDA-MB-231-BR. In animal studies, MBZ reduced leptomeningeal spread, and extended survival in brain metastasis model produced by MDA-MB-231-BR cells. MBZ did not have an effect in the non-migratory MCF7-BR model.CONCLUSIONS: We demonstrated that MBZ is a safe and effective oral agent in an animal model of TNBC CNS metastasis. Our findings are concordant with previous efforts involving MBZ and CNS pathology and support the drug's potential utility to slow down leptomeningeal spread.

  View details for DOI 10.1007/s11060-024-04654-x

  View details for PubMedID 38563850

• Repurposing mebendazole against triple-negative breast cancer leptomeningeal disease. Research square Rodrigues, A., Chernikova, S. B., Wang, Y., Trinh, T. T., Solow-Cordero, D. E., Alexandrova, L., Casey, K. M., Alli, E., Aggarwal, A., Quill, T., Koegel, A., Feldman, B. J., Ford, J. M., Hayden-Gephart, M. 2024

  Abstract

  Triple-negative breast cancer (TNBC) is an aggressive subtype that often metastasizes to the brain. Leptomeningeal disease (LMD), a devastating brain metastasis common in TNBC, has limited treatment options. We sought to test whether the common anti-helminthic drug mebendazole (MBZ) may be effective against murine TNBC LMD.A small-molecule screen involving TNBC cell lines identified benzimidazoles as potential therapeutic agents for further study. In vitro migration assays were used to evaluate cell migration capacity and the effect of MBZ. For in vivo testing, LMD was introduced into BALB/c athymic nude mice through internal carotid artery injections of brain-tropic MDA-MB-231-BR or MCF7-BR cells. Tumor growth and spread was monitored by bioluminescence imaging. MBZ was given orally at 50 and 100 mg/kg doses. MBZ bioavailability was assayed by mass spectrometry.Bioinformatic analysis and migration assays revealed higher migratory capacity of TNBC compared to other breast cancer subtypes. MBZ effectively slowed down migration of TNBC cell line MDA-MB-231 and its brain tropic derivative MDA-MB-231-BR. In animal studies, MBZ reduced tumor growth and extended survival in the LMD model produced by MDA-MB-231-BR cells. MBZ did not have an effect in the non-migratory MCF7-BR model.We demonstrated that MBZ is a safe and effective oral agent in an animal model of TNBC LMD. Our findings are concordant with previous efforts involving MBZ and central nervous system pathology and further support the drug's potential utility as an alternative therapeutic for TNBC LMD.

  View details for DOI 10.21203/rs.3.rs-3915392/v1

  View details for PubMedID 38405839

  View details for PubMedCentralID PMC10889063

• Identification of a potential chemoprevention agent for BRCA1- mutated cancers. Shanmugam, S., Hosch, E., Konar, D., Ford, J. M., Alli, E. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000920538200025

• Identification of a potential chemoprevention agent for BRCA1- mutated cancers Shanmugam, S., Hosch, E., Konar, D., Ford, J. M., Alli, E. AMER ASSOC CANCER RESEARCH. 2022

  View details for Web of Science ID 000896894200004

• Clinical Trial Development in TP53-Mutated Locally Advanced and Recurrent/Metastatic Head and Neck Squamous Cell Carcinoma. Journal of the National Cancer Institute Rodriguez, C. P., Kang, H., Geiger, J. L., Burtness, B., Chung, C. H., Pickering, C. R., Fakhry, C., Le, Q. T., Yom, S. S., Galloway, T. J., Golemis, E., Li, A., Shoop, J., Wong, S., Mehra, R., Skinner, H., Saba, N. F., Flores, E. R., Myers, J. N., Ford, J. M., Karchin, R., Ferris, R. L., Kunos, C., Lynn, J. M., Malik, S. 2022

  Abstract

  TP53 mutation is the most frequent genetic event in head and neck squamous cell carcinoma (HNSCC), found in over 80% of patients with HPV-negative disease. As mutations in the TP53 gene are associated with worse outcomes in HNSCC, novel therapeutic approaches are needed for patients with TP53 mutated tumors. The National Cancer Institute (NCI) sponsored a Clinical Trials Planning Meeting (CTPM) to address the issues of identifying and developing clinical trials for patients with TP53 mutations. Subcommittees, or Breakout Groups, were tasked with developing clinical studies in both the locally advanced and recurrent/metastatic disease settings as well consider signal seeking trial designs. A fourth Breakout Group was focused on identifying and standardizing biomarker integration into trial design; this information was provided to the other Breakout Groups prior to the meeting to aid in study development. A total of four concepts were prioritized to move forward for further development and implementation. This article summarizes the proceedings of the CTPM with the goal of developing clinical trials for patients with TP53 mutant HNSCC that can be conducted within the National Clinical Trials Network.

  View details for DOI 10.1093/jnci/djac163

  View details for PubMedID 36053203

• Targeting HER2 mutation-positive advanced biliary tract cancers with neratinib: Final results from the phase 2 SUMMIT basket trial. Harding, J. J., Piha-Paul, S., Shah, R. H., Cleary, J. M., Quinn, D. I., Brana, I., Moreno, V., Borad, M. J., Loi, S., Spanggaard, I., Ford, J. M., DiPrimeo, D., Berger, M. F., Eli, L., Meric-Bernstam, F., Solit, D. B., Abou-Alfa, G. K. LIPPINCOTT WILLIAMS & WILKINS. 2022

  View details for Web of Science ID 000863680301245

• Exploring homologous recombination deficiency thresholds for predicting response to platinum-based treatment in triple negative breast cancer. Timms, K., Lenz, L., Cogan, E. S., Mayer, E. L., Kaklamani, V. G., Stearns, V., Abramson, V. G., Falkson, C., Jankowitz, R., Marcom, P., Tung, N. M., Gradishar, W., Ford, J. M., Vinayak, S., Boughey, J., Goetz, M. P., Storniolo, A., Connolly, R. M., Richardson, A. L., Telli, M. L. LIPPINCOTT WILLIAMS & WILKINS. 2022

  View details for Web of Science ID 000863680301530

• MITI minimum information guidelines for highly multiplexed tissue images. Nature methods Schapiro, D., Yapp, C., Sokolov, A., Reynolds, S. M., Chen, Y., Sudar, D., Xie, Y., Muhlich, J., Arias-Camison, R., Arena, S., Taylor, A. J., Nikolov, M., Tyler, M., Lin, J., Burlingame, E. A., Human Tumor Atlas Network, Chang, Y. H., Farhi, S. L., Thorsson, V., Venkatamohan, N., Drewes, J. L., Pe'er, D., Gutman, D. A., Herrmann, M. D., Gehlenborg, N., Bankhead, P., Roland, J. T., Herndon, J. M., Snyder, M. P., Angelo, M., Nolan, G., Swedlow, J. R., Schultz, N., Merrick, D. T., Mazzili, S. A., Cerami, E., Rodig, S. J., Santagata, S., Sorger, P. K., Abravanel, D. L., Achilefu, S., Ademuyiwa, F. O., Adey, A. C., Aft, R., Ahn, K. J., Alikarami, F., Alon, S., Ashenberg, O., Baker, E., Baker, G. J., Bandyopadhyay, S., Bayguinov, P., Beane, J., Becker, W., Bernt, K., Betts, C. B., Bletz, J., Blosser, T., Boire, A., Boland, G. M., Boyden, E. S., Bucher, E., Bueno, R., Cai, Q., Cambuli, F., Campbell, J., Cao, S., Caravan, W., Chaligne, R., Chan, J. M., Chasnoff, S., Chatterjee, D., Chen, A. A., Chen, C., Chen, C., Chen, B., Chen, F., Chen, S., Chheda, M. G., Chin, K., Cho, H., Chun, J., Cisneros, L., Coffey, R. J., Cohen, O., Colditz, G. A., Cole, K. A., Collins, N., Cotter, D., Coussens, L. M., Coy, S., Creason, A. L., Cui, Y., Zhou, D. C., Curtis, C., Davies, S. R., Bruijn, I., Delorey, T. M., Demir, E., Denardo, D., Diep, D., Ding, L., DiPersio, J., Dubinett, S. M., Eberlein, T. J., Eddy, J. A., Esplin, E. D., Factor, R. E., Fatahalian, K., Feiler, H. S., Fernandez, J., Fields, A., Fields, R. C., Fitzpatrick, J. A., Ford, J. M., Franklin, J., Fulton, B., Gaglia, G., Galdieri, L., Ganesh, K., Gao, J., Gaudio, B. L., Getz, G., Gibbs, D. L., Gillanders, W. E., Goecks, J., Goodwin, D., Gray, J. W., Greenleaf, W., Grimm, L. J., Gu, Q., Guerriero, J. L., Guha, T., Guimaraes, A. R., Gutierrez, B., Hacohen, N., Hanson, C. R., Harris, C. R., Hawkins, W. G., Heiser, C. N., Hoffer, J., Hollmann, T. J., Hsieh, J. J., Huang, J., Hunger, S. P., Hwang, E., Iacobuzio-Donahue, C., Iglesia, M. D., Islam, M., Izar, B., Jacobson, C. A., Janes, S., Jayasinghe, R. G., Jeudi, T., Johnson, B. E., Johnson, B. E., Ju, T., Kadara, H., Karnoub, E., Karpova, A., Khan, A., Kibbe, W., Kim, A. H., King, L. M., Kozlowski, E., Krishnamoorthy, P., Krueger, R., Kundaje, A., Ladabaum, U., Laquindanum, R., Lau, C., Lau, K. S., LeBoeuf, N. R., Lee, H., Lenburg, M., Leshchiner, I., Levy, R., Li, Y., Lian, C. G., Liang, W., Lim, K., Lin, Y., Liu, D., Liu, Q., Liu, R., Lo, J., Lo, P., Longabaugh, W. J., Longacre, T., Luckett, K., Ma, C., Maher, C., Maier, A., Makowski, D., Maley, C., Maliga, Z., Manoj, P., Maris, J. M., Markham, N., Marks, J. R., Martinez, D., Mashl, J., Masilionis, I., Massague, J., Mazurowski, M. A., McKinley, E. T., McMichael, J., Meyerson, M., Mills, G. B., Mitri, Z. I., Moorman, A., Mudd, J., Murphy, G. F., Deen, N. N., Navin, N. E., Nawy, T., Ness, R. M., Nevins, S., Nirmal, A. J., Novikov, E., Oh, S. T., Oldridge, D. A., Owzar, K., Pant, S. M., Park, W., Patti, G. J., Paul, K., Pelletier, R., Persson, D., Petty, C., Pfister, H., Polyak, K., Puram, S. V., Qiu, Q., Villalonga, A. Q., Ramirez, M. A., Rashid, R., Reeb, A. N., Reid, M. E., Remsik, J., Riesterer, J. L., Risom, T., Ritch, C. C., Rolong, A., Rudin, C. M., Ryser, M. D., Sato, K., Sears, C. L., Semenov, Y. R., Shen, J., Shoghi, K. I., Shrubsole, M. J., Shyr, Y., Sibley, A. B., Simmons, A. J., Sinha, A., Sivagnanam, S., Song, S., Southar-Smith, A., Spira, A. E., Cyr, J. S., Stefankiewicz, S., Storrs, E. P., Stover, E. H., Strand, S. H., Straub, C., Street, C., Su, T., Surrey, L. F., Suver, C., Tan, K., Terekhanova, N. V., Ternes, L., Thadi, A., Thomas, G., Tibshirani, R., Umeda, S., Uzun, Y., Vallius, T., Van Allen, E. R., Vandekar, S., Vega, P. N., Veis, D. J., Vennam, S., Verma, A., Vigneau, S., Wagle, N., Wahl, R., Walle, T., Wang, L., Warchol, S., Washington, M. K., Watson, C., Weimer, A. K., Wendl, M. C., West, R. B., White, S., Windon, A. L., Wu, H., Wu, C., Wu, Y., Wyczalkowski, M. A., Xu, J., Yao, L., Yu, W., Zhang, K., Zhu, X. 2022; 19 (3): 262-267

  View details for DOI 10.1038/s41592-022-01415-4

  View details for PubMedID 35277708

• Phase II Study of Taselisib in PIK3CA-Mutated Solid Tumors Other Than Breast and Squamous Lung Cancer: Results From the NCI-MATCH ECOG-ACRIN Trial (EAY131) Subprotocol I. JCO precision oncology Krop, I. E., Jegede, O. A., Grilley-Olson, J. E., Lauring, J. D., Mitchell, E. P., Zwiebel, J. A., Gray, R. J., Wang, V., McShane, L. M., Rubinstein, L. V., Patton, D., Williams, P. M., Hamilton, S. R., Kono, S. A., Ford, J. M., Garcia, A. A., Sui, X. D., Siegel, R. D., Slomovitz, B. M., Conley, B. A., Arteaga, C. L., Harris, L. N., O'Dwyer, P. J., Chen, A. P., Flaherty, K. T. 2022; 6: e2100424

  Abstract

  PURPOSE: PIK3CA mutations frequently contribute to oncogenesis in solid tumors. Taselisib, a potent and selective inhibitor of phosphoinositide 3-kinase, has demonstrated clinical activity in PIK3CA-mutant breast cancer. Whether PIK3CA mutations predict sensitivity to taselisib in other cancer types is unknown. National Cancer Institute-Molecular Analysis for Therapy Choice Arm EAY131-I is a single-arm, phase II study of the safety and efficacy of taselisib in patients with advanced cancers.METHODS: Eligible patients had tumors with an activating PIK3CA mutation. Patients with breast or squamous cell lung carcinoma, or whose cancer had KRAS or PTEN mutations, were excluded. Patients received taselisib 4 mg, orally once daily continuously, until disease progression or unacceptable toxicity. The primary end point was objective response rate. Secondary end points included progression-free survival (PFS), 6-month PFS, overall survival (OS), and identification of predictive biomarkers.RESULTS: Seventy patients were enrolled, and 61 were eligible and initiated protocol therapy. Types of PIK3CA mutations included helical 41 of 61 (67%), kinase 11 of 61 (18%), and other 9 of 61 (15%). With a median follow-up of 35.7 months, there were no complete or partial responses. Six-month PFS was 19.9% (90% CI, 12.0 to 29.3) and median PFS was 3.1 months (90% CI, 1.8 to 3.7). Six-month OS was 60.7% (90% CI, 49.6 to 70.0) and median OS was 7.2 months (90% CI, 5.9 to 10.0). Individual comutations were too heterogeneous to correlate with clinical outcome. Fatigue, diarrhea, nausea, and hyperglycemia were the most common toxicities, and most were grade 1 and 2.CONCLUSION: In this study, taselisib monotherapy had very limited activity in a heterogeneous cohort of heavily pretreated cancer patients with PIK3CA-mutated tumors; the presence of a PIK3CA mutation alone does not appear to be a sufficient predictor of taselisib activity.

  View details for DOI 10.1200/PO.21.00424

  View details for PubMedID 35138919

• Surgery for Hereditary Diffuse Gastric Cancer: Long-Term Outcomes. Cancers Forrester, J. D., Foster, D., Ford, J. M., Longacre, T. A., Ladabaum, U., Fry, S., Norton, J. A. 2022; 14 (3)

  Abstract

  Gastric cancer is inherited as an autosomal dominant condition in hereditary diffuse gastric cancer (HDGC). The gene associated with HDGC is an E-cadherin gene CDH1. At the time of initiation of this study, it was estimated that 70% of patients who inherited the CDH1 gene mutation would develop gastric cancer. We hypothesized that the rate of signet ring cell cancer in asymptomatic patients with CDH1 mutations may be higher than anticipated and that the surgery could be conducted with acceptable short-term and long-term complications suggesting that the quality of life with the surgery is acceptable.We prospectively studied the role of total gastrectomy in symptomatic and asymptomatic patients with CDH1 mutations. A total of 43 patients with mutations of the CDH1 gene were studied prospectively, including 8 with symptoms and 35 without symptoms. Total gastrectomy was recommended to each. Quality of life was assessed in patients who underwent prophylactic gastrectomy. Proportions are compared with Fisher's exact test.In total, 13 (30%) asymptomatic patients declined surgery. Total gastrectomy was performed in 8 symptomatic patients and 22 asymptomatic patients of whom only 3 asymptomatic patients (14%) had endoscopically proven signet ring cell cancer preoperatively, while 21 of 22 (95%) had it on final pathology (p = 0.05). Each asymptomatic patient was T1, N0, while seven out of eight symptomatic patients had T3-T4 tumors and six had positive lymph nodes. None had operative complications or operative death. The median follow-up was 7 years. Five (63%) symptomatic patients died, while only one (95%) prophylactic patient died of a non-gastric cancer- or surgery-related issue (p = 0.05). A total of 15 prophylactic patients had long-term follow-up. Each had significant weight loss (mean 23%) but all had a normal body mass index. In total, 40% had bile reflux gastritis controlled with sucralfate. Each returned to work and, if given the choice, said that they would undergo the surgery again.Total gastrectomy is indicated for patients who have an inherented CDH1 mutation. Endoscopic screening is not reliable for diagnosing signet ring cell stomach cancer. If patients wait for symptoms, they will have a more advanced disease and significantly reduced survival. Operative complications of prophylactic gastrectomy are minimal, and long-term quality of life is acceptable.

  View details for DOI 10.3390/cancers14030728

  View details for PubMedID 35158993

• Genomic analysis from the talazoparib beyond BRCA clinical trial: Homologous recombination (HR) deficiency scores, loss-of-heterozygosity and mutations in non-BRCA1/2 mutant tumors with other HR mutations Gruber, J. J., Afghahi, A., Hatton, A., Gross, W., Foran, J., McMillan, A., Ford, J. M., Telli, M. L. AMER ASSOC CANCER RESEARCH. 2021

  View details for Web of Science ID 000618737700124

• Targeting HER2 (ERBB2) mutation-positive advanced biliary tract cancers with neratinib: Results from the phase II SUMMIT 'basket' trial. Harding, J. J., Cleary, J. M., Quinn, D. I., Brana, I., Moreno, V., Borad, M. J., Loi, S., Spanggaard, I., Park, H., Ford, J. M., Arnedos, M., Stemmer, S. M., De La Fouchardiere, C., Ramirez, S., Fountzilas, C., Zhang Jie, Xu Feng, Lalani, A. S., Piha-Paul, S., Abou-Alfa, G. K. LIPPINCOTT WILLIAMS & WILKINS. 2021

  View details for DOI 10.1200/JCO.2021.39.3_suppl.320

  View details for Web of Science ID 000636712800337

• Subtle endoscopic manifestations of diffuse signet cell gastric adenocarcinoma in patients with CDH1 mutations. Gastrointestinal endoscopy Ladabaum, U., Ford, J. M., Poultsides, G., Norton, J. 2021

  View details for DOI 10.1016/j.gie.2021.08.006

  View details for PubMedID 34416278

• A novel DDB2 mutation causes defective recognition of UV-induced DNA damages and prevalent equine squamous cell carcinoma. DNA repair Chen, L., Bellone, R. R., Wang, Y., Singer-Berk, M., Sugasawa, K., Ford, J. M., Artandi, S. E. 2020; 97: 103022

  Abstract

  Squamous cell carcinoma (SCC) occurs frequently in the human Xeroderma Pigmentosum (XP) syndrome and is characterized by deficient UV-damage repair. SCC is the most common equine ocular cancer and the only associated genetic risk factor is a UV-damage repair protein. Specifically, a missense mutation in horse DDB2 (T338M) was strongly associated with both limbal SCC and third eyelid SCC in three breeds of horses (Halflinger, Belgian, and Rocky Mountain Horses) and was hypothesized to impair binding to UV-damaged DNA. Here, we investigate DDB2-T338M mutant's capacity to recognize UV lesions in vitro and in vivo, together with human XP mutants DDB2-R273H and -K244E. We show that the recombinant DDB2-T338M assembles with DDB1, but fails to show any detectable binding to DNA substrates with or without UV lesions, due to a potential structural disruption of the rigid DNA recognition β-loop. Consistently, we demonstrate that the cellular DDB2-T338M is defective in its recruitment to focally radiated DNA damages, and in its access to chromatin. Thus, we provide direct functional evidence indicating the DDB2-T338M recapitulates molecular defects of human XP mutants, and is the causal loss-of-function allele that gives rise to equine ocular SCCs. Our findings shed new light on the mechanism of DNA recognition by UV-DDB and on the initiation of ocular malignancy.

  View details for DOI 10.1016/j.dnarep.2020.103022

  View details for PubMedID 33276309

• Universal Screening of Gastrointestinal Malignancies for Mismatch Repair Deficiency at Stanford. JNCI cancer spectrum Abrha, A., Shukla, N. D., Hodan, R., Longacre, T., Raghavan, S., Pritchard, C. C., Fisher, G., Ford, J., Haraldsdottir, S. 2020; 4 (5): pkaa054

  Abstract

  Background: In light of recent Food and Drug Administration (FDA) approval of immune checkpoint inhibitors for mismatch repair deficient (dMMR) malignancies, identifying patients with dMMR malignancies has become increasingly important. Although screening for dMMR in colorectal cancer (CRC) is recommended, it is less common for extracolonic gastrointestinal (GI) malignancies. At Stanford Comprehensive Cancer Institute (SCCI), all GI malignancies have been screened for dMMR via immunohistochemistry since January 2016.Methods: In this study, we conducted a retrospective review of all patients with GI malignancies screened for dMMR between January 2016 and December 2017. Tumor sequencing was performed on cases negative for germline pathogenic variants where tumor material was available.Results: A total of 1425 consecutive GI malignancies were screened for dMMR at SCCI during the study period, and 1374 were included for analysis. dMMR was detected in 7.2% of all GI malignancies. We detected the highest prevalence of dMMR in gastric (15 of 150, 10.0%) followed by colorectal (63 of 694, 9.1%), pancreatic (13 of 244, 5.3%), and gastroesophageal malignancy (6 of 132, 4.5%) patients. Lynch syndrome was the most common etiology for dMMR in colorectal cancer (41.5%), double somatic (confirmed or possible) pathogenic variants the most common etiology in pancreatic cancer (44.4%), and somatic MLH1 hypermethylation the most common etiology in gastric (73.3%) and gastroesophageal cancer (83.3%).Conclusions: Given the relatively high incidence of dMMR in GI malignancies, we recommend screening all GI malignancies. Our results suggest that although a rare occurrence, double somatic pathogenic variants may be a biologically significant pathway causing dMMR in pancreatic cancer.

  View details for DOI 10.1093/jncics/pkaa054

  View details for PubMedID 33225206

• Clinicopathologic features of invasive breast cancer (BC) diagnosed in carriers of germline PALB2, CHEK2 and ATM pathogenic variants. Scott, D., Kingham, K., Hodan, R., Ma, C., Mills, M., Ford, J. M., Kurian, A. W., Telli, M. L. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000560368301071

• Germline mutation in 1,338 BRCA-negative Chinese hereditary breast and/or ovarian cancer patients: clinical testing with a multigene test panel. The Journal of molecular diagnostics : JMD Kwong, A., Shin, V. Y., Chen, J., Wai-Yin Cheuk, I., Ho, C. Y., Au, C. H., Chan, K. K., Ngan, H. Y., Chan, T. L., Ford, J. M., Ma, E. S. 2020

  Abstract

  Differences in the mutation spectrum across ethnicities suggest that it is important to identify genes in addition to common high penetrant genes to estimate the associated breast cancer risk in Chinese. 1,338 high-risk breast cancer patients who tested negative for germline BRCA1, BRCA2, TP53 and PTEN mutations between 2007-2017 were selected from the Hong Kong Hereditary Breast Cancer Family Registry. Patient samples were subjected to next-generation DNA sequencing using a multigene panel (Color Genomics). All detected pathogenic variants were validated by bi-directional DNA sequencing. The sequencing data was co-analyzed by our in-house developed bioinformatics pipeline. Sixty-one pathogenic variants (4.6%) were identified in this cohort in 11 cancer predisposition genes. The majority of the carriers (77.1%) had early-onset of breast cancer (age <45), 32.8% had family members with breast cancer and 11.5% had triple-negative breast cancer (TNBC). The most common mutated genes were PALB2 (1.4%), RAD51D (0.8%) and ATM (0.8%). A total of 612 variants of unknown significance (VUS) were identified in 494 patients, and 87.4% of the VUS were missense mutations. Pathogenic variants in cancer predisposition genes beyond BRCA1, BRCA2, TP53 and PTEN were detected in an additional 4.6% of the patients using the multigene test panel. PALB2 (1.4%) and RAD51D (0.8%) were the most commonly mutated genes in patients who tested mutation-negative by a 4-gene panel.

  View details for DOI 10.1016/j.jmoldx.2020.01.013

  View details for PubMedID 32068069

• Gastric Cancer Registry: A comprehensive patient-reported resource for multidisciplinary and translational genomic approaches to gastric cancer Almeda, A., Hooker, A., Lee, H., Mills, M., Van Hummelen, P., Ford, J. M., Ji, H. AMER SOC CLINICAL ONCOLOGY. 2020

  View details for Web of Science ID 000530922700413

• Statistical Methods in Precision Oncology. Journal of clinical oncology : official journal of the American Society of Clinical Oncology Lu, Y. n., Lee, J. J., Ford, J. M. 2020: JCO1903173

  View details for DOI 10.1200/JCO.19.03173

  View details for PubMedID 31895607

• Clinical Outcome Event Adjudication in a 10-Year Prospective Study of Nucleos(t)ide Analogue Therapy for Chronic Hepatitis B. Journal of clinical and translational hepatology Lim, J. K., Chang, A. Y., Zaman, A. n., Martin, P. n., Fernandez-Rodriguez, C. M., Korkmaz, M. n., Rossi, S. n., Ford, J. M., Noonan, T. n., Cooney, E. n., Navarro, V. n., Colombato, L. n. 2020; 8 (4): 377–84

  Abstract

  Background and Aims: In the REALM (Randomized, Observational Study of Entecavir to Assess Long-Term Outcomes Associated with Nucleoside/Nucleotide Monotherapy for Patients with Chronic HBV Infection) study, 12,378 patients with chronic hepatitis B virus (HBV) infection received up to 10 years of randomized therapy with entecavir or another HBV nucleos(t)ide analogue. Monitored clinical outcome events (COEs) included malignant neoplasms, HBV disease progression events, and deaths. An external event adjudication committee (EAC) was convened to provide real-time review of reported COEs to optimize data quality, and minimize potential adverse effects of the large cohort, interdisciplinary outcome assessments, geographic scope, and long duration. Methods: The EAC comprised an international group of hepatologists and oncologists with expertise in diagnosis of targeted COEs. The EAC reviewed and adjudicated COEs according to prospectively defined diagnostic criteria captured in the EAC charter. Operational processes, including data collection and query procedures, were implemented to optimize efficiency of data recovery to maximize capture of adjudicated COEs, the primary study outcome measure. Results: A total of 1724 COEs were reported and 1465 of these events were adjudicated by the EAC as reported by the investigators (85.0% overall concordance). Concordance by COE type varied: deaths, 99.6%; hepatocellular carcinoma (HCC), 83.3%; non-HCC malignancies, 88.0%; non-HCC HBV disease progression, 68.2%. Reasons for lack of concordance were most commonly lack of adequate supporting data to support an adjudicated diagnosis or evidence that the event pre-dated the study. Conclusions: The REALM EAC performed a critical role in ensuring data quality and consistency; EAC performance was facilitated by well-defined diagnostic criteria, effective data capture, and efficient operational processes. Trial registration: ClinicalTrials.gov NCT00388674.

  View details for DOI 10.14218/JCTH.2020.00039

  View details for PubMedID 33447520

  View details for PubMedCentralID PMC7782110

• Psychosocial outcomes following germline multigene panel testing in an ethnically and economically diverse cohort of patients. Cancer Culver, J. O., Ricker, C. N., Bonner, J. n., Kidd, J. n., Sturgeon, D. n., Hodan, R. n., Kingham, K. n., Lowstuter, K. n., Chun, N. M., Lebensohn, A. P., Rowe-Teeter, C. n., Levonian, P. n., Partynski, K. n., Lara-Otero, K. n., Hong, C. n., Morales Pichardo, J. n., Mills, M. A., Brown, K. n., Lerman, C. n., Ladabaum, U. n., McDonnell, K. J., Ford, J. M., Gruber, S. B., Kurian, A. W., Idos, G. E. 2020

  Abstract

  Little is known about the psychological outcomes of germline multigene panel testing, particularly among diverse patients and those with moderate-risk pathogenic variants (PVs).Study participants (N = 1264) were counseled and tested with a 25- or 28-gene panel and completed a 3-month postresult survey including the Multidimensional Impact of Cancer Risk Assessment (MICRA).The mean age was 52 years, 80% were female, and 70% had cancer; 45% were non-Hispanic White, 37% were Hispanic, 10% were Asian, 3% were Black, and 5% had another race/ethnicity. Approximately 28% had a high school education or less, and 23% were non-English-speaking. The genetic test results were as follows: 7% had a high-risk PV, 6% had a moderate-risk PV, 35% had a variant of uncertain significance (VUS), and 52% were negative. Most participants (92%) had a total MICRA score ≤ 38, which corresponded to a mean response of "never," "rarely," or only "sometimes" reacting negatively to results. A multivariate analysis found that mean total MICRA scores were significantly higher (more uncertainty/distress) among high- and moderate-risk PV carriers (29.7 and 24.8, respectively) than those with a VUS or negative results (17.4 and 16.1, respectively). Having cancer or less education was associated with a significantly higher total MICRA score; race/ethnicity was not associated with the total MICRA score. High- and moderate-risk PV carriers did not differ significantly from one another in the total MICRA score, uncertainty, distress, or positive experiences.In a diverse population undergoing genetic counseling and multigene panel testing for hereditary cancer risk, the psychological response corresponded to test results and showed low distress and uncertainty. Further studies are needed to assess patient understanding and subsequent cancer screening among patients from diverse backgrounds.Multigene panel tests for hereditary cancer have become widespread despite concerns about adverse psychological reactions among carriers of moderate-risk pathogenic variants (mutations) and among carriers of variants of uncertain significance. This large study of an ethnically and economically diverse cohort of patients undergoing panel testing found that 92% "never," "rarely," or only "sometimes" reacted negatively to results. Somewhat higher uncertainty and distress were identified among carriers of high- and moderate-risk pathogenic variants, and lower levels were identified among those with a variant of uncertain significance or a negative result. Although the psychological response corresponded to risk, reactions to testing were favorable, regardless of results.

  View details for DOI 10.1002/cncr.33357

  View details for PubMedID 33320347

• A novel DDB2 mutation causes defective recognition of UV-induced DNA damages and prevalent equine squamous cell carcinoma DNA Repair Chen, L., Bellone, R. R., Wang, Y., Singer-Berk, M., Sugasawa, K., Ford, J. M., Artandi, S. E. 2020

  View details for DOI 10.1016/j.dnarep.2020.103022

• Whole genome analysis identifies the association of TP53 genomic deletions with lower survival in Stage III colorectal cancer. Scientific reports Xia, L. C., Van Hummelen, P. n., Kubit, M. n., Lee, H. n., Bell, J. M., Grimes, S. M., Wood-Bouwens, C. n., Greer, S. U., Barker, T. n., Haslem, D. S., Ford, J. M., Fulde, G. n., Ji, H. P., Nadauld, L. D. 2020; 10 (1): 5009

  Abstract

  DNA copy number aberrations (CNA) are frequently observed in colorectal cancers (CRC). There is an urgent need for CNA-based biomarkers in clinics,. n For Stage III CRC, if combined with imaging or pathologic evidence, these markers promise more precise care. We conducted this Stage III specific biomarker discovery with a cohort of 134 CRCs, and with a newly developed high-efficiency CNA profiling protocol. Specifically, we developed the profiling protocol for tumor-normal matched tissue samples based on low-coverage clinical whole-genome sequencing (WGS). We demonstrated the protocol's accuracy and robustness by a systematic benchmark with microarray, high-coverage whole-exome and -genome approaches, where the low-coverage WGS-derived CNA segments were highly accordant (PCC >0.95) with those derived from microarray, and they were substantially less variable if compared to exome-derived segments. A lasso-based model and multivariate cox regression analysis identified a chromosome 17p loss, containing the TP53 tumor suppressor gene, that was significantly associated with reduced survival (P = 0.0139, HR = 1.688, 95% CI = [1.112-2.562]), which was validated by an independent cohort of 187 Stage III CRCs. In summary, this low-coverage WGS protocol has high sensitivity, high resolution and low cost and the identified 17p-loss is an effective poor prognosis marker for Stage III patients.

  View details for DOI 10.1038/s41598-020-61643-6

  View details for PubMedID 32193467

• Talazoparib beyond BRCA: A phase II trial of talazoparib monotherapy in BRCA1 and BRCA2 wild-type patients with advanced HER2-negative breast cancer or other solid tumors with a mutation in homologous recombination (HR) pathway genes. Gruber, J., Afghahi, A., Hatton, A., Scott, D., McMillan, A., Ford, J. M., Telli, M. L. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.15_suppl.3006

  View details for Web of Science ID 000487345804596

• Preventive surgery after multiplex genetic panel testing (MGPT) Idos, G., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J., Kingham, K., Koff, R., Chun, N. M., Rowe-Teeter, C., Levonian, P., Hong, C., Mills, M., Ma, C., Lancaster, J. M., Brown, K., Kidd, J., McDonnell, K., Ladabaum, U., Ford, J. M., Gruber, S. B. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.15_suppl.1525

  View details for Web of Science ID 000487345804321

• JAVELIN BRCA/ATM: A phase 2 trial of avelumab (anti-PD-L1) plus talazoparib (PARP inhibitor) in patients with advanced solid tumors with a BRCA1/2 or ATM defect. Hyman, D., Zelnak, A. B., Bauer, T., Ulahannan, S., Ford, J. M., Cesari, R., Hoyle, M., Chappey, C., Stewart, R., Conte, U., Yap, T. A. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.15_suppl.TPS2660

  View details for Web of Science ID 000487345803277

• Clinical and pathological features of breast cancer among men and women with ATM and CDH1 mutations Tsang, A., Kingham, K., Kurian, A., Ford, J., Wapnir, I. SPRINGER. 2019: 69–70

  View details for Web of Science ID 000467382700043

• Multicenter Prospective Cohort Study of the Diagnostic Yield and Patient Experience of Multiplex Gene Panel Testing For Hereditary Cancer Risk. JCO precision oncology Idos, G. E., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J. O., Kingham, K. E., Koff, R., Chun, N. M., Rowe-Teeter, C., Lebensohn, A. P., Levonian, P., Lowstuter, K., Partynski, K., Hong, C., Mills, M. A., Petrovchich, I., Ma, C. S., Hartman, A. R., Allen, B., Wenstrup, R. J., Lancaster, J. M., Brown, K., Kidd, J., Evans, B., Mukherjee, B., McDonnell, K. J., Ladabaum, U., Ford, J. M., Gruber, S. B. 2019; 3

  Abstract

  Multiplex gene panel testing (MGPT) allows for the simultaneous analysis of germline cancer susceptibility genes. This study describes the diagnostic yield and patient experiences of MGPT in diverse populations.This multicenter, prospective cohort study enrolled participants from three cancer genetics clinics-University of Southern California Norris Comprehensive Cancer Center, Los Angeles County and University of Southern California Medical Center, and Stanford Cancer Institute-who met testing guidelines or had a 2.5% or greater probability of a pathogenic variant (N = 2,000). All patients underwent 25- or 28-gene MGPT and results were compared with differential genetic diagnoses generated by pretest expert clinical assessment. Post-test surveys on distress, uncertainty, and positive experiences were administered at 3 months (69% response rate) and 1 year (57% response rate).Of 2,000 participants, 81% were female, 41% were Hispanic, 26% were Spanish speaking only, and 30% completed high school or less education. A total of 242 participants (12%) carried one or more pathogenic variant (positive), 689 (34%) carried one or more variant of uncertain significance (VUS), and 1,069 (53%) carried no pathogenic variants or VUS (negative). More than one third of pathogenic variants (34%) were not included in the differential diagnosis. After testing, few patients (4%) had prophylactic surgery, most (92%) never regretted testing, and most (80%) wanted to know all results, even those of uncertain significance. Positive patients were twice as likely as negative/VUS patients (83% v 41%; P < .001) to encourage their relatives to be tested.In a racially/ethnically and socioeconomically diverse cohort, MGPT increased diagnostic yield. More than one third of identified pathogenic variants were not clinically anticipated. Patient regret and prophylactic surgery use were low, and patients appropriately encouraged relatives to be tested for clinically relevant results.

  View details for DOI 10.1200/PO.18.00217

  View details for PubMedID 34322651

  View details for PubMedCentralID PMC8260917

• Prevalence and molecular etiology of mismatch repair deficiency among gastrointestinal cancers. Shukla, N., Abrha, A., Longacre, T. A., Koff, R., Ford, J. M., Fisher, G. A., Haraldsdottir, S. AMER SOC CLINICAL ONCOLOGY. 2019

  View details for DOI 10.1200/JCO.2019.37.4_suppl.215

  View details for Web of Science ID 000489107600248

• Multicenter Prospective Cohort Study of the Diagnostic Yield and Patient Experience of Multiplex Gene Panel Testing For Hereditary Cancer Risk JCO Precision Oncology Idos, G. E., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J. O., Kingham, K. E., Koff, R., Chun, N. M., Rowe-Teeter, C., Lebensohn, A. P., Levonian, P., Lowstuter, K., Partynski, K., Hong, C., Mills, M. A., Petrovchich, I., Ma, C. S., Hartman, A., Allen, B., Wenstrup, R. J., Lancaster, J. M., Brown, K., Kidd, J., Evans, B., Mukherjee, B., et al 2019

  View details for DOI 10.1200/PO.18.00217

• Tumor Molecular Profiling Aids in Determining Tissue of Origin and Therapy for Metastatic Adenocarcinoma in a Patient With Multiple Primary Malignancies. JCO precision oncology Costa, H. A., Reyes, R., Mills, M., Zehnder, J. L., Sledge, G., Curtis, C., Ford, J. M., Suarez, C. J. 2018; 2: 1-4

  View details for DOI 10.1200/PO.18.00177

  View details for PubMedID 35135146

• Introducing the JCO Precision Oncology Molecular Tumor Board Case Discussion Series. JCO precision oncology Ford, J. M. 2018; 2: 1

  View details for DOI 10.1200/PO.17.00310

  View details for PubMedID 35135106

• Delivering Precision Oncology in a Community Cancer Program: Results From a Prospective Observational Study. JCO precision oncology Powell, S. F., Dib, E. G., Bleeker, J. S., Keppen, M. D., Mazurczak, M., Hack, K. M., Gitau, M. M., Steen, P. D., Terstriep, S. A., Reynolds, J., Landsverk, M. L., Chan, C. H., Nelson, M. E., Thompson, P. A., Ellison, C., Black, L. J., Ford, J. M., Chung, J. H., Anhorn, R., Gaba, A. G. 2018; 2: 1-12

  Abstract

  Precision oncology (PO) is a growing treatment approach in the era of next-generation sequencing (NGS) and matched therapies. Effective delivery of PO in the community has not been extensively studied. Our program developed a virtual molecular tumor board (MTB) strategy to help guide PO care.Over 18 months, eligible adult patients with advanced, incurable solid tumor malignancies were enrolled in a molecular profiling (MP) study using the Foundation Medicine NGS panel. Results were reviewed through a weekly, videoconferenced MTB conducted across our largely rural integrated health system. Recommendations from the MTB were used to identify actionable alterations (AAs). Feasibility of PO care delivery was assessed as the primary outcome. Secondary outcomes included the frequency of AAs, genomic matched treatments, genomic matched clinical trial enrollment, and clinical outcomes.A total of 120 participants with a variety of advanced tumor types were enrolled. Of these, 109 (90.8%) had successful MP. Treatment on the basis of an AA was recommended by the MTB in 58% of patients (63 of 109) who had a successful MP result. For those completing MP, treatments included enrollment in a genomic matched clinical trial (n = 16; 14.6%) and genomic matched treatment with a Food and Drug Administration-approved agent (n = 23; 21.1%). Response and survival data were similar regardless of the matched treatment option chosen.A video-conferenced MTB-facilitated NGS testing and treatment delivery system was implemented in our integrated community oncology program. Continued use of this model aims to increase understanding of the impact of PO in this setting.

  View details for DOI 10.1200/PO.17.00220

  View details for PubMedID 35135120

• Pathogenic Variants in Less Familiar Cancer Susceptibility Genes: What Happens After Genetic Testing? JCO precision oncology Hall, E. T., Parikh, D., Caswell-Jin, J. L., Gupta, T., Mills, M. A., Kingham, K. E., Koff, R., Ford, J. M., Kurian, A. W. 2018; 2: 1-10

  Abstract

  As genetic testing expands, patients are increasingly found to carry pathogenic variants in cancer susceptibility genes that are less familiar to most clinicians, specifically genes other than those causing hereditary breast ovarian cancer syndrome (BRCA1 and BRCA2) and Lynch syndrome. Little is known about the subsequent behaviors of such patients in terms of managing cancer risks and informing relatives.All adult patients who were counseled and tested at the Stanford Cancer Genetics Clinic from January 2013 to July 2015 and had a pathogenic variant in a non-BRCA1/2, non-Lynch syndrome gene were invited to participate in a telephone interview about adherence to risk-reducing recommendations, genetic testing by relatives, and new cancer incidence.Fifty-seven (40%) of 142 eligible patients were successfully contacted, and all 57 patients participated; median follow-up was 677 days (range, 247 to 1,401 days). Most patients (82%; 95% CI, 70% to 90%) recalled that a risk-reducing intervention (screening, medication, or surgery) was recommended, and most patients (85%; 95% CI, 72% to 93%) adhered to the recommendation. Nearly all patients (91%; 95% CI, 81% to 97%) shared results with relatives, and most patients (78%; 95% CI, 64% to 88%) reported that a relative was subsequently tested. During the follow-up period, 9% of patients (95% CI, 3% to 19%) developed second cancers, and in 14% of patients (95% CI, 7% to 26%), a first-degree relative developed cancer, some of which were detected by recommended screening.Patients with a pathogenic variant in a less familiar cancer susceptibility gene report high adherence to risk-reducing interventions. Furthermore, in the 57 carriers and subsequently tested relatives with two years of follow-up, a total of three cancers (one in a proband and two in relatives) were detected through interventions recommended on the basis of the pathogenic variant. These results suggest a potential benefit of genetic counseling and testing for pathogenic variants in less familiar genes.

  View details for DOI 10.1200/PO.18.00167

  View details for PubMedID 35135157

• Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst COLD SPRING HARBOR MOLECULAR CASE STUDIES Erdrich, J., Schaberg, K. B., Khodadoust, M. S., Zhou, L., Shelton, A. A., Visser, B. C., Ford, J. M., Alizadeh, A. A., Quake, S. R., Kunz, P. L., Beausang, J. F. 2018; 4 (5)

  View details for DOI 10.1101/mcs.a003004

  View details for Web of Science ID 000450957900005

• From the Past to the Present: Insurer Coverage Frameworks for Next-Generation Tumor Sequencing. Value in health : the journal of the International Society for Pharmacoeconomics and Outcomes Research Trosman, J. R., Weldon, C. B., Gradishar, W. J., Benson, A. B., Cristofanilli, M., Kurian, A. W., Ford, J. M., Balch, A., Watkins, J., Phillips, K. A. 2018; 21 (9): 1062-1068

  Abstract

  Next-generation sequencing promises major advancements in precision medicine but faces considerable challenges with insurance coverage. These challenges are especially important to address in oncology in which next-generation tumor sequencing (NGTS) holds a particular promise, guiding the use of life-saving or life-prolonging therapies. Payers' coverage decision making on NGTS is challenging because this revolutionary technology pushes the very boundaries of the underlying framework used in coverage decisions. Some experts have called for the adaptation of the coverage framework to make it better equipped for assessing NGTS. Medicare's recent decision to cover NGTS makes this topic particularly urgent to examine. In this article, we discussed the previously proposed approaches for adaptation of the NGTS coverage framework, highlighted their innovations, and outlined remaining gaps in their ability to assess the features of NGTS. We then compared the three approaches with Medicare's national coverage determination for NGTS and discussed its implications for US private payers as well as for other technologies and clinical areas. We focused on US payers because analyses of coverage approaches and policies in the large and complex US health care system may inform similar efforts in other countries. We concluded that further adaptation of the coverage framework will facilitate a better suited assessment of NGTS and future genomics innovations.

  View details for DOI 10.1016/j.jval.2018.06.011

  View details for PubMedID 30224110

• Small molecules facilitating DNA repair in breast cancer cells Pandrala, M., Hastak, K., Kumar, V., Gardiner, M., Ford, J., Malhotra, S. AMER CHEMICAL SOC. 2018

  View details for Web of Science ID 000447609102076

• Surgical and molecular characterization of primary and metastatic disease in a neuroendocrine tumor arising in a tailgut cyst. Cold Spring Harbor molecular case studies Erdrich, J., Schaberg, K., Khodadoust, M. S., Zhou, L., Shelton, A. A., Visser, B. C., Ford, J. M., Alizadeh, A. A., Quake, S. R., Kunz, P. L., Beausang, J. F. 2018

  Abstract

  Neuroendocrine tumors arising from tailgut cysts are rare but increasingly reported entity with gene expression profiles that may be indicative of the gastrointestinal cell of origin. We present a case report describing the unique pathological and genomic characteristics of a tailgut cyst neuroendocrine tumor that metastasized to liver. The histologic and immunohistochemical findings were consistent with a well-differentiated neuroendocrine tumor. Genomic testing indicates a germline frame-shift in BRCA1 and a few somatic mutations of unknown significance. Transcriptomic analysis suggests an enteroendocrine L-cell in the tailgut as a putative cell-of-origin. Genomic profiling of a rare neuroendocrine tumor and metastasis provides insight into its origin, development and potential therapeutic options.

  View details for PubMedID 30087100

• NCCN Guidelines Insights: Colorectal Cancer Screening, Version 1.2018. Journal of the National Comprehensive Cancer Network : JNCCN Provenzale, D., Gupta, S., Ahnen, D. J., Markowitz, A. J., Chung, D. C., Mayer, R. J., Regenbogen, S. E., Blanco, A. M., Bray, T., Cooper, G., Early, D. S., Ford, J. M., Giardiello, F. M., Grady, W., Hall, M. J., Halverson, A. L., Hamilton, S. R., Hampel, H., Klapman, J. B., Larson, D. W., Lazenby, A. J., Llor, X., Lynch, P. M., Mikkelson, J., Ness, R. M., Slavin, T. P., Sugandha, S., Weiss, J. M., Dwyer, M. A., Ogba, N. 2018; 16 (8): 939–49

  Abstract

  The NCCN Guidelines for Colorectal Cancer (CRC) Screening outline various screening modalities as well as recommended screening strategies for individuals at average or increased-risk of developing sporadic CRC. The NCCN panel meets at least annually to review comments from reviewers within their institutions, examine relevant data, and reevaluate and update their recommendations. These NCCN Guidelines Insights summarize 2018 updates to the NCCN Guidelines, with a primary focus on modalities used to screen individuals at average-risk for CRC.

  View details for DOI 10.6004/jnccn.2018.0067

  View details for PubMedID 30099370

• VISTA immune checkpoint deregulation in human triple-negative breast cancer Gruber, J. J., Juntilla, M. M., Yang, S., Geller, B., Jager, N., Lin, C., Lipchik, A. M., Chen, J., Ram, A., Vinayak, S., Telli, M. L., West, R. B., Ford, J. M., Snyder, M. P. AMER ASSOC CANCER RESEARCH. 2018

  View details for DOI 10.1158/1538-7445.AM2018-4749

  View details for Web of Science ID 000468819503369

• Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer CLINICAL CANCER RESEARCH Afghahi, A., Purington, N., Han, S. S., Desai, M., Pierson, E., Mathur, M. B., Seto, T., Thompson, C. A., Rigdon, J., Telli, M. L., Badve, S. S., Curtis, C. N., West, R. B., Horst, K., Gomez, S. L., Ford, J. M., Sledge, G. W., Kurian, A. W. 2018; 24 (12): 2851–58

  View details for DOI 10.1158/1078-0432.CCR-17-1323

  View details for Web of Science ID 000435462700016

• Promoting colorectal cancer (CRC) screening after multiplex genetic testing and genetic counseling Idos, G., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J., Kingham, K., Koff, R., Chun, N. M., Rowe-Teeter, C., Kidd, J., Evans, B., Brown, K., Mills, M., Ma, C., Hong, C., McDonnell, K., Ladabaum, U., Ford, J. M., Gruber, S. B. AMER SOC CLINICAL ONCOLOGY. 2018

  View details for DOI 10.1200/JCO.2018.36.15_suppl.1582

  View details for Web of Science ID 000442916001199

• Promoting breast cancer screening after multiplex genetic panel testing (MGPT) and genetic counseling Idos, G., Kurian, A. W., Ricker, C., Sturgeon, D., Culver, J., Kingham, K., Koff, R., Chun, N. M., Rowe-Teeter, C., Kidd, J., Evans, B., Brown, K., Mills, M., Ma, C., Hong, C., McDonnell, K. J., Ladabaum, U., Ford, J. M., Gruber, S. B. AMER SOC CLINICAL ONCOLOGY. 2018

  View details for DOI 10.1200/JCO.2018.36.15_suppl.1581

  View details for Web of Science ID 000442916001198

• Delivering Precision Oncology in a Community Cancer Program: Results From a Prospective Observational Study JCO PRECISION ONCOLOGY Powell, S. E., Dib, E. G., Bleeker, J. S., Keppen, M. D., Mazurczak, M., Hack, K. M., Gitau, M. M., Steen, P. D., Terstriep, S. A., Reynolds, J., Landsverk, M. L., Chan, C., Nelson, M. E., Thompson, P. A., Ellison, C., Black, L. J., Ford, J. M., Chung, J. H., Anhorn, R., Gaba, A. G. 2018; 2: 1–12

  View details for DOI 10.1200/PO.17.00220

  View details for Web of Science ID 000462085100001

• Molecular Characterization of Aggressive Estrogen Receptor Positive Breast Cancer Resistant to Palbociclib Therapy Lei, L., Lin, C., Steiner, D., Ford, J. M., Zehnder, J. L., Suarez, C. J. NATURE PUBLISHING GROUP. 2018: 703

  View details for Web of Science ID 000429308604325

• Molecular Characterization of Aggressive Estrogen Receptor Positive Breast Cancer Resistant to Palbociclib Therapy Lei, L., Lin, C., Steiner, D., Ford, J. M., Zehnder, J. L., Suarez, C. J. NATURE PUBLISHING GROUP. 2018: 703

  View details for Web of Science ID 000459341003278

• Introducing the JCO Precision Oncology Molecular Tumor Board Case Discussion Series JCO PRECISION ONCOLOGY Ford, J. M. 2018; 2

  View details for DOI 10.1200/PO.17.00310

  View details for Web of Science ID 000462118000002

• Patient communication of cancer genetic test results in a diverse population. Translational behavioral medicine Ricker, C. N., Koff, R. B., Qu, C. n., Culver, J. n., Sturgeon, D. n., Kingham, K. E., Lowstuter, K. n., Chun, N. M., Rowe-Teeter, C. n., Lebensohn, A. n., Levonian, P. n., Partynski, K. n., Lara-Otero, K. n., Hong, C. n., Petrovchich, I. M., Mills, M. A., Hartman, A. R., Allen, B. n., Ladabaum, U. n., McDonnell, K. n., Ford, J. M., Gruber, S. B., Kurian, A. W., Idos, G. E. 2018; 8 (1): 85–94

  Abstract

  Research on the communication of genetic test results has focused predominately on non-Hispanic White (NHW) mutation-positive families with high-risk hereditary cancer conditions. Little is known about this process for racially and ethnically diverse individuals or for those with mutations in moderate risk genes. The communication behaviors of study participants who carry a gene mutation were analyzed 3 months after disclosure of genetic test results. Participants were queried about communication of their results, as part of a prospective study of multi-gene panel genetic testing. The responses of particpants who tested positive were analyzed by race/ethnicity and by level of cancer risk (high vs. moderate). Of the 216 mutation-positive study participants, 136 (63%) responded. Self-reported race/ethnicity was 46% NHW, 41% Hispanic, 10% Asian, and 2% Black. The majority (99.0%, n = 135) had shared their results with someone and 96% had told a family member (n = 130). Hispanic respondents were less likely to have told a healthcare provider about their results than NHW (29% vs. 68%, p < .0001). Asian respondents were less likely than NHW to encourage family members to undergo testing (OR = 0.1, p = .03); but Asian family members were more likely to undergo testing (OR = 8.0, p = .03). There were no differences in communication between those with a mutation in a high- or moderate-risk gene. Three months post genetic testing, communication of results was very high; 30% reported a family member underwent genetic testing. Further studies are needed to better understand the communication process in individuals from diverse racial/ethnic backgrounds.

  View details for PubMedID 29385580

• Pathogenic variants in less familiar cancer susceptibility genes: what happens after genetic testing? JCO Precision Oncology Hall, E. T., Parikh, D., Caswell-Jin, J. L., Gupta, T., Mills, M. A., Kingham, K. E., Koff, R., Ford, J. M., Kurian, A. W. 2018

  View details for DOI 10.1200/PO.18.00167

• From the Past to the Present: Insurer Coverage Frameworks for Next-Generation Tumor Sequencing Value in Health Trosman, J. R., Weldon, C. B., Gradishar, W. J., Benson, A. B., Cristofanilli, M., Kurian, A. W., Ford, J. M., Balch, A., Watkins, J., Phillips, K. A. 2018: 1062-1068

  Abstract

  Next-generation sequencing promises major advancements in precision medicine but faces considerable challenges with insurance coverage. These challenges are especially important to address in oncology in which next-generation tumor sequencing (NGTS) holds a particular promise, guiding the use of life-saving or life-prolonging therapies. Payers' coverage decision making on NGTS is challenging because this revolutionary technology pushes the very boundaries of the underlying framework used in coverage decisions. Some experts have called for the adaptation of the coverage framework to make it better equipped for assessing NGTS. Medicare's recent decision to cover NGTS makes this topic particularly urgent to examine. In this article, we discussed the previously proposed approaches for adaptation of the NGTS coverage framework, highlighted their innovations, and outlined remaining gaps in their ability to assess the features of NGTS. We then compared the three approaches with Medicare's national coverage determination for NGTS and discussed its implications for US private payers as well as for other technologies and clinical areas. We focused on US payers because analyses of coverage approaches and policies in the large and complex US health care system may inform similar efforts in other countries. We concluded that further adaptation of the coverage framework will facilitate a better suited assessment of NGTS and future genomics innovations.

  View details for DOI 10.1016/j.jval.2018.06.011

• Higher Absolute Lymphocyte Counts Predict Lower Mortality from Early-Stage Triple-Negative Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research Afghahi, A. n., Purington, N. n., Han, S. S., Desai, M. n., Pierson, E. n., Mathur, M. B., Seto, T. n., Thompson, C. A., Rigdon, J. n., Telli, M. L., Badve, S. S., Curtis, C. n., West, R. B., Horst, K. n., Gomez, S. L., Ford, J. M., Sledge, G. W., Kurian, A. W. 2018

  Abstract

  Tumor-infiltrating lymphocytes (TILs) in pre-treatment biopsies are associated with improved survival in triple-negative breast cancer (TNBC). We investigated whether higher peripheral lymphocyte counts are associated with lower breast cancer-specific mortality (BCM) and overall mortality (OM) in TNBC.Data on treatments and diagnostic tests from electronic medical records of two healthcare systems were linked with demographic, clinical, pathologic, and mortality data from the California Cancer Registry. Multivariable regression models adjusted for age, race/ethnicity, socioeconomic status, cancer stage, grade, neoadjuvant/adjuvant chemotherapy use, radiotherapy use, and germline BRCA1/2 mutations were used to evaluate associations between absolute lymphocyte count (ALC), BCM and OM. For a subgroup with TILs data available, we explored the relationship between TILs and peripheral lymphocyte counts.1,463 Stage I-III TNBC patients were diagnosed from 2000-2014; 1113 (76%) received neoadjuvant/adjuvant chemotherapy within one year of diagnosis. Of 759 patients with available ALC data, 481 (63.4%) were ever lymphopenic (minimum ALC <1.0 K/μL). On multivariable analysis, higher minimum ALC, but not absolute neutrophil count, predicted lower OM (hazard ratio [HR]: 0.23, 95% confidence interval [CI]: 0.16-0.35) and BCM (HR: 0.19, CI: 0.11-0.34). Five-year probability of BCM was 15% for patients who were ever lymphopenic versus 4% for those who were not. An exploratory analysis (N=70) showed a significant association between TILs and higher peripheral lymphocyte counts during neoadjuvant chemotherapy.Higher peripheral lymphocyte counts predicted lower mortality from early-stage, potentially curable TNBC, suggesting that immune function may enhance the effectiveness of early TNBC treatment.

  View details for PubMedID 29581131

• Rapid detection ofBRCA1/2recurrent mutations in Chinese breast and ovarian cancer patients with multiplex SNaPshot genotyping panels. Oncotarget Kwong, A. n., Ho, J. C., Shin, V. Y., Kurian, A. W., Tai, E. n., Esserman, L. J., Weitzel, J. N., Lin, P. H., Field, M. n., Domchek, S. M., Lo, J. n., Ngan, H. Y., Ma, E. S., Chan, T. L., Ford, J. M. 2018; 9 (8): 7832–43

  Abstract

  BRCA1/2 mutations are significant risk factors for hereditary breast and ovarian cancer (HBOC), its mutation frequency in HBOC of Chinese ethnicity is around 9%, in which nearly half are recurrent mutations. In Hong Kong and China, genetic testing and counseling are not as common as in the West. To reduce the barrier of testing, a multiplex SNaPshot genotyping panel that targeted 25 ChineseBRCA1/2mutation hotspots was developed, and its feasibility was evaluated in a local cohort of 441 breast and 155 ovarian cancer patients. For those who tested negative, they were then subjected to full-gene testing with next-generation sequencing (NGS).BRCAmutation prevalence in this cohort was 8.05% and the yield of the recurrent panel was 3.52%, identifying over 40% of the mutation carriers. Moreover, from 79 Chinese breast cancer cases recruited overseas, 2 recurrent mutations and one novelBRCA2mutation were detected by the panel and NGS respectively. The developed genotyping panel showed to be an easy-to-perform and more affordable testing tool that can provide important contributions to improve the healthcare of Chinese women with cancer as well as family members that harbor high risk mutations for HBOC.

  View details for PubMedID 29487695

• NCCN Guidelines (R) Insights Genetic/Familial High-Risk Assessment: Colorectal, Version 3.2017 Featured Updates to the NCCN Guidelines JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK Gupta, S., Provenzale, D., Regenbogen, S. E., Hampel, H., Slavin, T. P., Hall, M. J., Llor, X., Chung, D. C., Ahnen, D. J., Bray, T., Cooper, G., Early, D. S., Ford, J. M., Giardiello, F. M., Grady, W., Halverson, A. L., Hamilton, S. R., Klapman, J. B., Larson, D. W., Lazenby, A. J., Lynch, P. M., Markowitz, A. J., Mayer, R. J., Ness, R. M., Samadder, N., Shike, M., Sugandha, S., Weiss, J. M., Dwyer, M. A., Ogba, N. 2017; 15 (12): 1465–74

  View details for DOI 10.6004/jnccn.2017.0176

  View details for Web of Science ID 000418536600006

• The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk (vol 3, 22, 2017) NPJ BREAST CANCER Slavin, T. P., Maxwell, K. N., Lilyquist, J., Vijai, J., Neuhausen, S. L., Hart, S. N., Ravichandran, V., Thomas, T., Maria, A., Villano, D., Schrader, K. A., Moore, R., Hu, C., Wubbenhorst, B., Wenz, B. M., D'Andrea, K., Robson, M. E., Peterlongo, P., Bonanni, B., Ford, J. M., Garber, J. E., Domchek, S. M., Szabo, C., Offit, K., Nathanson, K. L., Weitzel, J. N., Couch, F. J. 2017; 3: 44

  Abstract

  [This corrects the article DOI: 10.1038/s41523-017-0024-8.].

  View details for PubMedID 29119134

• Precision Oncology Strategy in Trastuzumab-Resistant Human Epidermal Growth Factor Receptor 2-Positive Colon Cancer: Case Report of Durable Response to Ado-Trastuzumab Emtansine. JCO precision oncology Haslem, D. S., Ji, H. P., Ford, J. M., Nadauld, L. D. 2017; 1

  View details for DOI 10.1200/PO.16.00055

  View details for PubMedID 32913966

  View details for PubMedCentralID PMC7446358

• The contribution of pathogenic variants in breast cancer susceptibility genes to familial breast cancer risk NPJ BREAST CANCER Slavin, T. P., Maxwell, K. N., Lilyquist, J., Vijai, J., Neuhausen, S. L., Hart, S. N., Ravichandran, V., Thomas, T., Maria, A., Villano, D., Schrader, K. A., Moore, R., Hu, C., Wubbenhorst, B., Wenz, B. M., D'Andrea, K., Robson, M. E., Peterlongo, P., Bonanni, B., Ford, J. M., Garber, J. E., Domchek, S. M., Szabo, C., Offit, K., Nathanson, K. L., Weitzel, J. N., Couch, F. J. 2017; 3: 22

  Abstract

  Understanding the gene-specific risks for development of breast cancer will lead to improved clinical care for those carrying germline mutations in cancer predisposition genes. We sought to detail the spectrum of mutations and refine risk estimates for known and proposed breast cancer susceptibility genes. Targeted massively-parallel sequencing was performed to identify mutations and copy number variants in 26 known or proposed breast cancer susceptibility genes in 2134 BRCA1/2-negative women with familial breast cancer (proband with breast cancer and a family history of breast or ovarian cancer) from a largely European-Caucasian multi-institutional cohort. Case-control analysis was performed comparing the frequency of internally classified mutations identified in familial breast cancer women to Exome Aggregation Consortium controls. Mutations were identified in 8.2% of familial breast cancer women, including mutations in high-risk (odds ratio > 5) (1.4%) and moderate-risk genes (2 < odds ratio < 5) (2.9%). The remaining familial breast cancer women had mutations in proposed breast cancer genes (1.7%), Lynch syndrome genes (0.5%), and six cases had two mutations (0.3%). Case-control analysis demonstrated associations with familial breast cancer for ATM, PALB2, and TP53 mutations (odds ratio > 3.0, p < 10-4), BARD1 mutations (odds ratio = 3.2, p = 0.012), and CHEK2 truncating mutations (odds ratio = 1.6, p = 0.041). Our results demonstrate that approximately 4.7% of BRCA1/2 negative familial breast cancer women have mutations in genes statistically associated with breast cancer. We classified PALB2 and TP53 as high-risk, ATM and BARD1 as moderate risk, and CHEK2 truncating mutations as low risk breast cancer predisposition genes. This study demonstrates that large case-control studies are needed to fully evaluate the breast cancer risks associated with mutations in moderate-risk and proposed susceptibility genes.

  View details for PubMedID 28649662

• Molecular receptor profiles in male mutation carriers with breast cancer Wapnir, I., Kingham, K., Mills, M., Ford, J., Kurian, A. SPRINGER. 2017: 112–13

  View details for Web of Science ID 000455441000079

• Long-read genome sequencing identifies causal structural variation in a Mendelian disease. Genetics in medicine : official journal of the American College of Medical Genetics Merker, J. D., Wenger, A. M., Sneddon, T. n., Grove, M. n., Zappala, Z. n., Fresard, L. n., Waggott, D. n., Utiramerur, S. n., Hou, Y. n., Smith, K. S., Montgomery, S. B., Wheeler, M. n., Buchan, J. G., Lambert, C. C., Eng, K. S., Hickey, L. n., Korlach, J. n., Ford, J. n., Ashley, E. A. 2017

  Abstract

  PurposeCurrent clinical genomics assays primarily utilize short-read sequencing (SRS), but SRS has limited ability to evaluate repetitive regions and structural variants. Long-read sequencing (LRS) has complementary strengths, and we aimed to determine whether LRS could offer a means to identify overlooked genetic variation in patients undiagnosed by SRS.MethodsWe performed low-coverage genome LRS to identify structural variants in a patient who presented with multiple neoplasia and cardiac myxomata, in whom the results of targeted clinical testing and genome SRS were negative.ResultsThis LRS approach yielded 6,971 deletions and 6,821 insertions > 50 bp. Filtering for variants that are absent in an unrelated control and overlap a disease gene coding exon identified three deletions and three insertions. One of these, a heterozygous 2,184 bp deletion, overlaps the first coding exon of PRKAR1A, which is implicated in autosomal dominant Carney complex. RNA sequencing demonstrated decreased PRKAR1A expression. The deletion was classified as pathogenic based on guidelines for interpretation of sequence variants.ConclusionThis first successful application of genome LRS to identify a pathogenic variant in a patient suggests that LRS has significant potential for the identification of disease-causing structural variation. Larger studies will ultimately be required to evaluate the potential clinical utility of LRS.GENETICS in MEDICINE advance online publication, 22 June 2017; doi:10.1038/gim.2017.86.

  View details for PubMedID 28640241

• Precision Oncology: A New Forum for an Emerging Field. JCO precision oncology Ford, J. M. 2017; 1: 1-2

  View details for DOI 10.1200/PO.16.00048

  View details for PubMedID 35172478

• Precision Oncology Strategy in Trastuzumab-Resistant Human Epidermal Growth Factor Receptor 2-Positive Colon Cancer: Case Report of Durable Response to Ado-Trastuzumab Emtansine JCO PRECISION ONCOLOGY Haslem, D. S., Ji, H. P., Ford, J. M., Nadauld, L. D. 2017; 1

  View details for DOI 10.1200/PO.16.00055

  View details for Web of Science ID 000462058200017

• Interferon-beta represses cancer stem cell properties in triple-negative breast cancer. Proceedings of the National Academy of Sciences of the United States of America Doherty, M. R., Cheon, H. n., Junk, D. J., Vinayak, S. n., Varadan, V. n., Telli, M. L., Ford, J. M., Stark, G. R., Jackson, M. W. 2017; 114 (52): 13792–97

  Abstract

  Triple-negative breast cancer (TNBC), the deadliest form of this disease, lacks a targeted therapy. TNBC tumors that fail to respond to chemotherapy are characterized by a repressed IFN/signal transducer and activator of transcription (IFN/STAT) gene signature and are often enriched for cancer stem cells (CSCs). We have found that human mammary epithelial cells that undergo an epithelial-to-mesenchymal transition (EMT) following transformation acquire CSC properties. These mesenchymal/CSCs have a significantly repressed IFN/STAT gene expression signature and an enhanced ability to migrate and form tumor spheres. Treatment with IFN-beta (IFN-β) led to a less aggressive epithelial/non-CSC-like state, with repressed expression of mesenchymal proteins (VIMENTIN, SLUG), reduced migration and tumor sphere formation, and reexpression of CD24 (a surface marker for non-CSCs), concomitant with an epithelium-like morphology. The CSC-like properties were correlated with high levels of unphosphorylated IFN-stimulated gene factor 3 (U-ISGF3), which was previously linked to resistance to DNA damage. Inhibiting the expression of IRF9 (the DNA-binding component of U-ISGF3) reduced the migration of mesenchymal/CSCs. Here we report a positive translational role for IFN-β, as gene expression profiling of patient-derived TNBC tumors demonstrates that an IFN-β metagene signature correlates with improved patient survival, an immune response linked with tumor-infiltrating lymphocytes (TILs), and a repressed CSC metagene signature. Taken together, our findings indicate that repressed IFN signaling in TNBCs with CSC-like properties is due to high levels of U-ISGF3 and that treatment with IFN-β reduces CSC properties, suggesting a therapeutic strategy to treat drug-resistant, highly aggressive TNBC tumors.

  View details for PubMedID 29229854

• Linked read sequencing resolves complex genomic rearrangements in gastric cancer metastases. Genome medicine Greer, S. U., Nadauld, L. D., Lau, B. T., Chen, J. n., Wood-Bouwens, C. n., Ford, J. M., Kuo, C. J., Ji, H. P. 2017; 9 (1): 57

  Abstract

  Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing.To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater. After sequencing, the barcoded sequence reads provide long range genomic information, identify individual high molecular weight DNA molecules, determine the haplotype context of genetic variants that occur across contiguous megabase-length segments of the genome and delineate the structure of complex rearrangements. We applied linked read sequencing of whole genomes to the analysis of a set of synchronous metastatic diffuse gastric cancers that occurred in the same individual.When comparing metastatic sites, our analysis implicated a complex somatic rearrangement that was present in the metastatic tumor. The oncogenic event associated with the identified complex rearrangement resulted in an amplification of the known cancer driver gene FGFR2. With further investigation using these linked read data, the FGFR2 copy number alteration was determined to be a deletion-inversion motif that underwent tandem duplication, with unique breakpoints in each metastasis. Using a three-dimensional organoid tissue model, we functionally validated the metastatic potential of an FGFR2 amplification in gastric cancer.Our study demonstrates that linked read sequencing is useful in characterizing oncogenic rearrangements in cancer metastasis.

  View details for PubMedID 28629429

• Genetic predisposition to gastric cancer SEMINARS IN ONCOLOGY Petrovchich, I., Ford, J. M. 2016; 43 (5): 554-559

  Abstract

  Gastric cancer ranks as the third leading cause of cancer mortality worldwide and confers a 5-year survival of 20%. While most gastric cancers are sporadic, ~1%-3% can be attributed to inherited cancer predisposition syndromes. Germline E-cadherin/CDH1 mutations have been identified in families with an autosomal dominant inherited predisposition to diffuse gastric cancer. The cumulative risk of gastric cancer for CDH1 mutation carriers by age 80 years is reportedly 70% for men and 56% for women. Female mutation carriers also have an estimated 42% risk for developing lobular breast cancer by age 80 years. However, most individuals meeting clinical criteria for hereditary diffuse gastric cancer syndrome (HDGC) do not have a germline CDH1 mutation, and germline CDH1 mutation carriers do not all exhibit similar clinical outcomes in terms of age of diagnosis or cancer types. E-cadherin (CDH1) as the one known causative gene for HDGC accounts for only 40% of cases, leaving 60% with an unknown genetic diagnosis. In addition to HDGC, we will review other genetic syndromes with elevated gastric cancer risk, as well as newly implicated alterations in other genes (CTNNA1, DOT1L, FBXO24, PRSS1, MAP3K6, MSR1, and INSR) that may affect gastric cancer susceptibility and age-specific penetrance.

  View details for DOI 10.1053/j.seminoncol.2016.08.006

  View details for PubMedID 27899187

• Homologous Recombination Deficiency (HRD) Score Predicts Response to Platinum-Containing Neoadjuvant Chemotherapy in Patients with Triple-Negative Breast Cancer. Clinical cancer research Telli, M. L., Timms, K. M., Reid, J., Hennessy, B., Mills, G. B., Jensen, K. C., Szallasi, Z., Barry, W. T., Winer, E. P., Tung, N. M., Isakoff, S. J., Ryan, P. D., Greene-Colozzi, A., Gutin, A., Sangale, Z., Iliev, D., Neff, C., Abkevich, V., Jones, J. T., Lanchbury, J. S., Hartman, A., Garber, J. E., Ford, J. M., Silver, D. P., Richardson, A. L. 2016; 22 (15): 3764-3773

  Abstract

  BRCA1/2 mutated and some sporadic triple negative breast cancers (TNBCs) have DNA repair defects and are sensitive to DNA-damaging therapeutics. Recently, three independent DNA-based measures of genomic instability were developed based on loss of heterozygosity (LOH), telomeric allelic imbalance (TAI), and large-scale state transitions (LST).We assessed a combined homologous recombination deficiency (HRD) score, an unweighted sum of LOH, TAI, and LST scores, in three neoadjuvant TNBC trials of platinum-containing therapy. We then tested the association of HR deficiency, defined as HRD score {greater than or equal to}42 or BRCA1/2 mutation, with response to platinum-based therapy.In a trial of neoadjuvant platinum, gemcitabine, and iniparib, HR deficiency predicted Residual Cancer Burden score of 0 or 1 (RCB 0/1) and pathologic complete response (pCR) (OR=4.96, p=0.0036; OR=6.52, p=0.0058). HR deficiency remained a significant predictor of RCB 0/1 when adjusted for clinical variables (OR=5.86, p=0.012). In two other trials of neoadjuvant cisplatin therapy, HR deficiency predicted RCB 0/1 and pCR (OR=10.18, p=0.0011; OR=17.00, p=0.0066). In a multivariable model of RCB 0/1, HR deficiency retained significance when clinical variables were included (OR=12.08, p=0.0017). When restricted to BRCA1/2 non-mutated tumors, response was higher in patients with high HRD scores: RCB 0/1 p=0.062, pCR p=0.063 in the neoadjuvant platinum, gemcitabine, and iniparib trial; RCB 0/1 p=0.0039, pCR p=0.018 in the neoadjuvant cisplatin trials.HR deficiency identifies TNBC tumors, including BRCA1/2 non-mutated tumors more likely to respond to platinum-containing therapy.

  View details for DOI 10.1158/1078-0432.CCR-15-2477

  View details for PubMedID 26957554

• Genetic/Familial High-Risk Assessment: Colorectal Version 1.2016 JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK Provenzale, D., Gupta, S., Ahnen, D. J., Bray, T., Cannon, J. A., Cooper, G., David, D. S., Early, D. S., Erwin, D., Ford, J. M., Giardiello, F. M., Grady, W., Halverson, A. L., Hamilton, S. R., Hampel, H., Ismail, M. K., Klapman, J. B., Larson, D. W., Lazenby, A. J., Lynch, P. M., Mayer, R. J., Ness, R. M., Regenbogen, S. E., Samadder, N. J., Shike, M., Steinbach, G., Weinberg, D., Dwyer, M., Darlow, S. 2016; 14 (8): 1010-1030

  Abstract

  This is a focused update highlighting the most current NCCN Guidelines for diagnosis and management of Lynch syndrome. Lynch syndrome is the most common cause of hereditary colorectal cancer, usually resulting from a germline mutation in 1 of 4 DNA mismatch repair genes (MLH1, MSH2, MSH6, or PMS2), or deletions in the EPCAM promoter. Patients with Lynch syndrome are at an increased lifetime risk, compared with the general population, for colorectal cancer, endometrial cancer, and other cancers, including of the stomach and ovary. As of 2016, the panel recommends screening all patients with colorectal cancer for Lynch syndrome and provides recommendations for surveillance for early detection and prevention of Lynch syndrome-associated cancers.

  View details for Web of Science ID 000380818400011

• A Chimeric ATP-Linked Nucleotide Enables Luminescence Signaling of Damage Surveillance by MTH1, a Cancer Target. Journal of the American Chemical Society Ji, D., Beharry, A. A., Ford, J. M., Kool, E. T. 2016; 138 (29): 9005-9008

  Abstract

  The enzyme MTH1 cleanses the cellular nucleotide pool of oxidatively damaged 8-oxo-dGTP, preventing mutagenesis by this nucleotide. The enzyme is considered a promising therapeutic target; however, methods to measure its activity are indirect and laborious and have low sensitivity. Here we describe a novel ATP-linked chimeric nucleotide (ARGO) that enables luminescence signaling of the enzymatic reaction, greatly simplifying the measurement of MTH1 activity. We show that the reporting system can be used to identify inhibitors of MTH1, and we use it to quantify enzyme activity in eight cell lines and in colorectal tumor tissue. The ARGO reporter is likely to have considerable utility in the study of the biology of MTH1 and potentially in analyzing patient samples during clinical testing.

  View details for DOI 10.1021/jacs.6b02895

  View details for PubMedID 27413803

• Detection of Germline Mutation in Hereditary Breast and/or Ovarian Cancers by Next-Generation Sequencing on a Four-Gene Panel JOURNAL OF MOLECULAR DIAGNOSTICS Kwong, A., Shin, V. Y., Au, C. H., Law, F. B., Ho, D. N., Ip, B. K., Wong, A. T., Lau, S. S., To, R. M., Choy, G., Ford, J. M., Ma, E. S., Chan, T. L. 2016; 18 (4): 580-594

  Abstract

  Mutation in BRCA1/BRCA2 genes accounts for 20% of familial breast cancers, 5% to 10% of which may be due to other less penetrant genes which are still incompletely studied. Herein, a four-gene panel was used to examine the prevalence of BRCA1, BRCA2, TP53, and PTEN in hereditary breast and ovarian cancers in Southern Chinese population. In this cohort, 948 high-risk breast and/or ovarian patients were recruited for genetic screening by next-generation sequencing (NGS). The performance of our NGS pipeline was evaluated with 80 Sanger-validated known mutations and eight negative cases. With appropriate bioinformatics analysis pipeline, the detection sensitivity of NGS is comparable with Sanger sequencing. The prevalence of BRCA1/BRCA2 germline mutations was 9.4% in our Chinese cohort, of which 48.8% of the mutations arose from hotspot mutations. With the use of a tailor-made algorithm, HomopolymerQZ, more mutations were detected compared with single mutation detection algorithm. The frequencies of PTEN and TP53 were 0.21% and 0.53%, respectively, in the Southern Chinese patients with breast and/or ovarian cancers. High-throughput NGS approach allows the incorporation of control cohort that provides an ethnicity-specific data for polymorphic variants. Our data suggest that hotspot mutations screening such as SNaPshot could be an effective preliminary screening alternative adopted in a standard clinical laboratory without NGS setup.

  View details for DOI 10.1016/j.jmoldx.2016.03.005

  View details for PubMedID 27157322

• DNA-repair defects in pancreatic neuroendocrine tumors and potential clinical applications CANCER TREATMENT REVIEWS Liu, I. H., Ford, J. M., Kunz, P. L. 2016; 44: 1-9

  Abstract

  The role of DNA repair in pathogenesis and response to treatment is not well understood in pancreatic neuroendocrine tumors (pNETs). However, the existing literature reveals important preliminary trends and targets in the genetic landscape of pNETs. Notably, pNETs have been shown to harbor defects in the direct reversal MGMT gene and the DNA mismatch repair genes, suggesting that these genes may be strong candidates for further prospective studies.PubMed searches were conducted for original studies assessing the DNA repair genes MGMT and MMR in pNETs, as well as for PTEN and MEN1, which are not directly DNA repair genes but are involved in DNA repair pathways. Searches were specific to pNETs, yielding five original studies on MGMT and four on MMR. Six original papers studied PTEN in pNETs. Five studied MEN1 in pNETs, and two others implicated MEN1 in DNA repair processes.The five studies on MGMT in pNET tumor samples found MGMT loss of between 24% and 51% of tumor samples by IHC staining and between 0% and 40% by promoter hypermethylation, revealing discrepancies in methods assessing MGMT expression as well as potential weaknesses in the correlation between MGMT IHC expression and promoter hypermethylation rates. Four studies on MMR in pNET tumor samples indicated similar ambiguities, as promoter hypermethylation of the MLH1 MMR gene ranged from 0% to 31% of pNETs, while IHC staining revealed loss of MMR genes in between 0% and 36% of pNETs sampled. Studies also indicated that PTEN and MEN1 are commonly mutated or underexpressed genes in pNETs, although frequency of mutation or loss of expression was again variable among different studies.Further studies are essential in determining a more thorough repertoire of DNA repair defects in pNETs and the clinical significance of these defects. This literature review synthesises the existing knowledge of relevant DNA repair pathways and studies of the specific genes that carry out these repair mechanisms in pNETs.

  View details for DOI 10.1016/j.ctrv.2015.11.006

  View details for Web of Science ID 000372379200001

• DNA-repair defects in pancreatic neuroendocrine tumors and potential clinical applications. Cancer treatment reviews Liu, I. H., Ford, J. M., Kunz, P. L. 2016; 44: 1-9

  Abstract

  The role of DNA repair in pathogenesis and response to treatment is not well understood in pancreatic neuroendocrine tumors (pNETs). However, the existing literature reveals important preliminary trends and targets in the genetic landscape of pNETs. Notably, pNETs have been shown to harbor defects in the direct reversal MGMT gene and the DNA mismatch repair genes, suggesting that these genes may be strong candidates for further prospective studies.PubMed searches were conducted for original studies assessing the DNA repair genes MGMT and MMR in pNETs, as well as for PTEN and MEN1, which are not directly DNA repair genes but are involved in DNA repair pathways. Searches were specific to pNETs, yielding five original studies on MGMT and four on MMR. Six original papers studied PTEN in pNETs. Five studied MEN1 in pNETs, and two others implicated MEN1 in DNA repair processes.The five studies on MGMT in pNET tumor samples found MGMT loss of between 24% and 51% of tumor samples by IHC staining and between 0% and 40% by promoter hypermethylation, revealing discrepancies in methods assessing MGMT expression as well as potential weaknesses in the correlation between MGMT IHC expression and promoter hypermethylation rates. Four studies on MMR in pNET tumor samples indicated similar ambiguities, as promoter hypermethylation of the MLH1 MMR gene ranged from 0% to 31% of pNETs, while IHC staining revealed loss of MMR genes in between 0% and 36% of pNETs sampled. Studies also indicated that PTEN and MEN1 are commonly mutated or underexpressed genes in pNETs, although frequency of mutation or loss of expression was again variable among different studies.Further studies are essential in determining a more thorough repertoire of DNA repair defects in pNETs and the clinical significance of these defects. This literature review synthesises the existing knowledge of relevant DNA repair pathways and studies of the specific genes that carry out these repair mechanisms in pNETs.

  View details for DOI 10.1016/j.ctrv.2015.11.006

  View details for PubMedID 26924193

• Comprehensive spectrum of BRCA1 and BRCA2 deleterious mutations in breast cancer in Asian countries JOURNAL OF MEDICAL GENETICS Kwong, A., Shin, V. Y., Ho, J. C., Kang, E., Nakamura, S., Teo, S., Lee, A. S., Sng, J., Ginsburg, O. M., Kurian, A. W., Weitzel, J. N., Siu, M., Law, F. B., Chan, T., Narod, S. A., Ford, J. M., Ma, E. S., Kim, S. 2016; 53 (1): 15-23

  Abstract

  Approximately 5%-10% of breast cancers are due to genetic predisposition caused by germline mutations; the most commonly tested genes are BRCA1 and BRCA2 mutations. Some mutations are unique to one family and others are recurrent; the spectrum of BRCA1/BRCA2 mutations varies depending on the geographical origins, populations or ethnic groups. In this review, we compiled data from 11 participating Asian countries (Bangladesh, Mainland China, Hong Kong SAR, Indonesia, Japan, Korea, Malaysia, Philippines, Singapore, Thailand and Vietnam), and from ethnic Asians residing in Canada and the USA. We have additionally conducted a literature review to include other Asian countries mainly in Central and Western Asia. We present the current pathogenic mutation spectrum of BRCA1/BRCA2 genes in patients with breast cancer in various Asian populations. Understanding BRCA1/BRCA2 mutations in Asians will help provide better risk assessment and clinical management of breast cancer.

  View details for DOI 10.1136/jmedgenet-2015-103132

  View details for PubMedID 26187060

• Discovery and functional characterization of a neomorphic PTEN mutation PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Costa, H. A., Leitner, M. G., Sos, M. L., Mavrantoni, A., Rychkova, A., Johnson, J. R., Newton, B. W., Yee, M., De La Vega, F. M., Ford, J. M., Krogan, N. J., Shokat, K. M., Oliver, D., Halaszovich, C. R., Bustamante, C. D. 2015; 112 (45): 13976-13981

  Abstract

  Although a variety of genetic alterations have been found across cancer types, the identification and functional characterization of candidate driver genetic lesions in an individual patient and their translation into clinically actionable strategies remain major hurdles. Here, we use whole genome sequencing of a prostate cancer tumor, computational analyses, and experimental validation to identify and predict novel oncogenic activity arising from a point mutation in the phosphatase and tensin homolog (PTEN) tumor suppressor protein. We demonstrate that this mutation (p.A126G) produces an enzymatic gain-of-function in PTEN, shifting its function from a phosphoinositide (PI) 3-phosphatase to a phosphoinositide (PI) 5-phosphatase. Using cellular assays, we demonstrate that this gain-of-function activity shifts cellular phosphoinositide levels, hyperactivates the PI3K/Akt cell proliferation pathway, and exhibits increased cell migration beyond canonical PTEN loss-of-function mutants. These findings suggest that mutationally modified PTEN can actively contribute to well-defined hallmarks of cancer. Lastly, we demonstrate that these effects can be substantially mitigated through chemical PI3K inhibitors. These results demonstrate a new dysfunction paradigm for PTEN cancer biology and suggest a potential framework for the translation of genomic data into actionable clinical strategies for targeted patient therapy.

  View details for DOI 10.1073/pnas.1422504112

  View details for PubMedID 26504226

• Clinical Actionability of Multigene Panel Testing for Hereditary Breast and Ovarian Cancer Risk Assessment. JAMA oncology Desmond, A., Kurian, A. W., Gabree, M., Mills, M. A., Anderson, M. J., Kobayashi, Y., Horick, N., Yang, S., Shannon, K. M., Tung, N., Ford, J. M., Lincoln, S. E., Ellisen, L. W. 2015; 1 (7): 943-951

  Abstract

  The practice of genetic testing for hereditary breast and/or ovarian cancer (HBOC) is rapidly evolving owing to the recent introduction of multigene panels. While these tests may identify 40% to 50% more individuals with hereditary cancer gene mutations than does testing for BRCA1/2 alone, whether finding such mutations will alter clinical management is unknown.To define the potential clinical effect of multigene panel testing for HBOC in a clinically representative cohort.Observational study of patients seen between 2001 and 2014 in 3 large academic medical centers. We prospectively enrolled 1046 individuals who were appropriate candidates for HBOC evaluation and who lacked BRCA1/2 mutations.We carried out multigene panel testing on all participants, then determined the clinical actionability, if any, of finding non-BRCA1/2 mutations in these and additional comparable individuals.We evaluated the likelihood of (1) a posttest management change and (2) an indication for additional familial testing, considering gene-specific consensus management guidelines, gene-associated cancer risks, and personal and family history.Among 1046 study participants, 40 BRCA1/2-negative patients (3.8%; 95% CI, 2.8%-5.2%) harbored deleterious mutations, most commonly in moderate-risk breast and ovarian cancer genes (CHEK2, ATM, and PALB2) and Lynch syndrome genes. Among these and an additional 23 mutation-positive individuals enrolled from our clinics, most of the mutations (92%) were consistent with the spectrum of cancer(s) observed in the patient or family, suggesting that these results are clinically significant. Among all 63 mutation-positive patients, additional disease-specific screening and/or prevention measures beyond those based on personal and family history alone would be considered for most (33 [52%] of 63; 95% CI, 40.3%-64.2%). Furthermore, additional familial testing would be considered for those with first-degree relatives (42 [72%] of 58; 95% CI, 59.8%-82.2%) based on potential management changes for mutation-positive relatives. This clinical effect was not restricted to a few of the tested genes because most identified genes could change clinical management for some patients.In a clinically representative cohort, multigene panel testing for HBOC risk assessment yielded findings likely to change clinical management for substantially more patients than does BRCA1/2 testing alone. Multigene testing in this setting is likely to alter near-term cancer risk assessment and management recommendations for mutation-affected individuals across a broad spectrum of cancer predisposition genes.

  View details for DOI 10.1001/jamaoncol.2015.2690

  View details for PubMedID 26270727

• A Systematic Comparison of Traditional and Multigene Panel Testing for Hereditary Breast and Ovarian Cancer Genes in More Than 1000 Patients JOURNAL OF MOLECULAR DIAGNOSTICS Lincoln, S. E., Kobayashi, Y., Anderson, M. J., Yang, S., Desmond, A. J., Mills, M. A., Nilsen, G. B., Jacobs, K. B., Monzon, F. A., Kurian, A. W., Ford, J. M., Ellisen, L. W. 2015; 17 (5): 533-544

  Abstract

  Gene panels for hereditary breast and ovarian cancer risk assessment are gaining acceptance, even though the clinical utility of these panels is not yet fully defined. Technical questions remain, however, about the performance and clinical interpretation of gene panels in comparison with traditional tests. We tested 1105 individuals using a 29-gene next-generation sequencing panel and observed 100% analytical concordance with traditional and reference data on >750 comparable variants. These 750 variants included technically challenging classes of sequence and copy number variation that together represent a significant fraction (13.4%) of the pathogenic variants observed. For BRCA1 and BRCA2, we also compared variant interpretations in traditional reports to those produced using only non-proprietary resources and following criteria based on recent (2015) guidelines. We observed 99.8% net report concordance, albeit with a slightly higher variant of uncertain significance rate. In 4.5% of BRCA-negative cases, we uncovered pathogenic variants in other genes, which appear clinically relevant. Previously unseen variants requiring interpretation accumulated rapidly, even after 1000 individuals had been tested. We conclude that next-generation sequencing panel testing can provide results highly comparable to traditional testing and can uncover potentially actionable findings that may be otherwise missed. Challenges remain for the broad adoption of panel tests, some of which will be addressed by the accumulation of large public databases of annotated clinical variants.

  View details for DOI 10.1016/j.jmoldx.2015.04.009

  View details for PubMedID 26207792

• The importance of analysis of long-range rearrangement of BRCA1 and BRCA2 in genetic diagnosis of familial breast cancer CANCER GENETICS Kwong, A., Chen, J., Shin, V. Y., Ho, J. C., Law, F. B., Au, C. H., Chan, T., Ma, E. S., Ford, J. M. 2015; 208 (9): 448-454

  Abstract

  Germline BRCA gene mutations are reportedly associated with hereditary breast and ovarian cancers. Identification of BRCA mutations greatly improves the preventive strategies and management of breast cancer. Sanger sequencing has been the gold standard in identifying these mutations. However, 4-28% of inherited BRCA mutations may be due to large genomic rearrangements (LGRs), which could be missed by using Sanger sequencing alone. Our aim is to evaluate the pick-up rate of LGRs in our cohort. A total of 1,236 clinically high-risk patients with breast and/or ovarian cancers were recruited through The Hong Kong Hereditary Breast Cancer Family Registry from 2007 to 2014. Full gene sequencing (either Sanger or next generation sequencing) and multiplex ligation-dependent probe amplification (MLPA) were performed. We identified 120 deleterious BRCA mutations: 57 (4.61%) were in BRCA1 and 63 (5.10%) were in BRCA2. LGRs accounted for 6.67% (8 of 120) of all BRCA mutations, whereas 8.77 % (5 of 57) were BRCA1 mutations and 4.76% (3 of 63) were BRCA2 mutations. Through this integrated approach, both small nucleotide variations and LGRs could be detected. We suggest that MLPA should be incorporated into the standard practice for genetic testing to avoid false-negative results, which would greatly affect the management of these high-risk families.

  View details for DOI 10.1016/j.cancergen.2015.05.031

  View details for PubMedID 26271414

• American Gastroenterological Association Technical Review on the Diagnosis and Management of Lynch Syndrome GASTROENTEROLOGY Ladabaum, U., Ford, J. M., Martel, M., Barkun, A. N. 2015; 149 (3): 783-?

  View details for DOI 10.1053/j.gastro.2015.07.037

  View details for Web of Science ID 000360269800046

• BRCA1: Beyond double-strand break repair DNA REPAIR Alli, E., Ford, J. M. 2015; 32: 165-171

  Abstract

  Since its discovery, the BRCA1 tumor suppressor has been shown to play a role in multiple DNA damage response pathways. Here, we will review the involvement of BRCA1 in base-excision DNA repair and highlight its clinical implications.

  View details for DOI 10.1016/j.dnarep.2015.04.028

  View details for PubMedID 25956865

• Colorectal Cancer Screening, Version 1.2015. Journal of the National Comprehensive Cancer Network Provenzale, D., Jasperson, K., Ahnen, D. J., Aslanian, H., Bray, T., Cannon, J. A., David, D. S., Early, D. S., Erwin, D., Ford, J. M., Giardiello, F. M., Gupta, S., Halverson, A. L., Hamilton, S. R., Hampel, H., Ismail, M. K., Klapman, J. B., Larson, D. W., Lazenby, A. J., Lynch, P. M., Mayer, R. J., Ness, R. M., Rao, M. S., Regenbogen, S. E., Shike, M., Steinbach, G., Weinberg, D., Dwyer, M. A., Freedman-Cass, D. A., Darlow, S. 2015; 13 (8): 959-968

  Abstract

  The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Colorectal Cancer Screening provide recommendations for selecting individuals for colorectal cancer screening, and for evaluation and follow-up of colon polyps. These NCCN Guidelines Insights summarize major discussion points of the 2015 NCCN Colorectal Cancer Screening panel meeting. Major discussion topics this year were the state of evidence for CT colonography and stool DNA testing, bowel preparation procedures for colonoscopy, and guidelines for patients with a positive family history of colorectal cancer.

  View details for PubMedID 26285241

• Colorectal Cancer Screening, Version 1.2015 Featured Updates to the NCCN Guidelines JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK Provenzale, D., Jasperson, K., Ahnen, D. J., Aslanian, H., Bray, T., Cannon, J. A., David, D. S., Early, D. S., Erwin, D., Ford, J. M., Giardiello, F. M., Gupta, S., Halverson, A. L., Hamilton, S. R., Hampel, H., Ismail, M. K., Klapman, J. B., Larson, D. W., Lazenby, A. J., Lynch, P. M., Mayer, R. J., Ness, R. M., Rao, M. S., Regenbogen, S. E., Shike, M., Steinbach, G., Weinberg, D., Dwyer, M. A., Freedman-Cass, D. A., Darlow, S. 2015; 13 (8): 959-968

  Abstract

  The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Colorectal Cancer Screening provide recommendations for selecting individuals for colorectal cancer screening, and for evaluation and follow-up of colon polyps. These NCCN Guidelines Insights summarize major discussion points of the 2015 NCCN Colorectal Cancer Screening panel meeting. Major discussion topics this year were the state of evidence for CT colonography and stool DNA testing, bowel preparation procedures for colonoscopy, and guidelines for patients with a positive family history of colorectal cancer.

  View details for Web of Science ID 000359470200006

• BRCA1: a movement toward cancer prevention. Molecular & cellular oncology Alli, E., Ford, J. M. 2015; 2 (3)

  Abstract

  Breast cancer susceptibility gene 1 (BRCA1) was first identified in 1994 and has since been shown to encode a tumor suppressor protein that maintains genetic stability through DNA damage response pathways. Carriers of mutations in BRCA1 are predisposed to breast and ovarian cancer; however, their cancers lack the targets for existing anticancer drugs. We describe a novel chemoprevention approach that uses DNA repair-activating agents to enhance the repair of oxidative DNA damage and, in turn, prevent tumorigenesis in the presence of mutant BRCA1.

  View details for DOI 10.4161/23723556.2014.979685

  View details for PubMedID 27308455

• Deconvoluting immune cell populations using 'in silico flow cytometry' with CIBERSORT: Association with neoadjuvant therapy response and genomic instability in TNBC Vinayak, S., Newman, A., Adams, S., Afghahi, A., Jensen, K. C., Badve, S. S., Ford, J. M., Alizadeh, A. A., Telli, M. L. AMER ASSOC CANCER RESEARCH. 2015

  View details for DOI 10.1158/1538-7445.SABCS14-P5-04-03

  View details for Web of Science ID 000356730203046

• Hereditary Gastric Cancer An Update at 15 Years JAMA ONCOLOGY Ford, J. M. 2015; 1 (1): 16–18

  View details for PubMedID 26182297

• DNA-Repair Defects in Pancreatic Neuroendocrine Tumors and Potential Clinical Applications Liu, I. H., Ford, J. M., Kunz, P. L. LIPPINCOTT WILLIAMS & WILKINS. 2015: 355

  View details for Web of Science ID 000349769400056

• Next-generation sequencing for hereditary breast and gynecologic cancer risk assessment. Current opinion in obstetrics & gynecology Kurian, A. W., Kingham, K. E., Ford, J. M. 2015; 27 (1): 23-33

  Abstract

  To summarize advances in next-generation sequencing and their application to breast and gynecologic cancer risk assessment.Next-generation sequencing panels of 6-112 cancer-associated genes are increasingly used in patient care. Studies report a 4-16% prevalence of mutations other than BRCA1/2 among patients who meet evidence-based practice guidelines for BRCA1/2 testing, with a high rate (15-88%) of uninterpretable variants of uncertain significance. Despite uncertainty about results interpretation and communication, there is early evidence of a benefit from multiple-gene sequencing panels for appropriately selected patients.Multiple-gene sequencing panels appear highly promising for the assessment of breast and gynecologic cancer risk, and they may usefully be administered in the context of cancer genetics expertise and/or clinical research protocols.

  View details for DOI 10.1097/GCO.0000000000000141

  View details for PubMedID 25502425

• Lynch Syndrome Screening: Discordance in MMR and Germline Test Results Mafnas, C., Martin, B., Ford, J., Longacre, T. NATURE PUBLISHING GROUP. 2015: 177A

  View details for Web of Science ID 000348948001204

• Lynch Syndrome Screening: Discordance in MMR and Germline Test Results Mafnas, C., Martin, B., Ford, J., Longacre, T. NATURE PUBLISHING GROUP. 2015: 177A

  View details for Web of Science ID 000349502201035

• Metastatic Lobular Breast Carcinoma Mimicking Primary Signet Ring Adenocarcinoma in a Patient With a Suspected CDH1 Mutation JOURNAL OF CLINICAL ONCOLOGY Mahmud, N., Ford, J. M., Longacre, T. A., Parent, R., Norton, J. A. 2015; 33 (4): E19-E21

  View details for DOI 10.1200/JCO.2013.49.1159

  View details for Web of Science ID 000352422900002

  View details for PubMedID 24590638

• Metastatic lobular breast carcinoma mimicking primary signet ring adenocarcinoma in a patient with a suspected CDH1 mutation. Journal of clinical oncology Mahmud, N., Ford, J. M., Longacre, T. A., Parent, R., Norton, J. A. 2015; 33 (4): e19-21

  View details for DOI 10.1200/JCO.2013.49.1159

  View details for PubMedID 24590638

• Parent Decision-Making Around the Genetic Testing of Children for Germline TP53 Mutations CANCER Alderfer, M. A., Zelley, K., Lindell, R. B., Novokmet, A., Mai, P. L., Garber, J. E., Nathan, D., Scollon, S., Chun, N. M., Patenaude, A. F., Ford, J. M., Plon, S. E., Schiffman, J. D., Diller, L. R., Savage, S. A., Malkin, D., Ford, C. A., Nichols, K. E. 2015; 121 (2): 286-293

  Abstract

  Li-Fraumeni syndrome is a rare genetic cancer predisposition syndrome caused by germline TP53 mutations. Up to 20% of mutation carriers develop cancer during childhood. The benefits of TP53 mutation testing of children are a matter of debate and knowledge of parent decision-making around such testing is limited. The current study examined how parents make decisions regarding TP53 testing for their children.Families offered and those pursuing TP53 testing for their children were identified across the study sites. Qualitative interviews with 46 parents (39 families) were analyzed to describe decision-making styles and perceived advantages and disadvantages of testing.TP53 mutation testing uptake was high (92%). Three decision-making styles emerged. Automatic decisions (44% of decisions) involved little thought and identified immediate benefit(s) in testing (100% pursued testing). Considered decisions (49%) weighed the risks and benefits but were made easily (77% pursued testing). Deliberated decisions (6%) were difficult and focused on psychosocial concerns (25% pursued testing). Perceived advantages of testing included promoting child health, satisfying a "need to know," understanding why cancer(s) occurred, suggesting family member risk, and benefiting research. Disadvantages included psychosocial risks and privacy/discrimination/insurance issues.Although empirical evidence regarding the benefits and risks of TP53 testing during childhood are lacking, the majority of parents in the current study decided easily in favor of testing and perceived a range of advantages. The authors conclude that in the context of a clinical diagnosis of Li-Fraumeni syndrome, parents should continue to be offered TP53 testing for their children, counseled regarding potential risks and benefits, and supported in their decision-making process. Cancer 2014. © 2014 American Cancer Society.

  View details for DOI 10.1002/cncr.29027

  View details for Web of Science ID 000347540900016

  View details for PubMedID 25223899

• Multiple-Gene Panels and the Future of Genetic Testing Current Breast Cancer Reports Kurian, A. W., Ford, J. M. 2015

  View details for DOI 10.1007/s12609-015-0181-4

• Single-versus Multifraction Stereotactic Body Radiation Therapy for Pancreatic Adenocarcinoma: Outcomes and Toxicity INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Pollom, E. L., Alagappan, M., von Eyben, R., Kunz, P. L., Fisher, G. A., Ford, J. A., Poultsides, G. A., Visser, B. C., Norton, J. A., Kamaya, A., Cox, V. L., Columbo, L. A., Koong, A. C., Chang, D. T. 2014; 90 (4): 918-925

  Abstract

  We report updated outcomes of single- versus multifraction stereotactic body radiation therapy (SBRT) for unresectable pancreatic adenocarcinoma.We included 167 patients with unresectable pancreatic adenocarcinoma treated at our institution from 2002 to 2013, with 1-fraction (45.5% of patient) or 5-fraction (54.5% of patients) SBRT. The majority of patients (87.5%) received chemotherapy.Median follow-up was 7.9 months (range: 0.1-63.6). The 6- and 12-month cumulative incidence rates (CIR) of local recurrence for patients treated with single-fraction SBRT were 5.3% (95% confidence interval [CI], 0.2%-10.4%) and 9.5% (95% CI, 2.7%-16.2%), respectively. The 6- and 12-month CIR with multifraction SBRT were 3.4% (95% CI, 0.0-7.2%) and 11.7% (95% CI, 4.8%-18.6%), respectively. Median survival from diagnosis for all patients was 13.6 months (95% CI, 12.2-15.0 months). The 6- and 12- month survival rates from SBRT for the single-fraction group were 67.0% (95% CI, 57.2%-78.5%) and 30.8% (95% CI, 21.9%-43.6%), respectively. The 6- and 12- month survival rates for the multifraction group were 75.7% (95% CI, 67.2%-85.3%) and 34.9% (95% CI, 26.1%-46.8%), respectively. There were no differences in CIR or survival rates between the single- and multifraction groups. The 6- and 12-month cumulative incidence rates of gastrointestinal toxicity grade ≥3 were 8.1% (95% CI, 1.8%-14.4%) and 12.3% (95% CI, 4.7%-20.0%), respectively, in the single-fraction group, and both were 5.6% (95% CI, 0.8%-10.5%) in the multifraction group. There were significantly fewer instances of toxicity grade ≥2 with multifraction SBRT (P=.005). Local recurrence and toxicity grade ≥2 were independent predictors of worse survival.Multifraction SBRT for pancreatic cancer significantly reduces gastrointestinal toxicity without compromising local control.

  View details for DOI 10.1016/j.ijrobp.2014.06.066

  View details for Web of Science ID 000344734300029

• Single- versus multifraction stereotactic body radiation therapy for pancreatic adenocarcinoma: outcomes and toxicity. International journal of radiation oncology, biology, physics Pollom, E. L., Alagappan, M., von Eyben, R., Kunz, P. L., Fisher, G. A., Ford, J. A., Poultsides, G. A., Visser, B. C., Norton, J. A., Kamaya, A., Cox, V. L., Columbo, L. A., Koong, A. C., Chang, D. T. 2014; 90 (4): 918-925

  Abstract

  We report updated outcomes of single- versus multifraction stereotactic body radiation therapy (SBRT) for unresectable pancreatic adenocarcinoma.We included 167 patients with unresectable pancreatic adenocarcinoma treated at our institution from 2002 to 2013, with 1-fraction (45.5% of patient) or 5-fraction (54.5% of patients) SBRT. The majority of patients (87.5%) received chemotherapy.Median follow-up was 7.9 months (range: 0.1-63.6). The 6- and 12-month cumulative incidence rates (CIR) of local recurrence for patients treated with single-fraction SBRT were 5.3% (95% confidence interval [CI], 0.2%-10.4%) and 9.5% (95% CI, 2.7%-16.2%), respectively. The 6- and 12-month CIR with multifraction SBRT were 3.4% (95% CI, 0.0-7.2%) and 11.7% (95% CI, 4.8%-18.6%), respectively. Median survival from diagnosis for all patients was 13.6 months (95% CI, 12.2-15.0 months). The 6- and 12- month survival rates from SBRT for the single-fraction group were 67.0% (95% CI, 57.2%-78.5%) and 30.8% (95% CI, 21.9%-43.6%), respectively. The 6- and 12- month survival rates for the multifraction group were 75.7% (95% CI, 67.2%-85.3%) and 34.9% (95% CI, 26.1%-46.8%), respectively. There were no differences in CIR or survival rates between the single- and multifraction groups. The 6- and 12-month cumulative incidence rates of gastrointestinal toxicity grade ≥3 were 8.1% (95% CI, 1.8%-14.4%) and 12.3% (95% CI, 4.7%-20.0%), respectively, in the single-fraction group, and both were 5.6% (95% CI, 0.8%-10.5%) in the multifraction group. There were significantly fewer instances of toxicity grade ≥2 with multifraction SBRT (P=.005). Local recurrence and toxicity grade ≥2 were independent predictors of worse survival.Multifraction SBRT for pancreatic cancer significantly reduces gastrointestinal toxicity without compromising local control.

  View details for DOI 10.1016/j.ijrobp.2014.06.066

  View details for PubMedID 25585785

• Lynch Syndrome Screening Should Be Considered for All Patients With Newly Diagnosed Endometrial Cancer AMERICAN JOURNAL OF SURGICAL PATHOLOGY Mills, A. M., Liou, S., Ford, J. M., Berek, J. S., Pai, R. K., Longacre, T. A. 2014; 38 (11): 1501-1509

  Abstract

  Lynch syndrome (LS) is an autosomal dominant inherited disorder caused by germline mutations in DNA mismatch repair (MMR) genes. Mutation carriers are at substantially increased risk of developing cancers of the colorectum and endometrium, among others. Given recent recommendations for universal, cost-effective screening of all patients with newly diagnosed colorectal cancer using MMR protein immunohistochemistry, we evaluated MMR protein expression in a series of endometrial cancers in the general population. A total of 605 consecutive cases of primary endometrial cancer at a single institution (1997 to 2013) were evaluated regardless of age, family history, or histologic features. Evaluation methods consisted of immunohistochemistry for the MMR proteins MLH1, MSH2, MSH6, and PMS2, followed by DNA methylation analysis for cases with MLH1/PMS2 deficiency. Germline mutation testing was performed on a subset of cases. Forty MMR-deficient, nonmethylated endometrial cancers were identified: 3 MLH1/PMS2 and 37 MSH6/MSH2 protein deficiencies. Only 25% occurred in women below 50 years of age (range, 39 to 88 y), 1 of which was in a risk-reducing hysterectomy specimen. Only 15% of patients had a prior history of carcinoma, including only 2 patients with prior colorectal carcinoma. Most (80%) of the endometrial cancers were purely endometrioid; there were 2 mixed endometrioid/mucinous, 1 mucinous, 1 serous, 2 clear cell, and 2 carcinosarcoma cases. When grading was applicable, 40% of the endometrial malignancies were FIGO grade 1, 34% grade 2, and 26% grade 3. Thirteen percent arose in the lower uterine segment, and 23% had tumor-infiltrating lymphocytes. Of the tumors with known germline testing, 41% with a LS-associated germline mutation were not associated with any of the traditional indicators that have been recommended for LS screening (ie, age 50 y or younger, personal/family cancer pedigree that meets Bethesda guideline criteria, presence of MMR-associated tumor morphology, or location in the lower uterine segment). These data suggest that a significant number of LS-associated endometrial carcinomas are missed using clinical, histologic, and locational screening parameters and provide support for universal screening of all newly diagnosed endometrial cancers.

  View details for PubMedID 25229768

• Association of increased tumor-infiltrating lymphocytes (TILs) with immunomodulatory (IM) triple-negative breast cancer (TNBC) subtype and response to neoadjuvant platinum-based therapy in PrECOG0105. Vinayak, S., Gray, R., Adams, S., Jensen, K. C., Manola, J., Afghahi, A., Goldstein, L. J., Ford, J. M., Badve, S. S., Telli, M. L. AMER SOC CLINICAL ONCOLOGY. 2014

  View details for DOI 10.1200/jco.2014.32.15_suppl.1000

  View details for Web of Science ID 000358613202425

• The MLH1 c.-27C>A and c.85G>T variants are linked to dominantly inherited MLH1 epimutation and are borne on a European ancestral haplotype. European journal of human genetics Kwok, C., Vogelaar, I. P., van Zelst-Stams, W. A., Mensenkamp, A. R., Ligtenberg, M. J., Rapkins, R. W., Ward, R. L., Chun, N., Ford, J. M., Ladabaum, U., McKinnon, W. C., Greenblatt, M. S., Hitchins, M. P. 2014; 22 (5): 617-624

  Abstract

  Germline mutations of the DNA mismatch repair genes MLH1, MSH2, MSH6 or PMS2, and deletions affecting the EPCAM gene adjacent to MSH2, underlie Lynch syndrome by predisposing to early-onset colorectal, endometrial and other cancers. An alternative but rare cause of Lynch syndrome is constitutional epimutation of MLH1, whereby promoter methylation and transcriptional silencing of one allele occurs throughout normal tissues. A dominantly transmitted constitutional MLH1 epimutation has been linked to an MLH1 haplotype bearing two single-nucleotide variants, NM_000249.2: c.-27C>A and c.85G>T, in a Caucasian family with Lynch syndrome from Western Australia. Subsequently, a second seemingly unrelated Caucasian Australian case with the same MLH1 haplotype and concomitant epimutation was reported. We now describe three additional, ostensibly unrelated, cancer-affected families of European heritage with this MLH1 haplotype in association with constitutional epimutation, bringing the number of index cases reported to five. Array-based genotyping in four of these families revealed shared haplotypes between individual families that extended across ≤2.6-≤6.4 megabase regions of chromosome 3p, indicating common ancestry. A minimal ≤2.6 megabase founder haplotype common to all four families was identified, which encompassed MLH1 and additional flanking genes and segregated with the MLH1 epimutation in each family. Our findings indicate that the MLH1 c.-27C>A and c.85G>T variants are borne on a European ancestral haplotype and provide conclusive evidence for its pathogenicity via a mechanism of epigenetic silencing of MLH1 within normal tissues. Additional descendants bearing this founder haplotype may exist who are also at high risk of developing Lynch syndrome-related cancers.

  View details for DOI 10.1038/ejhg.2013.200

  View details for PubMedID 24084575

• Clinical interpretation and implications of whole-genome sequencing. JAMA : the journal of the American Medical Association Dewey, F. E., Grove, M. E., Pan, C., Goldstein, B. A., Bernstein, J. A., Chaib, H., Merker, J. D., Goldfeder, R. L., Enns, G. M., David, S. P., Pakdaman, N., Ormond, K. E., Caleshu, C., Kingham, K., Klein, T. E., Whirl-Carrillo, M., Sakamoto, K., Wheeler, M. T., Butte, A. J., Ford, J. M., Boxer, L., Ioannidis, J. P., Yeung, A. C., Altman, R. B., Assimes, T. L., Snyder, M., Ashley, E. A., Quertermous, T. 2014; 311 (10): 1035-1045

  Abstract

  Whole-genome sequencing (WGS) is increasingly applied in clinical medicine and is expected to uncover clinically significant findings regardless of sequencing indication.To examine coverage and concordance of clinically relevant genetic variation provided by WGS technologies; to quantitate inherited disease risk and pharmacogenomic findings in WGS data and resources required for their discovery and interpretation; and to evaluate clinical action prompted by WGS findings.An exploratory study of 12 adult participants recruited at Stanford University Medical Center who underwent WGS between November 2011 and March 2012. A multidisciplinary team reviewed all potentially reportable genetic findings. Five physicians proposed initial clinical follow-up based on the genetic findings.Genome coverage and sequencing platform concordance in different categories of genetic disease risk, person-hours spent curating candidate disease-risk variants, interpretation agreement between trained curators and disease genetics databases, burden of inherited disease risk and pharmacogenomic findings, and burden and interrater agreement of proposed clinical follow-up.Depending on sequencing platform, 10% to 19% of inherited disease genes were not covered to accepted standards for single nucleotide variant discovery. Genotype concordance was high for previously described single nucleotide genetic variants (99%-100%) but low for small insertion/deletion variants (53%-59%). Curation of 90 to 127 genetic variants in each participant required a median of 54 minutes (range, 5-223 minutes) per genetic variant, resulted in moderate classification agreement between professionals (Gross κ, 0.52; 95% CI, 0.40-0.64), and reclassified 69% of genetic variants cataloged as disease causing in mutation databases to variants of uncertain or lesser significance. Two to 6 personal disease-risk findings were discovered in each participant, including 1 frameshift deletion in the BRCA1 gene implicated in hereditary breast and ovarian cancer. Physician review of sequencing findings prompted consideration of a median of 1 to 3 initial diagnostic tests and referrals per participant, with fair interrater agreement about the suitability of WGS findings for clinical follow-up (Fleiss κ, 0.24; P < 001).In this exploratory study of 12 volunteer adults, the use of WGS was associated with incomplete coverage of inherited disease genes, low reproducibility of detection of genetic variation with the highest potential clinical effects, and uncertainty about clinically reportable findings. In certain cases, WGS will identify clinically actionable genetic variants warranting early medical intervention. These issues should be considered when determining the role of WGS in clinical medicine.

  View details for DOI 10.1001/jama.2014.1717

  View details for PubMedID 24618965

  View details for PubMedCentralID PMC4119063

• American Society of Clinical Oncology Expert Statement: collection and use of a cancer family history for oncology providers. Journal of clinical oncology Lu, K. H., Wood, M. E., Daniels, M., Burke, C., Ford, J., Kauff, N. D., Kohlmann, W., Lindor, N. M., Mulvey, T. M., Robinson, L., Rubinstein, W. S., Stoffel, E. M., Snyder, C., Syngal, S., Merrill, J. K., Wollins, D. S., Hughes, K. S. 2014; 32 (8): 833-840

  View details for DOI 10.1200/JCO.2013.50.9257

  View details for PubMedID 24493721

  View details for PubMedCentralID PMC3940540

• American society of clinical oncology expert statement: collection and use of a cancer family history for oncology providers. Journal of clinical oncology Lu, K. H., Wood, M. E., Daniels, M., Burke, C., Ford, J., Kauff, N. D., Kohlmann, W., Lindor, N. M., Mulvey, T. M., Robinson, L., Rubinstein, W. S., Stoffel, E. M., Snyder, C., Syngal, S., Merrill, J. K., Wollins, D. S., Hughes, K. S. 2014; 32 (8): 833-840

  View details for DOI 10.1200/JCO.2013.50.9257

  View details for PubMedID 24493721

  View details for PubMedCentralID PMC3940540

• Colorectal Cancer Screening Clinical Practice Guidelines in Oncology JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK Burt, R. W., Cannon, J. A., David, D. S., Early, D. S., Ford, J. M., Giardiello, F. M., Halverson, A. L., Hamilton, S. R., Hampel, H., Ismail, M. K., Jasperson, K., Klapman, J. B., Lazenby, A. J., Lynch, P. M., Mayer, R. J., Ness, R. M., Provenzale, D., Rao, M. S., Shike, M., Steinbach, G., Terdiman, J. P., Weinberg, D., Dwyer, M., Freedman-Cass, D. 2013; 11 (12): 1538-1575

  Abstract

  Mortality from colorectal cancer can be reduced by early diagnosis and by cancer prevention through polypectomy. These NCCN Guidelines for Colorectal Cancer Screening describe various colorectal screening modalities and recommended screening schedules for patients at average or increased risk of developing colorectal cancer. In addition, the guidelines provide recommendations for the management of patients with high-risk colorectal cancer syndromes, including Lynch syndrome. Screening approaches for Lynch syndrome are also described.

  View details for Web of Science ID 000328639000011

• Colorectal cancer screening. Journal of the National Comprehensive Cancer Network Burt, R. W., Cannon, J. A., David, D. S., Early, D. S., Ford, J. M., Giardiello, F. M., Halverson, A. L., Hamilton, S. R., Hampel, H., Ismail, M. K., Jasperson, K., Klapman, J. B., Lazenby, A. J., Lynch, P. M., Mayer, R. J., Ness, R. M., Provenzale, D., Rao, M. S., Shike, M., Steinbach, G., Terdiman, J. P., Weinberg, D., Dwyer, M., Freedman-Cass, D. 2013; 11 (12): 1538-1575

  Abstract

  Mortality from colorectal cancer can be reduced by early diagnosis and by cancer prevention through polypectomy. These NCCN Guidelines for Colorectal Cancer Screening describe various colorectal screening modalities and recommended screening schedules for patients at average or increased risk of developing colorectal cancer. In addition, the guidelines provide recommendations for the management of patients with high-risk colorectal cancer syndromes, including Lynch syndrome. Screening approaches for Lynch syndrome are also described.

  View details for PubMedID 24335688

• Dynamic contrast-enhanced MRI-based biomarkers of therapeutic response in triple-negative breast cancer. Journal of the American Medical Informatics Association Golden, D. I., Lipson, J. A., Telli, M. L., Ford, J. M., Rubin, D. L. 2013; 20 (6): 1059-1066

  Abstract

  To predict the response of breast cancer patients to neoadjuvant chemotherapy (NAC) using features derived from dynamic contrast-enhanced (DCE) MRI.60 patients with triple-negative early-stage breast cancer receiving NAC were evaluated. Features assessed included clinical data, patterns of tumor response to treatment determined by DCE-MRI, MRI breast imaging-reporting and data system descriptors, and quantitative lesion kinetic texture derived from the gray-level co-occurrence matrix (GLCM). All features except for patterns of response were derived before chemotherapy; GLCM features were determined before and after chemotherapy. Treatment response was defined by the presence of residual invasive tumor and/or positive lymph nodes after chemotherapy. Statistical modeling was performed using Lasso logistic regression.Pre-chemotherapy imaging features predicted all measures of response except for residual tumor. Feature sets varied in effectiveness at predicting different definitions of treatment response, but in general, pre-chemotherapy imaging features were able to predict pathological complete response with area under the curve (AUC)=0.68, residual lymph node metastases with AUC=0.84 and residual tumor with lymph node metastases with AUC=0.83. Imaging features assessed after chemotherapy yielded significantly improved model performance over those assessed before chemotherapy for predicting residual tumor, but no other outcomes.DCE-MRI features can be used to predict whether triple-negative breast cancer patients will respond to NAC. Models such as the ones presented could help to identify patients not likely to respond to treatment and to direct them towards alternative therapies.

  View details for DOI 10.1136/amiajnl-2012-001460

  View details for PubMedID 23785100

• A clinical trial of lovastatin for modification of biomarkers associated with breast cancer risk. Breast cancer research and treatment Vinayak, S., Schwartz, E. J., Jensen, K., Lipson, J., Alli, E., McPherson, L., Fernandez, A. M., Sharma, V. B., Staton, A., Mills, M. A., Schackmann, E. A., Telli, M. L., Kardashian, A., Ford, J. M., Kurian, A. W. 2013; 142 (2): 389-398

  Abstract

  Pre-clinical and epidemiologic studies provide rationale for evaluating lipophilic statins for breast cancer prevention. We conducted a single-arm, biomarker modulation trial of lovastatin among women with increased risk of breast cancer. Eligibility criteria included a deleterious germline mutation in BRCA1, BRCA2, CDH1, or TP53; lifetime breast cancer risk of ≥20 % as estimated by the Claus model; or personal history of estrogen receptor and progesterone receptor-negative breast cancer. Participants received 40 mg of lovastatin orally twice daily for 6 months. We evaluated the following biomarkers before and after lovastatin use: breast duct cytology (primary endpoint), serum lipids, C-reactive protein, insulin-like growth factor-1, IGF binding protein-3, lipid peroxidation, oxidative DNA damage, 3-hydroxy-3-methylglutaryl CoA reductase genotype, and mammographic density. Thirty women were enrolled, and 26 (86.7 %) completed the study. For the primary endpoint of changes in breast duct cytology sampled by random periareolar fine needle aspiration, most participants [57.7 %, 95 % confidence interval (CI) 38.9-74.5 %] showed no change after lovastatin; 19.2 % (CI 8.1-38.3 %) had a favorable change in cytology, 7.7 % (95 % CI 1.0-25.3 %) had an unfavorable change, and 15.4 % (95 % CI 5.5-34.2 %) had equivocal results due to acellular specimens, usually after lovastatin. No significant changes were observed in secondary biomarker endpoints. The study was generally well-tolerated: 4 (13.3 %) participants did not complete the study, and one (3.8 %) required a dose reduction. This trial was technically feasible, but demonstrated no significant biomarker modulation; contributing factors may include insufficient sample size, drug dose and/or duration. The results are inconclusive and do not exclude a favorable effect on breast cancer risk.

  View details for DOI 10.1007/s10549-013-2739-z

  View details for PubMedID 24166281

• Seventh Edition (2010) of the AJCC/UICC Staging System for Gastric Adenocarcinoma: Is there Room for Improvement? ANNALS OF SURGICAL ONCOLOGY Patel, M. I., Rhoads, K. F., Ma, Y., Ford, J. M., Visser, B. C., Kunz, P. L., Fisher, G. A., Chang, D. T., Koong, A., Norton, J. A., Poultsides, G. A. 2013; 20 (5): 1631-1638

  Abstract

  The gastric cancer AJCC/UICC staging system recently underwent significant revisions, but studies on Asian patients have reported a lack of adequate discrimination between various consecutive stages. We sought to validate the new system on a U.S. population database.California Cancer Registry data linked to the Office of Statewide Health Planning and Development discharge abstracts were used to identify patients with gastric adenocarcinoma (esophagogastric junction and gastric cardia tumors excluded) who underwent curative-intent surgical resection in California from 2002 to 2006. AJCC/UICC stage was recalculated based on the latest seventh edition. Overall survival probabilities were calculated using the Kaplan-Meier method.Of 1905 patients analyzed, 54 % were males with a median age of 70 years. Median number of pathologically examined lymph nodes was 12 (range, 1-90); 40 % of patients received adjuvant chemotherapy, and 31 % received adjuvant radiotherapy. The seventh edition AJCC/UICC system did not distinguish outcome adequately between stages IB and IIA (P = 0.40), or IIB and IIIA (P = 0.34). By merging stage II into 1 category and moving T2N1 to stage IB and T2N2, T1N3 to stage IIIA, we propose a new grouping system with improved discriminatory abilityIn this first study validating the new seventh edition AJCC/UICC staging system for gastric cancer on a U.S. population with a relatively limited number of lymph nodes examined, we found stages IB and IIA, as well as IIB and IIIA to perform similarly. We propose a revised stage grouping for the AJCC/UICC staging system that better discriminates between outcomes.

  View details for DOI 10.1245/s10434-012-2724-5

  View details for PubMedID 23149854

• A young woman with bilateral breast cancer: identifying a genetic cause and implications for management. Journal of the National Comprehensive Cancer Network de Bruin, M. A., Ford, J. M., Kurian, A. W. 2013; 11 (5): 512-517

  Abstract

  Breast cancer is a common manifestation of an underlying genetic susceptibility to cancer, and 5% to 10% of all breast cancers are associated with a germline mutation in a known risk allele. Detection of mutations has implications for targeted screening and prevention strategies for probands, and for genetic counseling and testing of their family members. This report presents a case involving a 35-year-old woman with no family history of breast or ovarian cancer who presented with a palpable right breast lump. Imaging revealed multiple bilateral breast masses and right axillary adenopathy, and core needle biopsies showed invasive ductal carcinoma in both the right and left breast. This report discusses the appropriate genetics evaluation for a patient with bilateral breast cancer at a young age, including testing for mutations in BRCA1 and BRCA2, followed, if negative, by consideration of testing for mutations in TP53 (Li-Fraumeni syndrome). Given the specialized counseling and testing needs of patients with Li-Fraumeni syndrome, and the implications for targeted screening strategies if a mutation is found, referral to a cancer genetics expert is strongly recommended.

  View details for PubMedID 23667202

• Male Breast Cancer: A Comparison Between BRCA Mutation Carriers and Noncarriers in Hong Kong, Southern China Kwong, A., Chau, W., Law, F. F., Kurian, A., Ford, J. M., West, D. W., Ma, E. K. SPRINGER. 2013: 72

  View details for Web of Science ID 000318174800096

• Phase II Study Evaluating 2 Dosing Schedules of Oral Foretinib (GSK1363089), cMET/VEGFR2 Inhibitor, in Patients with Metastatic Gastric Cancer PLOS ONE Shah, M. A., Wainberg, Z. A., Catenacci, D. V., Hochster, H. S., Ford, J., Kunz, P., Lee, F., Kallender, H., Cecchi, F., Rabe, D. C., Keer, H., Martin, A., Liu, Y., Gagnon, R., Bonate, P., Liu, L., Gilmer, T., Bottaro, D. P. 2013; 8 (3)

  Abstract

  The receptors for hepatocyte and vascular endothelial cell growth factors (MET and VEGFR2, respectively) are critical oncogenic mediators in gastric adenocarcinoma. The purpose is to examine the safety and efficacy of foretinib, an oral multikinase inhibitor targeting MET, RON, AXL, TIE-2, and VEGFR2 receptors, for the treatment of metastatic gastric adenocarcinoma.Foretinib safety and tolerability, and objective response rate (ORR) were evaluated in patients using intermittent (240 mg/day, for 5 days every 2 weeks) or daily (80 mg/day) dosing schedules. Thirty evaluable patients were required to achieve alpha = 0.10 and beta = 0.2 to test the alternative hypothesis that single-agent foretinib would result in an ORR of ≥ 25%. Up to 10 additional patients could be enrolled to ensure at least eight with MET amplification. Correlative studies included tumor MET amplification, MET signaling, pharmacokinetics and plasma biomarkers of foretinib activity.From March 2007 until October 2009, 74 patients were enrolled; 74% male; median age, 61 years (range, 25-88); 93% had received prior therapy. Best response was stable disease (SD) in 10 (23%) patients receiving intermittent dosing and five (20%) receiving daily dosing; SD duration was 1.9-7.2 months (median 3.2 months). Of 67 patients with tumor samples, 3 had MET amplification, one of whom had SD. Treatment-related adverse events occurred in 91% of patients. Rates of hypertension (35% vs. 15%) and elevated aspartate aminotransferase (23% vs. 8%) were higher with intermittent dosing. In both patients with high baseline tumor phospho-MET (pMET), the pMET:total MET protein ratio decreased with foretinib treatment.These results indicate that few gastric carcinomas are driven solely by MET and VEGFR2, and underscore the diverse molecular oncogenesis of this disease. Despite evidence of MET inhibition by foretinib, single-agent foretinib lacked efficacy in unselected patients with metastatic gastric cancer.

  View details for DOI 10.1371/journal.pone.0054014

  View details for Web of Science ID 000316407400003

  View details for PubMedID 23516391

  View details for PubMedCentralID PMC3597709

• Qualitative and quantitative image-based biomarkers of therapeutic response in triple-negative breast cancer. AMIA Summits on Translational Science proceedings AMIA Summit on Translational Science Golden, D. I., Lipson, J. A., Telli, M. L., Ford, J. M., Rubin, D. L. 2013; 2013: 62-?

  Abstract

  Experimental targeted treatments for neoadjuvant chemotherapy for triple-negative breast cancer are currently underway, and a current challenge is predicting which patients will respond to these therapies. In this study, we use data from dynamic contrast-enhanced MRI (DCE-MRI) images to predict whether patients with triple negative breast cancer will respond to an experimental neoadjuvant chemotherapy regimen. Using pre-therapy image-based features that are both qualitative (e.g., morphological BI-RADS categories) and quantitative (e.g., lesion texture), we built a model that was able to predict whether patients will have residual invasive cancer with lymph nodes metastases following therapy (receiver operating characteristic area under the curve of 0.83, sensitivity=0.73, specificity=0.83). This model's performance is at a level that is potentially clinically valuable for predicting which patients may or may not benefit from similar treatments in the future.

  View details for PubMedID 24303300

• Novel BRCA1 and BRCA2 genomic rearrangements in Southern Chinese breast/ovarian cancer patients BREAST CANCER RESEARCH AND TREATMENT Kwong, A., Ng, E. K., Law, F. B., Wong, H. N., Wa, A., Wong, C. L., Kurian, A. W., West, D. W., Ford, J. M., Ma, E. S. 2012; 136 (3): 931-933

  View details for DOI 10.1007/s10549-012-2292-1

  View details for Web of Science ID 000312071000033

  View details for PubMedID 23099436

  View details for PubMedCentralID PMC3511694

• Li-Fraumeni syndrome: report of a clinical research workshop and creation of a research consortium CANCER GENETICS Mai, P. L., Malkin, D., Garber, J. E., Schiffman, J. D., Weitzel, J. N., Strong, L. C., Wyss, O., Locke, L., Means, V., Achatz, M. I., Hainaut, P., Frebourg, T., Evans, D. G., Bleiker, E., Patenaude, A., Schneider, K., Wilfond, B., Peters, J. A., Hwang, P. M., Ford, J., Tabori, U., Ognjanovic, S., Dennis, P. A., Wentzensen, I. M., Greene, M. H., Fraumeni, J. F., Savage, S. A. 2012; 205 (10): 479-487

  Abstract

  Li-Fraumeni syndrome (LFS) is a rare dominantly inherited cancer predisposition syndrome that was first described in 1969. In most families, it is caused by germline mutations in the TP53 gene and is characterized by early onset of multiple specific cancers and very high lifetime cumulative cancer risk. Despite significant progress in understanding the molecular biology of TP53, the optimal clinical management of this syndrome is poorly defined. We convened a workshop on November 2, 2010, at the National Institutes of Health in Bethesda, Maryland, bringing together clinicians and scientists, as well as individuals from families with LFS, to review the state of the science, address clinical management issues, stimulate collaborative research, and engage the LFS family community. This workshop also led to the creation of the Li-Fraumeni Exploration (LiFE) Research Consortium.

  View details for DOI 10.1016/j.cancergen.2012.06.008

  View details for Web of Science ID 000310665600001

  View details for PubMedID 22939227

  View details for PubMedCentralID PMC3593717

• Identification of BRCA1/2 Founder Mutations in Southern Chinese Breast Cancer Patients Using Gene Sequencing and High Resolution DNA Melting Analysis PLOS ONE Kwong, A., Ng, E. K., Wong, C. L., Law, F. B., Au, T., Wong, H. N., Kurian, A. W., West, D. W., Ford, J. M., Ma, E. S. 2012; 7 (9)

  Abstract

  Ethnic variations in breast cancer epidemiology and genetics have necessitated investigation of the spectra of BRCA1 and BRCA2 mutations in different populations. Knowledge of BRCA mutations in Chinese populations is still largely unknown. We conducted a multi-center study to characterize the spectra of BRCA mutations in Chinese breast and ovarian cancer patients from Southern China.A total of 651 clinically high-risk breast and/or ovarian cancer patients were recruited from the Hong Kong Hereditary Breast Cancer Family Registry from 2007 to 2011. Comprehensive BRCA1 and BRCA2 mutation screening was performed using bi-directional sequencing of all coding exons of BRCA1 and BRCA2. Sequencing results were confirmed by in-house developed full high resolution DNA melting (HRM) analysis. Among the 451 probands analyzed, 69 (15.3%) deleterious BRCA mutations were identified, comprising 29 in BRCA1 and 40 in BRCA2. The four recurrent BRCA1 mutations (c.470_471delCT, c.3342_3345delAGAA, c.5406+1_5406+3delGTA and c.981_982delAT) accounted for 34.5% (10/29) of all BRCA1 mutations in this cohort. The four recurrent BRCA2 mutations (c.2808_2811delACAA, c.3109C>T, c.7436_7805del370 and c.9097_9098insA) accounted for 40% (16/40) of all BRCA2 mutations. Haplotype analysis was performed to confirm 1 BRCA1 and 3 BRCA2 mutations are putative founder mutations. Rapid HRM mutation screening for a panel of the founder mutations were developed and validated.In this study, our findings suggest that BRCA mutations account for a substantial proportion of hereditary breast/ovarian cancer in Southern Chinese population. Knowing the spectrum and frequency of the founder mutations in this population will assist in the development of a cost-effective rapid screening assay, which in turn facilitates genetic counseling and testing for the purpose of cancer risk assessment.

  View details for DOI 10.1371/journal.pone.0043994

  View details for Web of Science ID 000308462000010

  View details for PubMedID 22970155

  View details for PubMedCentralID PMC3436879

• Breast cancer risk factors differ between Asian and white women with BRCA1/2 mutations FAMILIAL CANCER de Bruin, M. A., Kwong, A., Goldstein, B. A., Lipson, J. A., Ikeda, D. M., McPherson, L., Sharma, B., Kardashian, A., Schackmann, E., Kingham, K. E., Mills, M. A., West, D. W., Ford, J. M., Kurian, A. W. 2012; 11 (3): 429-439

  Abstract

  The prevalence and penetrance of BRCA1 and BRCA2 (BRCA1/2) mutations may differ between Asians and whites. We investigated BRCA1/2 mutations and cancer risk factors in a clinic-based sample. BRCA1/2 mutation carriers were enrolled from cancer genetics clinics in Hong Kong and California according to standardized entry criteria. We compared BRCA mutation position, cancer history, hormonal and reproductive exposures. We analyzed DNA samples for single-nucleotide polymorphisms reported to modify breast cancer risk. We performed logistic regression to identify independent predictors of breast cancer. Fifty Asian women and forty-nine white American women were enrolled. BRCA1 mutations were more common among whites (67 vs. 42 %, p = 0.02), and BRCA2 mutations among Asians (58 vs. 37 %, p = 0.04). More Asians had breast cancer (76 vs. 53 %, p = 0.03); more whites had relatives with breast cancer (86 vs. 50 %, p = 0.0003). More whites than Asians had breastfed (71 vs. 42 %, p = 0.005), had high BMI (median 24.3 vs. 21.2, p = 0.04), consumed alcohol (2 drinks/week vs. 0, p < 0.001), and had oophorectomy (61 vs. 34 %, p = 0.01). Asians had a higher frequency of risk-associated alleles in MAP3K1 (88 vs. 59 %, p = 0.005) and TOX3/TNRC9 (88 vs. 55 %, p = 0.0002). On logistic regression, MAP3K1 was associated with increased breast cancer risk for BRCA2, but not BRCA1 mutation carriers; breast density was associated with increased risk among Asians but not whites. We found significant differences in breast cancer risk factors between Asian and white BRCA1/2 mutation carriers. Further investigation of racial differences in BRCA1/2 mutation epidemiology could inform targeted cancer risk-reduction strategies.

  View details for DOI 10.1007/s10689-012-9531-9

  View details for PubMedID 22638769

• Clinicopathologic and molecular features of sporadic early-onset colorectal adenocarcinoma: an adenocarcinoma with frequent signet ring cell differentiation, rectal and sigmoid involvement, and adverse morphologic features MODERN PATHOLOGY Chang, D. T., Pai, R. K., Rybicki, L. A., DiMaio, M. A., Limaye, M., Jayachandran, P., Koong, A. C., Kunz, P. A., Fisher, G. A., Ford, J. M., Welton, M., Shelton, A., Ma, L., Arber, D. A., Pai, R. K. 2012; 25 (8): 1128-1139

  Abstract

  Recent literature suggests an increasing incidence of colorectal carcinoma in young patients. We performed a histologic, molecular, and immunophenotypic analysis of patients with sporadic early-onset (≤40 years of age) colorectal carcinoma seen at our institution from the years 2000-2010 and compared these tumors to a cohort of consecutively resected colorectal carcinomas seen in patients >40 years of age. A total of 1160 primary colorectal adenocarcinomas were surgically resected for the years 2000 through 2010. Of these, 75 (6%) were diagnoses in patients ≤40 years of age of which 13 (17%) demonstrated abnormalities in DNA mismatch repair, 4 (5%) were in patients with known germline genetic disorders (two patients with familial adenomatous polyposis, one patient with juvenile polyposis, and one patient with Li-Fraumeni syndrome), and three patients (4%) had long-standing chronic inflammatory bowel disease. The sporadic early-onset colorectal carcinoma group comprised a total of 55 patients (55/1160, 5%) and were compared with a control group comprising 73 consecutively resected colorectal carcinomas with proficient DNA mismatch repair in patients >40 years of age. For the early-onset colorectal carcinoma group, most cases (33/55, 60%) were diagnosed between the age of 35 and 40 years of age. Compared with the control group, the early-onset colorectal carcinoma group was significantly different with respect to tumor location (P<0.007) with 80% (44/55 cases) identified in either the sigmoid colon (24/55, 44%) or rectum (20/55, 36%). Morphologically, early-onset colorectal carcinomas more frequently displayed adverse histologic features compared with the control colorectal carcinoma group such as signet ring cell differentiation (7/55, 13% vs 1/73, 1%, P=0.021), perineural invasion (16/55, 29% vs 8/73, 11%, P=0.009) and venous invasion (12/55, 22% vs 4/73, 6%, P=0.006). A precursor adenomatous lesion was less frequently identified in the early-onset colorectal carcinoma group compared with the control group (19/55, 35% vs 39/73, 53%, P=0.034). Of the early-onset colorectal carcinomas, only 2/45 cases (4%) demonstrated KRAS mutations compared with 11/73 (15%) of the control group colorectal adenocarcinomas harboring KRAS mutations, although this difference did not reach statistical significance (P=0.13). BRAF V600E mutations were not identified in the early-onset colorectal carcinoma group. No difference was identified between the two groups with regard to tumor stage, tumor size, number of lymph node metastases, lymphatic invasion, tumor budding, mucinous histology, or tumor-infiltrating lymphocytes. Both groups had similar recurrence-free (P=0.28) and overall survival (P=0.73). However, patients in the early-onset colorectal carcinoma group more frequently either presented with or developed metastatic disease during their disease course compared with the control colorectal carcinoma group (25/55, 45% vs 18/73, 25%, P=0.014). In addition, 8/55 patients (15%) in the early-onset colorectal carcinoma group developed local recurrence of their tumor while no patients in the control colorectal carcinoma group developed local recurrence (P<0.001), likely due to the increased incidence of rectal carcinoma in the patients with early-onset colorectal carcinoma. Our study demonstrates that colorectal carcinoma is not infrequently diagnosed in patients ≤40 years of age and is not frequently the result of underlying Lynch syndrome or associated with other cancer-predisposing genetic conditions or chronic inflammatory conditions. These tumors have a striking predilection for the distal colon, particularly the sigmoid colon and rectum and are much more likely to demonstrate adverse histologic factors, including signet ring cell differentiation, venous invasion, and perineural invasion.

  View details for DOI 10.1038/modpathol.2012.61

  View details for PubMedID 22481281

• Chest Wall Leiomyosarcoma After Breast-Conservative Therapy for Early-Stage Breast Cancer in a Young Woman With Li-Fraumeni Syndrome JOURNAL OF THE NATIONAL COMPREHENSIVE CANCER NETWORK Henry, E., Villalobos, V., Million, L., Jensen, K. C., West, R., Ganjoo, K., Lebensohn, A., Ford, J. M., Telli, M. L. 2012; 10 (8): 939-942

  Abstract

  Li-Fraumeni syndrome (LFS) is one of the most penetrant forms of familial cancer susceptibility syndromes, characterized by early age at tumor onset and a wide spectrum of malignant tumors. Identifying LFS in patients with cancer is clinically imperative because they have an increased sensitivity to ionizing radiation and are more likely to develop radiation-induced secondary malignancies. This case report describes a young woman whose initial presentation of LFS was early-onset breast cancer and whose treatment of this primary malignancy with breast conservation likely resulted in a secondary malignancy arising in her radiation field. As seen in this case, most breast cancers in patients with LFS exhibit a triple-positive phenotype (estrogen receptor-positive/progesterone receptor-positive/HER2-positive). Although this patient met classic LFS criteria based on age and personal and family history of cancer, the NCCN Clinical Practice Guidelines in Oncology for Genetic/Familial High-Risk Assessment: Breast and Ovarian Cancer endorse genetic screening for TP53 mutations in a subset of patients with early-onset breast cancer, even in the absence of a suggestive family history, because of the potential for de novo TP53 mutations.

  View details for PubMedID 22878818

• Identification of a novel deletion mutant strain in Saccharomyces cerevisiae that results in a microsatellite instability phenotype. BioDiscovery Ji, H. P., Morales, S., Welch, K., Yuen, C., Farnam, K., Ford, J. M. 2012

  Abstract

  The DNA mismatch repair (MMR) pathway corrects specific types of DNA replication errors that affect microsatellites and thus is critical for maintaining genomic integrity. The genes of the MMR pathway are highly conserved across different organisms. Likewise, defective MMR function universally results in microsatellite instability (MSI) which is a hallmark of certain types of cancer associated with the Mendelian disorder hereditary nonpolyposis colorectal cancer. (Lynch syndrome). To identify previously unrecognized deleted genes or loci that can lead to MSI, we developed a functional genomics screen utilizing a plasmid containing a microsatellite sequence that is a host spot for MSI mutations and the comprehensive homozygous diploid deletion mutant resource for Saccharomyces cerevisiae. This pool represents a collection of non-essential homozygous yeast diploid (2N) mutants in which there are deletions for over four thousand yeast open reading frames (ORFs). From our screen, we identified a deletion mutant strain of the PAU24 gene that leads to MSI. In a series of validation experiments, we determined that this PAU24 mutant strain had an increased MSI-specific mutation rate in comparison to the original background wildtype strain, other deletion mutants and comparable to a MMR mutant involving the MLH1 gene. Likewise, in yeast strains with a deletion of PAU24, we identified specific de novo indel mutations that occurred within the targeted microsatellite used for this screen.

  View details for PubMedID 23667739

• Breast cancer phenotype in women with TP53 germline mutations: a Li-Fraumeni syndrome consortium effort BREAST CANCER RESEARCH AND TREATMENT Masciari, S., Dillon, D. A., Rath, M., Robson, M., Weitzel, J. N., Balmana, J., Gruber, S. B., Ford, J. M., Euhus, D., Lebensohn, A., Telli, M., Pochebit, S. M., Lypas, G., Garber, J. E. 2012; 133 (3): 1125-1130

  Abstract

  Breast cancer is the most common tumor in women with Li-Fraumeni Syndrome (LFS), an inherited cancer syndrome associated with germline mutations in the TP53 tumor suppressor gene. Their lifetime breast cancer risk is 49% by age 60. Breast cancers in TP53 mutation carriers recently have more often been reported to be hormone receptor and HER-2 positive by immunohistochemistry and FISH in small series. We seek to complement the existing small literature with this report of a histopathologic analysis of breast cancers from women with documented LFS. Unstained slides and paraffin-embedded tumor blocks from breast cancers from 39 germline TP53 mutation carriers were assembled from investigators in the LFS consortium. Central histology review was performed on 93% of the specimens by a single breast pathologist from a major university hospital. Histology, grade, and hormone receptor status were assessed by immunohistochemistry; HER-2 status was defined by immunohistochemistry and/or FISH. The 43 tumors from 39 women comprise 32 invasive ductal carcinomas and 11 ductal carcinomas in situ (DCIS). No other histologies were observed. The median age at diagnosis was 32 years (range 22-46). Of the invasive cancers, 84% were positive for ER and/or PR; and 81% were high grade. Sixty three percent of invasive and 73% of in situ carcinomas were positive for Her2/neu (IHC 3+ or FISH amplified). Of the invasive tumors, 53% were positive for both ER and HER2+; other ER/PR/HER2 combinations were observed. The DCIS were positive for ER and HER2 in 27% of the cases. This report of the phenotype of breast cancers from women with LFS nearly doubles the literature on this topic. Most DCIS and invasive ductal carcinomas in LFS are hormone receptor positive and/or HER-2 positive. These findings suggest that modern treatments may result in improved outcomes for women with LFS-associated breast cancer.

  View details for DOI 10.1007/s10549-012-1993-9

  View details for Web of Science ID 000305914900030

  View details for PubMedID 22392042

• Single Cell Profiling of Circulating Tumor Cells: Transcriptional Heterogeneity and Diversity from Breast Cancer Cell Lines PLOS ONE Powell, A. A., Talasaz, A. H., Zhang, H., Coram, M. A., Reddy, A., Deng, G., Telli, M. L., Advani, R. H., Carlson, R. W., Mollick, J. A., Sheth, S., Kurian, A. W., Ford, J. M., Stockdale, F. E., Quake, S. R., Pease, R. F., Mindrinos, M. N., Bhanot, G., Dairkee, S. H., Davis, R. W., Jeffrey, S. S. 2012; 7 (5)

  Abstract

  To improve cancer therapy, it is critical to target metastasizing cells. Circulating tumor cells (CTCs) are rare cells found in the blood of patients with solid tumors and may play a key role in cancer dissemination. Uncovering CTC phenotypes offers a potential avenue to inform treatment. However, CTC transcriptional profiling is limited by leukocyte contamination; an approach to surmount this problem is single cell analysis. Here we demonstrate feasibility of performing high dimensional single CTC profiling, providing early insight into CTC heterogeneity and allowing comparisons to breast cancer cell lines widely used for drug discovery.We purified CTCs using the MagSweeper, an immunomagnetic enrichment device that isolates live tumor cells from unfractionated blood. CTCs that met stringent criteria for further analysis were obtained from 70% (14/20) of primary and 70% (21/30) of metastatic breast cancer patients; none were captured from patients with non-epithelial cancer (n = 20) or healthy subjects (n = 25). Microfluidic-based single cell transcriptional profiling of 87 cancer-associated and reference genes showed heterogeneity among individual CTCs, separating them into two major subgroups, based on 31 highly expressed genes. In contrast, single cells from seven breast cancer cell lines were tightly clustered together by sample ID and ER status. CTC profiles were distinct from those of cancer cell lines, questioning the suitability of such lines for drug discovery efforts for late stage cancer therapy.For the first time, we directly measured high dimensional gene expression in individual CTCs without the common practice of pooling such cells. Elevated transcript levels of genes associated with metastasis NPTN, S100A4, S100A9, and with epithelial mesenchymal transition: VIM, TGFß1, ZEB2, FOXC1, CXCR4, were striking compared to cell lines. Our findings demonstrate that profiling CTCs on a cell-by-cell basis is possible and may facilitate the application of 'liquid biopsies' to better model drug discovery.

  View details for DOI 10.1371/journal.pone.0033788

  View details for PubMedID 22586443

• Breast cancers with compromised DNA repair exhibit selective sensitivity to elesclomol-induced oxidative DNA damage Alli, E., Ford, J. M. AMER ASSOC CANCER RESEARCH. 2012

  View details for DOI 10.1158/1538-7445.AM2012-1761

  View details for Web of Science ID 000209701603105

• Accuracy of BRCA1/2 Mutation Prediction Models for Different Ethnicities and Genders: Experience in a Southern Chinese Cohort WORLD JOURNAL OF SURGERY Kwong, A., Wong, C. H., Suen, D. T., Co, M., Kurian, A. W., West, D. W., Ford, J. M. 2012; 36 (4): 702-713

  Abstract

  BRCA1/2 mutation prediction models (BRCAPRO, Myriad II, Couch, Shattuck-Eidens, BOADICEA) are well established in western cohorts to estimate the probability of BRCA1/2 mutations. Results are conflicting in Asian populations. Most studies did not account for gender-specific prediction. We evaluated the performance of these models in a Chinese cohort, including males, before BRCA1/2 mutation testing.The five risk models were used to calculate the probability of BRCA mutations in probands with breast and ovarian cancers; 267 were non-BRCA mutation carriers (247 females and 20 males) and 43 were BRCA mutation carriers (38 females and 5 males).Mean BRCA prediction scores for all models were statistically better for carriers than noncarriers for females but not for males. BRCAPRO overestimated the numbers of female BRCA1/2 mutation carriers at thresholds ≥20% but underestimated if <20%. BRCAPRO and BOADICEA underestimated the number of male BRCA1/2 mutation carriers whilst Myriad II underestimated the number of both male and female carriers. In females, BRCAPRO showed similar discrimination, as measured by the area under the receiver operator characteristic curve (AUC) for BRCA1/2 combined mutation prediction to BOADICEA, but performed better than BOADICEA in BRCA1 mutation prediction (AUC 93% vs. 87%). BOADICEA had the best discrimination for BRCA1/2 combined mutation prediction (AUC 87%) in males.The variation in model performance underscores the need for research on larger Asian cohorts as prediction models, and the possible need for customizing these models for different ethnic groups and genders.

  View details for DOI 10.1007/s00268-011-1406-y

  View details for Web of Science ID 000301591200002

  View details for PubMedID 22290208

  View details for PubMedCentralID PMC3299960

• Intensity-Modulated Radiotherapy for Pancreatic Adenocarcinoma 51st Annual Meeting of the American-Society-for-Radiation-Oncology (ASTRO) Abelson, J. A., Murphy, J. D., Minn, A. Y., Chung, M., Fisher, G. A., Ford, J. M., Kunz, P., Norton, J. A., Visser, B. C., Poultsides, G. A., Koong, A. C., Chang, D. T. ELSEVIER SCIENCE INC. 2012: E595–E601

  Abstract

  To report the outcomes and toxicities in patients treated with intensity-modulated radiotherapy (IMRT) for pancreatic adenocarcinoma.Forty-seven patients with pancreatic adenocarcinoma were treated with IMRT between 2003 and 2008. Of these 47 patients, 29 were treated adjuvantly and 18 definitively. All received concurrent 5-fluorouracil chemotherapy. The treatment plans were optimized such that 95% of the planning target volume received the prescription dose. The median delivered dose for the adjuvant and definitive patients was 50.4 and 54.0 Gy, respectively.The median age at diagnosis was 63.9 years. For adjuvant patients, the 1- and 2-year overall survival rate was 79% and 40%, respectively. The 1- and 2-year recurrence-free survival rate was 58% and 17%, respectively. The local-regional control rate at 1 and 2 years was 92% and 80%, respectively. For definitive patients, the 1-year overall survival, recurrence-free survival, and local-regional control rate was 24%, 16%, and 64%, respectively. Four patients developed Grade 3 or greater acute toxicity (9%) and four developed Grade 3 late toxicity (9%).Survival for patients with pancreatic cancer remains poor. A small percentage of adjuvant patients have durable disease control, and with improved therapies, this proportion will increase. Systemic therapy offers the greatest opportunity. The present results have demonstrated that IMRT is well tolerated. Compared with those who received three-dimensional conformal radiotherapy in previously reported prospective clinical trials, patients with pancreatic adenocarcinoma treated with IMRT in our series had improved acute toxicity.

  View details for DOI 10.1016/j.ijrobp.2011.09.035

  View details for PubMedID 22197234

• Family History As a Positive Prognostic Factor in Gastric Cancer JOURNAL OF CLINICAL ONCOLOGY Nadauld, L. D., Ford, J. M. 2012; 30 (7): 683-684

  View details for DOI 10.1200/JCO.2011.40.1497

  View details for Web of Science ID 000302625400005

  View details for PubMedID 22271484

• Identification of a Functional In Vivo p53 Response Element in the Coding Sequence of the Xeroderma Pigmentosum Group C Gene. Genes & cancer Hastak, K., Adimoolam, S., Trinklein, N. D., Myers, R. M., Ford, J. M. 2012; 3 (2): 131-140

  Abstract

  The protein product of the xeroderma pigmentosum group C (XPC) gene is a DNA damage recognition factor that functions early in the process of global genomic nucleotide excision repair. Regulation of XPC expression is governed in part by p53 at the transcriptional level. To identify the regulatory elements involved in the p53-dependent control of XPC expression, we performed a quantitative PCR tiling experiment using multiple regularly spaced primer pairs over an 11-kb region centered around the XPC transcriptional start site. p53 chromatin immunoprecipitation was performed following ultraviolet irradiation, and DNA was analyzed for enrichment at each of 48 amplicons covering this region. A segment just upstream of the XPC translational initiation site was significantly enriched, whereas no enrichment of any other region was noted. In vitro promoter reporter assays and gel retardation assays were used to confirm the p53 responsiveness of this region and to define the minimal region with stimulating activity. We identified a p53 response element that has significant similarity to a consensus sequence, with 3 mismatches. This response element is unique in that part of the p53 binding site included the coding sequence for the first 2 amino acids in the XPC protein.

  View details for DOI 10.1177/1947601912456288

  View details for PubMedID 23050045

• HER2 Expression in Gastric and Gastroesophageal Junction Adenocarcinoma in a US Population: Clinicopathologic Analysis With Proposed Approach to HER2 Assessment APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY Kunz, P. L., Mojtahed, A., Fisher, G. A., Ford, J. M., Chang, D. T., Balise, R. R., Bangs, C. D., Cherry, A. M., Pai, R. K. 2012; 20 (1): 13-24

  Abstract

  Recent evidence suggests that trastuzumab, a monoclonal antibody which targets HER2, in combination with chemotherapy is a therapeutic option in patients with HER2-positive gastric or gastroesophageal junction cancer. Widely accepted guidelines for HER2 testing in gastric and gastroesophageal junction cancer have not been established. The purpose of this study was to analyze the incidence and patterns of HER2 expression in gastric and gastroesophageal junction cancer using a tissue microarray approach, which closely simulates small biopsies routinely tested for HER2. One hundred sixty-nine patients, including 99 primary gastric adenocarcinomas and 70 primary gastroesophageal junction carcinomas were analyzed for HER2 overexpression by immunohistochemistry and HER2 gene amplification by fluorescence in situ hybridization using scoring schemes proposed by both American Society of Clinical Oncology/College of American Pathologists (ASCO/CAP) and the results of the recently published Trastuzumab for Gastric Cancer (ToGA) trial. In our analysis, 19 adenocarcinomas were HER2 positive, defined as either a HER2/CEP17 ratio >2.2 and/or a 3+ HER2 immunohistochemistry score with either the ASCO/CAP or ToGA scoring schemes. Of the 19 HER2-positive adenocarcinomas, 8 (42%) exhibited a characteristic strongly intense basolateral membranous staining pattern which would be interpreted as negative (1+) using the accepted ASCO/CAP scoring scheme for HER2 assessment in breast carcinoma, but were correctly labeled as 3+ positive using the proposed ToGA scoring scheme. Of the 19 HER2-positive adenocarcinomas, 8 (42%) demonstrated heterogeneous HER2 protein expression by immunohistochemistry. Twelve of 99 (12%) gastric carcinomas were positive for HER2. Of these, HER2 was more often identified in intestinal-type adenocarcinomas (10 of 52, 19%) compared with diffuse (2 of 34, 6%) adenocarcinoma. Seven of 70 (10%) gastroesophageal junction carcinomas were positive for HER2 of which all were intestinal type (7 of 58, 12%). HER2 status or primary tumor site did not correlate with patient survival. Gastric and gastroesophageal junction adenocarcinomas typically display a characteristic basolateral membranous pattern of HER2 expression which is often heterogeneous rendering routine evaluation of HER2 status on small tissue samples challenging.

  View details for DOI 10.1097/PAI.0b013e31821c821c

  View details for PubMedID 21617522

• Quantitative and Sensitive Detection of Cancer Genome Amplifications from Formalin Fixed Paraffin Embedded Tumors with Droplet Digital PCR. Translational medicine (Sunnyvale, Calif.) Nadauld, L., Regan, J. F., Miotke, L., Pai, R. K., Longacre, T. A., Kwok, S. S., Saxonov, S., Ford, J. M., Ji, H. P. 2012; 2 (2)

  Abstract

  For the analysis of cancer, there is great interest in rapid and accurate detection of cancer genome amplifications containing oncogenes that are potential therapeutic targets. The vast majority of cancer tissue samples are formalin fixed and paraffin embedded (FFPE) which enables histopathological examination and long term archiving. However, FFPE cancer genomic DNA is oftentimes degraded and generally a poor substrate for many molecular biology assays. To overcome the issues of poor DNA quality from FFPE samples and detect oncogenic copy number amplifications with high accuracy and sensitivity, we developed a novel approach. Our assay requires nanogram amounts of genomic DNA, thus facilitating study of small amounts of clinical samples. Using droplet digital PCR (ddPCR), we can determine the relative copy number of specific genomic loci even in the presence of intermingled normal tissue. We used a control dilution series to determine the limits of detection for the ddPCR assay and report its improved sensitivity on minimal amounts of DNA compared to standard real-time PCR. To develop this approach, we designed an assay for the fibroblast growth factor receptor 2 gene (FGFR2) that is amplified in a gastric and breast cancers as well as others. We successfully utilized ddPCR to ascertain FGFR2 amplifications from FFPE-preserved gastrointestinal adenocarcinomas.

  View details for PubMedID 23682346

• A rare case of an aldosterone secreting metastatic adrenocortical carcinoma and papillary thyroid carcinoma in a 31-year-old male. Rare tumors Wanta, S. M., Basina, M., Chang, S. D., Chang, D. T., Ford, J. M., Greco, R., Kingham, K., Merritt, R. E., Kunz, P. L. 2011; 3 (4)

  Abstract

  We report a rare synchronous presentation of adrenocortical carcinoma (ACC) and papillary thyroid carcinoma (PTC). A 31-year-old male first presented with a large left adrenal mass that was identified during the workup for refractory hypertension due to hyperaldosteronism. The mass was removed surgically with pathology showing ACC. The patient was then treated with adjuvant radiation therapy and mitotane chemotherapy. Four months post ACC resection, metastatic ACC to the right upper lung and PTC in the left lobe of the thyroid were found in surveillance imaging. He subsequently developed pulmonary, contralateral adrenal and brain metastases from his ACC. Li Fraumeni syndrome and Multiple Endocrine Neoplasia Type I (MEN I) were considered, but testing of both P53 and menin genes showed no mutation. We also performed a review of the literature and found three similar cases, however gene mutation analysis was not performed..

  View details for DOI 10.4081/rt.2011.e45

  View details for PubMedID 22355500

  View details for PubMedCentralID PMC3282450

• A Prospective Study of Total Gastrectomy for CDH1-Positive Hereditary Diffuse Gastric Cancer ANNALS OF SURGICAL ONCOLOGY Chen, Y., Kingham, K., Ford, J. M., Rosing, J., Van Dam, J., Jeffrey, R. B., Longacre, T. A., Chun, N., Kurian, A., Norton, J. A. 2011; 18 (9): 2594-2598

  Abstract

  Hereditary diffuse gastric cancer (HDGC) is an autosomal dominant cancer syndrome. Up to 30% of families with HDGC have mutations in the E-cadherin gene, CDH1. The role of prophylactic versus therapeutic gastrectomy for HDGC was studied prospectively.Eighteen consecutive patients with CDH1 mutations and positive family history were studied prospectively, including 13 without and 5 with symptoms. Proportions were compared by Fisher's exact test, and survival by the Breslow modification of the Wilcoxon rank-sum test.Each patient underwent total gastrectomy (TG), and 17 (94%) were found to have signet ring cell adenocarcinoma. Twelve of 13 asymptomatic patients had T1, N0 cancer, and only 2/12 (16%) had it diagnosed preoperatively despite state-of-the-art screening methods. Each asymptomatic patient did well postoperatively, and no patient has recurred. For five symptomatic patients, each (100%) was found to have signet ring cell adenocarcinoma (P = 0.002 versus asymptomatic) by preoperative endoscopy; three (60%) had lymph node involvement and two (40%) had distant metastases at time of operation. Two-year survival was 100% for asymptomatic and 40% for symptomatic patients (P < 0.01).The data show that asymptomatic patients with family history of HDGC and CDH1 mutation have high probability of having signet ring cell adenocarcinoma of the stomach that is not able to be diagnosed on endoscopy; when symptoms arise, the diagnosis can be made by endoscopy, but they have metastases and decreased survival. Surveillance endoscopy is of limited value, and prophylactic gastrectomy (PG) is recommended for patients with family history of HDGC and CDH1 mutations.

  View details for DOI 10.1245/s10434-011-1648-9

  View details for PubMedID 21424370

• SINGLE-FRACTION STEREOTACTIC BODY RADIATION THERAPY AND SEQUENTIAL GEMCITABINE FOR THE TREATMENT OF LOCALLY ADVANCED PANCREATIC CANCER INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Schellenberg, D., Kim, J., Ciristman-Skieller, C., Chun, C. L., Columbo, L. A., Ford, J. M., Fisher, G. A., Kunz, P. L., Van Dam, J., Quon, A., Desser, T. S., Norton, J., Hsu, A., Maxim, P. G., Xing, L., Goodman, K. A., Chang, D. T., Koong, A. C. 2011; 81 (1): 181-188

  Abstract

  This Phase II trial evaluated the toxicity, local control, and overall survival in patients treated with sequential gemcitabine and linear accelerator-based single-fraction stereotactic body radiotherapy (SBRT).Twenty patients with locally advanced, nonmetastatic pancreatic adenocarcinoma were enrolled on this prospective single-institution, institutional review board-approved study. Gemcitabine was administered on Days 1, 8, and 15, and SBRT on Day 29. Gemcitabine was restarted on Day 43 and continued for 3-5 cycles. SBRT of 25 Gy in a single fraction was delivered to the internal target volume with a 2- 3-mm margin using a nine-field intensity-modulated radiotherapy technique. Respiratory gating was used to account for breathing motion. Follow-up evaluations occurred at 4-6 weeks, 10-12 weeks, and every 3 months after SBRT.All patients completed SBRT and a median of five cycles of chemotherapy. Follow-up for the 2 remaining alive patients was 25.1 and 36.4 months. No acute Grade 3 or greater nonhematologic toxicity was observed. Late Grade 3 or greater toxicities occurred in 1 patient (5%) and consisted of a duodenal perforation (G4). Three patients (15%) developed ulcers (G2) that were medically managed. Overall, median survival was 11.8 months, with 1-year survival of 50% and 2-year survival of 20%. Using serial computed tomography, the freedom from local progression was 94% at 1 year.Linear accelerator-delivered SBRT with sequential gemcitabine resulted in excellent local control of locally advanced pancreatic cancer. Future studies will address strategies for reducing long-term duodenal toxicity associated with SBRT.

  View details for DOI 10.1016/j.ijrobp.2010.05.006

  View details for Web of Science ID 000294093300025

  View details for PubMedID 21549517

• Intensity-Modulated Radiation Therapy Versus Conventional Radiation Therapy for Squamous Cell Carcinoma of the Anal Canal CANCER Bazan, J. G., Hara, W., Hsu, A., Kunz, P. A., Ford, J., Fisher, G. A., Welton, M. L., Shelton, A., Kapp, D. S., Koong, A. C., Goodman, K. A., Chang, D. T. 2011; 117 (15): 3342-3351

  Abstract

  The purpose of this study was to compare outcomes in patients with anal canal squamous cell carcinoma (SCCA) who were treated with definitive chemoradiotherapy by either intensity-modulated radiation therapy (IMRT) or conventional radiotherapy (CRT).Forty-six patients who received definitive chemoradiotherapy from January 1993 to August 2009 were included. Forty-five patients received 5-fluorouracil with mitomycin C (n = 39) or cisplatin (n = 6). Seventeen (37%) were treated with CRT and 29 (63%) with IMRT. The median dose was 54 Gy in both groups. Median follow-up was 26 months (CRT) and 32 months (IMRT). T3-T4 stage (P = .18) and lymph node-positive disease (P = .6) were similar between groups.The CRT group required longer treatment duration (57 days vs 40 days, P < .0001), more treatment breaks (88% vs 34.5%, P = .001), and longer breaks (12 days vs 1.5 days, P < .0001) than patients treated with IMRT. Eleven (65%) patients in the CRT group experienced grade >2 nonhematologic toxicity compared with 6 (21%) patients in the IMRT group (P = .003). The 3-year overall survival (OS), locoregional control (LRC), and progression-free survival were 87.8%, 91.9%, and 84.2%, respectively, for the IMRT groups and 51.8%, 56.7%, and 56.7%, respectively, for the CRT group (all P < .01). On multivariate analysis, T stage, use of IMRT, and treatment duration were associated with OS, and T stage and use of IMRT were associated with LRC.The use of IMRT was associated with less toxicity, reduced need for treatment breaks, and excellent LRC and OS compared with CRT in patients with SCCA of the anal canal.

  View details for DOI 10.1002/cncr.25901

  View details for PubMedID 21287530

• A two-antibody mismatch repair protein immunohistochemistry screening approach for colorectal carcinomas, skin sebaceous tumors, and gynecologic tract carcinomas MODERN PATHOLOGY Mojtahed, A., Schrijver, I., Ford, J. M., Longacre, T. A., Pai, R. K. 2011; 24 (7): 1004-1014

  Abstract

  Mismatch repair protein immunohistochemistry is a widely used method for detecting patients at risk for Lynch syndrome. Recent data suggest that a two-antibody panel approach using PMS2 and MSH6 is an effective screening protocol for colorectal carcinoma, but there are limited data concerning this approach for extraintestinal tumors. The purpose of this study was to review the utility of a two-antibody panel approach in colorectal carcinoma and extraintestinal tumors. We evaluated mismatch repair protein expression in two cohorts: (1) a retrospective analysis of intestinal and extraintestinal tumors (n=334) tested for mismatch repair protein immunohistochemistry and (2) a prospectively accrued series of intestinal, gynecologic tract, and skin sebaceous neoplasms (n=98). A total of 432 cases were analyzed, including 323 colorectal, 50 gynecologic tract, 49 skin sebaceous, and 10 other neoplasms. Overall, 102/432 tumors (24%) demonstrated loss of at least one mismatch repair protein. Concurrent loss of MLH1 and PMS2 was the most common pattern of abnormal expression (50/432, 12%) followed by concurrent loss of MSH2 and MSH6 (33/432, 8%). Of 55 cases with abnormal PMS2 expression, 5 (9%) demonstrated isolated loss of PMS2 expression. Of 47 cases with abnormal MSH6 expression, 14 (30%) demonstrated isolated loss of MSH6 expression. Isolated loss of MLH1 or MSH2 was not observed. Colorectal carcinomas more frequently demonstrated abnormal expression of PMS2 (39/59, 66%). Skin sebaceous neoplasms more frequently demonstrated abnormal expression of MSH6 (18/24, 75%, respectively). A total of 65 tumors with abnormal mismatch repair protein expression were tested for microsatellite instability (MSI): 47 (72%) MSI high, 9 (14%) MSI low, and 9 (14%) microsatellite stable (MSS). Abnormal MSH6 expression accounted for 14/18 (78%) cases that were MSS or MSI low. Our findings confirm the utility of a two-antibody approach using PMS2 and MSH6 in colorectal carcinoma and indicate that this approach is effective in extraintestinal neoplasms associated with Lynch syndrome.

  View details for DOI 10.1038/modpathol.2011.55

  View details for PubMedID 21499234

• Asian ethnicity and breast cancer subtypes: a study from the California Cancer Registry BREAST CANCER RESEARCH AND TREATMENT Telli, M. L., Chang, E. T., Kurian, A. W., Keegan, T. H., McClure, L. A., Lichtensztajn, D., Ford, J. M., Gomez, S. L. 2011; 127 (2): 471-478

  Abstract

  The distribution of breast cancer molecular subtypes has been shown to vary by race/ethnicity, highlighting the importance of host factors in breast tumor biology. We undertook the current analysis to determine population-based distributions of breast cancer subtypes among six ethnic Asian groups in California. We defined immunohistochemical (IHC) surrogates for each breast cancer subtype among Chinese, Japanese, Filipina, Korean, Vietnamese, and South Asian patients diagnosed with incident, primary, invasive breast cancer between 2002 and 2007 in the California Cancer Registry as: hormone receptor-positive (HR+)/HER2- [estrogen receptor-positive (ER+) and/or progesterone receptor-positive (PR+), human epidermal growth factor receptor 2-negative (HER2-)], triple-negative (ER-, PR-, and HER2-), and HER2-positive (ER±, PR±, and HER2+). We calculated frequencies of breast cancer subtypes among Asian ethnic groups and evaluated their associations with clinical and demographic factors. Complete IHC data were available for 8,140 Asian women. Compared to non-Hispanic White women, Korean [odds ratio (OR) = 1.8, 95% confidence interval (CI) = 1.5-2.2], Filipina (OR = 1.3, 95% CI = 1.2-1.5), Vietnamese (OR = 1.3, 95% CI = 1.1-1.6), and Chinese (OR = 1.1, 95% CI = 1.0-1.3) women had a significantly increased risk of being diagnosed with HER2-positive breast cancer subtypes after adjusting for age, stage, grade, socioeconomic status, histology, diagnosis year, nativity, and hospital ownership status. We report a significant ethnic disparity in HER2-positive breast cancer in a large population-based cohort enriched for Asian-Americans. Given the poor prognosis and high treatment costs of HER2-positive breast cancer, our results have implications for healthcare resource utilization, cancer biology, and clinical care.

  View details for DOI 10.1007/s10549-010-1173-8

  View details for PubMedID 20957431

• A novel de novo BRCA1 mutation in a Chinese woman with early onset breast cancer FAMILIAL CANCER Kwong, A., Ng, E. K., Tang, E. Y., Wong, C. L., Law, F. B., Leung, C. P., Chan, A., Cheung, M. T., To, M. Y., Ma, E. S., West, D. W., Ford, J. M. 2011; 10 (2): 233-237

  Abstract

  Germline mutations in the two breast cancer susceptibility genes, BRCA1 and BRCA2 account for a significant portion of hereditary breast/ovarian cancer. De novo mutations such as multiple exon deletion are rarely occurred in BRCA1 and BRCA2. During our mutation screening for BRCA1/2 genes to Chinese women with risk factors for hereditary breast/ovarian cancer, we identified a novel germline mutation, consisting of a deletion from exons 1 to 12 in BRCA1 gene, in a patient diagnosed with early onset triple negative breast cancer with no family history of cancer. None of her parents carried the mutation and molecular analysis showed that this novel de novo germline mutation resulted in down-regulation of BRCA1 gene expression.

  View details for DOI 10.1007/s10689-011-9429-y

  View details for Web of Science ID 000290937500008

  View details for PubMedID 21404118

  View details for PubMedCentralID PMC3100488

• Germline mutations in CDH1 are infrequent in women with early-onset or familial lobular breast cancers JOURNAL OF MEDICAL GENETICS Schrader, K. A., Masciari, S., Boyd, N., Salamanca, C., Senz, J., Saunders, D. N., Yorida, E., Maines-Bandiera, S., Kaurah, P., Tung, N., Robson, M. E., Ryan, P. D., Olopade, O. I., Domchek, S. M., Ford, J., Isaacs, C., BROWN, P., Balmana, J., Razzak, A. R., Miron, P., Coffey, K., Terry, M. B., John, E. M., Andrulis, I. L., Knight, J. A., O'Malley, F. P., Daly, M., Bender, P., Moore, R., Southey, M. C., Hopper, J. L., Garber, J. E., Huntsman, D. G. 2011; 48 (1): 64-68

  Abstract

  Germline mutations in CDH1 are associated with hereditary diffuse gastric cancer; lobular breast cancer also occurs excessively in families with such condition.To determine if CDH1 is a susceptibility gene for lobular breast cancer in women without a family history of diffuse gastric cancer, germline DNA was analysed for the presence of CDH1 mutations in 318 women with lobular breast cancer who were diagnosed before the age of 45 years or had a family history of breast cancer and were not known, or known not, to be carriers of germline mutations in BRCA1 or BRCA2. Cases were ascertained through breast cancer registries and high-risk cancer genetic clinics (Breast Cancer Family Registry, the kConFab and a consortium of breast cancer genetics clinics in the United States and Spain). Additionally, Multiplex Ligation-dependent Probe Amplification was performed for 134 cases to detect large deletions.No truncating mutations and no large deletions were detected. Six non-synonymous variants were found in seven families. Four (4/318 or 1.3%) are considered to be potentially pathogenic through in vitro and in silico analysis.Potentially pathogenic germline CDH1 mutations in women with early-onset or familial lobular breast cancer are at most infrequent.

  View details for DOI 10.1136/jmg.2010.079814

  View details for Web of Science ID 000285383600009

  View details for PubMedID 20921021

  View details for PubMedCentralID PMC3003879

• Multimodality Therapy for Esophageal Cancer: The Benefit of Chemoradiation Vossler, S. R., Bavan, B., Kunz, P., Ford, J. M., Fisher, G. A., Whyte, R., Koong, A. C., Chang, D. T. ELSEVIER SCIENCE INC. 2011: S309–S309

  View details for Web of Science ID 000296411700630

• PARP Inhibitors for the Treatment and Prevention of Breast Cancer. Current breast cancer reports Vinayak, S., Ford, J. M. 2010; 2 (4): 190-197

  Abstract

  Poly (ADP-ribose) polymerase (PARP) inhibitors, a novel class of drugs that target tumors with DNA repair defects, have received tremendous enthusiasm. Early preclinical studies identified BRCA1 and BRCA2 tumors to be highly sensitive to PARP inhibitors as a result of homologous recombination defect. Based on this premise, PARP inhibitors have been tested in early phase clinical trials as a single agent in BRCA1 or BRCA2 mutation carriers and in combination with chemotherapy in triple-negative breast cancer patients. For high-risk populations, use of PARP inhibition as a prevention agent has been postulated, but no robust preclinical or clinical studies exist yet. We review the preclinical and clinical studies in treatment of breast cancer and rationale for use of PARP inhibitors as a prevention agent for high-risk populations. Of significance, PARP inhibitors vary significantly in mechanism of action, dosing intervals, and toxicities, which are highlighted in this review.

  View details for PubMedID 22655123

• Expression of p16(INK4A) But Not Hypoxia Markers or Poly Adenosine Diphosphate-Ribose Polymerase Is Associated With Improved Survival in Patients With Pancreatic Adenocarcinoma 51st Annual Meeting of the American-Society-for-Radiation-Oncology (ASTRO) Chang, D. T., Chapman, C. H., Norton, J. A., Visser, B., Fisher, G. A., Kunz, P., Ford, J. M., Koong, A. C., Pai, R. K. WILEY-BLACKWELL. 2010: 5179–87

  Abstract

  Pancreatic cancer is associated with mutations in the tumor suppressor gene cyclin-dependent kinase inhibitor 2A (p16(INK4A) ), a regulator of the cell cycle and apoptosis. This study investigates whether immunohistochemical expression of p16(INK4A) as well as hypoxia markers and poly adenosine diphosphate-ribose polymerase (PARP) correlates with survival in patients with resected pancreatic adenocarcinoma.Seventy-three patients with pancreatic adenocarcinoma who underwent curative resection at Stanford University were included. From the surgical specimens, a tissue microarray was constructed using triplicate tissue cores from the primary tumor and used for immunohistochemical staining for the following markers: carbonic anhydrase IX, dihydrofolate reductase, p16(INK4A) , and PARP1/2. Staining was scored as either positive or negative and percentage positive staining. Staining score was correlated with overall survival (OS) and progression-free survival (PFS).Of the markers tested, only immunohistochemical expression of p16(INK4A) correlated with clinical outcome. On univariate analysis, p16(INK4A) expression in the tumor was associated with improved OS (P = .038) but not PFS (P = .28). The median survival for patients with positive versus negative p16(INK4A) staining was 28.8 months versus 18 months. On multivariate analysis, p16(INK4A) expression was associated with improved OS (P = .026) but not PFS (P = .25). Age (P = .0019) and number of nodes involved (P = .025) were also significant for OS. Adjuvant chemotherapy and margin status did not correlate with OS or PFS.Expression of p16(INK4A) is associated with improved OS in patients with resected pancreatic adenocarcinoma. Further investigation is needed for validation, given conflicting data in the published literature. .

  View details for DOI 10.1002/cncr.25481

  View details for PubMedID 20665497

• Poly(ADP-Ribose) Polymerase Inhibition: "Targeted" Therapy for Triple-Negative Breast Cancer CLINICAL CANCER RESEARCH Anders, C. K., Winer, E. P., Ford, J. M., Dent, R., Silver, D. P., Sledge, G. W., Carey, L. A. 2010; 16 (19): 4702-4710

  Abstract

  In contrast to endocrine-sensitive and human epidermal growth factor receptor 2 (HER2)-positive breast cancer, novel agents capable of treating advanced triple-negative breast cancer (TNBC) are lacking. Poly(ADP-ribose) polymerase (PARP) inhibitors are emerging as one of the most promising "targeted" therapeutics to treat TNBC, with the intended "target" being DNA repair. PARPs are a family of enzymes involved in multiple cellular processes, including DNA repair. TNBC shares multiple clinico-pathologic features with BRCA-mutated breast cancers, which harbor dysfunctional DNA repair mechanisms. Investigators hypothesized that PARP inhibition, in conjunction with the loss of DNA repair via BRCA-dependent mechanisms, would result in synthetic lethality and augmented cell death. This hypothesis has borne out in both preclinical models and in clinical trials testing PARP inhibitors in both BRCA-deficient and triple-negative breast cancer. The focus of this review includes an overview of the preclinical rationale for evaluating PARP inhibitors in TNBC, the presumed mechanism of action of this novel therapeutic class, promising results from several influential clinical trials of PARP inhibition in advanced breast cancer (both TNBC and BRCA deficient), proposed mechanisms of acquired resistance to PARP inhibitors, and, finally, concludes with current challenges and future directions for the development of PARP inhibitors in the treatment of breast cancer.

  View details for DOI 10.1158/1078-0432.CCR-10-0939

  View details for Web of Science ID 000282647900004

  View details for PubMedID 20858840

  View details for PubMedCentralID PMC2948607

• PARP inhibitors in breast cancer. Clinical advances in hematology & oncology : H&O Telli, M. L., Ford, J. M. 2010; 8 (9): 629-635

  Abstract

  The therapeutic implications of DNA damage in cancer therapy have long been appreciated and form the basis of many successful cytotoxic chemotherapy and radiotherapy treatment strategies. A novel class of DNA repair defect targeted therapeutics that inhibit poly (ADP-Ribose) polymerase (PARP) are being rapidly developed in breast cancer based on exciting preliminary clinical activity as single agents in BRCA mutation-associated breast cancer and in combination with chemotherapy in triple-negative breast cancer. Though there is widespread enthusiasm to move these drugs forward quickly, much remains to be understood about the optimal use of the novel agents. Here we review the clinical development of PARP inhibitors in breast cancer and highlight clinical trials in progress. We also provide commentary on a series of outstanding questions in the field, the answers to which will be critical for the successful development of PARP inhibitor-based strategies in early- and late-stage breast cancer.

  View details for PubMedID 21157412

• Comparison of Intensity-Modulated Radiotherapy and 3-Dimensional Conformal Radiotherapy as Adjuvant Therapy for Gastric Cancer 51st Annual Meeting of the American-Society-for-Radiation-Oncology (ASTRO) Minn, A. Y., Hsu, A., La, T., Kunz, P., Fisher, G. A., Ford, J. M., Norton, J. A., Visser, B., Goodman, K. A., Koong, A. C., Chang, D. T. JOHN WILEY & SONS INC. 2010: 3943–52

  Abstract

  The current study was performed to compare the clinical outcomes and toxicity in patients treated with postoperative chemoradiotherapy for gastric cancer using intensity-modulated radiotherapy (IMRT) versus 3-dimensional conformal radiotherapy (3D CRT).Fifty-seven patients with gastric or gastroesophageal junction cancer were treated postoperatively: 26 with 3D CRT and 31 with IMRT. Concurrent chemotherapy was capecitabine (n=31), 5-fluorouracil (5-FU) (n=25), or none (n=1). The median radiation dose was 45 Gy. Dose volume histogram parameters for kidney and liver were compared between treatment groups.The 2-year overall survival rates for 3D CRT versus IMRT were 51% and 65%, respectively (P=.5). Four locoregional failures occurred each in the 3D CRT (15%) and the IMRT (13%) patients. Grade>or=2 acute gastrointestinal toxicity was found to be similar between the 3D CRT and IMRT patients (61.5% vs 61.2%, respectively) but more treatment breaks were needed (3 vs 0, respectively). The median serum creatinine from before radiotherapy to most recent creatinine was unchanged in the IMRT group (0.80 mg/dL) but increased in the 3D CRT group from 0.80 mg/dL to 1.0 mg/dL (P=.02). The median kidney mean dose was higher in the IMRT versus the 3D CRT group (13.9 Gy vs 11.1 Gy; P=.05). The median kidney V20 was lower for the IMRT versus the 3D CRT group (17.5% vs 22%; P=.17). The median liver mean dose for IMRT and 3D CRT was 13.6 Gy and 18.6 Gy, respectively (P=.19). The median liver V30 was 16.1% and 28%, respectively (P<.001).Adjuvant chemoradiotherapy was well tolerated. IMRT was found to provide sparing to the liver and possibly renal function.

  View details for DOI 10.1002/cncr.25246

  View details for PubMedID 20564136

• (18)FLUORODEOXYGLUCOSE PET IS PROGNOSTIC OF PROGRESSION-FREE AND OVERALL SURVIVAL IN LOCALLY ADVANCED PANCREAS CANCER TREATED WITH STEREOTACTIC RADIOTHERAPY INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Schellenberg, D., Quon, A., Minn, A. Y., Graves, E. E., Kunz, P., Ford, J. M., Fisher, G. A., Goodman, K. A., Koong, A. C., Chang, D. T. 2010; 77 (5): 1420-1425

  Abstract

  This study analyzed the prognostic value of positron emission tomography (PET) for locally advanced pancreas cancer patients undergoing stereotactic body radiotherapy (SBRT).Fifty-five previously untreated, unresectable pancreas cancer patients received a single fraction of 25-Gy SBRT sequentially with gemcitabine-based chemotherapy. On the preradiation PET-CT, the tumor was contoured and the maximum standardized uptake value (SUVmax) and metabolic tumor burden (MTB) were calculated using an in-house software application. High-SUVmax and low-SUVmax subgroups were created by categorizing patients above or below the median SUVmax. The analysis was repeated to form high-MTB and low-MTB subgroups as well as clinically relevant subgroups with SUVmax values of <5, 5-10, or >10. Multivariate analysis analyzing SUVmax, MTB, age, chemotherapy cycles, and pretreatment carbohydrate antigen (CA)19-9 was performed.For the entire population, median survival was 12.7 months. Median survival was 9.8 vs.15.3 months for the high- and low- SUVmax subgroups (p <0.01). Similarly, median survival was 10.1 vs. 18.0 months for the high MTB and low MTB subgroups (p <0.01). When clinical SUVmax cutoffs were used, median survival was 6.4 months in those with SUVmax >10, 9.5 months with SUVmax 5.0-10.0, and 17.7 months in those with SUVmax <5 (p <0.01). On multivariate analysis, clinical SUVmax was an independent predictor for overall survival (p = 0.03) and progression-free survival (p = 0.03).PET scan parameters can predict for length of survival in locally advanced pancreas cancer patients.

  View details for DOI 10.1016/j.ijrobp.2009.06.049

  View details for Web of Science ID 000280459700020

  View details for PubMedID 20056345

• Hereditary diffuse gastric cancer due to a previously undescribed CDH1 splice site mutation HUMAN PATHOLOGY Matsukuma, K. E., Mullins, F. M., Dietz, L., Zehnder, J. L., Ford, J. M., Chun, N. M., Schrijver, I. 2010; 41 (8): 1200-1203

  Abstract

  Our patient was a 52-year-old man who was diagnosed with signet ring cell gastric adenocarcinoma. An extensive family history of gastric cancer raised suspicion for hereditary diffuse gastric cancer. Sequencing of the patient's CDH1 gene revealed a novel point mutation in a strictly conserved splice site within intron 6, c.833-2 A > G. This mutation was predicted to result in loss of function due to defective RNA splicing. To characterize the pathogenic mechanism of this mutation, we amplified the patient's CDH1 gene products by reverse transcriptase polymerase chain reaction. Primers flanking the region of the mutation detected 3 distinct transcripts. In addition to the wild-type product, a larger product consistent with activation of a cryptic splice site within intron 6 and a smaller product shown to result from exon 7 skipping were detected. In summary, we have identified a novel CDH1 mutation in a large hereditary diffuse gastric cancer kindred and identified its pathogenic mechanism.

  View details for DOI 10.1016/j.humpath.2010.01.022

  View details for PubMedID 20624523

• Pathological response after chemoradiation for T3 rectal cancer. Colorectal disease Chennupati, S. K., Kamaya, A., Fisher, G. A., Ford, J. M., Kunz, P., Itakura, H., Welton, M. L., Shelton, A., Van Dam, J., Koong, A. C., Chang, D. T. 2010; 12 (7 Online): e24-30

  Abstract

  The aim of this study was to investigate the effect of preoperative chemoradiotherapy (CRT) on nodal disease in locally advanced rectal adenocarcinoma.Thirty-two patients staged uT3N0 and 27 patients staged uT3N1 rectal adenocarcinoma who underwent pre-CRT staging using endoscopic ultrasound or rectal protocol CT were included. The median radiation dose was 50.4 Gy (range: 45-50.4 Gy) at 1.8 Gy per fraction and all patients received concurrent 5-FU or capecitabine-based chemotherapy. Low anterior resection or abdomino-perineal resection occurred at a median of 46 days (range: 27-112 days) after CRT.Eleven of 32 uT3N0 patients (34.4%) and 13 of 26 uT3N1 patients (50.0%) had ypN+ (P = 0.29). For patients with uT3N0, 10 of 20 (50.0%) with ypT2-3 and 1 of 12 (8.3%) with ypT0-1 were ypN+ (P = 0.02). For patients with uT3N1, 12 of 20 (60.0%) with ypT2-3 and 1 of 6 (16.7%) with ypT0-1 were ypN+ (P = 0.16). Overall, the ypN+ rate was 11.1% in the ypT0-yT1 group compared with 55.0% in the ypT2-yT3 group (P = 003). Among patients with uT3N0 disease, the ypN+ rate in patients who had surgery > 46 days vs 46 days vs 46 days vs

  View details for DOI 10.1111/j.1463-1318.2009.02013.x

  View details for PubMedID 19614668

• Pathological response after chemoradiation for T3 rectal cancer COLORECTAL DISEASE Chennupati, S. K., Kamaya, A., Fisher, G. A., Ford, J. M., Kunz, P., Itakura, H., Welton, M. L., Shelton, A., Van Dam, J., Koong, A. C., Chang, D. T. 2010; 12 (7): E24-E30

  Abstract

  The aim of this study was to investigate the effect of preoperative chemoradiotherapy (CRT) on nodal disease in locally advanced rectal adenocarcinoma.Thirty-two patients staged uT3N0 and 27 patients staged uT3N1 rectal adenocarcinoma who underwent pre-CRT staging using endoscopic ultrasound or rectal protocol CT were included. The median radiation dose was 50.4 Gy (range: 45-50.4 Gy) at 1.8 Gy per fraction and all patients received concurrent 5-FU or capecitabine-based chemotherapy. Low anterior resection or abdomino-perineal resection occurred at a median of 46 days (range: 27-112 days) after CRT.Eleven of 32 uT3N0 patients (34.4%) and 13 of 26 uT3N1 patients (50.0%) had ypN+ (P = 0.29). For patients with uT3N0, 10 of 20 (50.0%) with ypT2-3 and 1 of 12 (8.3%) with ypT0-1 were ypN+ (P = 0.02). For patients with uT3N1, 12 of 20 (60.0%) with ypT2-3 and 1 of 6 (16.7%) with ypT0-1 were ypN+ (P = 0.16). Overall, the ypN+ rate was 11.1% in the ypT0-yT1 group compared with 55.0% in the ypT2-yT3 group (P = 003). Among patients with uT3N0 disease, the ypN+ rate in patients who had surgery > 46 days vs 46 days vs 46 days vs

  View details for DOI 10.1111/j.1463-1318.2009.02013.x

  View details for Web of Science ID 000208355900003

• High-resolution melting analysis for rapid screening of BRCA2 founder mutations in Southern Chinese breast cancer patients BREAST CANCER RESEARCH AND TREATMENT Kwong, A., Ng, E. K., Law, F. B., Wong, L. P., To, M. Y., Cheung, M. T., Wong, H. N., Chan, V. W., Kurian, A., West, D. W., Ford, J. M., Ma, E. S. 2010; 122 (2): 605-607

  View details for DOI 10.1007/s10549-010-0882-3

  View details for Web of Science ID 000278810700034

  View details for PubMedID 20396944

• Novel Treatment Approaches for Triple-Negative Breast Cancer CLINICAL BREAST CANCER Telli, M. L., Ford, J. M. 2010; 10: E16-E22

  Abstract

  Triple-negative breast cancers share an aggressive biology, marked by increased recurrence risk and poorer survival compared with hormone receptor-positive subtypes. Few therapeutic trials have specifically focused on triple-negative breast cancer, and the treatment of patients with early-stage triple-negative breast cancer has changed little in the past decade. Over this time, however, attention has shifted to treatment approaches based on molecular subtypes of breast cancer, and investigation into the mechanistic underpinnings of these distinct subtypes has exploded. Converging preclinical rationales combined with early provocative clinical efficacy has focused recent attention on strategies targeting DNA repair defects for the treatment of patients with triple-negative and BRCA mutation-associated breast cancers. These developments are very promising and suggest that major advances in the targeted treatment of patients with triple-negative breast cancer are in sight. This review provides an overview of the clinical features of triple-negative breast cancer and current treatment strategies in the adjuvant setting. Mechanisms of DNA repair and the DNA damage response are reviewed to provide background for understanding novel approaches targeting DNA repair defects in this disease with DNA-damaging chemotherapeutic agents and poly(ADP-ribose) polymerase inhibitors. Ongoing studies, including those investigating the role of antiangiogenic therapies, are also reviewed.

  View details for DOI 10.3816/CBC.2010.s.003

  View details for PubMedID 20587403

• Longer Relative Telomere Length in Blood from Women with Sporadic and Familial Breast Cancer Compared with Healthy Controls CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Gramatges, M. M., Telli, M. L., Balise, R., Ford, J. M. 2010; 19 (2): 605-613

  Abstract

  Telomeres cap the ends of chromosomes and are composed of a series of noncoding hexamer repeats. Telomeres protect the integrity of DNA coding sequences and are integral to the maintenance of genomic stability. Previous studies have shown an association between shortened lymphocyte telomeres and increased risk for specific cancers. However, the association between telomere length and breast cancer risk is less clear. We examined the relative telomere length (RTL) in blood from women with no personal or family history of cancer (controls) compared with different populations of women with breast cancer and women at high genetic risk for developing breast cancer. RTL was determined as the telomere to single gene copy number ratio assessed by quantitative PCR. Breast cancer cases (low risk, n = 40; high risk, n = 62) had significantly longer RTL compared with unaffected controls (n = 50; mean RTL = 1.11 versus 0.84; P < 0.0001). The assessment of risk by RTL quartile showed an increased risk for breast cancer with each longer quartile, with the most significant risk observed in the longest quartile (odds ratio, 23.3; confidence interval, 4.4-122.3; P < 0.0003). Women without breast cancer but at high risk due to family history (n = 30) also showed longer telomeres than controls (mean RTL = 1.09 versus 0.84; P < 0.0001). Our analysis supports previous findings of longer RTL in breast cancer cases compared with controls, and is the first to observe longer RTL in women without breast cancer identified as high risk based on family history.

  View details for DOI 10.1158/1055-9965.EPI-09-0896

  View details for Web of Science ID 000278403900035

  View details for PubMedID 20142254

• Oncogenic BRAF Mutation with CDKN2A Inactivation Is Characteristic of a Subset of Pediatric Malignant Astrocytomas CANCER RESEARCH Schiffman, J. D., Hodgson, J. G., VandenBerg, S. R., Flaherty, P., Polley, M. C., Yu, M., Fisher, P. G., Rowitch, D. H., Ford, J. M., Berger, M. S., Ji, H., Gutmann, D. H., James, C. D. 2010; 70 (2): 512-519

  Abstract

  Malignant astrocytomas are a deadly solid tumor in children. Limited understanding of their underlying genetic basis has contributed to modest progress in developing more effective therapies. In an effort to identify such alterations, we performed a genome-wide search for DNA copy number aberrations (CNA) in a panel of 33 tumors encompassing grade 1 through grade 4 tumors. Genomic amplifications of 10-fold or greater were restricted to grade 3 and 4 astrocytomas and included the MDM4 (1q32), PDGFRA (4q12), MET (7q21), CMYC (8q24), PVT1 (8q24), WNT5B (12p13), and IGF1R (15q26) genes. Homozygous deletions of CDKN2A (9p21), PTEN (10q26), and TP53 (17p3.1) were evident among grade 2 to 4 tumors. BRAF gene rearrangements that were indicated in three tumors prompted the discovery of KIAA1549-BRAF fusion transcripts expressed in 10 of 10 grade 1 astrocytomas and in none of the grade 2 to 4 tumors. In contrast, an oncogenic missense BRAF mutation (BRAF(V600E)) was detected in 7 of 31 grade 2 to 4 tumors but in none of the grade 1 tumors. BRAF(V600E) mutation seems to define a subset of malignant astrocytomas in children, in which there is frequent concomitant homozygous deletion of CDKN2A (five of seven cases). Taken together, these findings highlight BRAF as a frequent mutation target in pediatric astrocytomas, with distinct types of BRAF alteration occurring in grade 1 versus grade 2 to 4 tumors.

  View details for DOI 10.1158/0008-5472.CAN-09-1851

  View details for Web of Science ID 000278485500011

  View details for PubMedID 20068183

  View details for PubMedCentralID PMC2851233

• Multimodality treatment with intensity modulated radiation therapy for esophageal cancer DISEASES OF THE ESOPHAGUS La, T. H., Minn, A. Y., Su, Z., Fisher, G. A., Ford, J. M., Kunz, P., Goodman, K. A., Koong, A. C., Chang, D. T. 2010; 23 (4): 300-308

  Abstract

  The objective of this study is to determine the feasibility and report the outcome of patients with locally advanced esophageal cancer treated with preoperative or definitive chemoradiotherapy (CRT) using intensity-modulated radiation therapy (IMRT). Between 2003 and 2007, 30 patients with non-cervical esophageal cancer received concurrent chemotherapy and IMRT at Stanford University. Eighteen patients were planned for definitive CRT and 12 were planned for preoperative CRT. All patients had computed tomography-based treatment planning and received IMRT. The median dose delivered was 50.4 Gy. Patients planned for preoperative CRT underwent surgery 4-13 weeks (median 8.3 weeks) following completion of CRT. Median follow-up of surviving patients from start of RT was 24.2 months (range 8.2-38.3 months). The majority of tumors were adenocarcinomas (67%) and poorly differentiated (57%). Tumor location was 7% upper, 20% mid, 47% lower, and 27% gastroesophageal junction. Actuarial 2-year local-regional control (LRC) was 64%. High tumor grade was an adverse prognostic factor for LRC and overall survival (OS) (P= 0.015 and 0.012, respectively). The 2-year LRC was 83% vs. 51% for patients treated preoperatively vs. definitively (P= 0.32). The 2-year disease-free and OS were 38% and 56%, respectively. Twelve patients (40%) required feeding tube placement, and the average weight loss from baseline was 4.8%. Twelve (40%) patients experienced grade 3+ acute complications and one patient died of complications following feeding tube placement. Three patients (10%) required a treatment break. Eight patients (27%) experienced grade 3 late complications. No grade 4 complications were seen. IMRT was effective and well tolerated. Disease recurrence remains a challenge and further investigation with dose escalation to improve LRC and OS is warranted.

  View details for DOI 10.1111/j.1442-2050.2009.01004.x

  View details for PubMedID 19732129

• NCCN clinical practice guidelines in oncology. Colorectal cancer screening. Journal of the National Comprehensive Cancer Network Burt, R. W., Barthel, J. S., Dunn, K. B., David, D. S., Drelichman, E., Ford, J. M., Giardiello, F. M., Gruber, S. B., Halverson, A. L., Hamilton, S. R., Ismail, M. K., Jasperson, K., Lazenby, A. J., Lynch, P. M., Martin, E. W., Mayer, R. J., Ness, R. M., Provenzale, D., Rao, M. S., Shike, M., Steinbach, G., Terdiman, J. P., Weinberg, D. 2010; 8 (1): 8-61

  View details for PubMedID 20064289

• Intensity Modulated Radiation Therapy vs. Conventional Radiation Therapy for Squamous Cell Carcinoma of the Anal Canal 52nd Annual Meeting of the American-Society-for-Therapeutic-Radiation-Oncology (ASTRO) Bazan, J. G., Hara, W., Kunz, P., Fisher, G. A., Ford, J. M., Welton, M. L., Koong, A., Shelton, A., Goodman, K. A., Chang, D. T. ELSEVIER SCIENCE INC. 2010: S300–S301

  View details for Web of Science ID 000288775700650

• Identification of a biomarker panel using a multiplex proximity ligation assay improves accuracy of pancreatic cancer diagnosis JOURNAL OF TRANSLATIONAL MEDICINE Chang, S. T., Zahn, J. M., Horecka, J., Kunz, P. L., Ford, J. M., Fisher, G. A., Le, Q. T., Chang, D. T., Ji, H., Koong, A. C. 2009; 7

  Abstract

  Pancreatic cancer continues to prove difficult to clinically diagnose. Multiple simultaneous measurements of plasma biomarkers can increase sensitivity and selectivity of diagnosis. Proximity ligation assay (PLA) is a highly sensitive technique for multiplex detection of biomarkers in plasma with little or no interfering background signal.We examined the plasma levels of 21 biomarkers in a clinically defined cohort of 52 locally advanced (Stage II/III) pancreatic ductal adenocarcinoma cases and 43 age-matched controls using a multiplex proximity ligation assay. The optimal biomarker panel for diagnosis was computed using a combination of the PAM algorithm and logistic regression modeling. Biomarkers that were significantly prognostic for survival in combination were determined using univariate and multivariate Cox survival models.Three markers, CA19-9, OPN and CHI3L1, measured in multiplex were found to have superior sensitivity for pancreatic cancer vs. CA19-9 alone (93% vs. 80%). In addition, we identified two markers, CEA and CA125, that when measured simultaneously have prognostic significance for survival for this clinical stage of pancreatic cancer (p < 0.003).A multiplex panel assaying CA19-9, OPN and CHI3L1 in plasma improves accuracy of pancreatic cancer diagnosis. A panel assaying CEA and CA125 in plasma can predict survival for this clinical cohort of pancreatic cancer patients.

  View details for DOI 10.1186/1479-5876-7-105

  View details for PubMedID 20003342

• ASSOCIATION OF 7Q34 COPY NUMBER GAINS AND KIAA1549-BRAF GENE FUSIONS WITH JUVENILE PILOCYTIC ASTROCYTOMA Hodgson, J., VandenBerg, S. R., James, C., Perry, A., Gutmann, D., Fisher, P., Ford, J., Ji, H., Schiffman, J. OXFORD UNIV PRESS INC. 2009: 960

  View details for Web of Science ID 000272974100393

• A BRCA2 founder mutation and seven novel deleterious BRCA mutations in southern Chinese women with breast and ovarian cancer BREAST CANCER RESEARCH AND TREATMENT Kwong, A., Wong, L. P., Wong, H. N., Law, F. B., Ng, E. K., Tang, Y. H., Chan, W. K., Ho, L. S., Kwan, K. H., Poon, M., Wong, T. T., Leung, F. C., Chan, S. W., Ying, M. W., Ma, E. S., Ford, J. M. 2009; 117 (3): 683-686

  View details for DOI 10.1007/s10549-009-0385-2

  View details for Web of Science ID 000269916700028

  View details for PubMedID 19353265

• Molecular inversion probes reveal patterns of 9p21 deletion and copy number aberrations in childhood leukemia CANCER GENETICS AND CYTOGENETICS Schiffman, J. D., Wang, Y., McPherson, L. A., Welch, K., Zhang, N., Davis, R., Lacayo, N. J., Dahl, G. V., Faham, M., Ford, J. M., Ji, H. P. 2009; 193 (1): 9-18

  Abstract

  Childhood leukemia, which accounts for >30% of newly diagnosed childhood malignancies, is one of the leading causes of death for children with cancer. Genome-wide studies using microarray chips to identify copy number changes in human cancer are becoming more common. In this pilot study, 45 pediatric leukemia samples were analyzed for gene copy aberrations using novel molecular inversion probe (MIP) technology. Acute leukemia subtypes included precursor B-cell acute lymphoblastic leukemia (ALL) (n=23), precursor T-cell ALL (n=6), and acute myeloid leukemia (n=14). The MIP analysis identified 69 regions of recurring copy number changes, of which 41 have not been identified with other DNA microarray platforms. Copy number gains and losses were validated in 98% of clinical karyotypes and 100% of fluorescence in situ hybridization studies available. We report unique patterns of copy number loss in samples with 9p21.3 (CDKN2A) deletion in the precursor B-cell ALL patients, compared with the precursor T-cell ALL patients. MIPs represent an attractive technology for identifying novel copy number aberrations, validating previously reported copy number changes, and translating molecular findings into clinically relevant targets for further investigation.

  View details for DOI 10.1016/j.cancergencyto.2009.03.005

  View details for Web of Science ID 000268922900002

  View details for PubMedID 19602459

  View details for PubMedCentralID PMC2776674

• The role of the retinoblastoma/E2F1 tumor suppressor pathway in the lesion recognition step of nucleotide excision repair DNA REPAIR Lin, P. S., McPherson, L. A., Chen, A. Y., Sage, J., Ford, J. M. 2009; 8 (7): 795-802

  Abstract

  The retinoblastoma Rb/E2F tumor suppressor pathway plays a major role in the regulation of mammalian cell cycle progression. The pRb protein, along with closely related proteins p107 and p130, exerts its anti-proliferative effects by binding to the E2F family of transcription factors known to regulate essential genes throughout the cell cycle. We sought to investigate the role of the Rb/E2F1 pathway in the lesion recognition step of nucleotide excision repair (NER) in mouse embryonic fibroblasts (MEFs). Rb-/-, p107-/-, p130-/- MEFs repaired both cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4PPs) at higher efficiency than did wildtype cells following UV-C irradiation. The expression of damaged DNA binding gene DDB2 involved in the DNA lesion recognition step was elevated in the Rb family-deficient MEFs. To determine if the enhanced DNA repair in the absence of the Rb gene family is due to the derepression of E2F1, we assayed the ability of E2F1-deficient cells to repair damaged DNA and demonstrated that E2F1-/- MEFs are impaired for the removal of both CPDs and 6-4PPs. Furthermore, wildtype cells induced a higher expression of DDB2 and xeroderma pigmentosum gene XPC transcript levels than did E2F1-/- cells following UV-C irradiation. Using an E2F SiteScan algorithm, we uncovered a putative E2F-responsive element in the XPC promoter upstream of the transcription start site. We showed with chromatin immunoprecipitation assays the binding of E2F1 to the XPC promoter in a UV-dependent manner, suggesting that E2F1 is a transcriptional regulator of XPC. Our study identifies a novel E2F1 gene target and further supports the growing body of evidence that the Rb/E2F1 tumor suppressor pathway is involved in the regulation of the DNA lesion recognition step of nucleotide excision repair.

  View details for DOI 10.1016/j.dnarep.2009.03.003

  View details for PubMedID 19376752

• Detection of Solitary Humeral Metastasis From Pancreatic Adenocarcinoma With F-18 FDG PET/CT CLINICAL NUCLEAR MEDICINE Kim, J., Quon, A., Humke, E., Ford, J. M., Koong, A. C. 2009; 34 (5): 312-313

  View details for PubMedID 19387214

• Stereotactic Radiotherapy for Unresectable Adenocarcinoma of the Pancreas CANCER Chang, D. T., Schellenberg, D., Shen, J., Kim, J., Goodman, K. A., Fisher, G. A., Ford, J. M., Desser, T., Quon, A., Koong, A. C. 2009; 115 (3): 665-672

  Abstract

  The authors report on the local control and toxicity of stereotactic body radiotherapy (SBRT) for patients with unresectable pancreatic adenocarcinoma.Seventy-seven patients with unresectable adenocarcinoma of the pancreas received 25 gray (Gy) in 1 fraction. Forty-five patients (58%) had locally advanced disease, 11 patients (14%) had medically inoperable disease, 15 patients (19%) had metastatic disease, and 6 patients (8%) had locally recurrent disease. Nine patients (12%) had received prior chemoradiotherapy. Sixteen patients (21%) received between 45 to 54 Gy of fractionated radiotherapy and SBRT. Various gemcitabine-based chemotherapy regimens were received by 74 patients (96%), but 3 patients (4%) did not receive chemotherapy until they had distant failure.The median follow-up was 6 months (range, 3-31 months) and, among surviving patients, it was 12 months (range, 3-31 months). The overall rates of freedom from local progression (FFLP) at 6 months and 12 months were 91% and 84%, respectively. The 6- and 12-month isolated local recurrence rates were 5% and 5%, respectively. There was no difference in the 12-month FFLP rate based on tumor location (head/uncinate, 91% vs body/tail, 86%; P = .52). The progression-free survival (PFS) rates at 6 months and 12 months were 26% and 9%, respectively. The PFS rate at 6 months was superior for patients who had nonmetastatic disease versus patients who had metastatic disease (28% vs 15%; P = .05). The overall survival (OS) rates at 6 months and 12 months from SBRT were 56% and 21%, respectively. Four patients (5%) experienced grade > or = 2 acute toxicity. Three patients (4%) experienced grade 2 late toxicity, and 7 patients (9%) experienced grade > or = 3 late toxicity. At 6 months and 12 months, the rates of grade > or = 2 late toxicity were 11% and 25%, respectively.SBRT for pancreatic adenocarcinoma was effective for local control with associated risk of toxicity and should be used with rigorous attention to quality assurance. Efforts to reduce complications are warranted. Distant metastases account for the vast majority of disease-related mortality.

  View details for DOI 10.1002/cncr.24059

  View details for PubMedID 19117351

• Tailoring BRCAPRO to Asian-Americans IN REPLY JOURNAL OF CLINICAL ONCOLOGY Kurian, A. W., Whittemore, A. S., Ford, J. M. 2009; 27 (4): 643–44

  View details for DOI 10.1200/JCO.2008.20.7191

  View details for Web of Science ID 000262894400031

• Gemcitabine chemotherapy and single-fraction stereotactic body radiotherapy for locally advanced pancreatic cancer INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Schellenberg, D., Goodman, K. A., Lee, F., Chang, S., Kuo, T., Ford, J. M., Fisher, G. A., Quon, A., Desser, T. S., Norton, J., Greco, R., Yang, G. P., Koong, A. C. 2008; 72 (3): 678-686

  Abstract

  Fractionated radiotherapy and chemotherapy for locally advanced pancreatic cancer achieves only modest local control. This prospective trial evaluated the efficacy of a single fraction of 25 Gy stereotactic body radiotherapy (SBRT) delivered between Cycle 1 and 2 of gemcitabine chemotherapy.A total of 16 patients with locally advanced, nonmetastatic, pancreatic adenocarcinoma received gemcitabine with SBRT delivered 2 weeks after completion of the first cycle. Gemcitabine was resumed 2 weeks after SBRT and was continued until progression or dose-limiting toxicity. The gross tumor volume, with a 2-3-mm margin, was treated in a single 25-Gy fraction by Cyberknife. Patients were evaluated at 4-6 weeks, 10-12 weeks, and every 3 months after SBRT.All 16 patients completed SBRT. A median of four cycles (range one to nine) of chemotherapy was delivered. Three patients (19%) developed local disease progression at 14, 16, and 21 months after SBRT. The median survival was 11.4 months, with 50% of patients alive at 1 year. Patients with normal carbohydrate antigen (CA)19-9 levels either at diagnosis or after Cyberknife SBRT had longer survival (p <0.01). Acute gastrointestinal toxicity was mild, with 2 cases of Grade 2 (13%) and 1 of Grade 3 (6%) toxicity. Late gastrointestinal toxicity was more common, with five ulcers (Grade 2), one duodenal stenosis (Grade 3), and one duodenal perforation (Grade 4). A trend toward increased duodenal volumes radiated was observed in those experiencing late effects (p = 0.13).SBRT with gemcitabine resulted in comparable survival to conventional chemoradiotherapy and good local control. However, the rate of duodenal ulcer development was significant.

  View details for DOI 10.1016/j.ijrobp.2008.01.051

  View details for PubMedID 18395362

• Microsatellite instability and mismatch repair protein defects in ovarian epithelial neoplasms in patients 50 years of age and younger 95th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology Jensen, K. C., Mariappan, M. R., Putcha, G. V., Husain, A., Chun, N., Ford, J. M., Schrijver, I., Longacre, T. A. LIPPINCOTT WILLIAMS & WILKINS. 2008: 1029–37

  Abstract

  Ovarian malignancies occurring in the setting of hereditary nonpolyposis colorectal carcinoma syndrome typically present in young women, often as the first or "sentinel" cancer, but the frequency of microsatellite instability (MSI) and mismatch repair (MMR) defects in ovarian surface epithelial malignancies in women

  View details for PubMedID 18469706

• Characterization of the pathogenic mechanism of a novel BRCA2 variant in a Chinese family FAMILIAL CANCER Kwong, A., Wong, L. P., Chan, K. Y., Ma, E. S., Khoo, U. S., Ford, J. M. 2008; 7 (2): 125-133

  Abstract

  Germline mutations of BRCA1 and BRCA2 account for the majority of hereditary breast cancers, many of which are classified as variants of unknown significance (VUS). We report the identification of a novel BRCA2 variant (c.7806-9T > G) in a Chinese family with multiple breast cancers and document it as a pathogenic mutation.The proband in this family was diagnosed with breast cancer at age 50 with a strong family history of breast cancer. DNA and RNA were extracted from the blood of the proband and her family, and was used for BRCA gene mutation/deletion screening and RNA splicing analysis.BRCA2 c.7806-9T > G was identified in the proband, which was suggestive of a variant. This change was also found in two sisters of the proband with a history of breast cancer, as well as from the proband's maternal gastric cancer. The only sibling free of breast cancer did not carry the BRCA2 variant, thus demonstrating that the mutation segregates with the clinical phenotype in this family. RNA analysis on the proband blood sample revealed three aberrant splicing variants: c.7806_7874del, c.7806_7976del, and c.7806-8_7806-1ins. The latter causes a frameshift and creates a truncated protein, whilst the other two splicing variants resulted in shorter forms of the protein.The identified BRCA2 c.7806-9T > G [Genbank: DQ889340] was found to be pathogenic, based on aberrant splicing events resulting in the formation of truncated protein products. Thus, better understanding and classification of BRCA variants as neutral or disease causing has important implications for genetic counseling so that appropriate management can be given.

  View details for DOI 10.1007/s10689-007-9155-7

  View details for Web of Science ID 000256823500003

  View details for PubMedID 17657584

• Risk-reducing total gastrectomy for germline mutations in E-cadherin (CDH1): Pathologic findings with clinical implications AMERICAN JOURNAL OF SURGICAL PATHOLOGY Rogers, W. M., Dobo, E., Norton, J. A., Van Dam, J., Jeffrey, R. B., Huntsman, D. G., Kingham, K., Chun, N., Ford, J. M., Longacre, T. A. 2008; 32A (6): 799-809

  Abstract

  Hereditary diffuse gastric cancer is a rare autosomal dominant cancer susceptibility syndrome caused by germline E-cadherin (CDH1) mutations in 40% of cases with a high degree of penetrance. Screening endoscopy has not been useful in identifying early cancer, in part owing to conflicting data concerning site(s) of involvement in the stomach and the lack of endoscopically detectable pathology. Risk-reducing total gastrectomy specimens from 8 asymptomatic adults with germline mutations in the CDH1 gene (3 different pedigrees) were studied using a sequential serial sectioning protocol with submission of the entire stomach for histologic analysis. The presence, size, and distribution of signet ring cell clusters were determined for each section and geographic maps of the invasive foci were constructed and compared with gastrectomy specimens from patients with germline E-cadherin mutation and symptomatic gastric cancer. All but 1 of the asymptomatic patients with germline mutations in the CDH1 gene had negative endoscopic screening. All risk-reducing gastrectomy specimens were macroscopically normal. All contained multiple foci (mean, 10.9) of microscopic intramucosal signet ring cell carcinoma confined to the superficial gastric mucosa; no invasion of submucosa was identified. In situ carcinoma was present in 6/8 cases. The majority of signet ring foci were located in the proximal one third of the stomach, most within oxyntic-type mucosa. The number and size of foci were not related to age, but there was a trend toward more severe disease burden in women. Stomachs from the symptomatic group of patients with germline CDH1 mutations exhibited infiltrative foci with higher Ki-67 labeling that extended well beyond the superficial mucosa. In addition, while superficial signet ring cancer exhibited decreased or absent E-cadherin and beta-catenin protein expression in all cases studied, deeply invasive signet ring cancer showed reversion to E-cadherin and beta-catenin protein expression in a subset of mutation carriers. Our study indicates that superficial intramucosal signet ring carcinoma, although widespread, is predominantly located in the proximal one third of the stomach in patients with E-cadherin gene mutations. The observed site predilection suggests a possible role for geographically targeted endoscopic surveillance biopsy in patients who elect to delay surgical intervention.

  View details for Web of Science ID 000256553000001

• Risk-reducing total gastrectomy for germline mutations in E-cadherin (CDH1): pathologic findings with clinical implications. American journal of surgical pathology Rogers, W. M., Dobo, E., Norton, J. A., Van Dam, J., Jeffrey, R. B., Huntsman, D. G., Kingham, K., Chun, N., Ford, J. M., Longacre, T. A. 2008; 32 (6): 799-809

  Abstract

  Hereditary diffuse gastric cancer is a rare autosomal dominant cancer susceptibility syndrome caused by germline E-cadherin (CDH1) mutations in 40% of cases with a high degree of penetrance. Screening endoscopy has not been useful in identifying early cancer, in part owing to conflicting data concerning site(s) of involvement in the stomach and the lack of endoscopically detectable pathology. Risk-reducing total gastrectomy specimens from 8 asymptomatic adults with germline mutations in the CDH1 gene (3 different pedigrees) were studied using a sequential serial sectioning protocol with submission of the entire stomach for histologic analysis. The presence, size, and distribution of signet ring cell clusters were determined for each section and geographic maps of the invasive foci were constructed and compared with gastrectomy specimens from patients with germline E-cadherin mutation and symptomatic gastric cancer. All but 1 of the asymptomatic patients with germline mutations in the CDH1 gene had negative endoscopic screening. All risk-reducing gastrectomy specimens were macroscopically normal. All contained multiple foci (mean, 10.9) of microscopic intramucosal signet ring cell carcinoma confined to the superficial gastric mucosa; no invasion of submucosa was identified. In situ carcinoma was present in 6/8 cases. The majority of signet ring foci were located in the proximal one third of the stomach, most within oxyntic-type mucosa. The number and size of foci were not related to age, but there was a trend toward more severe disease burden in women. Stomachs from the symptomatic group of patients with germline CDH1 mutations exhibited infiltrative foci with higher Ki-67 labeling that extended well beyond the superficial mucosa. In addition, while superficial signet ring cancer exhibited decreased or absent E-cadherin and beta-catenin protein expression in all cases studied, deeply invasive signet ring cancer showed reversion to E-cadherin and beta-catenin protein expression in a subset of mutation carriers. Our study indicates that superficial intramucosal signet ring carcinoma, although widespread, is predominantly located in the proximal one third of the stomach in patients with E-cadherin gene mutations. The observed site predilection suggests a possible role for geographically targeted endoscopic surveillance biopsy in patients who elect to delay surgical intervention.

  View details for DOI 10.1097/PAS.0b013e31815e7f1a

  View details for PubMedID 18391748

• Cancer risk reduction and reproductive concerns in female BRCA1/2 mutation carriers FAMILIAL CANCER Staton, A. D., Kurian, A. W., Cobb, K., Mills, M. A., Ford, J. M. 2008; 7 (2): 179-186

  Abstract

  Women with mutations in the BRCA1 or BRCA2 cancer susceptibility genes face unique choices regarding management of their high risk for breast and ovarian cancer that impact their reproductive options. In order to explore women's preferences for management of elevated cancer risk, we evaluated the decisions of BRCA1/2 mutation carriers about contraception, prophylactic surgery, and family planning.An internet-based questionnaire assessing high-risk women's preferences about cancer risk management and reproductive options was designed, pilot-tested and administered electronically to 284 participants of an internet-based advocacy group for women with BRCA1/2 mutations.Two hundred and thirteen eligible participants completed the majority of the survey. Mean age was 34 years; 66% were BRCA1 mutation carriers and 34% were BRCA2 mutation carriers. Most women (92%) had used oral contraceptive pills. About 88% of responders reported frequent or extreme worry about transmitting the mutation to their children. Despite their high level of worry, few responders said they would likely consider using assisted reproduction technologies such as a pregnancy surrogate (3%), cryopreservation of oocytes or embryos (8%), or pre-implantation genetic diagnosis (PGD) to select embryos without BRCA1/2 mutations (13%).Although they expressed substantial concern about transmitting BRCA1/2 mutations to their children, only a minority of the high-risk women surveyed were likely to consider currently available assisted reproductive strategies. Further research is necessary to explore the risk management preferences of patients with inherited cancer predisposition, and to incorporate these preferences into clinical care.

  View details for DOI 10.1007/s10689-007-9171-7

  View details for PubMedID 18026853

• Preliminary activity of XL880, a dual MET/VEGFR2 inhibitor, in MET amplified poorly differentiated gastric cancer (PDGC): Interim results of a multicenter phase II study Jhawer, M. P., Kindler, H. L., Wainberg, Z. A., Hecht, J. R., Kerr, R. O., Ford, J. M., Henderson, C., Mueller, T., KEER, H. N., Shah, M. A. AMER SOC CLINICAL ONCOLOGY. 2008

  View details for Web of Science ID 000208457401683

• Identification of a novel p53 in-frame deletion in a Li-Fraumeni-like family PEDIATRIC BLOOD & CANCER Schiffman, J. D., Chun, N., Fisher, P. G., Dahl, G. V., Ford, J. M., Eggerding, F. A. 2008; 50 (4): 914-916

  Abstract

  We describe a 2-year-old female with a completely resected cerebral pilocytic astrocytoma who subsequently developed B-progenitor acute lymphoblastic leukemia (ALL). Her father and paternal uncle were previously diagnosed with glioblastoma multiforme. Sequence analysis of the patient's p53 gene revealed a novel germline three base-pair deletion (339_341delCTT) in exon 4, resulting in removal of an evolutionarily conserved phenylalanine amino acid residue at codon 113. The same mutation was found in the patient's two clinically unaffected siblings. The in-frame deletion we describe has not previously been reported and adds to our understanding of the biologic effects of p53 gene mutation in Li-Fraumeni syndrome (LFS).

  View details for DOI 10.1002/pbc.21247

  View details for PubMedID 17554785

• Identifying and preventing high-risk gastric cancer individuals with CDH1 mutations - Reply ANNALS OF SURGERY Norton, J. A., Ford, J. M. 2008; 247 (4): 715–16

  View details for DOI 10.1097/SLA.0b013e31816a5092

  View details for Web of Science ID 000254546900026

• Magnetic resonance galactography: A feasibility study in women with prior atypical breast duct cytology BREAST JOURNAL Kurian, A. W., Hartman, A., Mills, M. A., Logan, L. J., Sawyer, A. M., Ford, J. M., Daniel, B. L. 2008; 14 (2): 211-214

  View details for Web of Science ID 000253712200022

  View details for PubMedID 18248552

• HDAC inhibitor PCI-24781 decreases RAD51 expression and inhibits homologous recombination PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Adimoolam, S., Sirisawad, M., Chen, J., Thiemann, P., Ford, J. M., Buggy, J. J. 2007; 104 (49): 19482-19487

  Abstract

  Histone deacetylase (HDAC) inhibitors such as the phenyl hydroxamic acid PCI-24781 have emerged recently as a class of therapeutic agents for the treatment of cancer. Recent data showing synergy of HDAC inhibitors with ionizing radiation and other DNA-damaging agents have suggested that HDAC inhibitors may act, in part, by inhibiting DNA repair. Here we present evidence that HDAC enzymes are important for homologous recombinational repair of DNA double-strand breaks. Combination studies of PCI-24781 with the poly(ADP-ribose) polymerase inhibitor PJ34, an agent thought to produce lesions repaired by homologous recombination (HR), resulted in a synergistic effect on apoptosis. Immunofluorescence analysis demonstrated that HDAC inhibition caused a complete inhibition of subnuclear repair foci in response to ionizing radiation. Mechanistic investigations revealed that inhibition of HDAC enzymes by PCI-24781 led to a significant reduction in the transcription of genes specifically associated with HR, including RAD51. RAD51 protein levels were significantly decreased after 24 h of drug exposure both in vitro and in vivo. Consistent with inhibition of HR, treatment with PCI-24781 resulted in a decreased ability to perform homology directed repair of I-SceI-induced chromosome breaks in transfected CHO cells. In addition, an enhancement of cell killing was observed in Ku mutant cells lacking functional nonhomologous end joining compared with WT cells. Together these results demonstrate that HDAC enzymes are critically important to enable functional HR by controlling the expression of HR-related genes and promoting the proper assembly of HR-directed subnuclear foci.

  View details for DOI 10.1073/pnas.0707828104

  View details for Web of Science ID 000251525800057

  View details for PubMedID 18042714

  View details for PubMedCentralID PMC2148315

• A carrier of both MEN1 and BRCA2 mutations: case report a-lid review of the literature CANCER GENETICS AND CYTOGENETICS Ghataorhe, P., Kurian, A. W., Pickart, A., Trapane, P., Norton, J. A., Kingham, K., Ford, J. M. 2007; 179 (2): 89-92

  Abstract

  High-penetrance autosomal dominant cancer susceptibility genes such as BRCA2 and MEN1 result in specific patterns of cancers in individuals who inherit germline mutations. Their incidence in the population is relatively low, however, and it is highly unusual to identify individuals with two or more inherited cancer gene mutations. We describe a family with multiple cases of MEN1-associated cancers as well as pancreatic adenocarcinoma, ovarian cancer, and male breast cancer, in which we identified germline mutations in both MEN1 and BRCA2. To our knowledge, this is the first report of a patient with both MEN1 and BRCA2 mutations and with a personal history of hyperparathyroidism and pancreatic neuroendocrine tumors.

  View details for DOI 10.1016/j.cancergencyto.2007.08.009

  View details for Web of Science ID 000251478000001

  View details for PubMedID 18036394

• Identification of an intronic single nucleotide polymorphism leading to allele dropout during validation of a CDH1 sequencing assay: implications for designing polymerase chain reaction-based assays GENETICS IN MEDICINE Mullins, F. M., Dietz, L., Lay, M., Zehnder, J. L., Ford, J., Chun, N., Schrijver, I. 2007; 9 (11): 752-760

  Abstract

  The CDH1 gene encodes the cell adhesion protein E-cadherin, and CDH1 germline mutations are associated with hereditary diffuse gastric cancer. Identification of individuals at high risk of developing diffuse gastric cancer affords the opportunity for endoscopic screening or elective prophylactic gastrectomy. We set out to develop a CDH1 sequencing assay for clinical use.All exons of the CDH1 gene were amplified and sequenced with published and modified primers.While validating the assay, we encountered a case in which a single nucleotide polymorphism located in intron 15 led to allele dropout and therefore to a false-negative result. The polymorphism leading to allele dropout was located within a primer-binding sequence, five bases away from the 3' end of the primer. A frameshift mutation in exon 15 was detected by an alternative primer that binds away from the polymorphic site. A search of the University of California Santa Cruz single nucleotide polymorphism database revealed other polymorphisms located within primer-binding sites. A total of 12 primers in nine primer sets were modified to minimize allele dropout risk.The approach of designing primers to avoid known single nucleotide polymorphisms can be generalized to the design of any polymerase chain reaction-based assay and should be employed whenever possible.

  View details for DOI 10.1097/GIM.0b013e318159a369

  View details for PubMedID 18007144

• Founder and recurrent CDH1 mutations in families with hereditary diffuse gastric cancer JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION Kaurah, P., MacMillan, A., Boyd, N., Senz, J., De Luca, A., Chun, N., Suriano, G., Zaor, S., Van Manen, L., Gilpin, C., Nikkel, S., Connolly-Wilson, M., Weissman, S., Rubinstein, W. S., Sebold, C., Greenstein, R., Stroop, J., Yim, D., Panzini, B., McKinnon, W., Greenblatt, M., Wirtzfeld, D., Fontaine, D., Coit, D., Yoon, S., Chung, D., Lauwers, G., Pizzuti, A., Vaccaro, C., Redal, M. A., Oliveira, C., Tischkowitz, M., Olschwang, S., Gallinger, S., Lynch, H., Green, J., Ford, J., Pharoah, P., Fernandez, B., Huntsman, D. 2007; 297 (21): 2360-2372

  Abstract

  Hereditary diffuse gastric cancer is caused by germline mutations in the epithelial cadherin (CDH1) gene and is characterized by an increased risk for diffuse gastric cancer and lobular breast cancer.To determine whether recurring germline CDH1 mutations occurred due to independent mutational events or common ancestry.Thirty-eight families diagnosed clinically with hereditary diffuse gastric cancer were accrued between November 2004 and January 2006 and were analyzed for CDH1 mutations as part of an ongoing study at the British Columbia Cancer Agency. Twenty-six families had at least 2 gastric cancer cases with 1 case of diffuse gastric cancer in a person younger than 50 years; 12 families had either a single case of diffuse gastric cancer diagnosed in a person younger than 35 years or multiple cases of diffuse gastric cancer diagnosed in persons older than 50 years.Classification of family members as carriers or noncarriers of CDH1 mutations. Haplotype analysis to assess recurring mutations for common ancestry was performed on 7 families from this study and 7 previously reported families with the same mutations.Thirteen mutations (6 novel) were identified in 15 of the 38 families (40% detection rate). The 1137G>A splicing mutation and the 1901C>T (A634V) missense/splicing mutation occurred on common haplotypes in 2 families but on different haplotypes in a third family. The 2195G>A (R732Q) missense/splicing mutation occurred in 2 families on different haplotypes. The 2064-2065delTG mutation occurred on a common haplotype in 2 families. Two families from this study plus 2 additional families carrying the novel 2398delC mutation shared a common haplotype, suggesting a founder effect. All 4 families originate from the southeast coast of Newfoundland. Due to concentrations of lobular breast cancer cases, 2 branches of this family had been diagnosed as having hereditary breast cancer and were tested for BRCA mutations. Within these 4 families, the cumulative risk by age 75 years in mutation carriers for clinically detected gastric cancer was 40% (95% confidence interval [CI], 12%-91%) for males and 63% (95% CI, 19%-99%) for females and the risk for breast cancer in female mutation carriers was 52% (95% CI, 29%-94%).Recurrent CDH1 mutations in families with hereditary diffuse gastric cancer are due to both independent mutational events and common ancestry. The presence of a founder mutation from Newfoundland is strongly supported.

  View details for Web of Science ID 000247007200018

  View details for PubMedID 17545690

• Reversal of stathmin-mediated resistance to paclitaxel and vinblastine in human breast carcinoma cells MOLECULAR PHARMACOLOGY Alli, E., Yang, J., Ford, J. M., Hait, W. N. 2007; 71 (5): 1233-1240

  Abstract

  Antimicrotubule agents are commonly used chemotherapy drugs for the treatment of breast and other cancers. However, these agents have variable activity partly because of microtubule regulatory proteins. Stathmin, an 18-kDa phosphoprotein that promotes microtubule depolymerization, was found to be frequently overexpressed in breast cancer. We previously identified stathmin-mediated mechanisms of resistance to antimicrotubule agents, including altered drug binding and delayed transit from G(2) into M phase, where these agents are effective in disrupting microtubule dynamics. We hypothesized that by reversing stathmin-mediated depolymerization of microtubules or by promoting entry into mitosis, this could increase sensitivity to antimicrotubule agents in human breast cancer cells overexpressing stathmin. We found that targeting stathmin or wee-1 expression with RNA interference can induce microtubule polymerization and promote G(2)/M progression, respectively, and sensitize stathmin-overexpressing breast cancer cells to paclitaxel and vinblastine. Furthermore, targeting wee-1 led to the phosphorylation of stathmin, which is known to attenuate its activity. Therefore, these data suggest a novel approach to improving the efficacy of certain antimicrotubule agents against breast cancer by regulating the function of stathmin.

  View details for DOI 10.1124/mol.106.029702

  View details for Web of Science ID 000245974900008

  View details for PubMedID 17272681

• Ductal pattern enhancement on magnetic resonance imaging of the breast due to ductal lavage BREAST JOURNAL Ghanouni, P., Kurian, A. W., Margolis, D., Hartman, A., Mills, M. A., Plevritis, S. K., Ford, J. M., Daniel, B. L. 2007; 13 (3): 281-286

  Abstract

  Our purpose is to describe the appearance of breast ductal enhancement found on magnetic resonance imaging (MRI) after breast ductal lavage (DL). We describe a novel etiology of enhancement in a ductal pattern on postcontrast MRI of the breast. Knowledge of the potential for breast MRI enhancement subsequent to DL, which can mimic the appearance of a pathologic lesion, is critical to the care of patients who undergo breast MRI and DL or other intraductal cannulation procedures.

  View details for PubMedID 17461903

• Germ line mutations of mismatch repair genes in hereditary nonpolyposis colorectal cancer patients with small bowel cancer: International Society for Gastrointestinal Hereditary Tumours Collaborative Study CLINICAL CANCER RESEARCH Park, J., Kim, D., Hong, C. W., Nam, B., Shin, Y., Hong, S., Kim, I., Lim, S., Aronson, M., Bisgaard, M. L., Brown, G. J., Burn, J., Chow, E., Conrad, P., Douglas, F., Dunlop, M., Ford, J., Greenblatt, M. S., Heikki, J., Heinimann, K., Lynch, E. L., Macrae, F., McKinnon, W. C., Moeeslein, G., Rossi, B. M., Rozen, P., Schofield, L., Vaccaro, C., Vasen, H., Velthuizen, M., Viel, A., Wijnen, J. 2006; 12 (11): 3389-3393

  Abstract

  The aim of study was to determine the clinical characteristics and mutational profiles of the mismatch repair genes in hereditary nonpolyposis colorectal cancer (HNPCC) patients with small bowel cancer (SBC).A questionnaire was mailed to 55 members of the International Society for Gastrointestinal Hereditary Tumours, requesting information regarding patients with HNPCC-associated SBC and germ line mismatch repair gene mutations.The study population consisted of 85 HNPCC patients with identified mismatch repair gene mutations and SBCs. SBC was the first HNPCC-associated malignancy in 14 of 41 (34.1%) patients for whom a personal history of HNPCC-associated cancers was available. The study population harbored 69 different germ line mismatch repair gene mutations, including 31 mutations in MLH1, 34 in MSH2, 3 in MSH6, and 1 in PMS2. We compared the distribution of the mismatch repair mutations in our study population with that in a control group, including all pathogenic mismatch repair mutations of the International Society for Gastrointestinal Hereditary Tumours database (excluding those in our study population). In patients with MSH2 mutations, patients with HNPCC-associated SBCs had fewer mutations in the MutL homologue interaction domain (2.9% versus 19.9%, P = 0.019) but an increased frequency of mutations in codons 626 to 733, a domain that has not previously been associated with a known function, versus the control group (26.5% versus 2.8%, P < 0.001).In HNPCC patients, SBC can be the first and only cancer and may develop as soon as the early teens. The distribution of MSH2 mutations found in patients with HNPCC-associated SBCs significantly differed from that found in the control group (P < 0.001).

  View details for DOI 10.1158/1078-0432.CCR-05-2452

  View details for Web of Science ID 000238169800023

  View details for PubMedID 16740762

• A kinase-independent function of c-Abl in promoting proteolytic destruction of damaged DNA binding proteins MOLECULAR CELL Chen, X., Zhang, J., Lee, J., Lin, P. S., Ford, J. M., Zheng, N., Zhou, P. 2006; 22 (4): 489-499

  Abstract

  Damaged DNA binding proteins (DDBs) play a critical role in the initial recognition of UV-damaged DNA and mediate recruitment of nucleotide excision repair factors. Previous studies identified DDB2 as a target of the CUL-4A ubiquitin ligase. However, the biochemical mechanism governing DDB proteolysis and its underlying physiological function in the removal of UV-induced DNA damage are largely unknown. Here, we report that the c-Abl nonreceptor tyrosine kinase negatively regulates the repair of UV-induced photolesions on genomic DNA. Biochemical studies revealed that c-Abl promotes CUL-4A-mediated DDB ubiquitination and degradation in a manner that does not require its tyrosine kinase activity both under normal growth conditions and following UV irradiation. Moreover, c-Abl activates DDB degradation in part by alleviating the inhibitory effect of CAND1/TIP120A on CUL-4A. These results revealed a kinase-independent function of c-Abl in a ubiquitin-proteolytic pathway that regulates the damage recognition step of nucleotide excision repair.

  View details for DOI 10.1016/j.molcel.2006.04.021

  View details for Web of Science ID 000237813300010

  View details for PubMedID 16713579

• Colorectal Cancer Screening Clinical Practice Guidelines. Journal of the National Comprehensive Cancer Network Levin, B., Barthel, J. S., Burt, R. W., David, D. S., Ford, J. M., Giardiello, F. M., Gruber, S. B., Halverson, A. L., Hamilton, S., Kohlmann, W., Ludwig, K. A., Lynch, P. M., Marino, C., Martin, E. W., Mayer, R. J., Pasche, B., Pirruccello, S. J., Rajput, A., Rao, M. S., Shike, M., Steinbach, G., Terdiman, J. P., Weinberg, D., Winawer, S. J. 2006; 4 (4): 384-420

  View details for PubMedID 16569391

• Genetic/familial high-risk assessment: breast and ovarian. Journal of the National Comprehensive Cancer Network Daly, M. B., Axilbund, J. E., Bryant, E., Buys, S., Eng, C., Friedman, S., Esserman, L. J., Farrell, C. D., Ford, J. M., Garber, J. E., Jeter, J. M., Kohlmann, W., Lynch, P. M., Marcom, P. K., Nabell, L. M., Offit, K., Osarogiagbon, R. U., Pasche, B., Reiser, G., Sutphen, R., Weitzel, J. N. 2006; 4 (2): 156-176

  View details for PubMedID 16451772

• Phase II study to assess the efficacy of conventionally fractionated radiotherapy followed by a stereotactic radiosurgery boost in patients with locally advanced pancreatic cancer INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Koong, A. C., Christofferson, E., Le, Q. T., Goodman, K. A., Ho, A., Kuo, T., Ford, J. M., Fisher, G. A., Greco, R., Norton, J., Yang, G. P. 2005; 63 (2): 320-323

  Abstract

  To determine the efficacy of concurrent 5-fluorouracil (5-FU) and intensity-modulated radiotherapy (IMRT) followed by body stereotactic radiosurgery (SRS) in patients with locally advanced pancreatic cancer.In this prospective study, all patients (19) had pathologically confirmed adenocarcinoma and were uniformly staged. Our treatment protocol consisted of 45 Gy IMRT with concurrent 5-FU followed by a 25 Gy SRS boost to the primary tumor.Sixteen patients completed the planned therapy. Two patients experienced Grade 3 toxicity (none had more than Grade 3 toxicity). Fifteen of these 16 patients were free from local progression until death. Median overall survival was 33 weeks.Concurrent IMRT and 5-FU followed by SRS in patients with locally advanced pancreatic cancer results in excellent local control, but does not improve overall survival and is associated with more toxicity than SRS, alone.

  View details for DOI 10.1016/j.ijrobp.2005.07.002

  View details for PubMedID 16168826

• Regulation of DNA damage recognition and nucleotide excision repair: Another role for p53 MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS Ford, J. M. 2005; 577 (1-2): 195-202

  Abstract

  In response to DNA damage, the p53 tumor suppressor gene product is activated leading to the induction of several downstream cellular processes including cell cycle checkpoints, DNA repair or apoptosis. Experiments first performed in the Hanawalt laboratory identified a p53-dependent pathway affecting global genomic nucleotide excision repair. The mechanisms involved in this process include both transcriptional and post-translational regulation by p53 of the DDB2 and XPC gene products, two critical DNA damage recognition proteins required for GGR. A historical review of this work is presented.

  View details for DOI 10.1016/j.mrfmmm.2005.04.005

  View details for PubMedID 15927209

• Opinions of women with high inherited breast cancer risk about prophylactic mastectomy: an initial evaluation from a screening trial including magnetic resonance imaging and ductal lavage HEALTH EXPECTATIONS Kurian, A. W., Hartman, A. R., Mills, M. A., Ford, J. M., Daniel, B. L., Plevritis, S. K. 2005; 8 (3): 221-233

  Abstract

  Prophylactic mastectomy (PM) is often considered, but variably chosen by women at high inherited risk of breast cancer; few data exist on patient tolerance of intensive breast screening as an alternative to PM. We performed an evaluation of high-risk women's tolerance of a breast screening protocol using clinical breast examination, mammography, breast magnetic resonance imaging (MRI) and ductal lavage (DL), and of change in attitudes toward PM after screening.A questionnaire assessing tolerance of screening procedures and change in opinion towards PM was designed and administered to 43 study participants, after a median follow-up of 13 months. Responses were evaluated according to patient characteristics, including type of study-prompted interventions, BRCA mutation status, and prior history of cancer, via univariate analysis.Most patients [85.3% (68.9-95.1%)] were more opposed or unchanged in their attitudes towards PM after study participation, with only 14.7% (5.0-31.1%) less opposed (P = 0.017) despite a short-interval follow-up MRI rate of 71.7% and a biopsy rate of 37%. Lower rates of maximal discomfort were reported with mammogram [2.8% (0-14.5%)] and MRI [5.6% (0-18.7%)] than with DL [28.6% (14.6-46.3%)], with P = 0.035.Most high-risk women tolerated intensive breast screening well; they were not more inclined towards PM after participating. Future studies should prospectively evaluate larger numbers of high-risk women via multivariate analysis, to determine characteristics associated with preference for breast screening vs. PM.

  View details for PubMedID 16098152

• Phase II study of gefitinib, fluorouracil, leucovorin, and oxaliplatin therapy in previously treated patients with metastatic colorectal cancer 40th Annual Meeting of the American-Society-of-Clinical-Oncology Kuo, T., Cho, C. D., Halsey, J., Wakelee, H. A., Advani, R. H., Ford, J. M., Fisher, G. A., Sikic, B. I. AMER SOC CLINICAL ONCOLOGY. 2005: 5613–19

  Abstract

  To investigate the gefitinib, fluorouracil (FU), leucovorin, and oxaliplatin regimen (IFOX) in previously treated patients with metastatic colorectal cancer.Eligible patients had stage IV colorectal adenocarcinoma and had demonstrated progression or intolerance to a prior chemotherapy regimen not including oxaliplatin. Each cycle consisted of 14 days. Cycle 1 consisted of oxaliplatin 85 mg/m2 intravenously (IV) during 2 hours on day 1, hours 0 to 2; leucovorin 200 mg/m2 IV on days 1 and 2, hours 0 to 2; FU 400 mg/m2 IV push on days 1 and 2; and FU 600 mg/m2 IV on days 1 and 2, hours 2 to 24 (FOLFOX-4). All subsequent cycles consisted of FOLFOX-4 with gefitinib at 500 mg/d administered orally throughout the 14-day cycle.Twenty-seven patients were enrolled onto the study. The median number of prior chemotherapy regimens was two, and 74% of all patients received prior irinotecan. Nine of the 27 patients (33%) and six of the 20 patients (30%) who had prior FU and irinotecan had a partial response by Response Evaluation Criteria in Solid Tumors Group criteria. Median overall survival was 12.0 months. Median event-free survival was 5.4 months. Grade 3 to 4 toxicities included neutropenia (48%), diarrhea (48%), nausea (22%), and vomiting (15%).IFOX is an active regimen in patients with previously treated metastatic colorectal adenocarcinoma, demonstrating higher response rates than those reported with FOLFOX-4 alone in a similar patient population.

  View details for DOI 10.1200/JCO.2005.08.359

  View details for PubMedID 16110021

• Characterization of a recurrent germ line mutation of the E-cadherin gene: Implications for genetic testing and clinical management CLINICAL CANCER RESEARCH Suriano, G., Yew, S., Ferreira, P., Senz, J., Kaurah, P., Ford, J. M., Longacre, T. A., NORTON, J. A., Chun, N., Young, S., Oliveira, M. J., MacGillivray, B., Rao, A., Sears, D., Jackson, C. E., Boyd, J., Yee, C., Deters, C., Pai, G. S., Hammond, L. S., McGivern, B. J., Medgyesy, D., Sartz, D., Arun, B., Oelschlager, B. K., Upton, M. P., Neufeld-Kaiser, W., Silva, O. E., Donenberg, T. R., Kooby, D. A., Sharma, S., Jonsson, B. A., Gronberg, H., Gallinger, S., Seruca, R., Lynch, H., Huntsman, D. G. 2005; 11 (15): 5401-5409

  Abstract

  To identify germ line CDH1 mutations in hereditary diffuse gastric cancer (HDGC) families and develop guidelines for management of at risk individuals.We ascertained 31 HDGC previously unreported families, including 10 isolated early-onset diffuse gastric cancer (DGC) cases. Screening for CDH1 germ line mutations was done by denaturing high-performance liquid chromatography and automated DNA sequencing.We identified eight inactivating and one missense CDH1 germ line mutation. The missense mutation conferred in vitro loss of protein function. Two families had the previously described 1003C>T nonsense mutation. Haplotype analysis revealed this to be a recurrent and not a founder mutation. Thirty-six percent (5 of 14) of the families with a documented DGC diagnosed before the age of 50 and other cases of gastric cancer carried CDH1 germ line mutations. Two of 10 isolated cases of DGC in individuals ages <35 years harbored CDH1 germ line mutations. One mutation positive family was ascertained through a family history of lobular breast cancer (LBC) and another through an individual with both DGC and LBC. Occult DGC was identified in five of six prophylactic gastrectomies done on asymptomatic, endoscopically negative 1003C>T mutation carriers.In addition to families with a strong history of early-onset DGC, CDH1 mutation screening should be offered to isolated cases of DGC in individuals ages <35 years and for families with multiple cases of LBC, with any history of DGC or unspecified GI malignancies. Prophylactic gastrectomy is potentially a lifesaving procedure and clinical breast screening is recommended for asymptomatic mutation carriers.

  View details for Web of Science ID 000230878900012

  View details for PubMedID 16061854

• Ductal lavage of fluid-yielding and non-fluid-yielding ducts in BRCA1 and BRCA2 mutation carriers and other women at high inherited breast cancer risk CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION Kurian, A. W., Mills, M. A., Jaffee, M., Sigal, B. M., Chun, N. M., Kingham, K. E., Collins, L. C., Nowels, K. W., Plevritis, S. K., Garber, J. E., Ford, J. M., Hartman, A. R. 2005; 14 (5): 1082-1089

  Abstract

  Nipple fluid production and atypical breast duct cells in women at high risk of breast cancer have been associated with further increased risk. Most publications on ductal lavage for cell collection report cannulating fluid-yielding ducts only. We report lavage of fluid-yielding and non-fluid-yielding ducts in women at high inherited breast cancer risk.A pilot breast cancer screening study including ductal lavage was conducted in 75 women at high inherited risk, 56 (74.7%) of whom had BRCA1/2 mutations. Ductal lavage was attempted in any duct identifiable with a catheter.Ducts were successfully catheterized in 60 of 75 patients (80%). Successfully catheterized patients were younger (median age 41 versus 53 years, P = 0.0003) and more often premenopausal (51.7% versus 20%, P = 0.041). Thirty-one successfully catheterized patients [51.6%, 95% confidence interval (39.4-63.9%)] had non-fluid-yielding ducts only. Seventeen patients [28.3% (18.5-40.9%)] had atypical cells. Twelve of seventeen [70.6% (46.8-87.2%)] samples with atypia were from non-fluid-yielding ducts. Patients with non-fluid-yielding ducts (versus fluid-yielding ducts) were more likely to have had prior cancer (48.4% versus 17.2%, P = 0.014) or chemotherapy (45.2% versus 17.2%, P = 0.027); this was also true in patients with atypia from non-fluid-yielding ducts.Successfully lavaged women were younger and more often premenopausal. Atypical cells can be found in non-fluid-yielding ducts in patients at high inherited breast cancer risk. Non-fluid-yielding ducts, and atypia from non-fluid-yielding ducts, are more common in patients with prior cancer and chemotherapy. Larger studies are needed to identify risk factors and prognostic significance associated with atypia and non-fluid-yielding ducts in high-risk populations, and define their role as biomarkers.

  View details for PubMedID 15894656

• Phase I study of stereotactic radiosurgery in patients with locally advanced pancreatic cancer INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Koong, A. C., Le, Q. T., Ho, A., Fong, B., Fisher, G., Cho, C., Ford, J., Poen, J., Gibbs, I. C., Mehta, V. K., Kee, S., Trueblood, W., Yang, G., Bastidas, J. A. 2004; 58 (4): 1017-1021

  Abstract

  To determine the feasibility and toxicity of delivering stereotactic radiosurgery to patients with locally advanced pancreatic cancer.Patients with Eastern Cooperative Oncology Group performance status < or=2 and locally advanced pancreatic cancer were enrolled on this Phase I dose escalation study. Patients received a single fraction of radiosurgery consisting of either 15 Gy, 20 Gy, or 25 Gy to the primary tumor. Acute gastrointestinal toxicity was scored according to the Radiation Therapy Oncology Group criteria. Response to treatment was determined by serial high-resolution computed tomography scanning.Fifteen patients were treated at 3 dose levels (3 patients received 15 Gy, 5 patients received 20 Gy, and 7 patients received 25 Gy). At these doses, no Grade 3 or higher acute gastrointestinal toxicity was observed. This trial was stopped before any dose-limiting toxicity was reached, because the clinical objective of local control was achieved in all 6 evaluable patients treated at 25 Gy.It is feasible to deliver stereotactic radiosurgery to patients with locally advanced pancreatic cancer. The recommended dose to achieve local control without significant acute gastrointestinal toxicity is 25 Gy.

  View details for DOI 10.1016/j.ijrobp.2003.11.004

  View details for PubMedID 15001240

• Breast magnetic resonance image screening and ductal lavage in women at high genetic risk for breast carcinoma CANCER Hartman, A. R., Daniel, B. L., Kurian, A. W., Mills, M. A., Nowels, K. W., Dirbas, F. M., Kingham, K. E., Chun, N. M., Herfkens, R. J., Ford, J. M., Plevritis, S. K. 2004; 100 (3): 479-489

  Abstract

  Intensive screening is an alternative to prophylactic mastectomy in women at high risk for developing breast carcinoma. The current article reports preliminary results from a screening protocol using high-quality magnetic resonance imaging (MRI), ductal lavage (DL), clinical breast examination, and mammography to identify early malignancy and high-risk lesions in women at increased genetic risk of breast carcinoma.Women with inherited BRCA1 or BRCA2 mutations or women with a >10% risk of developing breast carcinoma at 10 years, as estimated by the Claus model, were eligible. Patients were accrued from September 2001 to May 2003. Enrolled patients underwent biannual clinical breast examinations and annual mammography, breast MRI, and DL.Forty-one women underwent an initial screen. Fifteen of 41 enrolled women (36.6%) either had undergone previous bilateral oophorectomy and/or were on tamoxifen at the time of the initial screen. One patient who was a BRCA1 carrier had high-grade ductal carcinoma in situ (DCIS) that was screen detected by MRI but that was missed on mammography. High-risk lesions that were screen detected by MRI in three women included radial scars and atypical lobular hyperplasia. DL detected seven women with cellular atypia, including one woman who had a normal MRI and mammogram.Breast MRI identified high-grade DCIS and high-risk lesions that were missed by mammography. DL detected cytologic atypia in a high-risk cohort. A larger screening trial is needed to determine which subgroups of high-risk women will benefit and whether the identification of malignant and high-risk lesions at an early stage will impact breast carcinoma incidence and mortality.

  View details for DOI 10.1002/cncr.11926

  View details for PubMedID 14745863

• BRCA1 and p53: compensatory roles in DNA repair JOURNAL OF MOLECULAR MEDICINE-JMM Hartman, A. R., Ford, J. M. 2003; 81 (11): 700-707

  Abstract

  The BRCA1 breast cancer susceptibility gene has been implicated in many cellular processes, yet its specific mechanism of tumor suppression remains unclear. BRCA1 plays a role in several DNA repair pathways including nucleotide excision repair (NER). Loss of the p53 tumor suppressor gene, a key regulator of NER, is an important and necessary event in the pathogenesis of BRCA1-mutated tumors. Here we discuss the role of BRCA1 and NER in breast cancer and the interactions of BRCA1 with p53 in breast tumorigenesis and suggest approaches for risk assessment and chemotherapeutic management of BRCA1-related breast cancer.

  View details for DOI 10.1007/s00109-003-0477-0

  View details for PubMedID 13679996

• Functional characterization of global genomic DNA repair and its implications for cancer 4th International Conference on Environmental Mutagens in Human Populations (ICEMHP) Hanawalt, P. C., Ford, J. A., Lloyd, D. R. ELSEVIER SCIENCE BV. 2003: 107–14

  Abstract

  The most versatile cellular pathway for dealing with a large variety of structurally-unrelated DNA alterations is nucleotide excision repair (NER). Most genomic damage, if not repaired, may contribute to mutagenesis and carcinogenesis, as well as to cellular lethality. There are two subpathways of NER, termed global genomic repair (GGR) and transcription-coupled repair (TCR); While GGR deals with all repairable lesions throughout the genome, TCR is selective for the transcribed DNA strand in expressed genes. Proteins involved in the initial recognition of lesions for GGR as well as for TCR (i.e. RNA polymerase) may sometimes initiate gratuitous repair events in undamaged DNA. However, the damage recognition enzymes for GGR are normally maintained at very low levels unless the cells are genomically stressed. Following UV irradiation in human fibroblasts the efficiency of GGR is upregulated through activation of the p53 tumor suppressor gene. The transactivation role of p53 includes control of expression of the genes, XPC and XPE, which are implicated in GGR but not TCR. These inducible responses are essential for the efficient repair of the most prominent lesion produced by UV, the cyclobutane pyrimidine dimer (CPD). They are also clinically relevant, as we have shown them to operate upon chemical carcinogen DNA damage at levels to which humans are environmentally exposed (e.g. through smoking). Thus, for benzo(a)pyrene (at 10-50 adducts per 10(8) nucleotides) repair was essentially complete within 1 day in p53(+/+) human fibroblasts while no repair was detected within 3 days in p53(-/-) cells. The levels of all four DNA adducts formed by benzo(g)chrysene, also exhibited p53-dependent control in human fibroblasts. However, unlike humans most rodent tissues are deficient in the p53-dependent GGR pathway. Since rodents are used as surrogates for humans in environmental cancer risk assessment it is very important that we determine how they differ from humans with respect to DNA repair and oncogenic responses to environmental genotoxins.

  View details for DOI 10.1016/j.mrrev.2003.06.002

  View details for PubMedID 14644313

• Defective double-strand DNA break repair and chromosomal translocations by MYC overexpression PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Karlsson, A., Deb-Basu, D., Cherry, A., Turner, S., Ford, J., Felsher, D. W. 2003; 100 (17): 9974-9979

  Abstract

  DNA repair mechanisms are essential for the maintenance of genomic integrity. Disruption of gene products responsible for DNA repair can result in chromosomal damage. Improperly repaired chromosomal damage can result in the loss of chromosomes or the generation of chromosomal deletions or translocations, which can lead to tumorigenesis. The MYC protooncogene is a transcription factor whose overexpression is frequently associated with human neoplasia. MYC has not been previously implicated in a role in DNA repair. Here we report that the overexpression of MYC disrupts the repair of double-strand DNA breaks, resulting in a several-magnitude increase in chromosomal breaks and translocations. We found that MYC inhibited the repair of gamma irradiation DNA breaks in normal human cells and blocked the repair of a single double-strand break engineered to occur in an immortal cell line. By spectral karyotypic analysis, we found that MYC even within one cell division cycle resulted in a several-magnitude increase in the frequency of chromosomal breaks and translocations in normal human cells. Hence, MYC overexpression may be a previously undescribed example of a dominant mutator that may fuel tumorigenesis by inducing chromosomal damage.

  View details for DOI 10.1073/pnas.1732638100

  View details for PubMedID 12909717

• Phase II trial of preoperative 3D conformal radiotherapy, protracted venous infusion 5-fluorouracil, and weekly CPT-11, followed by surgery for ultrasound-staged T3 rectal cancer INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Mehta, V. K., Cho, C., Ford, J. M., Jambalos, C., Poen, J., Koong, A., Lin, A., Bastidas, J. A., Young, H., Dunphy, E. P., Fisher, G. 2003; 55 (1): 132-137

  Abstract

  CPT-11 sensitizes tumor cells to radiation and in combination therapy with 5-fluorouracil (5-FU) results in enhanced cytotoxicity to metastatic colorectal cancer. We report the results from a Phase II trial of preoperative radiotherapy (RT), CPT-11, and 5-FU for patients with ultrasound-staged T3 rectal cancer.Between April 1999 and August 2001, 32 patients (21 men, 11 women; median age 52 years, range 40-74) with biopsy-proven adenocarcinoma of the rectum were enrolled in the study. All patients underwent endorectal ultrasonography for staging (uT3N0 = 19; uT3N1 = 13; uT2N1 = 1). RT was prescribed to the draining lymph nodes (45 Gy in 1.8-Gy daily fractions) and tumor (50.4 Gy in 1.8-Gy daily fractions). Patients also received concurrent CPT-11 (50 mg/m(2), Days 1, 8, 15, and 22) and 5-FU (200 mg/m(2) daily, 7 d/wk, Days 1-33). Surgical resection was performed 6-10 weeks after completing chemoradiotherapy.Acute toxicity was frequently observed, and 18 patients (56%) required either a chemotherapy dose reduction or RT interruption of >3 days. One patient withdrew because of diarrhea and abdominal cramping (Grade III) after 10 days of treatment. Although no Grade IV toxicity was observed, Grade III diarrhea (n = 9, 28%), mucositis (n = 7, 21%), rectal sores (n = 7, 21%), abdominal cramping (n = 3, 9%) were noted. Of the 32 patients who underwent surgery, 12 had a complete pathologic response. Of the 32 patients, the disease of 23 (71%) was downstaged. The average length of hospitalization was between 5 and 12 days, with 1 patient staying 33 days. All patients were followed for disease-free survival.Although associated with frequent acute toxicity, the regimen is associated with significant tumor "downstaging." Additional patients and longer follow-up are necessary to define the role of this regimen fully.

  View details for PubMedID 12504045

• DNA Damage, Repair, and Diseases. Journal of biomedicine & biotechnology Wiesmüller, L., Ford, J. M., Schiestl, R. H. 2002; 2 (2): 45

  View details for DOI 10.1155/S1110724302001985

  View details for PubMedID 12488582

  View details for PubMedCentralID PMC153783

• The p53-regulated cyclin-dependent kinase inhibitor, p21 (cip1, waf1, sdi1), is not required for global genomic and transcription-coupled nucleotide excision repair of UV-induced DNA photoproducts JOURNAL OF BIOLOGICAL CHEMISTRY Adimoolam, S., Lin, C. X., Ford, J. M. 2001; 276 (28): 25813-25822

  Abstract

  The p53 tumor suppressor gene is a transcriptional activator involved in cell cycle regulation, apoptosis, and DNA repair. We have shown that p53 is required for efficient nucleotide excision repair of UV-induced DNA photoproducts from global genomic DNA but has no effect on transcription-coupled repair. In order to evaluate whether p53 influences repair indirectly through cell cycle arrest following DNA damage or plays a direct role, we examined repair in vivo in human cells genetically altered to disrupt or regulate the function of p53 and p21. Both primary human fibroblasts and HCT116 colon carcinoma cells wild type for p53 but in which the p21 gene was inactivated through targeted homologous recombination showed no decrease in global repair of UV photoproducts. Human bladder carcinoma cells mutant for p53 and containing a tetracycline-regulated p21 cDNA showed no significant enhancement of repair upon induction of p21 expression. All of the cell lines, including the mismatch repair-deficient, MLH1 mutant HCT116 cells, were proficient for transcription-coupled repair. Clonogenic survival of HCT116 cells following UV irradiation showed no dependence on p21. Therefore, our results indicate that p53-dependent nucleotide excision repair does not require the function of the p21 gene product and is independent of p53-regulated cell cycle checkpoints.

  View details for Web of Science ID 000169823300025

  View details for PubMedID 11331289

• Protracted venous infusion 5-fluorouracil with concomitant radiotherapy compared with bolus 5-fluorouracil for unresectable pancreatic cancer AMERICAN JOURNAL OF CLINICAL ONCOLOGY-CANCER CLINICAL TRIALS Mehta, V. K., Poen, J. C., Ford, J. M., Oberhelman, H. A., Vierra, M. A., Bastidas, A. J., Fisher, G. A. 2001; 24 (2): 155-159

  Abstract

  Radiation therapy (RT) with concurrent 5-fluorouracil (5-FU) administered by protracted venous infusion (PVI) replaced our prior institutional protocol of RT with bolus administration of 5-FU as standard therapy for unresectable pancreatic cancer in 1994. In this article, we compare the treatment intensity, toxicity, and outcome for patients with unresectable pancreatic cancer treated on these sequential protocols. Fifty-four patients, 27 on each protocol, with biopsy-confirmed pancreatic cancer received chemoradiotherapy. The radiotherapy field included the gross tumor volume and regional lymph nodes to a dose of 45 Gy, followed by "boost" to the gross tumor volume to 54 Gy to 60 Gy. From 1987 to 1994, patients received concurrent 5-FU administered by bolus injection, at a dose of 500 mg/m2 on days 1 to 3 and days 29 to 31 of RT. After December 1994, 5-FU was administered by PVI (200-250 mg/m2) beginning on day 1 and continuing until the completion of RT. The chemotherapy treatment intensity was increased in the group receiving 5-FU by PVI, as evidenced by an increased average weekly and cumulative dose of 5-FU (p < 0.01). The radiotherapy treatment intensity was equivalent between the two groups. The incidence of objectively quantified toxicity was not statistically different between treatment groups. Overall survival remained poor in both treatment groups. With a median follow-up of 18 months (range: 3-30 months) for surviving patients, the 6-month, 1-year, and 2-year survivals for the PVI 5-FU-treated group versus the bolus 5-FU-treated group were 56% versus 52%, 34% versus 18%, and 22% versus 13%, respectively (p = 0.9). Radiotherapy with concomitant 5-FU by PVI results in a greater weekly and total dose of chemotherapy. The method of 5-FU administration (bolus versus PVI) did not change the RT treatment intensity, experienced toxicity, or overall survival.

  View details for Web of Science ID 000168186300012

  View details for PubMedID 11319291

• Adjuvant chemoradiotherapy for "unfavorable" carcinoma of the ampulla of vater - Preliminary report ARCHIVES OF SURGERY Mehta, V. K., Fisher, G. A., Ford, J. M., Poen, J. C., Vierra, M. A., Oberhelman, H. A., Bastidas, A. J. 2001; 136 (1): 65-69

  Abstract

  Adjuvant chemoradiotherapy decreases the risk of local recurrence in patients with adenocarcinoma of the ampulla of Vater and high-risk features. Adjuvant chemoradiotherapy for this population can be administered safely and without much morbidity.Controlled, prospective, single-arm study.Tertiary care referral hospital.From June 1995 to March 1999, 12 patients (7 men and 5 women; median age, 66 years; age range, 38-78 years) with "unfavorable" ampullary carcinoma were treated with adjuvant chemoradiotherapy. All patients underwent pancreaticoduodenectomy, and all pathologic findings were confirmed at Stanford University Medical Center, Stanford, Calif. Unfavorable features were defined as involved lymph nodes (n = 10), involved surgical margins (n = 1), poorly differentiated histological features (n = 3), tumor size greater than 2 cm (n = 6), or the presence of neurovascular invasion (n = 4).Four to 6 weeks after undergoing pylorus-preserving pancreaticoduodenectomy with regional lymphadenectomy, patients began adjuvant chemoradiotherapy consisting of concurrent radiotherapy (45 Gy) and fluorouracil by protracted venous infusion (225-250 mg/m(2) per day, 7 days per week) for 5 weeks.Local recurrence, distant recurrence, overall survival rate, and treatment-related toxic effects.All patients completed the prescribed treatment course. Toxic effects were assessed twice a week during treatment and graded according to the National Cancer Institute Common Toxicity Criteria Scale. One patient required a treatment interruption of 1 week for grade III nausea/vomiting. No grade IV or V toxic effects were observed. At median follow-up of 24 months (range, 13-50 months), 8 of 12 patients were alive and disease free. One patient was alive but had disease recurrence. Three patients died of this disease (liver metastases). Actuarial overall survival at 2 years was 89%, and median survival was 34 months. One surviving patient developed a local recurrence and a lung lesion. Actuarial overall survival and median survival were better than in a parallel cohort with resected high-risk pancreatic cancer (n = 26) treated with the same adjuvant chemoradiotherapy regimen (median survival, 34 vs 14 months; P<.004).Adjuvant chemoradiotherapy for carcinoma of the ampulla of Vater is well tolerated and might improve control of this disease in patients with unfavorable features.

  View details for Web of Science ID 000166307500014

  View details for PubMedID 11146780

• Radiotherapy, concomitant protracted-venous-infusion 5-fluorouracil, and surgery for ultrasound-staged T3 or T4 rectal cancer 36th Annual Meeting of the American-Society-of-Clinical-Oncology Mehta, V. K., Poen, J., Ford, J., Edelstein, P. S., Vierra, M., Bastidas, A. J., Young, H., Fisher, G. SPRINGER. 2001: 52–58

  Abstract

  A prospective study was undertaken to evaluate the response and toxicity of neoadjuvant chemoradiotherapy for ultrasound-staged T3 or T4 rectal cancer.Since 1995, 30 patients (18 males; median age, 56 (range, 25-83) years) have received preoperative chemoradiotherapy for ultrasound-staged T3 or T4 rectal cancer. All patients underwent an endorectal ultrasound, CT scan, and review in our multidisciplinary Gastrointestinal Tumor Board before treatment. All patients had pathology-demonstrated invasive adenocarcinoma of the rectum. Eleven patients were Stage T3N0, 14 were T3N1, and five were T4N1. Patients received radiotherapy to the primary tumor and draining lymph nodes (45 Gy) followed by a tumor boost (50.4-54 Gy). Protracted-venous-infusion 5-fluorouracil (225 mg/m2 per day, seven days per week) was administered throughout treatment. Surgical resection was performed six to ten weeks after completing chemoradiotherapy. Using endorectal ultrasound measurements, the primary tumor was a median of 4 (range, 0-12) cm from the anal verge, encompassed 50 (range, 20-90) percent of the rectal circumference, and was 6 (range, 3-12) cm in diameter.No Grade 4 toxicity was observed during chemoradiotherapy. Three patients experienced Grade 3 toxicity (diarrhea), and four patients required a treatment interruption of greater than three days. All patients completed at least 90 percent of the prescribed radiotherapy dose. All patients underwent surgical resection. Ninety-four percent had clear surgical margins. All pathologic specimens had significant evidence of necrosis, hyalinization, and fibrosis. Thirty-three percent of the specimens had a complete pathologic response (defined as no evidence of viable tumor cells). Of the 19 patients with ultrasound-staged N1 disease, only five had pathologic evidence of nodal involvement after chemoradiotherapy. Of the 25 patients with ultrasound-staged T3 disease, pathologic staging revealed eight with T0, two with T1, five with T2, and ten with T3 disease. Of the five patients with ultrasound-staged T4 disease, pathologic staging revealed two with T0, one with T2, and two with T3 disease. No patient developed progressive disease while on treatment. Two patients have experienced local failure at 6 and 20 months, and one patient failed in the liver at seven months. Twenty-seven patients remain free of disease with a median follow-up of 20 (range, 3-53) months.Our experience suggests that preoperative chemoradiotherapy is well tolerated, down-stages tumors, and sterilizes regional lymph nodes.

  View details for Web of Science ID 000166587400015

  View details for PubMedID 11805563

• Preoperative chemoradiation for marginally resectable adenocarcinoma of the pancreas 82nd Annual Meeting of the American-Radium-Society Mehta, V. K., Fisher, G., Ford, J. A., Poen, J. C., Vierra, M. A., Oberbelman, H., Niederhuber, J., Bastidas, J. A. SPRINGER. 2001: 27–35

  Abstract

  Only 10% to 20% of patients with pancreatic cancer are considered candidates for curative resection at the time of diagnosis. We postulated that preoperative chemoradiation therapy might promote tumor regression, eradicate nodal metastases, and allow for definitive surgical resection in marginally resectable patients. The objective of this study was to evaluate the effect of a preoperative chemoradiation therapy regimen on tumor response, resectability, and local control among patients with marginally resectable adenocarcinoma of the pancreas and to report potential treatment-related toxicity. Patients with marginally resectable adenocarcinoma of the pancreas (defined as portal vein, superior mesenteric vein, or artery involvement) were eligible for this protocol. Patients received 50.4 to 56 Gy in 1.8 to 2.0 Gy/day fractions with concurrent protracted venous infusion of 5-fluorouracil (250 mg/m2/day). Reevaluation for surgical resection occurred 4 to 6 weeks after therapy. Fifteen patients (9 men and 6 women) completed preoperative chemoradiation without interruption. One patient required a reduction in the dosage of 5-fluorouracil because of stomatitis. Acute toxicity from chemoradiation consisted of grade 1 or 2 nausea, vomiting, diarrhea, stomatitis, palmar and plantar erythrodysesthesia, and hematologic suppression. CA 19-9 levels declined in all nine of the patients with elevated pretreatment levels. Nine of the 15 patients underwent a pancreaticoduodenectomy, and all had uninvolved surgical margins. Two of these patients had a complete pathologic response, and two had microscopic involvement of a single lymph node. With a median follow-up of 30 months, the median survival for resected patients was 30 months, whereas in the unresected group median survival was 8 months. Six of the nine patients who underwent resection remain alive and disease free with follow-up of 12, 30, 30, 34, 39, and 72 months, respectively. Preoperative chemoradiation therapy is well tolerated. It may downstage tumors, sterilize regional lymph nodes, and improve resectability in patients with marginally resectable pancreatic cancer. Greater patient accrual and longer follow-up are needed to more accurately assess its future role in therapy.

  View details for Web of Science ID 000167919800010

  View details for PubMedID 11309645

• Adjuvant radiotherapy and concomitant 5-fluorouracil by protracted venous infusion for resected pancreatic cancer INTERNATIONAL JOURNAL OF RADIATION ONCOLOGY BIOLOGY PHYSICS Mehta, V. K., Fisher, G. A., Ford, J. M., Oberhelman, H. A., Vierra, M. A., Bastidas, A. J., Poen, J. C. 2000; 48 (5): 1483-1487

  Abstract

  To assess the toxicity and clinical benefit from adjuvant chemoradiotherapy consisting of protracted venous infusion 5-fluorouracil (5-FU) and concomitant radiotherapy in patients with resected pancreatic cancer.Between 1994 and 1999, 52 patients who underwent pancreaticoduodenectomy received adjuvant chemoradiotherapy. The tumor bed and regional nodes received a dose of 45 Gy in fractions of 1.8 Gy followed by boost to the tumor bed if the surgical margins were involved (total dose, 54 Gy). The patients also received concomitant 5-FU by protracted venous infusion (200-250 mg/m(2)/day, 7 days/week) during the entire radiotherapy course.Fifty-two patients (30 men, 22 women) were enrolled and treated on this protocol. The median age was 63 years (range, 38-78 years), and the median Karnofsky Performance Status was 80 (range, 70-100). Thirty-five percent had involved surgical margins and 59% had involved lymph nodes. All patients completed therapy, and there were no Grade IV/V toxicities observed. With median follow-up of 24 months (range, 3-52 months) for surviving patients, the median survival is 32 months, and 2-year and 3-year survivals are 62%, and 39%, respectively.Radiotherapy with concomitant 5-FU by protracted venous infusion as adjuvant treatment for resected pancreatic cancer is well tolerated. This approach allows for greater dose intensity with reduced toxicity. The median survival of this cohort of patients compares favorably with our earlier experience and other published series.

  View details for Web of Science ID 000165604600030

  View details for PubMedID 11121652

• Proapoptotic p53-interacting protein 53BP2 is induced by UV irradiation but suppressed by p53 MOLECULAR AND CELLULAR BIOLOGY Lopez, C. D., Ao, Y., Rohde, L. H., Perez, T. D., O'Connor, D. J., Lu, X., Ford, J. M., Naumovski, L. 2000; 20 (21): 8018-8025

  Abstract

  p53 is an important mediator of the cellular stress response with roles in cell cycle control, DNA repair, and apoptosis. 53BP2, a p53-interacting protein, enhances p53 transactivation, impedes cell cycle progression, and promotes apoptosis through unknown mechanisms. We now demonstrate that endogenous 53BP2 levels increase following UV irradiation induced DNA damage in a p53-independent manner. In contrast, we found that the presence of a wild-type (but not mutant) p53 gene suppressed 53BP2 steady-state levels in cell lines with defined p53 genotypes. Likewise, expression of a tetracycline-regulated wild-type p53 cDNA in p53-null fibroblasts caused a reduction in 53BP2 protein levels. However, 53BP2 levels were not reduced if the tetracycline-regulated p53 cDNA was expressed after UV damage in these cells. This suggests that UV damage activates cellular factors that can relieve the p53-mediated suppression of 53BP2 protein. To address the physiologic significance of 53BP2 induction, we utilized stable cell lines with a ponasterone A-regulated 53BP2 cDNA. Conditional expression of 53BP2 cDNA lowered the apoptotic threshold and decreased clonogenic survival following UV irradiation. Conversely, attenuation of endogenous 53BP2 induction with an antisense oligonucleotide resulted in enhanced clonogenic survival following UV irradiation. These results demonstrate that 53BP2 is a DNA damage-inducible protein that promotes DNA damage-induced apoptosis. Furthermore, 53BP2 expression is highly regulated and involves both p53-dependent and p53-independent mechanisms. Our data provide new insight into 53BP2 function and open new avenues for investigation into the cellular response to genotoxic stress.

  View details for Web of Science ID 000089794200018

  View details for PubMedID 11027272

  View details for PubMedCentralID PMC86412

• Reduced global genomic repair of ultraviolet light-induced cyclobutane pyrimidine dimers in simian virus 40-transformed human cells MOLECULAR CARCINOGENESIS Bowman, K. K., Sicard, D. M., Ford, J. M., Hanawalt, P. C. 2000; 29 (1): 17-24

  Abstract

  The p53 tumor-suppressor gene has been implicated in the inducible activation of excision repair of ultraviolet (UV)-induced cyclobutane pyrimidine dimers (CPDs) in human cells. Because the large T antigen (LTAg) of the simian virus 40 (SV40) binds p53 protein and can interfere with its function, it was of interest to study DNA repair in normal human fibroblasts that had been transformed by SV40 compared with that in their nontransformed parental counterparts and to determine whether such transformation attenuated global genomic repair (GGR) of CPDs. Three methods were used to measure GGR in UV-irradiated cells: (i) an immunoassay using monoclonal antibodies specific for CPDs or 6-4 photoproducts (6-4PPs), (ii) zone sedimentation in alkaline sucrose gradients to measure the average DNA strand size after specific nicking at CPD sites in duplex DNA with T4 endonuclease V (TEV), and (iii) Southern hybridization of TEV-treated DNA with strand-specific mRNA probes to assess removal of CPDs from either strand of a defined genetic sequence in an expressed gene. Whereas repair of 6-4PPs was very similar in paired SV40-transformed and primary fibroblasts, GGR of CPDs was significantly reduced in the SV40-transformed cells. In contrast, SV40 transformation did not appreciably affect the efficiency of transcription-coupled repair. These data support the hypothesis that SV40 transformation can result in reduced levels of GGR, most likely because of the inhibition of normal p53 function by LTAg.

  View details for Web of Science ID 000089690900003

  View details for PubMedID 11020243

• Decreased UV sensitivity, mismatch repair activity and abnormal cell cycle checkpoints in skin cancer cell lines derived from UVB-irradiated XPA-deficient mice MUTATION RESEARCH-DNA REPAIR Ichikawa, M., Nakane, H., Marra, G., Corti, C., Jiricny, J., Fitch, M., Ford, J. M., Ikejima, M., Shimada, T., Yoshino, M., Takeuchi, S., Nakatsu, Y., Tanaka, K. 2000; 459 (4): 285-298

  Abstract

  Xeroderma pigmentosum group A gene (XPA)-deficient mice are defective in nucleotide excision repair (NER) and are therefore highly sensitive to ultraviolet (UV)-induced skin carcinogenesis. We established cell lines from skin cancers of UVB-irradiated XPA-deficient mice to investigate the phenotypic changes occurring during skin carcinogenesis. As anticipated, the skin cancer cell lines were devoid of NER activity but were less sensitive to killing by UV-irradiation than the XPA(-/-) fibroblast cell line. The lines were also more resistant to 6-thioguanine (6-TG) than XPA(-/-) and XPA(+/+) fibroblasts, which was suggestive of a mismatch repair (MMR) defect. Indeed, in vitro mismatch binding and MMR activity were impaired in several of these cell lines. Moreover, these cell lines displayed cell cycle checkpoint derangements following UV-irradiation and 6-TG exposure. The above findings suggest that MMR downregulation may help cells escape killing by UVB, as was seen previously for methylating agents and cisplatin, and thus that MMR deficient clones are selected for during the tumorigenic transformation of XPA(-/-) cells.

  View details for Web of Science ID 000087610300003

  View details for PubMedID 10844242

• p53-mediated DNA repair responses to UV radiation: Studies of mouse cells lacking p53, p21, and/or gadd45 genes MOLECULAR AND CELLULAR BIOLOGY Smith, M. L., Ford, J. M., Hollander, M. C., Bortnick, R. A., Amundson, S. A., Seo, Y. R., Deng, C. X., Hanawalt, P. C., Fornace, A. J. 2000; 20 (10): 3705-3714

  Abstract

  Human cells lacking functional p53 exhibit a partial deficiency in nucleotide excision repair (NER), the pathway for repair of UV-induced DNA damage. The global genomic repair (GGR) subpathway of NER, but not transcription-coupled repair (TCR), is mainly affected by p53 loss or inactivation. We have utilized mouse embryo fibroblasts (MEFs) lacking p53 genes or downstream effector genes of the p53 pathway, gadd45 (Gadd45a) or p21 (Cdkn1a), as well as MEFs lacking both gadd45 and p21 genes to address the potential contribution of these downstream effectors to p53-associated DNA repair. Loss of p53 or gadd45 had a pronounced effect on GGR, while p21 loss had only a marginal effect, determined by measurements of repair synthesis (unscheduled DNA synthesis), by immunoassays to detect removal of UV photoproducts from genomic DNA, and by assays determining strand-specific removal of CPDs from the mouse dhfr gene. Taken together, the evidence suggests a role for Gadd45, but relatively little role for p21, in DNA repair responses to UV radiation. Recent evidence suggests that Gadd45 binds to UV-damaged chromatin and may affect lesion accessibility. MEFs lacking p53 or gadd45 genes exhibited decreased colony-forming ability after UV radiation and cisplatin compared to wild-type MEFs, indicating their sensitivity to DNA damage. We provide evidence that Gadd45 affects chromatin remodelling of templates concurrent with DNA repair, thus indicating that Gadd45 may participate in the coupling between chromatin assembly and DNA repair.

  View details for Web of Science ID 000086698100038

  View details for PubMedID 10779360

  View details for PubMedCentralID PMC85670

• Chemoradiotherapy in the management of localized tumors of the pancreas ANNALS OF SURGICAL ONCOLOGY Poen, J. C., Ford, J. M., Niederhuber, J. E. 1999; 6 (1): 117-122

  Abstract

  In western countries, carcinoma of the pancreas remains the most lethal of the common malignancies. Even the favorable "organ-confined" tumors present a considerable challenge. The lack of anatomic barriers to local infiltration and the biological propensity for early lymphatic, perineural, and vascular invasion are nearly insurmountable obstacles to complete surgical eradication of this malignancy. Various combinations of chemotherapy and radiotherapy (RT) have been used with marginal but measurable success. Earlier trials conducted by the Gastrointestinal Tumor Study Group established roles for 5-fluorouracil chemotherapy and RT in the treatment of patients with resectable or locally advanced pancreatic cancer. More recently, computed tomography-guided conformal RT and a variety of intraoperative RT techniques have enabled more reliable sterilization of the local surgical field and escalation of doses to potentially curative levels (7000 cGy) for unresectable lesions. Chemotherapy dose intensification through the use of portable programmable pumps for protracted venous infusions and the development of active systemic agents in addition to 5-fluorouracil suggest that an effective combination chemotherapeutic regimen might soon be developed. This report reviews the current standards of practice and integrates recent developments to construct a modern algorithm for the use of chemoradiotherapy in the management of localized (nonmetastatic) pancreatic cancer. The likely directions of future investigations are also discussed.

  View details for Web of Science ID 000078475800023

  View details for PubMedID 10030424

• Hepatitis B x protein inhibits p53-dependent DNA repair in primary mouse hepatocytes JOURNAL OF BIOLOGICAL CHEMISTRY Prost, S., Ford, J. M., Taylor, G., Doig, J., Harrison, D. J. 1998; 273 (50): 33327-33332

  Abstract

  The mechanisms by which the hepatitis B x protein (HBx) contributes to hepatocarcinogenesis remain unclear. However, interaction with the tumor suppressor gene p53 and inhibition of p53-dependent cellular functions, including nucleotide excision repair, could be central to this process. We studied the levels of global repair (removal of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts) and transcription-coupled repair (removal of CPDs in both strands of the dihydrofolate reductase gene) in primary wild-type and p53-null mouse hepatocytes. We show that global repair of CPDs appears to be more efficient in mouse hepatocytes than in other commonly studied rodent cells and approaches the levels of human cells and that p53 is required for global genomic DNA repair of CPDs but not for transcription-coupled repair. We then investigated the effect of HBx expression on hepatocyte nucleotide excision repair. We demonstrate that HBx expression affects DNA repair in a p53-dependent manner. Transient HBx expression reduces global DNA repair in wild-type cells to the level of p53-null hepatocytes and has no effect on the repair of a transfected damaged plasmid. Therefore, in viral hepatitis, the hepatitis B virus could inhibit the p53-dependent component of global repair leading, over time, to accumulation of genetic defects and fostering carcinogenesis.

  View details for Web of Science ID 000077462500036

  View details for PubMedID 9837906

• Human fibroblasts expressing the human papillomavirus E6 gene are deficient in global genomic nucleotide excision repair and sensitive to ultraviolet irradiation CANCER RESEARCH Ford, J. M., Baron, E. L., Hanawalt, P. C. 1998; 58 (4): 599-603

  Abstract

  We investigated the role of wild-type p53 activity in modulating nucleotide excision repair after UV irradiation in normal and p53-deficient primary human fibroblasts created by expression of the human papillomavirus 16 E6 gene. Compared with parental cells, the E6-expressing fibroblasts were deficient in global genomic repair of both UV-induced cyclobutane pyrimidine dimers and 6-4 photoproducts but exhibited normal transcription-coupled repair. The E6-expressing cells were also more sensitive than their parental counterparts to UV irradiation and displayed similar levels of UV-induced apoptosis. These results suggest that disruption of wild-type p53 function by E6 expression results in selective loss of p53-dependent global genomic nucleotide excision repair, but not UV-induced apoptosis, leading to enhanced UV sensitivity.

  View details for PubMedID 9485006

• Role of DNA excision repair gene defects in the etiology of cancer GENETIC INSTABILITY AND TUMORIGENESIS Ford, J. M., Hanawalt, P. C. 1997; 221: 47-70

  View details for Web of Science ID A1997BJ47J00005

  View details for PubMedID 8979440

• Experimental reversal of P-glycoprotein-mediated multidrug resistance by pharmacological chemosensitisers EUROPEAN JOURNAL OF CANCER Ford, J. M. 1996; 32A (6): 991-1001

  View details for Web of Science ID A1996UT29600010

  View details for PubMedID 8763340

• P-glycoprotein-mediated multidrug resistance: experimental and clinical strategies for its reversal. Cancer treatment and research Ford, J. M., Yang, J. M., Hait, W. N. 1996; 87: 3-38

  Abstract

  The study of the cellular, biochemical, and molecular biology and pharmacology of MDR has provided one of the most active and exciting areas within cancer research and one that holds great promise for translation into clinical benefit. While convincing evidence for the functional role of P-gp in mediating clinical drug resistance in humans remains elusive, studies of the clinical expression of P-gp and trials of chemosensitizers with cancer chemotherapy suggest "resistance modification" strategies may be effective in some tumors with intrinsic or acquired drug resistance. However, even if P-gp-associated MDR proves to be a relevant and reversible cause of clinical drug resistance, numerous problems remain to be solved before effective clinical chemosensitization may be achieved. Such factors as absorption, distribution, and metabolism; the effect of chemosensitizers on chemotherapeutic drug clearance; toxicity to normal tissues expressing P-gp; and the most efficacious modulator regimens all remain to be defined in vivo. Clearly, the identification of more specific, potent, and less clinically toxic chemosensitizers for clinical use remains critical to the possible success of this approach. Nonetheless, the finding that a number of pharmacological agents can antagonize a well-characterized form of experimental drug resistance provides promise for potential clinical applications. Further study of chemosensitizers in humans and the rational design of novel chemosensitizers with improved activity should define the importance of MDR in clinically resistant cancer.

  View details for PubMedID 8886447

• MODULATORS OF MULTIDRUG-RESISTANCE - PRECLINICAL STUDIES HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA Ford, J. M. 1995; 9 (2): 337-361

  Abstract

  The study of the cellular, biochemical, and molecular biology and pharmacology of MDR has provided one of the most active and exciting areas within cancer research for translation into potential clinical benefit. Although convincing evidence for the functional role of P-gp in mediating clinical drug resistance in humans remains scant, studies of the clinical expression of P-gp and trials of chemosensitizers with cancer chemotherapy suggest "resistance modification" strategies may be effective in some tumors with intrinsic or acquired drug resistance. However, even if P-gp-associated MDR proves to be a relevant and reversible cause of clinical drug resistance, numerous problems remain to be solved before effective clinical chemosensitization may be achieved. Such factors as absorption, distribution, and metabolism, the effect of chemosensitizers on chemotherapeutic drug clearance, toxicity to normal tissues expressing P-gp, and the most efficacious modulator regimens all remain to be defined in vivo. Clearly, the identification of more specific, more potent, and less clinically toxic chemosensitizers for clinical use remains critical to the possible success of this approach. However, the finding that a number of pharmacologic agents can antagonize a well-characterized form of experimental drug resistance provides promise for potential clinical applications. Further study of chemosensitizers in humans and the rational design of novel chemosensitizers with improved activity should define the importance of MDR to clinically resistant cancer.

  View details for Web of Science ID A1995QT66400006

  View details for PubMedID 7642467

• PREFERENTIAL REPAIR OF ULTRAVIOLET LIGHT-INDUCED DNA-DAMAGE IN THE TRANSCRIBED STRAND OF THE HUMAN P53 GENE MOLECULAR CARCINOGENESIS Ford, J. M., Lommel, L., Hanawalt, P. C. 1994; 10 (2): 105-109

  Abstract

  Mutations in the p53 tumor suppressor gene have been found in most human tumors. Analyses of the spectrum of p53 mutations in certain tumor types have shown a bias for mutations originating from lesions presumed to be in the untranscribed strand of the gene. This implies strand specificity for the formation or repair of DNA damage. We measured the induction and repair of ultraviolet light-induced cyclobutane pyrimidine dimers (CPD) in each strand of the human p53 gene in a normal human lung fibroblast cell line using quantitative Southern hybridization. We found that the removal of CPD from the transcribed strand was more rapid than that from the untranscribed strand of this gene, although the frequency of CPD induction was similar in both strands. Preferential repair of the transcribed strand of the p53 gene may account for the mutational spectra of this gene in human tumors.

  View details for Web of Science ID A1994NV25200007

  View details for PubMedID 8031463

• PHARMACOLOGICAL CIRCUMVENTION OF MULTIDRUG-RESISTANCE CYTOTECHNOLOGY Ford, J. M., Hait, W. N. 1993; 12 (1-3): 171-212

  Abstract

  The ability of malignant cells to develop resistance to chemotherapeutic drugs is a major obstacle to the successful treatment of clinical tumors. The phenomenon multidrug resistance (MDR) in cancer cells results in cross-resistance to a broad range of structurally diverse antineoplastic agents, due to outward efflux of cytotoxic substrates by the mdr1 gene product, P-glycoprotein (P-gp). Numerous pharmacologic agents have been identified which inhibit the efflux pump and modulate MDR. The biochemical, cellular and clinical pharmacology of agents used to circumvent MDR is analyzed in terms of their mechanism of action and potential clinical utility. MDR antagonists, termed chemosensitizers, may be grouped into several classes, and include calcium channel blockers, calmodulin antagonists, anthracycline and Vinca alkaloid analogs, cyclosporines, dipyridamole, and other hydrophobic, cationic compounds. Structural features important for chemosensitizer activity have been identified, and a model for the interaction of these drugs with P-gp is proposed. Other possible cellular targets for the reversal of MDR are also discussed, such as protein kinase C. Strategies for the clinical modulation of MDR and trials combining chemosensitizers with chemotherapeutic drugs in humans are reviewed. Several novel approaches for the modulation of MDR are examined.

  View details for Web of Science ID A1993MU79000010

  View details for PubMedID 7765325

• EFFECT OF BUTHIONINE SULFOXIMINE ON TOXICITY OF VERAPAMIL AND DOXORUBICIN TO MULTIDRUG RESISTANT CELLS AND TO MICE CANCER RESEARCH Ford, J. M., Yang, J. M., Hait, W. N. 1991; 51 (1): 67-72

  Abstract

  Resistance of tumor cells to chemotherapeutic drugs may be due to several mechanisms within a single cell line. Resistance to doxorubicin in the human multidrug resistant breast cancer cell line, MCF-7 AdrR, has been attributed to increased glutathione (GSH) S-transferase and GSH peroxidase activity, as well as to increased expression of the mdr1 gene product, P-glycoprotein. We studied the potentiation of doxorubicin activity in these cells by buthionine sulfoximine (BSO), a specific inhibitor of gamma-glutamylcysteine synthetase, and by verapamil and trans-flupenthixol, agents which interact with P-glycoprotein. Treatment with BSO enhanced the effect of doxorubicin by 1.5-fold, while verapamil or transflupenthixol caused a greater reversal of drug resistance. The combination of BSO with trans-flupenthixol produced no further potentiation of doxorubicin activity. However, the combination of BSO with verapamil and doxorubicin caused up to a 10-fold increment in antiproliferative effect. To explore the mechanism by which BSO interacted with this drug combination, we determined whether or not BSO might potentiate the effects of verapamil. These studies demonstrated that the effects of BSO were predominantly due to an increase in verapamil toxicity rather than to doxorubicin toxicity. In addition, when mice received concentrations of BSO in their drinking water sufficient to deplete GSH and were treated with verapamil, the calcium channel blocker was lethal to 9 of 12 mice receiving BSO compared to 1 of 10 control animals receiving verapamil alone. These studies demonstrate that BSO does not markedly increase the pharmacological effect of doxorubicin against MCF-7 AdrR cells and suggest that alterations in GSH and related enzymes are not a major factor in drug resistance in this cell line. Furthermore, BSO can increase the toxicity of verapamil, a finding which may have important implications for clinical trials.

  View details for Web of Science ID A1991EQ68300012

  View details for PubMedID 1988108

• MODULATION OF RESISTANCE TO ALKYLATING-AGENTS IN CANCER CELL BY GOSSYPOL ENANTIOMERS CANCER LETTERS Ford, J. M., Hait, W. N., Matlin, S. A., Benz, C. C. 1991; 56 (1): 85-94

  Abstract

  Several cell lines resistant to alkylating agents possess increased activity of glutathione-S-transferase (GST) drug detoxifying enzymes. Inhibition of certain enzymes of the glutathione redox system may affect cellular sensitivity to alkylators. We report that the (-.)enantiomer of gossypol is a potent and selective inhibitor of GST alpha and GST pi isozymes, and that in combination with buthionine sulfoximine (BSO), causes the enhanced modulation of alkylator resistance in two drug resistant cell lines with increased GST activity. The use of (-)gossypol alone had no effect on the 2-5-fold resistance of MCF-7 Adr and Walker resistant cells to chlorambucil, melphalan and BCNU. Cellular depletion of glutathione with BSO resulted in a 2-4-fold modulation of cell sensitivity to these alkylators. However, the combination of (-)gossypol with BSO resulted in a markedly greater modulation of alkylator sensitivity than with either inhibitor alone. Therefore, the complementary inhibition of glutathione and GST by BSO and (-)gossypol, respectively, produced a synergistic modulation of alkylator cytotoxicity in these drug resistant cell lines. The favorable clinical pharmacokinetics of (-)gossypol suggest its further evaluation for use in combination with BSO and alkylating agents in clinical trials.

  View details for Web of Science ID A1991EZ78300013

  View details for PubMedID 2004358

• PHARMACOLOGY OF DRUGS THAT ALTER MULTIDRUG RESISTANCE IN CANCER PHARMACOLOGICAL REVIEWS Ford, J. M., Hait, W. N. 1990; 42 (3): 155-199

  View details for Web of Science ID A1990EA43800001

  View details for PubMedID 2217530

• BIOCHEMICAL CORRELATES OF THE ANTITUMOR AND ANTIMITOCHONDRIAL PROPERTIES OF GOSSYPOL ENANTIOMERS MOLECULAR PHARMACOLOGY Benz, C. C., Keniry, M. A., Ford, J. M., Townsend, A. J., COX, F. W., PALAYOOR, S., Matlin, S. A., Hait, W. N., COWAN, K. H. 1990; 37 (6): 840-847

  Abstract

  Racemic gossypol has been shown to have antitumor properties that may be due to its ability to uncouple tumor mitochondria or to its inhibitory effects on a variety of nonmitochondrial enzymes. We have studied the antimitochondrial and enzyme-inhibiting properties of gossypol in human carcinoma cell lines of breast (MCF-7, T47-D), ovarian (OVCAR-3) colon (HCT-8), and pancreatic (MiaPaCa) origin by comparing the effects of its purified (+)- and (-)-enantiomers. (-)-Gossypol shows up to 10-fold greater antiproliferative activity than (+)-gossypol in the cancer cell lines and in normal hematopoietic stem cells grown in vitro, with IC50 values ranging from 1.5 to 4.0 microM for the cancer cells and from 10 to 20 microM for the human marrow stem cells. As well, multidrug-resistant MCF/Adr cells appear more resistant to (-)-gossypol than their parental cell line. Electron microscopy indicates that the earliest ultrastructural change in tumor cells exposed to a cytotoxic (10 microM) concentration of (-)-gossypol is the selective destruction of their mitochondria. Consistent with this observation, 31P magnetic resonance spectroscopy detects pronounced changes in tumor cell high energy phosphate metabolism within 24 hr of (-)-gossypol treatment, manifest by 1.6- to greater than 50-fold differential reductions in the intracellular ratios of ATP/Pi, relative to (+)-gossypol-treated cell lines; the magnitude of these antimitochondrial effects correlates with the antiproliferative activity of (-)-gossypol. Northern blot RNA analyses suggest that treatment with a 5-10 microM dose of (-)-gossypol induces a transient increase in the expression of heat shock gene products, particularly hsp-70 transcripts. The mean 5-fold increase in (-)-gossypol-induced hsp-70 mRNA appears coincident with a comparable heat-stimulated increase in transcript levels, as compared with control or (+)-gossypol-treated cells. The enzyme-inhibiting properties of gossypol enantiomers were compared in cell-free assays measuring glutathione-S-transferase-alpha, -mu, and pi activities, calmodulin stimulation of cyclic nucleotide phosphodiesterase, and protein kinase C activity. Both enantiomers are near equivalent antagonists of calmodulin stimulation and protein kinase C activity, exceeding the potency of known inhibitors such as phenothiazines by as much as 50-fold. In contrast, (-)-gossypol is a 3-fold more potent inhibitor of glutathione-S-transferase-alpha and -pi isozyme activity, resulting in IC50 values of 1.6 and 7.0 microM, respectively, for these two isozymes.(ABSTRACT TRUNCATED AT 400 WORDS)

  View details for Web of Science ID A1990DK97800011

  View details for PubMedID 2193225

• CELLULAR AND BIOCHEMICAL-CHARACTERIZATION OF THIOXANTHENES FOR REVERSAL OF MULTIDRUG RESISTANCE IN HUMAN AND MURINE CELL-LINES CANCER RESEARCH Ford, J. M., Bruggemann, E. P., Pastan, I., Gottesman, M. M., Hait, W. N. 1990; 50 (6): 1748-1756

  Abstract

  We have previously shown that phenothiazines sensitize multidrug resistant (MDR) cells to chemotherapeutic drugs in a manner related to specific structural features, and have identified structurally related thioxanthenes with increased anti-MDR activity. We have now studied the structure-activity relationships of 16 thioxanthenes in the human breast cancer line MCF-7 AdrR. trans-Thioxanthene stereoisomers were 2- to 7-fold more potent than cis-thioxanthenes for antagonizing MDR. The most potent thioxanthenes possessed a halogenated tricyclic ring connected by a 3-carbon alkyl bridge to a piperazinyl or piperadinyl side group. The chemosensitizing effects of the lead compound, trans-flupenthixol, its stereoisomer cis-flupenthixol, its phenothiazine homologue fluphenazine, and the calcium channel blocker verapamil, were further studied in a series of sensitive and MDR cell lines. trans-Flupenthixol caused a greater reversal of cellular resistance to doxorubicin, vinblastine, vincristine, and colchicine in MCF-7 AdrR, KB-V1, and P388/DOX MDR cells than the other chemosensitizers. In particular, trans-flupenthixol was 2- to 3-fold more potent for reversing MDR than equimolar concentrations of verapamil. Furthermore, trans-flupenthixol fully reversed resistance to doxorubicin, vincristine, and colchicine in MDR MCF-7 and NIH 3T3 cells transfected with the mdr1 gene. None of these agents altered MDR in a non-P-glycoprotein expressing MCF-7 cell line selected with mitoxantrone, nor in any of the parental cell lines. The stereoselective antagonism of the flupenthixol isomers on several putative cellular targets was studied to explore the mechanism of their chemosensitizing activity. cis- and trans-flupenthixol were equally active inhibitors of protein kinase C and calmodulin. Both cis- and trans-flupenthixol were also potent inhibitors of [3H]azidopine binding to P-glycoprotein. The apparent lack of clinical toxicity of trans-flupenthixol makes it an attractive drug for possible use in the modulation of tumor resistance in vivo if appropriate tissue concentrations can be achieved.

  View details for Web of Science ID A1990CU24000014

  View details for PubMedID 1968358

• TOREMIFENE - PHARMACOLOGIC AND PHARMACOKINETIC BASIS OF REVERSING MULTIDRUG RESISTANCE JOURNAL OF CLINICAL ONCOLOGY DeGregorio, M. W., Ford, J. M., Benz, C. C., Wiebe, V. J. 1989; 7 (9): 1359-1364

  Abstract

  Triphenylethylene compounds, such as tamoxifen, have shown chemosensitizing activity independent of estrogen receptor status in doxorubicin-resistant cells. We examined the chemosensitizing activity of a new triphenylethylene, toremifene, and its major metabolites in a doxorubicin-resistant human breast cell line, MCF-7/DOX. In addition, we examined the chemosensitizing activity of unbound plasma toremifene and its metabolites isolated from patients treated with toremifene doses of 20 to 400 mg/d. MCF-7/DOX cells were exposed to ultrafiltrate plasma specimens in the absence and presence of doxorubicin. These latter studies were single-blinded. Toremifene and its major metabolites were capable of sensitizing multidrug-resistant cells to doxorubicin. The degree of chemosensitizing activity in vitro correlated with the plasma concentrations of toremifene and its metabolites (P less than .05). Plasma samples isolated from patients receiving high-dose toremifene (400 mg/d) had the greatest chemosensitizing activity. We present evidence that toremifene and its metabolites can sensitize resistant MCF-7/DOX cells to doxorubicin, that this effect is concentration-dependent, and that sensitizing activity can be detected at clinically achieved concentrations.

  View details for Web of Science ID A1989AM61500026

  View details for PubMedID 2527971

• STRUCTURAL FEATURES DETERMINING ACTIVITY OF PHENOTHIAZINES AND RELATED DRUGS FOR INHIBITION OF CELL-GROWTH AND REVERSAL OF MULTIDRUG RESISTANCE MOLECULAR PHARMACOLOGY Ford, J. M., Prozialeck, W. C., Hait, W. N. 1989; 35 (1): 105-115

  Abstract

  Phenothiazines and structurally related compounds inhibit cellular proliferation and sensitize multidrug-resistant (MDR) cells to chemotherapeutic agents. To identify more potent pharmaceuticals, we studied the structure-activity relationships of 30 phenothiazines and related compounds on cellular proliferation and MDR in sensitive MCF-7 and resistant MCF-7/DOX human breast cancer cells. Substitutions on the phenothiazine ring that increased hydrophobicity increased antiproliferative and anti-MDR activities. For example, -Cl and -CF3 groups increased whereas -OH groups decreased potency. Modifying the length of the alkyl bridge and the type of amino side chain also influenced potency. Compounds with increased activity against cellular proliferation and MDR possessed a four-carbon bridge rather than a three- or two-carbon bridge and a piperazinyl amine rather than a noncyclic amino group. Compounds with tertiary amines were better anti-MDR agents than those with secondary or primary amines but were equipotent antiproliferative agents. The effects of these substituents were unrelated to hydrophobicity. The structure-activity relationships suggest that an ideal phenothiazine structure for reversing MDR has a hydrophobic nucleus with a -CF3 ring substitution at position 2, connected by a four-carbon alkyl bridge to a para-methyl-substituted piperazinyl amine. We subsequently studied related compounds having certain of these properties. Substitution of a carbon for a nitrogen at position 10 of the tricyclic ring, with a double bond to the side chain (thioxanthene), further increased activity against MDR. For example, (trans)-flupenthixol, the most potent of these compounds, increased the potency of doxorubicin against MDR cells by 15-fold, as compared with its stereoisomer (cis)-flupenthixol (5-fold) or its phenothiazine homolog fluphenazine (3-fold). (cis)- and (trans)-flupenthixol were equipotent antiproliferative agents. (trans)-flupenthixol was not accumulated more than (cis)-flupenthixol in MDR cells, implying that their stereospecific anti-MDR effects were not the result of selective differences in the access of the drugs to intracellular targets. Both drugs increased the accumulation of doxorubicin in MDR cells, but not in sensitive cells, suggesting that they modulate MDR by interacting with a uniquely overexpressed cellular target in these resistant cells. The apparent lack of clinical toxicity of (trans)-flupenthixol makes it an attractive drug for further investigation.

  View details for Web of Science ID A1989T094200015

  View details for PubMedID 2563302