Bio


Dr. Dong is the Associate Director of Molecular Pathology at Stanford Health Care. His clinical interests include the implementation and interpretation of laboratory developed tests in diagnosis and patient care. Previous accomplishments include the development of novel bioinformatics algorithms to infer microsatellite instability and allogeneic contamination from cancer sequencing data. Before arriving at Stanford, Dr. Dong was on faculty at Brigham and Women’s Hospital/Harvard Medical School for nine years, where he established a track record in education and mentorship and was the recipient of both the Anatomic Pathology and Clinical Pathology resident teaching awards. Dr. Dong has served on national/international committees for the Association for Molecular Pathology, the Clinical and Laboratory Standards Institute, and the College of American Pathologists and serves on the editorial boards of multiple academic journals, including the Archives of Pathology and Laboratory Medicine, the Journal of Molecular Diagnostics, and Modern Pathology.

Clinical Focus


  • Molecular Pathology
  • Anatomic and Clinical Pathology

Academic Appointments


Professional Education


  • Board Certification: American Board of Pathology, Molecular Genetic Pathology (2014)
  • Board Certification: American Board of Pathology, Anatomic Pathology (2013)
  • Fellowship: Brigham and Women's Hospital Pathology Fellowships (2014) MA
  • Residency: Massachusetts General Hospital Dept of Pathology (2013) MA
  • Medical Education: Case Western Reserve School of Medicine (2010) OH

All Publications


  • Atypical Droplet Digital Polymerase Chain Reaction Patterns That Indicate Uncommon but Clinically Actionable EGFR Mutations in Lung Cancer. Archives of pathology & laboratory medicine Lechner, A., Rai, A., Rojas-Rudilla, V., Kuang, Y., Paweletz, C. P., Sholl, L. M., Dong, F. 2023

    Abstract

    Droplet digital polymerase chain reaction (ddPCR) is a sensitive method to detect common pathogenic EGFR mutations in non-small cell lung cancer. Although targeted assays have not been specifically designed to detect them, uncommon EGFR mutations have been linked to response to targeted therapy.To describe atypical ddPCR patterns that correspond to uncommon but clinically actionable EGFR mutations.A cohort of 1134 consecutive non-small cell lung cancers that underwent targeted next-generation sequencing was reviewed. Uncommon EGFR mutations involving probe binding sites were evaluated by ddPCR.Two hundred fifty-five of 1134 cancers (22.5%) harbored pathogenic EGFR mutations. One hundred eighty-six of 255 (72.9%) had canonical EGFR exon 19 deletion or exon 21 p.L858R variants designed for detection by ddPCR. An additional 25 of 255 cases (9.8%) had uncommon EGFR mutations within the probe-binding site, including one case with concurrent uncommon mutations in both exon 19 and exon 21. These mutations included uncommon EGFR exon 19 deletions (n = 6), EGFR exon 19 substitutions p.L747P (n = 3) and p.L747A (n = 1), dinucleotide substitutions leading to EGFR p.L858R (n = 5), EGFR exon 21 substitutions p.K860I (n = 1) and p.L861Q (n = 9), and EGFR p.[L858R;K860I] (n = 1). Droplet digital polymerase chain reaction generated atypical but reproducible signal for each of these uncommon variants.Droplet digital polymerase chain reaction analysis of uncommon pathogenic EGFR variants can yield unique and reproducible results. Recognition of atypical patterns in EGFR ddPCR testing can prompt confirmatory molecular testing and aid appropriate targeted therapy selection for patients with non-small cell lung cancer.

    View details for DOI 10.5858/arpa.2023-0088-OA

    View details for PubMedID 37639432

  • Mutational Signatures in Cancer: Laboratory Considerations and Emerging Applications. The Journal of molecular diagnostics : JMD Dong, F., Davies, K. D. 2023

    Abstract

    Patterns of somatic mutations have emerged from the broad sequencing of human cancer genomes. These mutational signatures reflect mechanisms of mutagenesis and DNA repair defects and represent an emerging class of cancer biomarkers. The appropriate interpretation of mutational signatures from sequencing assays holds implications in the reporting of molecular diagnostic results for patients with cancer. This brief review describes the scientific principles, laboratory considerations, and emerging clinical applications of mutational signature analysis from clinical cancer genomes.

    View details for DOI 10.1016/j.jmoldx.2023.08.002

    View details for PubMedID 37633594

  • SMARCA4 mutations in carcinomas of the esophagus, esophagogastric junction, and stomach Modern Pathology Neil, A. J., Zhao, L., Isidro, R. A., Srivastava, A., Cleary, J. M., Dong, F. 2023; 36 (6): 100183

    Abstract

    Deficiency of SMARCA4, a member of the SWI/SNF chromatin remodeling complex, has been described in a subset of undifferentiated gastroesophageal carcinomas with an aggressive clinical course. The full spectrum and frequency of SMARCA4 mutations in gastroesophageal cancer are unknown. We interrogated our institutional database and identified patients with gastroesophageal carcinomas who underwent cancer next-generation sequencing. We classified SMARCA4 mutations, assessed histologic features, and correlated SMARCA4 mutations with SMARCA4 protein expression by immunohistochemistry. SMARCA4 mutations were identified in gastroesophageal carcinomas from 107 (9.1%) of 1174 patients. Forty-nine SMARCA4 mutations, including 26 missense variants and 23 protein-truncating variants, were interpreted as pathogenic in 42 (3.6%) of 1174 patients. Thirty (71%) of 42 cancers with pathogenic SMARCA4 mutations were located in the esophagus or esophagogastric junction, and 12 cancers (29%) were located in the stomach. Sixty-four percent of carcinomas with pathogenic truncating SMARCA4 variants were poorly differentiated or undifferentiated compared with 25% of carcinomas with pathogenic missense variants. Eight of 12 carcinomas with truncating SMARCA4 variants and none of the 7 carcinomas with pathogenic SMARCA4 missense variants showed loss of SMARCA4 expression by immunohistochemistry. Four carcinomas with pathogenic truncating SMARCA4 variants were associated with Barrett esophagus. SMARCA4-mutated gastroesophageal cancers were enriched for APC (31%) and CTNNB1 (14%) mutations and exhibited similar frequency of TP53 (76%) and ARID1A (31%) mutations compared with gastroesophageal cancers without pathogenic SMARCA4 mutations. The median overall survival was 13.6 months for patients who presented with metastasis at diagnosis and 22.7 months for patients without metastasis. Overall, SMARCA4-mutated gastroesophageal cancers exhibit a spectrum of histologic grade, an association with Barrett esophagus, and a concurrent mutational pattern similar to SMARCA4-wild-type gastroesophageal adenocarcinomas. Although SMARCA4-deficient gastroesophageal carcinomas are associated with poorly differentiated and undifferentiated histology, the spectrum of histologic and molecular features suggests overlapping pathogenic pathways with conventional gastroesophageal adenocarcinomas.

    View details for DOI 10.1016/j.modpat.2023.100183

  • Loss of function SMAD4 nonstop mutations in human cancer Histopathology Bauer, A. H., Basta, D. W., Hornick, J. L., Dong, F. 2023; 82 (7): 1098-1104

    Abstract

    SMAD4 is a tumour suppressor gene that is mutated in a variety of cancers. SMAD4 nonstop mutations, which convert stop codons to sense codons that extend transcription, have been identified in genomic databases but have not been characterised in human pathology samples. The frequency of SMAD4 nonstop mutations and the consequences of nonstop mutations on SMAD4 protein expression are unknown.We retrospectively analysed our cancer sequencing database of 38,002 tumour specimens and evaluated the spectrum of SMAD4 mutations. SMAD4 protein expression was evaluated by immunohistochemistry in tumours with SMAD4 nonstop mutations.In total, 1956 SMAD4 mutations were identified in 1822 tumours. SMAD4 mutations were most common in tumours of the gastrointestinal tract and included nonsense variants (n = 344), frameshift indels (n = 258), splice site variants (n = 104), and missense variants at codon R361 (n = 245). In a subset of cases with immunohistochemistry, SMAD4 expression was lost in 23 of 25 tumours (92%) with protein truncating variants and in 7 of 27 tumours (26%) with missense variants. Four cases harboured SMAD4 nonstop mutations. SMAD4 nonstop mutations were identified in two pancreatic adenocarcinomas, one colonic adenocarcinoma, and one non-small cell lung carcinoma. Immunohistochemistry demonstrated loss of SMAD4 protein expression in each of the four tumours with SMAD4 nonstop mutations.SMAD4 nonstop mutations are associated with loss of SMAD4 protein expression in multiple tumour types. SMAD4 nonstop mutations should be clinically interpreted as pathogenic loss of function alterations when identified in cancer sequencing panels.

    View details for DOI 10.1111/his.14880

  • Integrating molecular sequencing into the pathological diagnosis of clinically suspected non-small cell lung carcinomas Modern Pathology Lo, Y., Bauer, A. H., Siegmund, S. E., Sholl, L. M., Dong, F. 2023; 36 (5): 100126
  • Deriving tumor purity from cancer next generation sequencing data: applications for quantitative ERBB2 (HER2) copy number analysis and germline inference of BRCA1 and BRCA2 mutations Modern Pathology Siegmund, S. E., Manning, D. K., Davineni, P. K., Dong, F. 2022; 35 (10): 1458-1467
  • The success rates of clinical cancer next-generation sequencing based on pathologic diagnosis: Experience from a single academic laboratory. American journal of clinical pathology Latham, K., Dong, F. 2023

    Abstract

    OBJECTIVES: This article aims to establish the relationship between pathologic diagnosis and the rate of success in cancer next-generation sequencing testing.METHODS: Clinical next-generation sequencing results performed for solid tumors were reviewed. The rate of success was analyzed in the context of tumor type and accompanying variables.RESULTS: Out of 683 total specimens, 533 (78.0%) underwent successful sequencing. The rate of success was 91.8% for ovarian carcinomas, 87.5% for lung non-small cell carcinomas, 82.0% for colorectal adenocarcinomas, 78.3% for melanomas, 75.9% for breast carcinomas, and 64.7% for pancreatic adenocarcinomas. For specimens that successfully underwent sequencing, pancreatic adenocarcinomas had the lowest median tumor proportion and somatic RAS and TP53 mutation allele fractions compared with other tumor types. Cytology specimens had a 33.3% success rate for pancreatic adenocarcinomas (5 of 15) and a 93.3% success rate for lung carcinomas (14 of 15). Compared with tissue from primary sites, tissue from metastatic sites showed a higher success rate for pancreatic adenocarcinomas and lower success rates for colorectal adenocarcinomas and melanomas.CONCLUSIONS: The success rate of cancer next-generation sequencing testing is dependent on pathologic diagnosis, tissue site, and diagnostic procedure. Understanding which specimens are at higher risk for failing molecular testing may help pathologists and clinical care teams optimize tissue acquisition and usage for patient care.

    View details for DOI 10.1093/ajcp/aqad092

    View details for PubMedID 37543867

  • A Clinicopathologic and Molecular Characterization of Uterine Sarcomas Classified as Malignant PEComa AMERICAN JOURNAL OF SURGICAL PATHOLOGY Anderson, W. J., Dong, F., Fletcher, C. M., Hirsch, M. S., Nucci, M. R. 2023; 47 (5): 535-546

    Abstract

    Perivascular epithelioid cell tumors (PEComas) are a distinctive group of mesenchymal neoplasms that demonstrate features of smooth muscle and melanocytic differentiation. Here, we present the clinicopathologic, immunohistochemical, and molecular features of 15 uterine sarcomas diagnosed as malignant PEComa. The median patient age was 56 years (range: 27 to 86 y). The median tumor size was 8.0 cm (range: 5.0 to 14.0 cm). All tumors were classified as malignant based on the presence of mitoses (15/15; 100%), necrosis (15/15; 100%), lymphovascular invasion (8/15; 53%), and high nuclear grade (13/15; 87%). Molecular analysis revealed the mammalian target of rapamycin pathway gene mutations in 7 cases (47%), including mutually exclusive variants in TSC1 (27%) and TSC2 (20%). Recurrent alterations were also identified in TP53 (53%), RB1 (30%), ATRX (33%), and BRCA2 (13%). Tumors with inactivating ATRX mutations all demonstrated loss of ATRX expression by immunohistochemistry. Loss of expression was also observed in 2 tumors without demonstrable ATRX alterations. Clinical follow-up was available for 14 patients (range: 5 to 92 mo; median: 15 mo). Five patients developed local recurrence and 9 developed metastases; 2 patients died of their disease. Our series expands the spectrum of molecular events in tumors diagnosed as malignant PEComa and further highlights the important role of targeted sequencing in tumors with focal melanocytic marker expression.

    View details for DOI 10.1097/PAS.0000000000002028

    View details for Web of Science ID 000973641800002

    View details for PubMedID 36856023

  • Molecular Landscape of Mullerian Clear Cell Carcinomas Identifies The Cancer Genome Atlas-like Prognostic Subgroups MODERN PATHOLOGY Irshaid, L., Costigan, D. C., Dong, F., Matulonis, U. A., Nucci, M. R., Kolin, D. L. 2023; 36 (5): 100123

    Abstract

    Mullerian clear cell carcinoma (CCC) is often aggressive and chemoresistant. The prognostic significance of molecular subclassification of endometrioid carcinomas is well established. However, less is known about the molecular landscape of CCC. The aim of this study was to better characterize the genetic landscape of a large cohort of CCC and correlate these findings with clinicopathologic features. CCC of the ovary (n = 72), endometrium (n = 24), and peritoneum/abdominal wall (n = 5) were retrospectively identified. Tumors had undergone tumor-only targeted sequencing using a hybrid capture next-generation sequencing panel. Median tumor mutational burden was 6.8 mutations/megabase (range, 1.3-185, 21% were ≥10 mutations/Mb). The most frequently mutated genes were ARID1A (48%), PIK3CA (45%), TP53 (23%), and PTEN (10%). ERBB2 amplification occurred in 4%. When classified according to the Cancer Genome Atlas/the Proactive Molecular Risk Classifier for Endometrial Cancer endometrial carcinoma molecular subgroups, 3 (3%) were POLE ultramutated, 5 (5%) were microsatellite instability-high (MSI-H), 20 (20%) were TP53-mutant subgroup, and 73 (72%) were no specific molecular profile (NSMP). Immunohistochemical expression of estrogen receptor, progesterone receptor, and programmed death-ligand 1 were not associated with the molecular subgroup. POLE and MSI-H tumors were characterized by an excellent prognosis, and the TP53-mutant subgroup had a worse disease-free survival than NSMP. NSMP tumors could be further substratified as high-risk NSMP if they lacked PIK3CA, PIK3R1, and ARID1A mutations, and/or harbored a TERT-promoter mutation. The Cancer Genome Atlas and NSMP-specific stratifications were prognostic for both the entire cohort and the subset of stage I ovarian tumors. On multivariable analysis, stage, lymphovascular invasion, and tumor mutational burden were prognostic for disease-free survival, whereas advanced stage and TP53-mutant subgroup - but not a TP53 mutation in isolation - were negative prognostic factors for overall survival. These data suggest that routine molecular profiling of Mullerian CCC may be warranted for both prognosis and identification of potential targeted treatments, such as immunotherapy and anti-HER2 agents.

    View details for DOI 10.1016/j.modpat.2023.100123

    View details for Web of Science ID 000949830600001

    View details for PubMedID 36857998

  • Epithelioid and Spindle Cell Hemangioma Clinicopathologic Analysis of 18 Primary Bone and Soft Tissue Tumors Highlighting a Predilection for the Hands and Feet, Frequent Multicentricity, and Benign Behavior AMERICAN JOURNAL OF SURGICAL PATHOLOGY Papke Jr, D. J., Jagannathan, J., Dong, F., Dickson, B. C., Mertens, F., Hornick, J. L., Fletcher, C. M. 2023; 47 (2): 147-156

    Abstract

    Epithelioid and spindle cell hemangioma was initially described in 1999 in a series of primary bone tumors and was subsequently suggested by some to represent a variant of epithelioid hemangioma. Here, we studied 18 epithelioid and spindle cell hemangiomas. Nine patients (50%) were male. Age at presentation ranged from 12 to 78 years (median: 38.5 y). Nine patients (50%) had tumor(s) limited to bone, 5 (28%) had tumor(s) limited to soft tissue, and 4 (22%) had tumor(s) involving bone and soft tissue. Nine patients (50%) had multiple tumors, all in a unilateral anatomic region involving the wrist, hand, ankle, or foot. Seventeen tumors (94%) occurred in an extremity, including 12 (67%) in the hands and feet, and 1 occurred in a vertebra. In imaging studies, primary bone tumors were lobulated, expansile, and lytic, and 7 bone tumors with available imaging (58%) showed cortical breakthrough. Tumor sizes were 0.8 to 7.2 cm (median: 2.2 cm). Epithelioid and spindle cell hemangioma is composed of lobules of epithelioid and spindled endothelial cells with bland, vesicular nuclei. Neoplastic cells show orderly vasoformative growth, with hemorrhagic stroma and no endothelial atypia or multilayering. Immunohistochemistry demonstrated uniform positivity for CD31 and ERG. Where positive, SMA highlighted pericytes (11/13 tumors). FOSB was strongly positive in 4 of 16 tumors (25%), and FOS was strongly positive in 5 of 10 stained tumors (50%). Break-apart fluorescence in situ hybridization confirmed the presence of FOS split signals in 4 tumors positive for FOS by immunohistochemistry and FOSB split signals in 2 FOSB-positive tumors. DNA sequencing demonstrated a GATA6 :: FOXO1 fusion in 1 of 3 sequenced tumors. Clinical follow-up was available for 15 patients (83%; range: 5 mo to 11 y; median: 3.5 y). Seven patients (47%) had no evidence of disease at most recent follow-up. Seven of 13 patients (54%) who underwent surgery experienced local recurrence at the primary tumor site: 5 patients within a year, 1 at 2.4 years, and 1 thrice at 2, 3, and 5 years. Six patients were alive with multifocal disease (median: 3.5 y; range: 5 mo to 6 y). No tumors gave rise to distant metastases. The clinicopathologic and genetic findings in this study support the notion that epithelioid and spindle cell hemangioma is a morphologic variant of epithelioid hemangioma that can occur in soft tissue as well as bone and that shows a striking predilection for the extremities. Given that most recurrences and primary tumors behaved indolently, watchful waiting would be reasonable for patients with multicentric disease that is not readily amenable to surgery.

    View details for DOI 10.1097/PAS.0000000000001974

    View details for Web of Science ID 000916492700001

    View details for PubMedID 36206448

  • The Medical Practice of Molecular Oncology Diagnostics Preface CLINICS IN LABORATORY MEDICINE Dong, F. 2022; 42 (3): XIII-XIV

    View details for DOI 10.1016/j.cll.2022.06.001

    View details for Web of Science ID 000892865200001

    View details for PubMedID 36150827

  • Recurrent PTPN14 Mutations in Trichilemmoma: Evidence for Distinct Pathways of Molecular Pathogenesis AMERICAN JOURNAL OF DERMATOPATHOLOGY Russell-Goldman, E., Dong, F., Hanna, J. 2022; 44 (8): 545-552

    Abstract

    Trichilemmoma is a benign cutaneous neoplasm that recapitulates the outer root sheath of the hair follicle. Trichilemmomas may occur sporadically or in association with Cowden syndrome, which is characterized by germline mutations in the lipid phosphatase PTEN (phosphatase and tensin homolog on chromosome 10). Interestingly, most sporadic trichilemmomas do not show PTEN aberrations, but rather activating mutations in HRAS. Despite these important advances, a comprehensive genetic analysis of trichilemmoma has not been reported. Here, we used a next-generation DNA sequencing platform to study 9 sporadic trichilemmoma cases. Seven cases (7/9; 78%) harbored activating mutations in HRAS, consistent with previous findings. Unexpectedly, we identified recurrent mutations in the tyrosine phosphatase PTPN14 (protein tyrosine phosphatase nonreceptor type 14) in 4 cases (4/9; 44%). Three of these cases also harbored HRAS mutations, whereas one case occurred in the absence of a HRAS mutation and showed evidence of biallelic inactivation of PTPN14. Finally, one case (1/9; 11%) showed biallelic inactivation of PTEN in the absence of a HRAS (or PTPN14) mutation. These data suggest at least 3 distinct pathways of molecular pathogenesis in sporadic trichilemmoma and identify PTPN14 as a potentially important contributor to trichilemmoma biology.

    View details for DOI 10.1097/DAD.0000000000002015

    View details for Web of Science ID 000823968400006

    View details for PubMedID 35830698

  • Esophageal squamous cell carcinoma with basaloid features are genetically and prognostically similar to conventional squamous cell carcinoma MODERN PATHOLOGY Sauer, M. A., Yang, J., Isidro, R. A., Dong, F., Patil, D. T., Wee, J. O., Agoston, A. T., Deshpande, V., Zhao, L. 2022; 35 (9): 1247-1253

    Abstract

    We compared clinicopathologic and molecular features of esophageal squamous cell carcinoma (SCC) with basaloid features to conventional SCC using surgical resections of treatment naïve esophageal carcinomas and cases available from the TCGA database. Twenty-two cases of SCC with basaloid features were identified in the Mass General Brigham pathology archives, including 9 cases with pure basaloid morphology and 13 cases with mixed other features such as conventional well- or poorly differentiated areas or sarcomatoid areas. Thirty-eight cases of conventional SCC matched by tumor stage were used as controls. HPV infection status was tested by p16 immunohistochemistry and HPV mRNA ISH. Digital slides for 94 cases of esophageal SCC from TCGA found in the Genomic Data Commons (GDC) Data Portal were reviewed. Five cases of SCC with basaloid features were identified. Genomic profiles of SCC with basaloid features were compared to the rest of 89 SCCs without basaloid features. In addition, eight tumor sections from six patients selected from our cohort underwent in-house molecular profiling. Compared to conventional SCC, SCC with basaloid features were more frequently associated with diffuse or multifocal squamous dysplasia (p < 0.001). P16 IHC was positive in 2/13 cases, whereas HPV mRNA ISH was negative in 17/17 cases (including both p16-positive cases). SCC with basaloid features and conventional SCC from TCGA showed similar rates of TP53 mutations, CDKN2A/B deletions, and CCDN1 amplifications. TP53 variants were identified in all in-house samples that had sufficient coverage. Survival analyses between SCC with basaloid features versus conventional SCC (matched for tumor stage) did not reveal any statistically significant differences. In conclusion, esophageal SCC with basaloid features has similar survival and genomic alterations to those of conventional SCC, are more frequently associated with diffuse or multifocal dysplasia, and are not associated with HPV (high-risk strains) infection.

    View details for DOI 10.1038/s41379-022-01060-4

    View details for Web of Science ID 000774687000001

    View details for PubMedID 35351978

    View details for PubMedCentralID 6708531

  • Detection of EGFR mutations in non-small cell lung cancer by droplet digital PCR PLoS One Williamson, D. F., Marris, S. R., Rojas-Rudilla, V., Bruce, J. L., Paweletz, C. P., Oxnard, G. R., Sholl, L. M., Dong, F. 2022; 17 (2): e0264201
  • Contamination assessment for cancer next generation sequencing: method development and clinical implementation Archives of Pathology & Laboratory Medicine Li, Y. Y., Schmidt, R. J., Manning, D. K., Jia, Y., Dong, F. 2022; 146 (2): 227-232
  • Pan-Cancer Molecular Biomarkers: A Paradigm Shift in Diagnostic Pathology. Surgical pathology clinics Dong, F. 2021; 14 (3): 507-516

    Abstract

    The rapid adoption of next-generation sequencing in clinical oncology has enabled the detection of molecular biomarkers shared between multiple tumor types. These pan-cancer biomarkers include sequence-altering mutations, copy number changes, gene rearrangements, and mutational signatures and have been demonstrated to predict response to targeted therapy. This article reviews issues surrounding current and emerging pan-cancer molecular biomarkers in clinical oncology: technological advances that enable the broad detection of cancer mutations across hundreds of genes, the spectrum of driver and passenger mutations derived from human cancer genomes, and implications for patient care now and in the near future.

    View details for DOI 10.1016/j.path.2021.05.012

    View details for PubMedID 34373099

  • Verrucous carcinoma of the oesophagus is a genetically distinct subtype of oesophageal squamous cell carcinoma HISTOPATHOLOGY Isidro, R. A., Dong, F., Hornick, J. L., Wee, J. O., Agoston, A., Patil, D. T., Deshpande, V., Zhao, L. 2021; 79 (4): 642-649

    Abstract

    Oesophageal verrucous carcinoma (VSCC) is a rare and morphologically distinct type of oesophageal squamous cell carcinoma (SCC). Diagnosing VSCC on biopsy material is challenging, given the lack of significant atypia and the presence of keratinising epithelium and exophytic growth. The molecular pathogenesis of VSCC remains unclear. The aim of this study was to characterise the genomic landscape of VSCC in comparison to conventional oesophageal SCC.Three cases of VSCC from the Brigham and Women's Hospital pathology archive were identified. Formalin-fixed, paraffin-embedded (FFPE) tumour tissue was used for p16 immunohistochemistry (IHC), high-risk human papillomavirus (HPV) in-situ mRNA hybridisation (ISH) and DNA isolation. Tumour DNA was sequenced using a targeted massively parallel sequencing assay enriched for cancer-associated genes. Three additional cases of VSCC were identified by image review of The Cancer Genome Atlas (TCGA) oesophageal SCC cohort. VSCC cases were negative for p16 IHC and high-risk HPV ISH. TP53 mutations (P < 0.001) and copy number variants (CNVs) for CDKN2A (P < 0.001), CDKN2B (P < 0.01) and CCND1 (P < 0.01) were absent in VSCC and significantly less frequent in comparison to conventional SCC. Five VSCC cases featured SMARCA4 missense mutations or in-frame deletions compared to only four of 88 conventional SCC cases (P < 0.001). VSCC featured driver mutations in PIK3CA, HRAS and GNAS. Recurrent CNVs were rare in VSCC.VSCC is not only morphologically but also genetically distinct from conventional oesophageal SCC, featuring frequent SMARCA4 mutations and infrequent TP53 mutations or CDKN2A/B CNVs. Molecular findings may aid in establishing the challenging diagnosis of VSCC.

    View details for DOI 10.1111/his.14395

    View details for Web of Science ID 000670551100001

    View details for PubMedID 33960520

  • Genomic profile of columnar cell variant of papillary thyroid carcinoma HISTOPATHOLOGY Janovitz, T., Williamson, D. K., Wong, K. S., Dong, F., Barletta, J. A. 2021; 79 (4): 491-498

    Abstract

    Columnar cell variant (CCV) is a rare papillary thyroid carcinoma subtype. The majority of CCV occur in older patients and are large, invasive tumours that pursue an aggressive clinical course. Rare well-circumscribed CCV occur in younger female patients and are comparatively indolent.We retrospectively identified CCV with material available to perform targeted next-generation sequencing and correlated molecular results with clinicopathological features and outcome. Our cohort was comprised of nine CCV. Nearly all were aggressive tumours; however, one was predominantly well-circumscribed and arose in a thyroglossal duct cyst of a 26-year-old woman who had no evidence of disease at last follow-up. Seven (78%) cases demonstrated activating oncogenic driver alterations in BRAF, including BRAF V600E, an activating N486_P490del deletion, and BRAF-AGK fusions. Activating RAS mutations were seen in two (22%) cases. Additionally, three (33%) cases had TERT promoter mutations, four (44%) had loss of the tumour suppressor CDKN2A and one (11%) case had a loss of function TP53 mutation. Most cases (89%) also demonstrated copy number alterations, including recurrent gain of chromosome 1q (five cases) and losses of chromosome 9p (three cases) and 22q (four cases). The one case without secondary pathogenic mutations or copy number alterations was the tumour in the 26-year-old woman.We found that CCV is primarily a BRAF-driven tumour, with most also harbouring secondary oncogenic mutations and multiple chromosomal gains and losses. Moreover, our findings suggest that molecular analysis could potentially be used to help risk stratify CCV.

    View details for DOI 10.1111/his.14374

    View details for Web of Science ID 000661391100001

    View details for PubMedID 33783022

  • Evaluation of grade in a genotyped cohort of sporadic medullary thyroid carcinomas HISTOPATHOLOGY Najdawi, F., Ahmadi, S., Capelletti, M., Dong, F., Chau, N. G., Barletta, J. A. 2021; 79 (3): 427-436

    Abstract

    Tumour grade and RET mutation status, especially the presence of high-risk exon 15 and 16 RET mutations, have been reported to be prognostic in patients with sporadic medullary thyroid carcinoma (MTC). The aims of our study were to evaluate the performance of two recently proposed grading systems and to assess the association between grade and genotype in a cohort of sporadic MTCs.We identified 44 sporadic MTCs. All available tumour slides were examined, and cases were assigned a grade on the basis of either mitotic count and tumour necrosis, or mitotic count, tumour necrosis, and Ki-67 proliferative index, as described in two recent studies. Additional clinicopathological features and outcome information were obtained from the pathology reports and electronic medical records. The presence of RET and RAS mutations was determined either with direct sequencing or with massively parallel sequencing. Both grading systems were prognostic for progression-free survival and disease-specific survival on univariate analysis. There was no correlation between grade and mutation status. Specifically, neither RET nor high-risk RET mutations were enriched in high-grade tumours, as assessed by either grading scheme.Our findings suggest that grade is not correlated with RET/RAS mutation status, indicating that grade and genotype may give independent prognostic information.

    View details for DOI 10.1111/his.14370

    View details for Web of Science ID 000661412500001

    View details for PubMedID 33763905

  • Calcifying nested stromal-epithelial tumor: a clinicopathologic and molecular genetic study of eight cases highlighting metastatic potential and recurrent CTNNB1 and TERT promoter alterations MODERN PATHOLOGY Papke Jr., D. J., Dong, F., Zhang, X., Kozielski, R., Basturk, O., Fletcher, C. M., Zhao, L. 2021; 34 (9): 1696-1703

    Abstract

    Calcifying nested stromal-epithelial tumor (CNSET) is a rare hepatic tumor that occurs in children and young adults. With <40 cases in the literature, the mechanism for tumorigenesis and the biological behavior of CNSET remain uncertain. Here, we studied the clinicopathologic and molecular genetic features of eight CNSETs. Six patients (75%) were female, and the median age at presentation was 22.5 years (range 14-34 years). The median tumor size was 14 cm (range 2.7-18 cm). All tumors had fibrous stroma that contained organoid nests of epithelioid to spindled tumor cells with moderate amounts of palely eosinophilic cytoplasm and ovoid, vesicular nuclei. Five tumors showed calcifications, and one showed lymphovascular invasion. Necrosis was absent in all. Immunohistochemistry demonstrated nuclear β-catenin expression in five of five tested tumors and focal to diffuse nuclear WT-1 positivity in five of seven. Hepatocellular markers (HepPar-1, arginase-1, and albumin in situ hybridization) and neuroendocrine markers (synaptophysin, chromogranin, and INSM1) were uniformly negative. Next-generation sequencing demonstrated CTNNB1 alterations in all seven sequenced tumors. Sanger sequencing demonstrated TERT promoter mutations in all six sequenced tumors. Clinical follow-up was available for seven patients (median duration 4.4 years; range 1.2-6.2 years): four (57%) developed metastatic disease; all four developed lung metastases; and two also had abdominal metastases. All four patients with metastatic disease also had persistent or recurrent liver tumors. Three patients with metastases were alive with disease at the most recent follow-up and one died of disease. The other three patients with available follow-up did not develop metastasis or recurrence. One tumor treated with neoadjuvant chemotherapy showed no response, and another showed 90% tumor fibrosis; the latter patient remained disease-free at 6.2 years of follow-up. Our series demonstrates the presence of TERT promoter mutations and CTNNB1 alterations in all sequenced tumors and suggests that CNSET might perhaps be more aggressive than previously reported.

    View details for DOI 10.1038/s41379-021-00822-w

    View details for Web of Science ID 000651022300001

    View details for PubMedID 33994539

  • Re-evaluating tumors of purported specialized prostatic stromal origin reveals molecular heterogeneity, including non-recurring gene fusions characteristic of uterine and soft tissue sarcoma subtypes MODERN PATHOLOGY Acosta, A. M., Sholl, L. M., Dickson, B. C., McKenney, J. K., Gordetsky, J. B., Pins, M. R., Marino-Enriquez, A., Dong, F., Dubuc, A. M., Cin, P., Fletcher, C. M. 2021; 34 (9): 1763-1779

    Abstract

    Tumors of purported specialized prostatic stromal origin comprise prostatic stromal sarcomas (PSS) and stromal tumors of uncertain malignant potential (STUMP). Prior studies have described their clinicopathologic characteristics, but the molecular features remain incompletely understood. Moreover, these neoplasms are morphologically heterogeneous and the lack of specific adjunctive markers of prostatic stromal lineage make precise definition more difficult, leading some to question whether they represent a specific tumor type. In this study, we used next-generation DNA and RNA sequencing to profile 25 primary prostatic mesenchymal neoplasms of possible specialized prostatic stromal origin, including cases originally diagnosed as PSS (11) and STUMP (14). Morphologically, the series comprised 20 cases with solid architecture (11 PSS and 9 STUMP) and 5 cases with phyllodes-like growth pattern (all STUMP). Combined DNA and RNA sequencing results demonstrated that 19/22 (86%) cases that underwent successful sequencing (either DNA or RNA) harbored pathogenic somatic variants. Except for TP53 alterations (6 cases), ATRX mutations (2 cases), and a few copy number variants (-13q, -14q, -16q and +8/8p), the findings were largely nonrecurrent. Eight gene rearrangements were found, and 4 (NAB2-STAT6, JAZF1-SUZ12, TPM3-NTRK1 and BCOR-MAML3) were useful for reclassification of the cases as specific entities. The present study shows that mesenchymal neoplasms of the prostate are morphologically and molecularly heterogeneous and include neoplasms that harbor genetic aberrations seen in specific mesenchymal tumors arising in other anatomic sites, including soft tissue and the uterus. These data suggest that tumors of purported specialized prostatic stromal origin may perhaps not represent a single diagnostic entity or specific disease group and that alternative diagnoses should be carefully considered.

    View details for DOI 10.1038/s41379-021-00818-6

    View details for Web of Science ID 000650156000002

    View details for PubMedID 33986460

    View details for PubMedCentralID 16723846

  • Papillary Thyroid Carcinoma with High-Grade Features Versus Poorly Differentiated Thyroid Carcinoma: An Analysis of Clinicopathologic and Molecular Features and Outcome THYROID Wong, K. S., Dong, F., Telatar, M., Lorch, J. H., Alexander, E. K., Marqusee, E., Cho, N. L., Nehs, M. A., Doherty, G. M., Afkhami, M., Barletta, J. A. 2021; 31 (6): 933-940

    Abstract

    Background: Similar to poorly differentiated thyroid carcinoma (PDTC), papillary thyroid carcinoma with high-grade features (PTC HGF) demonstrates increased mitotic activity and/or necrosis; however, PTC HGF is excluded from the World Health Organization (WHO) definition of PDTC based on maintained nuclear features of PTC. Methods: Consecutive tumors that met criteria for PTC HGF, defined as tumors with maintained nuclear features of PTC and mitoses numbering 5 or more per 10 contiguous high-power fields and/or tumor necrosis, and PDTC (defined as per the WHO criteria) were identified. Clinicopathologic characteristics, follow-up data, and targeted next-generation sequencing results were compared between groups. Results: There were 15 PTC HGF and 47 PDTC. PTC HGF was associated with a higher rate of pT4 disease (53% vs. 13%, p = 0.0027) and lymph node metastases (73% vs. 38%, p = 0.049). The disease-specific survival was worse for patients with PTC HGF compared with those with PDTC using Kaplan-Meier estimation (p < 0.001) and was worse in subgroup analysis evaluating patients with widely invasive PDTC (i.e., those with a similar rate of pT4 disease) and PTC HGF (p = 0.040). PTC HGF had a higher BRAFV600E mutation rate (42% vs. 3%; p = 0.003), a trend toward more gene fusions (25% vs. 3%; p = 0.052), and a higher rate of relative gain of 1q (67% vs. 15%; p = 0.002) than PDTC. Conclusions: Our results demonstrate that PTC HGF are important to recognize based on their aggressive behavior. The molecular differences between PTC HGF and PDTC suggest that PTC HGF should be considered a distinct group from PDTC.

    View details for DOI 10.1089/thy.2020.0668

    View details for Web of Science ID 000610615200001

    View details for PubMedID 33143568

  • Novel Pathogenic Germline Variant of the Adenomatous Polyposis Coli (APC) Gene, p.S2627Gfs*12 Identified in a Mild Phenotype of APC-Associated Polyposis: A Case Report AMERICAN JOURNAL OF CASE REPORTS Koeller, D. R., Schwartz, A., Manning, D. K., Dong, F., Lindeman, N., Garber, J. E., Ghazani, A. A. 2020; 21: e927293

    Abstract

    BACKGROUND The diagnoses of adenomatous polyposis coli (APC)-associated polyposis conditions are typically based on suggestive personal features and/or family history, and the identification of a pathogenic variant in the APC gene. However, with large-scale genome sequencing, it is now possible to identify pathogenic variants before or even without the presentation of the expected clinical features. This case describes a novel pathogenic APC variant. CASE REPORT We report the unexpected identification of a rare, pathogenic germline APC variant, p.S2627Gfs*12 in an 80-year-old man with a diagnosis of renal cell carcinoma, without any family history of APC-associated polyposis or personal history of colorectal cancer. After the identification of the APC variant, a review of the patient's medical records showed a personal history of 15 adenomatous polyps over a decade ago, with no follow-up genetic testing at the time. CONCLUSIONS This novel APC variant has not been characterized to date. The presence of the APC-p.S2627Gfs*12 variant in this patient led to the recommendation of additional cascade genetic testing and surveillance measures for any family members who tested positive for this variant. This report highlights the broad spectrum of the APC-associated polyposis features, and a mild phenotype associated with the pathogenic APC p.S2627Gfs*12 variant.

    View details for DOI 10.12659/AJCR.927293

    View details for Web of Science ID 000599347900001

    View details for PubMedID 33303731

    View details for PubMedCentralID PMC7737709

  • Detection ofERBB2amplification in uterine serous carcinoma by next-generation sequencing: an approach highly concordant with standard assays MODERN PATHOLOGY Robinson, C. L., Harrison, B. T., Ligon, A. H., Dong, F., Maffeis, V., Matulonis, U., Nucci, M. R., Kolin, D. L. 2021; 34 (3): 603-612

    Abstract

    Uterine serous carcinoma is an aggressive subtype of endometrial cancer that accounts for fewer than 10% of endometrial carcinomas but is responsible for about half of deaths. A subset of cases has HER2 overexpression secondary to ERBB2 gene amplification, and these patients may benefit from anti-HER2 therapies, such as trastuzumab. HER2 protein overexpression is currently assessed by immunohistochemistry (IHC) and ERBB2 gene amplification by fluorescence in situ hybridization (FISH). Targeted next-generation sequencing (NGS) is increasingly used to routinely identify predictive and prognostic molecular abnormalities in endometrial carcinoma. To investigate the ability of a targeted NGS panel to detect ERBB2 amplification, we identified cases of uterine serous carcinoma (n = 93) and compared HER2 expression by IHC and copy number assessed by FISH with copy number status assessed by NGS. ERBB2 copy number status using a combination of IHC and FISH was interpreted using the 2018 ASCO/CAP guidelines for breast carcinoma. ERBB2 amplification by NGS was determined by the relative number of reads mapping to ERBB2 in tumor DNA compared to control nonneoplastic DNA. Cases with copy number ≥6 were considered amplified and copy number <6 were non-amplified. By IHC, 70 specimens were classified as negative (0 or 1+), 19 were classified as equivocal (2+), and 4 were classified as positive (3+). Using combined IHC/FISH, ERBB2 amplification was observed in 8 of 93 cases (9%). NGS identified the same 8 cases with copy number ≥6; all 85 others had copy number <6. In this series, NGS had 100% concordance with combined IHC/FISH in identifying ERBB2 amplification. NGS is highly accurate in detecting ERBB2 amplification in uterine serous carcinoma and provides an alternative to measurement by IHC and FISH.

    View details for DOI 10.1038/s41379-020-00695-5

    View details for Web of Science ID 000580713500004

    View details for PubMedID 33077919

    View details for PubMedCentralID 2361201

  • Molecular Characterization of Neuroendocrine Carcinomas of the Endometrium: Representation in All 4 TCGA Groups. The American journal of surgical pathology Howitt, B. E., Dong, F., Vivero, M., Shah, V., Lindeman, N., Schoolmeester, J. K., Baltay, M., MacConaill, L., Sholl, L. M., Nucci, M. R., McCluggage, W. G. 2020

    Abstract

    High-grade neuroendocrine carcinomas (NEC) of the endometrium are rare and account for <1% of all endometrial carcinomas. Both small cell neuroendocrine carcinoma (SCNEC) and large cell neuroendocrine carcinoma (LCNEC) morphologies have been reported. Little is known regarding the molecular features of endometrial NEC including how they compare to pulmonary NEC (the most common site for these neoplasms) and the more common endometrial carcinoma histotypes. In this study, we investigated the molecular alterations in a series of endometrial NEC using a targeted next generation sequencing panel (Oncopanel). Fourteen NEC were sequenced; pure NEC (n=4) and mixed (n=10) with endometrioid adenocarcinoma (n=9) or carcinosarcoma (n=1). The NEC components of mixed tumors comprised LCNEC (n=6) and SCNEC (n=4). The 4 pure NEC comprised LCNEC (n=2) and SCNEC (n=2). Molecular analysis classified tumors into the 4 The Cancer Genome Atlas groups: (1) POLE-mutated/ultramutated (1/14; 7%), (2) microsatellite instability/hypermutated (6/14; 43%), (3) TP53 mutated/copy number high (2/14; 14%), or (4) no specific molecular profile (5/14; 36%). Overall, 50% of cases were ultramutated or hypermutated. In 8 cases of mixed carcinomas, the different histologic components were macrodissected and separately sequenced; molecular alterations were nearly identical among the 2 components, with the non-NEC component harboring slightly increased tumor mutational burden. Only 2 carcinomas (both with pure SCNEC morphology) had a molecular profile that would be expected in typical pulmonary SCNEC (RB1 deletion and TP53 mutations). Our findings, similar to data from NECs of other anatomic sites, suggest that the molecular context may be important when selecting therapies for women with endometrial NEC. Immune checkpoint inhibition may be a reasonable approach to treatment of microsatellite instability-NEC and we thus recommend that all endometrial NEC be tested for mismatch repair abnormalities, either molecularly or by mismatch repair protein immunohistochemistry.

    View details for DOI 10.1097/PAS.0000000000001560

    View details for PubMedID 32773531

  • Molecular and clinicopathologic features of gliomas harboring NTRK fusions ACTA NEUROPATHOLOGICA COMMUNICATIONS Torre, M., Vasudevaraja, V., Serrano, J., DeLorenzo, M., Malinowski, S., Blandin, A., Pages, M., Ligon, A. H., Dong, F., Meredith, D. M., Nasrallah, M. P., Horbinski, C., Dahiya, S., Ligon, K. L., Santi, M., Ramkissoon, S. H., Filbin, M. G., Snuderl, M., Alexandrescu, S. 2020; 8 (1): 107

    Abstract

    Fusions involving neurotrophic tyrosine receptor kinase (NTRK) genes are detected in ≤2% of gliomas and can promote gliomagenesis. The remarkable therapeutic efficacy of TRK inhibitors, which are among the first Food and Drug Administration-approved targeted therapies for NTRK-fused gliomas, has generated significant clinical interest in characterizing these tumors. In this multi-institutional retrospective study of 42 gliomas with NTRK fusions, next generation DNA sequencing (n = 41), next generation RNA sequencing (n = 1), RNA-sequencing fusion panel (n = 16), methylation profile analysis (n = 18), and histologic evaluation (n = 42) were performed. All infantile NTRK-fused gliomas (n = 7) had high-grade histology and, with one exception, no other significant genetic alterations. Pediatric NTRK-fused gliomas (n = 13) typically involved NTRK2, ranged from low- to high-histologic grade, and demonstrated histologic overlap with desmoplastic infantile ganglioglioma, pilocytic astrocytoma, ganglioglioma, and glioblastoma, among other entities, but they rarely matched with high confidence to known methylation class families or with each other; alterations involving ATRX, PTEN, and CDKN2A/2B were present in a subset of cases. Adult NTRK-fused gliomas (n = 22) typically involved NTRK1 and had predominantly high-grade histology; genetic alterations involving IDH1, ATRX, TP53, PTEN, TERT promoter, RB1, CDKN2A/2B, NF1, and polysomy 7 were common. Unsupervised principal component analysis of methylation profiles demonstrated no obvious grouping by histologic grade, NTRK gene involved, or age group. KEGG pathway analysis detected methylation differences in genes involved in PI3K/AKT, MAPK, and other pathways. In summary, the study highlights the clinical, histologic, and molecular heterogeneity of NTRK-fused gliomas, particularly when stratified by age group.

    View details for DOI 10.1186/s40478-020-00980-z

    View details for Web of Science ID 000553109000002

    View details for PubMedID 32665022

    View details for PubMedCentralID PMC7362646

  • Molecular characterization of diffuse malignant peritoneal mesothelioma MODERN PATHOLOGY Hung, Y. P., Dong, F., Torre, M., Crum, C. P., Bueno, R., Chirieac, L. R. 2020; 33 (11): 2269-2279

    Abstract

    Malignant peritoneal mesothelioma is a rare aggressive tumor that arises from the peritoneal lining. While recurrent BAP1 mutations have been identified in a subset of mesotheliomas, molecular characteristics of peritoneal mesotheliomas, including those lacking BAP1 alterations, remain poorly understood. Using targeted next-generation sequencing, we examined the molecular features of 26 diffuse malignant peritoneal mesotheliomas. As part of an exploratory analysis, we analyzed an additional localized peritoneal mesothelioma and one well-differentiated papillary mesothelioma with invasive foci. Genomic characterization identified categories of diffuse malignant peritoneal mesotheliomas: The first group included 18 (69%) tumors with recurrent BAP1 alterations, with eight (31%) having more than one BAP1 alterations, and concomitant alterations in PBRM1 (46%) and SETD2 (35%). All tumors with complete loss of BAP1 expression by immunohistochemistry harbored BAP1 molecular alterations. PBRM1 alterations were significantly enriched in the BAP1-altered cohort. Frequent copy number loss of BAP1, ARID1B, PRDM1, PBRM1, SETD2, NF2, and CDKN2A was noted. The second group included eight (31%) BAP1-wild-type tumors: two with TP53 mutations, one with a TRAF7 activating mutation, one with a SUZ12 inactivating mutation, and three with ALK rearrangements that we previously published. One TP53-mutant biphasic mesothelioma showed evidence of genomic near-haploidization showing loss of heterozygosity of all chromosomes except 5, 7, 16, and 20. The localized peritoneal mesothelioma harbored a nonsense CHEK2 mutation, and the well-differentiated papillary mesothelioma with invasive foci harbored no reportable variants. In conclusion, we described the genetic categories of diffuse malignant peritoneal mesotheliomas, with BAP1-mutant and BAP1-wild-type groups. Our findings implicated DNA repair, epigenetics, and cell cycle regulation in the pathogenesis of peritoneal mesotheliomas, with identification of potential therapeutic targets.

    View details for DOI 10.1038/s41379-020-0588-y

    View details for Web of Science ID 000538222500001

    View details for PubMedID 32504035

    View details for PubMedCentralID 5657894

  • Clinicopathologic and Immunohistochemical Correlates of CTNNB1 Mutated Endometrial Endometrioid Carcinoma INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY Costigan, D. C., Dong, F., Nucci, M. R., Howitt, B. E. 2020; 39 (2): 119–27
  • A model combining clinical and genomic factors to predict response to PD-1/PD-L1 blockade in advanced urothelial carcinoma BRITISH JOURNAL OF CANCER Nassar, A. H., Mouw, K. W., Jegede, O., Shinagare, A. B., Kim, J., Liu, C., Pomerantz, M., Harshman, L. C., Van Allen, E. M., Wei, X. X., McGregor, B., Choudhury, A. D., Preston, M. A., Dong, F., Signoretti, S., Lindeman, N. I., Bellmunt, J., Choueiri, T. K., Sonpavde, G., Kwiatkowski, D. J. 2020; 122 (4): 555-563

    Abstract

    In metastatic urothelial carcinoma (mUC), predictive biomarkers that correlate with response to immune checkpoint inhibitors (ICIs) are lacking. Here, we interrogated genomic and clinical features associated with response to ICIs in mUC.Sixty two mUC patients treated with ICI who had targeted tumour sequencing were studied. We examined associations between candidate biomarkers and clinical benefit (CB, any objective reduction in tumour size) versus no clinical benefit (NCB, no change or objective increase in tumour size). Both univariable and multivariable analyses for associations were conducted. A comparator cohort of 39 mUC patients treated with taxanes was analysed by using the same methodology.Nine clinical and seven genomic factors correlated with clinical outcomes in univariable analysis in the ICI cohort. Among the 16 factors, neutrophil-to-lymphocyte ratio (NLR) ≥5 (OR = 0.12, 95% CI, 0.01-1.15), visceral metastasis (OR = 0.05, 95% CI, 0.01-0.43) and single-nucleotide variant (SNV) count < 10 (OR = 0.04, 95% CI, 0.006-0.27) were identified as independent predictors of NCB to ICI in multivariable analysis (c-statistic = 0.90). None of the 16 variables were associated with clinical benefit in the taxane cohort.This three-factor model includes genomic (SNV count >9) and clinical (NLR <5, lack of visceral metastasis) variables predictive for benefit to ICI but not taxane therapy for mUC. External validation of these hypothesis-generating results is warranted to enable use in routine clinical care.

    View details for DOI 10.1038/s41416-019-0686-0

    View details for Web of Science ID 000515028200013

    View details for PubMedID 31857723

    View details for PubMedCentralID PMC7028947

  • Molecular characterization of localized pleural mesothelioma MODERN PATHOLOGY Hung, Y. P., Dong, F., Dubuc, A. M., Dal Cin, P., Bueno, R., Chirieac, L. R. 2020; 33 (2): 271-280

    Abstract

    Localized pleural mesothelioma is a rare solitary circumscribed pleural tumor that is microscopically similar to diffuse malignant pleural mesothelioma. However, the molecular characteristics and nosologic relationship with its diffuse counterpart remain unknown. In a consecutive cohort of 1110 patients with pleural mesotheliomas diagnosed in 2005-2018, we identified six (0.5%) patients diagnosed with localized pleural mesotheliomas. We gathered clinical history, evaluated the histopathology, and in select cases performed karyotypic analysis and targeted next-generation sequencing. The cohort included three women and three men (median age 63; range 28-76), often presenting incidentally during radiologic evaluation for unrelated conditions. Neoadjuvant chemotherapy was administered in two patients. All tumors (median size 5.0 cm; range 2.7-13.5 cm) demonstrated gross circumscription (with microscopic invasion into lung, soft tissue, and/or rib in four cases), mesothelioma histology (four biphasic and two epithelioid types), and mesothelial immunophenotype. Of four patients with at least 6-month follow-up, three were alive (up to 8.9 years). Genomic characterization identified several subgroups: (1) BAP1 mutations with deletions of CDKN2A and NF2 in two tumors; (2) TRAF7 mutations in two tumors, including one harboring trisomies of chromosomes 3, 5, 7, and X; and (3) genomic near-haploidization, characterized by extensive loss of heterozygosity sparing chromosomes 5 and 7. Localized pleural mesotheliomas appear genetically heterogeneous and include BAP1-mutated, TRAF7-mutated, and near-haploid subgroups. While the BAP1-mutated subgroup is similar to diffuse malignant pleural mesotheliomas, the TRAF7-mutated subgroup overlaps genetically with adenomatoid tumors and well-differentiated papillary mesotheliomas, in which recurrent TRAF7 mutations have been described. Genomic near-haploidization, identified recently in a subset of diffuse malignant pleural mesotheliomas, suggests a novel mechanism in the pathogenesis of both localized pleural mesothelioma and diffuse malignant pleural mesothelioma. Our findings describe distinctive genetic features of localized pleural mesothelioma, with both similarities to and differences from diffuse malignant pleural mesothelioma.

    View details for DOI 10.1038/s41379-019-0330-9

    View details for Web of Science ID 000511195600012

    View details for PubMedID 31371807

    View details for PubMedCentralID PMC7359734

  • Uterine Tumor Resembling Ovarian Sex Cord Tumor (UTROSCT) A Morphologic and Molecular Study of 26 Cases Confirms Recurrent NCOA1-3 Rearrangement AMERICAN JOURNAL OF SURGICAL PATHOLOGY Goebel, E. A., Hernandez Bonilla, S., Dong, F., Dickson, B. C., Hoang, L. N., Hardisson, D., Lacambra, M. D., Lu, F., Fletcher, C. M., Crum, C. P., Antonescu, C. R., Nucci, M. R., Kolin, D. L. 2020; 44 (1): 30-42

    Abstract

    Uterine tumor resembling ovarian sex cord tumor (UTROSCT) is a rare mesenchymal neoplasm, of uncertain biological potential, that was recently reported to exhibit recurrent gene fusions involving NCOA2-3. The purpose of this study was to, using a larger sample size, better characterize the histopathologic and molecular diversity of UTROSCT. Twenty-six cases of UTROSCT from 5 institutions were selected for further study. Fluorescence in situ hybridization for NCOA1, NCOA2, NCOA3, ESR1 and GREB1, and targeted RNA sequencing was performed on 17 and 8 UTROSCTs, respectively. Eight cases underwent massively parallel sequencing to detect single nucleotide variants (SNV), copy number variations, and structural variants using a targeted hybrid-capture based assay. NCOA1-3 rearrangement was identified in 81.8% (18/22) of cases. The most common fusion was ESR1-NCOA3, occurring in 40.9% (9/22). GREB1-NCOA1 (n=4), ESR1-NCOA2 (n=3), and GREB1-NCOA2 (n=1) rearrangements were also identified. No recurrent SNVs were identified and no tumor had SNVs in FOXL2, DICER1, STK11, or AKT1, which can be seen in ovarian sex cord-stromal tumors. Copy number variations were infrequent. Clinical follow-up was available for 11 cases with a mean follow-up interval of 94.4 (range, 1 to 319) months. Only one case had a recurrence 66 months after the initial diagnosis and this was the single case with a GREB1-NCOA2 fusion. This study reports the morphologic spectrum of UTROSCT and confirms the recently reported recurrent NCOA2-3 gene fusions, in addition to identifying novel rearrangements involving NCOA1 in these tumors.

    View details for DOI 10.1097/PAS.0000000000001348

    View details for Web of Science ID 000504091900004

    View details for PubMedID 31464709

    View details for PubMedCentralID PMC8223168

  • The extended spectrum of RAS-MAPK pathway mutations in colorectal cancer Genes Chromosomes & Cancer Costigan, D. C., Dong, F. 2020; 59 (3): 152-159

    View details for DOI 10.1002/gcc.22813

  • Targeted Genomic Profiling of Female Adnexal Tumors of Probable Wolffian Origin (FATWO) INTERNATIONAL JOURNAL OF GYNECOLOGICAL PATHOLOGY Mirkovic, J., Dong, F., Sholl, L. M., Garcia, E., Lindeman, N., MacConaill, L., Crum, C. P., Nucci, M. R., McCluggage, W., Howitt, B. E. 2019; 38 (6): 543–51
  • Recurrent SMARCB1 Inactivation in Epithelioid Malignant Peripheral Nerve Sheath Tumors AMERICAN JOURNAL OF SURGICAL PATHOLOGY Schaefer, I., Dong, F., Garcia, E. P., Fletcher, C. M., Jo, V. Y. 2019; 43 (6): 835-843

    Abstract

    Epithelioid malignant peripheral nerve sheath tumors (EMPNST) are characterized by diffuse S-100 and SOX10 positivity, frequent immunohistochemical loss of SMARCB1 expression (70%), and rare association with neurofibromatosis type 1. Some cases arise in a preexisting epithelioid schwannoma (ESCW), which also show SMARCB1 loss in 40% of cases. To date, little is known about the genomic landscape of this distinctive variant of malignant peripheral nerve sheath tumor. The aim of this study was to use targeted next-generation sequencing to identify recurrent genomic aberrations in EMPNST and a subset of ESCW, including the basis of SMARCB1 loss. Sixteen EMPNSTs (13 SMARCB1-lost, 3 SMARCB1-retained) and 5 ESCWs with SMARCB1 loss were selected for the cohort. Sequencing identified SMARCB1 gene inactivation in 12/16 (75%) EMPNST and all 5 (100%) ESCW through homozygous deletion (N=8), nonsense (N=7), frameshift (N=2), or splice site (N=2) mutations; 2 EMPNSTs harbored 2 concurrent mutations each. SMARCB1 immunohistochemistry status and SMARCB1 alterations were concordant in 20/21 of the sequenced tumors. Additional genetic alterations in a subset of EMPNST included inactivation of CDKN2A and gain of chromosome 2q. Among SMARCB1-wild-type EMPNSTs there were single cases each with NF1 and NF2 mutations. No cases had SUZ12 or EED mutations. In summary, we identified recurrent SMARCB1 alterations in EMPNST (and all 5 SMARCB1-negative ESCWs tested), supporting loss of SMARCB1 tumor suppressor function as a key oncogenic event. SMARCB1-retained EMPNSTs lack SMARCB1 mutations and harbor different driver events.

    View details for DOI 10.1097/PAS.0000000000001242

    View details for Web of Science ID 000468310500013

    View details for PubMedID 30864974

    View details for PubMedCentralID PMC6520153

  • Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites CLINICAL CANCER RESEARCH Nassar, A. H., Umeton, R., Kim, J., Lundgren, K., Harshman, L., Van Allen, E. M., Preston, M., Dong, F., Bellmunt, J., Mouw, K. W., Choueiri, T. K., Sonpavde, G., Kwiatkowski, D. J. 2019; 25 (8): 2458-2470

    Abstract

    The purpose of this study is to characterize the mutational landscape across the spectrum of urothelial carcinoma (UC) to identify mutational features and potential therapeutic targets.Using targeted exome sequencing (n = 237 genes), we analyzed the mutation spectra of 82 low-grade nonmuscle-invasive bladder cancers (LG-NMIBC), 126 high-grade (HG) NMIBC, 199 muscle-invasive bladder cancers (MIBC), 10 LG-upper tract urothelial cancers (LG-UTUC), and 55 HG-UTUC.FGFR3 and KDM6A mutations were significantly more common in LG-NMIBC (72% and 44%, respectively) versus other bladder subtypes. FGFR3 alterations were also enriched in LG-UTUC versus HG-UTUC tumors (80% vs. 16%). In contrast, TP53 and RB1 mutations were significantly more frequent in all 3 HG urothelial carcinoma subtypes than in LG-NIMBC (45%-58% vs. 4%; 9%-22% vs. 0; respectively). Among LG-NMIBC tumors, KDM6A mutations were more common in women than in men (71% vs. 38%). HG-NMIBC and MIBC had higher tumor mutational burden (TMB) than LG-NMIBC (P = 0.001 and P < 0.01, respectively). DNA-damage repair (DDR) alterations were associated with a higher TMB in HG-NMIBC and MIBC tumors, and these two tumor types were also enriched for an APOBEC mutational signature compared with LG-NMIBC and HG-UTUC. Alterations in FGFR3, PIK3CA, and EP300 correlated with worse overall survival in HG-UTUC and occurred concurrently.Our analysis suggests that a fraction of MIBCs likely arise from precursor lesions other than LG-NMIBC. KDM6A mutations are twice as common in women with LG-NIMBC than those in men. DDR gene mutations and APOBEC mutagenesis drive mutations in HG-NMIBC and MIBC. UTUC has a distinct mutation profile from bladder cancer.

    View details for DOI 10.1158/1078-0432.CCR-18-3147

    View details for Web of Science ID 000464654200014

    View details for PubMedID 30593515

  • A Combined Morphologic and Molecular Approach to Retrospectively Identify KRAS-Mutated Mesonephric-like Adenocarcinomas of the Endometrium AMERICAN JOURNAL OF SURGICAL PATHOLOGY Kolin, D. L., Costigan, D. C., Dong, F., Nucci, M. R., Howitt, B. E. 2019; 43 (3): 389-398
  • SMARCA4-deficient Uterine Sarcoma and Undifferentiated Endometrial Carcinoma are Distinct Clinicopathologic Entities. The American journal of surgical pathology Kolin, D. L., Quick, C. M., Dong, F. n., Fletcher, C. D., Stewart, C. J., Soma, A. n., Hornick, J. L., Nucci, M. R., Howitt, B. E. 2019

    Abstract

    Undifferentiated and dedifferentiated endometrial carcinomas (UDEC) are aggressive uterine tumors which may show loss of expression of SMARCA4 (BRG1) or SMARCB1 (INI-1). The recently described SMARCA4-deficient undifferentiated uterine sarcoma (SDUS) has a morphology which overlaps with UDEC. In this study, we compared clinical, morphologic, immunohistochemical, and molecular characteristics to identify features which differentiate SDUS from UDEC. Cases of SDUS (n=12) were compared with cases of UDEC (n=84, 55 of which were previously published). Immunohistochemistry was performed for p53, mismatch repair proteins, claudin-4, SMARCA4, and SMARCB1. Targeted molecular profiling was performed on 15 cases. Patients with SDUS were significantly younger than those with UDEC (mean 35.8 vs. 61.2 y, P=0.0001). UDEC and SDUS showed morphologic overlap; however, phyllodiform architecture favored a diagnosis of SDUS (36% vs. 0%, P=0.005), while prominent nuclear pleomorphism was only seen in some cases of UDEC (0% vs. 24%, P=0.15). Compared with SDUS, UDEC more frequently showed TP53 mutations (0% vs. 34%, P=0.03), microsatellite instability (0% vs. 44%, P=0.006), and intact SMARCA4 and SMARCB1 (0% vs. 80%); a panel combining these immunohistochemical markers had a sensitivity of 100% and specificity of 92% in distinguishing SDUS and UDEC. Cases of UDEC had mutations in genes associated with endometrial adenocarcinomas (eg, TP53, PTEN, PIK3CA) and occasionally SMARCA4, while SDUS was characterized solely by inactivating mutations in SMARCA4. Disease-specific survival was shorter in SDUS than UDEC (median survival 9 and 36 mo, P=0.01). In conclusion, SDUS occurs in younger patients than UDEC, has a worse prognosis, and in most cases has a distinct molecular and immunohistochemical profile.

    View details for DOI 10.1097/PAS.0000000000001375

    View details for PubMedID 31567195

  • Targeted cancer next generation sequencing as a primary screening tool for microsatellite instability and Lynch syndrome in upper gastrointestinal tract cancers Cancer Epidemiology Biomarkers & Prevention Christakis, A. G., Papke, D. J., Nowak, J. A., Yurgelun, M. B., Agoston, A. T., Lindeman, N. I., MacConaill, L. E., Sholl, L. M., Dong, F. 2019; 28 (7): 1252-1258
  • Targeted next generation sequencing in the detection of mismatch repair deficiency in endometrial cancers Modern Pathology Dong, F., Costigan, D. C., Howitt, B. E. 2019; 32 (2): 252-257
  • Expanding the spectrum of translocations in sclerosing epitheloid fibrosarcoma: A new case with EWSR1-CREB3L3 fusion GENES CHROMOSOMES & CANCER Dong, F., Quade, B. J., Dal Cin, P., Jo, V. Y. 2018; 57 (12): 675-677

    View details for DOI 10.1002/gcc.22677

    View details for Web of Science ID 000450359000009

    View details for PubMedID 30136738

  • SMARCA4-deficient undifferentiated uterine sarcoma (malignant rhabdoid tumor of the uterus): a clinicopathologic entity distinct from undifferentiated carcinoma MODERN PATHOLOGY Kolin, D. L., Dong, F., Baltay, M., Lindeman, N., MacConaill, L., Nucci, M. R., Crum, C. P., Howitt, B. E. 2018; 31 (9): 1442–56

    Abstract

    Small cell carcinoma of the ovary, hypercalcemic type is a rare, aggressive malignancy which usually occurs in young women and is characterized by mutations in SMARCA4, with few other alterations. We recently encountered uterine tumors with morphologic, immunohistochemical, and genetic similarities to small cell carcinoma of the ovary, hypercalcemic type. Herein we report the clinicopathologic and molecular features (using a targeted massively parallel sequencing [MPS] assay) of these tumors. The cases were diagnosed on cervical and endometrial biopsies (n = 2, 34, and 29 years) or hysterectomy and bilateral salpingo-oophorectomy (n = 3, 25, 33, and 58 years). The tumors were composed of sheets of large atypical epithelioid cells with prominent rhabdoid morphology, indistinguishable from the "large cell" variant of small cell carcinoma of the ovary, hypercalcemic type. In three cases, the ovaries were pathologically examined to exclude a primary ovarian malignancy. Immunohistochemically, four of four cases showed SMARCA4 loss, and were negative or only focally positive for keratins, EMA, and claudin-4. One of three cases was positive for WT-1. Targeted MPS was successfully performed on 4 of 5 tumors, and showed recurrent mutations in SMARCA4, with few other alterations. Of the cases diagnosed on hysterectomy, all had extensive lymphovascular invasion, extra-uterine spread, and marked infiltrative growth. These tumors were uniformly aggressive; all patients died of disease (median survival 7 months, range 1-43 months). We propose this entity be called "SMARCA4-deficient undifferentiated uterine sarcoma (malignant rhabdoid tumor of the uterus)", a term which describes both the tumor's underlying molecular abnormality and its morphology. Its unique clinicopathologic and molecular features differentiate it from other related malignancies, including undifferentiated endometrial carcinoma, small cell carcinoma of the ovary (hypercalcemic type), and epithelioid sarcoma. We review and discuss previously reported "rhabdoid tumors of the uterus;" while they are a heterogenous group of tumors, some of them are likely examples of this entity. Correctly identifying cases of SMARCA4-deficient uterine sarcoma from histologic mimics is important as it may have prognostic, predictive, and germline implications.

    View details for PubMedID 29700418

  • Identification of ALK Rearrangements in Malignant Peritoneal Mesothelioma JAMA ONCOLOGY Hung, Y. P., Dong, F., Watkins, J. C., Nardi, V., Bueno, R., Dal Cin, P., Godleski, J. J., Crum, C. P., Chirieac, L. R. 2018; 4 (2): 235-238

    Abstract

    Malignant peritoneal mesothelioma is a rare, aggressive tumor arising from the peritoneal lining, induced by asbestos, therapeutic radiation, or germline mutations. Nevertheless, the molecular features remain largely unknown.To investigate anaplastic lymphoma kinase (ALK) rearrangements in a large series of peritoneal mesothelioma and characterize the mutational landscape of these tumors.We studied 88 consecutive patients (39 men, 49 women; median age 61, range 17-84 years) with peritoneal mesotheliomas diagnosed at a single institution between 2005 and 2015. We identified ALK-positive mesotheliomas by immunohistochemistry and confirmed ALK rearrangement by fluorescence in situ hybridization (FISH). In ALK-rearranged cases, we characterized the fusion partners using targeted next-generation sequencing of both tumor DNA and RNA. In select cases, we quantified asbestos fibers by combined scanning electron microscopy and x-ray spectroscopy. We also explored ALK rearrangement in a separate series of 205 patients with pleural mesothelioma.Identification and characterization of novel ALK rearrangements and correlations with clinicopathologic characteristics.Anaplastic lymphoma kinase was positive by immunohistochemistry in 11 (13%) peritoneal mesotheliomas (focal weak in 8, diffuse strong in 3). In focal weak ALK-positive cases, no ALK rearrangement was detected by FISH or next-generation sequencing. In strong diffuse ALK-positive cases, FISH confirmed ALK rearrangements, and next-generation sequencing identified novel fusion partners ATG16L1, STRN, and TPM1. Patients with ALK-rearranged peritoneal mesotheliomas were women and younger than patients without ALK rearrangement (median age 36 vs 62; Mann-Whitney test, P = .02), but all other clinicopathologic characteristics (size of tumor nodules, histology, treatment, and survival) were not different. No asbestos fibers were detected in ALK-rearranged cases. Furthermore, loss of chromosomal region 9p or 22q or genetic alterations in BAP1, SETD2, or NF2 typically present in peritoneal mesothelioma were absent in the ALK-rearranged cases. All pleural mesotheliomas were ALK-negative by immunohistochemistry.We identified unique ALK rearrangements in a subset of patients with peritoneal mesothelioma, each lacking asbestos fibers, therapeutic radiation, and cytogenetic and molecular alterations typically found in these tumors. Identification of clinically actionable ALK rearrangements may represent a novel pathogenetic mechanism of malignant peritoneal mesothelioma with promise for targeted therapy.

    View details for DOI 10.1001/jamaoncol.2017.2918

    View details for Web of Science ID 000424778600018

    View details for PubMedID 28910456

    View details for PubMedCentralID PMC5838580

  • Targeted Genomic Profiling Reveals Recurrent KRAS Mutations in Mesonephric-like Adenocarcinomas of the Female Genital Tract. The American journal of surgical pathology Mirkovic, J., McFarland, M., Garcia, E., Sholl, L. M., Lindeman, N., MacConaill, L., Dong, F., Hirsch, M., Nucci, M. R., Quick, C. M., Crum, C. P., McCluggage, W. G., Howitt, B. E. 2018; 42 (2): 227-233

    Abstract

    Mesonephric adenocarcinoma most commonly arises in the cervix and is presumed to be derived from normal or hyperplastic mesonephric remnants. It is characterized by recurrent KRAS mutations and lack of PIK3CA/PTEN alterations. Adenocarcinomas of the uterine corpus and ovary characterized by morphologic and immunophenotypic similarities to mesonephric adenocarcinoma have been reported. The pathogenesis of these tumors, which have been designated "mesonephric-like adenocarcinomas" is unknown, and it has been debated whether these represent mesonephric adenocarcinomas that arise in the endometrium/ovary or endometrioid adenocarcinomas that closely mimic mesonephric adenocarcinoma. The relationship at the molecular level between mesonephric adenocarcinomas and mesonephric-like adenocarcinomas is unknown. The aim of this study was to examine the molecular alterations in mesonephric-like adenocarcinomas to identify driver mutations and potential therapeutically targetable mutations, and to determine the relationship between mesonephric-like adenocarcinomas and mesonephric adenocarcinomas using targeted next-generation sequencing. Seven mesonephric-like adenocarcinomas (4 ovarian, 3 uterine corpus) underwent targeted next-generation sequencing to detect mutations, copy number variations and structural variants in exonic regions of 300 cancer genes, and 113 selected intronic regions across 35 genes. All 7 tumors (100%) harbored canonical activating KRAS mutations (4 G12D, 3 G12V). PIK3CA activating mutations were identified in 3 of 7 (43%) cases. There were no alterations in PTEN, ARID1A, or TP53 in any of the tumors. In copy number analysis, 5 of 7 (71%) tumors exhibited 1q gain, which was accompanied by 1p loss in 2 cases. In addition, 4 of 7 (57%) tumors had chromosome 10 gain, which was accompanied by gain of chromosome 12 in 3 cases. Mesonephric-like adenocarcinomas, similar to mesonephric adenocarcinomas, are characterized by recurrent KRAS mutations, gain of 1q, lack of PTEN mutations, and gains of chromosomes 10 and 12. PIK3CA mutations, which have not previously been identified in mesonephric adenocarcinoma, were found in 3 of 7 (43%) mesonephric-like adenocarcinomas in our study. Mesonephric-like adenocarcinomas exhibit strikingly similar molecular aberrations to mesonephric adenocarcinomas, but also frequently harbor PIK3CA mutations, demonstrating biological overlap with carcinomas of both mesonephric and Mullerian (endometrioid) differentiation. Given the previously documented association with endometriosis (ovarian neoplasms) and the prominent endometrial involvement (uterine corpus neoplasms), we believe these are best regarded as of Mullerian origin and representing adenocarcinomas which differentiate along mesonephric lines; as such, we propose the term mesonephric-like Mullerian adenocarcinoma.

    View details for DOI 10.1097/PAS.0000000000000958

    View details for PubMedID 28984674

  • Validation of a targeted next-generation sequencing approach to detect mismatch repair deficiency in colorectal adenocarcinoma Modern Pathology Papke, D. J., Nowak, J. A., Yurgelun, M. B., Frieden, A., Srivastava, A., Lindeman, N. I., Sholl, L. M., MacConaill, L. E., Dong, F. 2018; 31 (12): 1882-1890
  • Differentiated exophytic vulvar intraepithelial lesions are genetically distinct from keratinizing squamous cell carcinomas and contain mutations in PIK3CA. Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc Watkins, J. C., Howitt, B. E., Horowitz, N. S., Ritterhouse, L. L., Dong, F., MacConaill, L. E., Garcia, E., Lindeman, N. I., Lee, L. J., Berkowitz, R. S., Nucci, M. R., Crum, C. P. 2017; 30 (3): 448-458

    Abstract

    Human papillomavirus-negative keratinizing vulvar cancers typically harbor TP53 mutations as do their precursors, differentiated vulvar intraepithelial neoplasia. However, atypical verruciform proliferations are also associated with these malignancies and their pathogenesis is poorly understood. This study compared 11 atypical verruciform lesions, including atypical verruciform hyperplasia, vulvar acanthosis with altered differentiation, and verruciform lichen simplex chronicus, with 14 human papillomavirus-negative keratinizing squamous cell carcinomas. Extracted tissue DNA was subjected to targeted massively parallel sequencing of the exonic regions of 300 genes. Eight (73%) and six (55%) of eleven atypical verruciform lesions contained mutations in PIK3CA and ARID2, respectively. No TP53 mutations were identified. Eleven (79%) and five (36%) of fourteen keratinizing squamous cell carcinomas tested contained TP53 and CDKN2A mutations, respectively. Keratinizing squamous cell carcinomas displayed the majority of copy number variations with some variations (7p gain and 8p loss) shared by some cases in both groups. One patient developed atypical verruciform lesions with PIK3CA mutations followed by a keratinizing carcinoma with mutations in both PIK3CA and TP53. This study, for the first time segregates atypical verruciform lesions by virtue of a unique genotype (PIK3CA mutant/TP53 wild type) illustrating an example of progression to a TP53-mutated keratinizing carcinoma. The findings indicate that although PIK3CA mutations are found in <10% of vulvar squamous cell carcinomas, they may be specific for a particular pathway involving atypical verruciform lesions, which could function as either a direct precursor or a risk factor for vulvar squamous cell carcinoma. Given the presence of a molecular signature, we propose the term 'differentiated exophytic vulvar intraepithelial lesion' for this group. Whether they function as direct precursors to a less common form of squamous cell carcinoma will require further study, but carcinomas associated with these lesions might warrant testing for PIK3CA mutations to address this question.

    View details for DOI 10.1038/modpathol.2016.187

    View details for PubMedID 27834349

  • GNAS mutations in primary mucinous and non-mucinous lung adenocarcinomas Modern Pathology Ritterhouse, L. L., Vivero, M., Mino-Kenudson, M., Sholl, L. M., Iafrate, A. J., Nardi, V., Dong, F. 2017; 30 (12): 1720-1727
  • Detection of mismatch repair deficiency and microsatellite instability in colorectal adenocarcinoma by targeted next generation sequencing Journal of Molecular Diagnostics Nowak, J. A., Yurgelun, M. B., Bruce, J. L., Rojas-Rudilla, V., Hall, D. L., Shivdasani, P., Garcia, E. P., Agoston, A. T., Srivastava, A., Ogino, S., Kuo, F. C., Lindeman, N. I., Dong, F. 2017; 19 (1): 84-91
  • Validation of OncoPanel: a targeted next generation sequencing assay for the detection of somatic variants in cancer Archives of Pathology & Laboratory Medicine Garcia, E. P., Minkovsky, A., Jia, Y., Ducar, M. D., Shivdasani, P., Gong, X., Ligon, A. H., Sholl, L. M., Kuo, F. C., MacConaill, L. E., Lindeman, N. I., Dong, F. 2017; 141 (6): 751-758
  • Melanoma arising in a nevus of Ito: novel genetic mutations and a review of the literature on cutaneous malignant transformation of dermal melanocytosis JOURNAL OF CUTANEOUS PATHOLOGY Tse, J. Y., Walls, B. E., Pomerantz, H., Yoon, C. H., Buchbinder, E. I., Werchniak, A. E., Dong, F., Lian, C. G., Granter, S. R. 2016; 43 (1): 57-63

    Abstract

    Dermal melanocytosis refers to a spectrum of benign melanocytic proliferations that includes Mongolian spot, nevus of Ota and nevus of Ito. These lesions most commonly occur in persons of Asian or African descent and are often present at birth or develop during childhood. Very rarely, dermal melanocytoses undergo malignant transformation. There have been only 13 reports in the literature of primary cutaneous melanoma arising in dermal melanocytoses. We report a case of a Chinese woman with melanoma arising in a congenital nevus of Ito. We performed targeted next-generation sequencing of the tumor which revealed mutations of GNAQ and BAP1, suggesting that alterations in these two genes led to malignant transformation of the nevus of Ito. We also provide a summary of reports in the literature regarding primary cutaneous melanoma arising in the context of dermal melanocytosis.

    View details for DOI 10.1111/cup.12568

    View details for Web of Science ID 000369303700010

    View details for PubMedID 26260725

  • KRAS and NKX2-1 mutations in invasive mucinous adenocarcinoma of the lung Journal of Thoracic Oncology Hwang, D. H., Sholl, L. M., Rojas-Rudilla, V., Hall, D. L., Shivdasani, P., Garcia, E. P., MacConaill, L. E., Vivero, M., Hornick, J. L., Kuo, F. C., Lindeman, N. I., Dong, F. 2016; 11 (4): 496-503
  • A BRCA1/2 mutational signature and survival in ovarian high-grade serous carcinoma Cancer Epidemiology Biomarkers & Prevention Dong, F., Davineni, P. K., Howitt, B. E., Beck, A. H. 2016; 25 (11): 1511-1516
  • Papillary renal cell carcinoma: correlation of tumor grade and histologic characteristics with clinical outcome HUMAN PATHOLOGY Cornejo, K. M., Dong, F., Zhou, A. G., Wu, C., Young, R. H., Braaten, K., Sadow, P. M., Nielsen, G. P., Oliva, E. 2015; 46 (10): 1411-1417

    Abstract

    Histologic prognostic parameters in papillary renal cell carcinoma (PRCC) are unclear. The aims were to review the clinicopathological features of PRCC, including Fuhrman grade and International Society of Urological Pathology (ISUP) nucleolar grade, and to identify parameters that may be independent prognostic indicators. PRCCs in patients treated by nephrectomy were retrieved from the pathology files from 1984 to 2010. Parameters studied included tumor multifocality, size, PRCC type (1 or 2), Fuhrman grade, ISUP nucleolar grade, presence of necrosis, lymphovascular invasion, and stage at presentation. Cancer-specific survival (CSS) and overall survival (OS) were used as prognostic measures. Of 154 PRCCs, 112 (73%) were type 1, and 42 (27%), type 2. A total of 125 patients were male, and 29, female, with ages from 26 to 86 (mean, 62.7) years. Fuhrman grade was 1 in 8 (5%), 2 in 95 (62%), 3 in 49 (32%), and 4 in 2 (1%) tumors, respectively. ISUP nucleolar grade was 1 in 47 (31%), 2 in 56 (36%), 3 in 49 (32%), and 4 in 2 (1%) tumors, respectively. Mean follow-up interval was 73.9 months (0.13-222 months). ISUP nucleolar grade was a significant predictor of both CSS and OS in univariate (CSS, P = .001; OS, P = .004) and multivariate (CSS, P = .04; OS, P = .008) analyses, whereas Fuhrman grade was only predictive of CSS in univariate (P = .001) and multivariate (P = .04) analyses. Only ISUP nucleolar grade and lymphovascular invasion were independently prognostic for CSS and OS in univariate and multivariate analyses. Therefore, the ISUP nucleolar grade appears to be superior in predicting survival in patients with PRCC.

    View details for DOI 10.1016/j.humpath.2015.07.001

    View details for Web of Science ID 000362061400001

    View details for PubMedID 26297250

  • Squamous Cell Carcinoma of the Vulva A Subclassification of 97 Cases by Clinicopathologic, Immunohistochemical, and Molecular Features (p16, p53, and EGFR) AMERICAN JOURNAL OF SURGICAL PATHOLOGY Dong, F., Kojiro, S., Borger, D. R., Growdon, W. B., Oliva, E. 2015; 39 (8): 1045-1053

    Abstract

    Squamous cell carcinomas (SCCs) of the vulva develop through human papilloma virus (HPV)-associated or HPV-independent pathways, but the relationship between pathogenesis, classification, and prognosis of these tumors is controversial. Therefore, we review the morphology, immunophenotype, and select molecular features of a consecutive series of 97 patients with vulvar SCC with a median clinical follow-up of 3.6 years. Tumors were histologically classified as basaloid (13), warty (11), mixed basaloid and warty (1), keratinizing (68), nonkeratinizing (3), and sarcomatoid (1). Diffuse p16 expression was associated with younger age at presentation (P<0.0001), basaloid and warty carcinoma subtypes (P<0.0001), and usual vulvar intraepithelial neoplasia (P<0.0001) and was negatively associated with p53 immunopositivity (P=0.0008). Five keratinizing SCCs showed p16 and p53 coexpression, but only 1 was positive for high-risk HPV by in situ hybridization. Among 8 of 36 tumors with EGFR gene amplification, 4 were p53 positive but none p16 positive. In a Cox regression model, early clinical stage (P<0.006), p16 expression (P=0.002), and absent p53 expression (P=0.02) were independent predictors of improved overall survival. These findings utilize morphologic and immunohistochemical analysis to support HPV-associated and HPV-independent pathogenesis of vulvar SCCs and support p16 and p53 immunohistochemistry as markers of disease biology and clinical outcome.

    View details for DOI 10.1097/PAS.0000000000000454

    View details for Web of Science ID 000358417800004

    View details for PubMedID 26171917

  • Next-Generation Sequencing-Based Panel Testing for Myeloid Neoplasms CURRENT HEMATOLOGIC MALIGNANCY REPORTS Kuo, F. C., Dong, F. 2015; 10 (2): 104-111

    Abstract

    Our ability to interrogate a broad array of genetic alterations in myeloid neoplasm has increased significantly with the advance in next-generation sequencing (NGS). In addition to morphologic examination, flow cytometry, and cytogenetics, NGS-based testing can add additional information to the diagnostic workup. More than a dozen myeloid-focused NGS-based panels are now available from commercial and academic laboratories. In this review, we examine the content of these panels in the context of our current understanding of driver alterations in myeloid neoplasms. With improved turnaround time, decreasing costs, and an expanding knowledge of the therapeutic and prognostic significance of the detected variants, NGS-based panel testing is likely to play a major role in the management of patients with myeloid neoplasm in the coming decade.

    View details for DOI 10.1007/s11899-015-0256-3

    View details for Web of Science ID 000355214100005

    View details for PubMedID 25933675

  • Clear cell carcinoma of the ovary: evaluation of prognostic parameters based on a clinicopathological analysis of 100 cases HISTOPATHOLOGY Bennett, J. A., Dong, F., Young, R. H., Oliva, E. 2015; 66 (6): 808-815

    Abstract

    The aim of this study was to evaluate the clinicopathological features of ovarian clear cell carcinomas in order to identify which, if any, are prognostically significant, and to determine whether there is value in grading these tumours.One hundred tumours with clinical follow-up were reviewed. Features evaluated included age, preoperative/intraoperative rupture, size, architectural pattern(s), presence of oxyphilic cells, degree of cytological atypia, nucleolar grade, mitoses, background precursor and stage. Survival differences were analysed using the log-rank test and Kaplan-Meier estimator. Stage and lymph node status were the only parameters that were statistically significant (P < 0.0001). Patients with stage I disease (71%) had a 92% 5-year survival compared to a 31% 5-year survival in advanced stage disease (29%). Those with negative lymph nodes (92%) had an 80% 5-year survival compared to a 22% 5-year survival for those with positive nodes (8%).This study shows that stage and lymph node status are the only prognostically significant parameters in patients with ovarian clear cell carcinoma. It also confirms that most patients with clear cell carcinoma present with disease confined to the ovary, and have an excellent prognosis. Grading ovarian clear cell carcinomas based on morphological features is not recommended, as none are of prognostic significance.

    View details for DOI 10.1111/his.12514

    View details for Web of Science ID 000352809600006

    View details for PubMedID 25065903

  • Crowdsourcing image annotation for nucleus detection and segmentation in computational pathology: evaluating experts, automated methods, and the crowd. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Irshad, H., Montaser-Kouhsari, L., Waltz, G., Bucur, O., Nowak, J. A., Dong, F., Knoblauch, N. W., Beck, A. H. 2015: 294-305

    Abstract

    The development of tools in computational pathology to assist physicians and biomedical scientists in the diagnosis of disease requires access to high-quality annotated images for algorithm learning and evaluation. Generating high-quality expert-derived annotations is time-consuming and expensive. We explore the use of crowdsourcing for rapidly obtaining annotations for two core tasks in com- putational pathology: nucleus detection and nucleus segmentation. We designed and implemented crowdsourcing experiments using the CrowdFlower platform, which provides access to a large set of labor channel partners that accesses and manages millions of contributors worldwide. We obtained annotations from four types of annotators and compared concordance across these groups. We obtained: crowdsourced annotations for nucleus detection and segmentation on a total of 810 images; annotations using automated methods on 810 images; annotations from research fellows for detection and segmentation on 477 and 455 images, respectively; and expert pathologist-derived annotations for detection and segmentation on 80 and 63 images, respectively. For the crowdsourced annotations, we evaluated performance across a range of contributor skill levels (1, 2, or 3). The crowdsourced annotations (4,860 images in total) were completed in only a fraction of the time and cost required for obtaining annotations using traditional methods. For the nucleus detection task, the research fellow-derived annotations showed the strongest concordance with the expert pathologist- derived annotations (F-M =93.68%), followed by the crowd-sourced contributor levels 1,2, and 3 and the automated method, which showed relatively similar performance (F-M = 87.84%, 88.49%, 87.26%, and 86.99%, respectively). For the nucleus segmentation task, the crowdsourced contributor level 3-derived annotations, research fellow-derived annotations, and automated method showed the strongest concordance with the expert pathologist-derived annotations (F-M = 66.41%, 65.93%, and 65.36%, respectively), followed by the contributor levels 2 and 1 (60.89% and 60.87%, respectively). When the research fellows were used as a gold-standard for the segmentation task, all three con- tributor levels of the crowdsourced annotations significantly outperformed the automated method (F-M = 62.21%, 62.47%, and 65.15% vs. 51.92%). Aggregating multiple annotations from the crowd to obtain a consensus annotation resulted in the strongest performance for the crowd-sourced segmentation. For both detection and segmentation, crowd-sourced performance is strongest with small images (400 × 400 pixels) and degrades significantly with the use of larger images (600 × 600 and 800 × 800 pixels). We conclude that crowdsourcing to non-experts can be used for large-scale labeling microtasks in computational pathology and offers a new approach for the rapid generation of labeled images for algorithm development and evaluation.

    View details for DOI 10.1142/9789814644730_0029

    View details for PubMedID 25592590

    View details for PubMedCentralID PMC4299942

  • Computational Pathology to Discriminate Benign from Malignant Intraductal Proliferations of the Breast PLOS ONE Dong, F., Irshad, H., Oh, E., Lerwill, M. F., Brachtel, E. F., Jones, N. C., Knoblauch, N. W., Montaser-Kouhsari, L., Johnson, N. B., Rao, L. F., Faulkner-Jones, B., Wilbur, D. C., Schnitt, S. J., Beck, A. H. 2014; 9 (12): e114885

    Abstract

    The categorization of intraductal proliferative lesions of the breast based on routine light microscopic examination of histopathologic sections is in many cases challenging, even for experienced pathologists. The development of computational tools to aid pathologists in the characterization of these lesions would have great diagnostic and clinical value. As a first step to address this issue, we evaluated the ability of computational image analysis to accurately classify DCIS and UDH and to stratify nuclear grade within DCIS. Using 116 breast biopsies diagnosed as DCIS or UDH from the Massachusetts General Hospital (MGH), we developed a computational method to extract 392 features corresponding to the mean and standard deviation in nuclear size and shape, intensity, and texture across 8 color channels. We used L1-regularized logistic regression to build classification models to discriminate DCIS from UDH. The top-performing model contained 22 active features and achieved an AUC of 0.95 in cross-validation on the MGH data-set. We applied this model to an external validation set of 51 breast biopsies diagnosed as DCIS or UDH from the Beth Israel Deaconess Medical Center, and the model achieved an AUC of 0.86. The top-performing model contained active features from all color-spaces and from the three classes of features (morphology, intensity, and texture), suggesting the value of each for prediction. We built models to stratify grade within DCIS and obtained strong performance for stratifying low nuclear grade vs. high nuclear grade DCIS (AUC = 0.98 in cross-validation) with only moderate performance for discriminating low nuclear grade vs. intermediate nuclear grade and intermediate nuclear grade vs. high nuclear grade DCIS (AUC = 0.83 and 0.69, respectively). These data show that computational pathology models can robustly discriminate benign from malignant intraductal proliferative lesions of the breast and may aid pathologists in the diagnosis and classification of these lesions.

    View details for DOI 10.1371/journal.pone.0114885

    View details for Web of Science ID 000347515300091

    View details for PubMedID 25490766

    View details for PubMedCentralID PMC4260962

  • Not all mixed-type intraductal papillary mucinous neoplasms behave like main-duct lesions: Implications of minimal involvement of the main pancreatic duct SURGERY Sahora, K., Fernandez-del Castillo, C., Dong, F., Marchegiani, G., Thayer, S. P., Ferrone, C. R., Sahani, D. V., Brugge, W. R., Warshaw, A. L., Lillemoe, K. D., Mino-Kenudson, M. 2014; 156 (3): 611-621

    Abstract

    The malignant potential of intraductal mucinous neoplasm of the pancreas (IPMN) is associated closely with main pancreatic duct (MPD) involvement. Because mixed-type IPMN is thought to have the same malignant potential as that of main-duct (MD)-IPMN, resection is recommended; however, the biological nature of mixed-type IPMN with only minimal involvement of MPD (min-mix-IPMN) may be different.A prospective database of 404 resected IPMNs was re-reviewed to subclassify mixed-type IPMNs. We defined min-mix-IPMN as absence of gross abnormalities (except for dilatation) of MPD and noncircumferential microscopic involvement of MPD limited to few sections.We identified 46 min-mix-IPMNs, 163 IPMNs with extensive involvement of MPD (ex-mix-IPMN), 175 branch-duct (BD)-IPMNs, and 20 MD-IPMNs. The majority of min-mix-IPMNs were found incidentally and increased cyst size on surveillance was the leading operative indication. The median diameter of MPD was 2 mm in min-mix-IPMN versus 9 mm in ex-mix-IPMN (P < .0001), and cysts ≥10 mm were present in 62% of ex-mix-IPMNs versus 93% of min-mix-IPMNs (P < .0001). Most importantly, the vast majority of min-mix-IPMNs exhibited gastric-type epithelium, similar to BD-IPMNs, whereas intestinal-type epithelium was present in half of ex-mix-IPMNs, similar to MD-IPMNs. The prevalence of high-grade lesions was less in min-mix-IPMN than ex-mix-IPMN (P < .0001). These differences were reflected in better disease-specific outcomes of min-mix-IPMN compared with ex-mix-IPMN (P = .046).Min-mix-IPMN often presents with no MPD dilation and is an incidental finding by microscopic examination. min-mix-IPMN shares the pathologic features and less aggressive biology with BD-IPMN. We propose that min-mix-IPMN be categorized differently than ex-mix-IPMN.

    View details for DOI 10.1016/j.surg.2014.04.023

    View details for Web of Science ID 000341228200016

    View details for PubMedID 25081232

    View details for PubMedCentralID PMC5614499

  • Modulation of miR-29 Expression by Alpha-Fetoprotein Is Linked to the Hepatocellular Carcinoma Epigenome HEPATOLOGY Parpart, S., Roessler, S., Dong, F., Rao, V., Takai, A., Ji, J., Qin, L., Ye, Q., Jia, H., Tang, Z., Wang, X. 2014; 60 (3): 872-883

    Abstract

    Globally, hepatocellular carcinoma (HCC) accounts for 70%-85% of primary liver cancers and ranks as the second leading cause of male cancer death. Serum alpha-fetoprotein (AFP), normally highly expressed in the liver only during fetal development, is reactivated in 60% of HCC tumors and associated with poor patient outcome. We hypothesize that AFP+ and AFP- tumors differ biologically. Multivariable analysis in 237 HCC cases demonstrates that AFP level predicts poor survival independent of tumor stage (P<0.043). Using microarray-based global microRNA (miRNA) profiling, we found that miRNA-29 (miR-29) family members were the most significantly (P<0.001) down-regulated miRNAs in AFP+ tumors. Consistent with miR-29's role in targeting DNA methyltransferase 3A (DNMT3A), a key enzyme regulating DNA methylation, we found a significant inverse correlation (P<0.001) between miR-29 and DNMT3A gene expression, suggesting that they might be functionally antagonistic. Moreover, global DNA methylation profiling reveals that AFP+ and AFP- HCC tumors have distinct global DNA methylation patterns and that increased DNA methylation is associated with AFP+ HCC. Experimentally, we found that AFP expression in AFP- HCC cells induces cell proliferation, migration, and invasion. Overexpression of AFP, or conditioned media from AFP+ cells, inhibits miR-29a expression and induces DNMT3A expression in AFP- HCC cells. AFP also inhibited transcription of the miR-29a/b-1 locus, and this effect is mediated through c-MYC binding to the transcript of miR-29a/b-1. Furthermore, AFP expression promotes tumor growth of AFP- HCC cells in nude mice.Tumor biology differs considerably between AFP+ HCC and AFP- HCC; AFP is a functional antagonist of miR-29, which may contribute to global epigenetic alterations and poor prognosis in HCC.

    View details for DOI 10.1002/hep.27200

    View details for Web of Science ID 000341239200015

    View details for PubMedID 24798303

    View details for PubMedCentralID PMC4146718

  • Standardized decision support in next generation sequencing reports of somatic cancer variants MOLECULAR ONCOLOGY Dienstmann, R., Dong, F., Borger, D., Dias-Santagata, D., Ellisen, L. W., Le, L. P., Iafrate, A. 2014; 8 (5): 859-873

    Abstract

    Of hundreds to thousands of somatic mutations that exist in each cancer genome, a large number are unique and non-recurrent variants. Prioritizing genetic variants identified via next generation sequencing technologies remains a major challenge. Many such variants occur in tumor genes that have well-established biological and clinical relevance and are putative targets of molecular therapy, however, most variants are still of unknown significance. With large amounts of data being generated as high throughput sequencing assays enter the clinical realm, there is a growing need to better communicate relevant findings in a timely manner while remaining cognizant of the potential consequences of misuse or overinterpretation of genomic information. Herein we describe a systematic framework for variant annotation and prioritization, and we propose a structured molecular pathology report using standardized terminology in order to best inform oncology clinical practice. We hope that our experience developing a comprehensive knowledge database of emerging predictive markers matched to targeted therapies will help other institutions implement similar programs.

    View details for DOI 10.1016/j.molonc.2014.03.021

    View details for Web of Science ID 000339774900001

    View details for PubMedID 24768039

    View details for PubMedCentralID PMC5528527

  • Architectural Heterogeneity and Cribriform Pattern Predict Adverse Clinical Outcome for Gleason Grade 4 Prostatic Adenocarcinoma AMERICAN JOURNAL OF SURGICAL PATHOLOGY Dong, F., Yang, P., Wang, C., Wu, S., Xiao, Y., McDougal, W., Young, R. H., Wu, C. 2013; 37 (12): 1855–61

    Abstract

    Gleason grade 4 defines a group of prostatic adenocarcinomas with a variety of architectural patterns, including poorly formed glands, fused glands, and cribriform pattern. To address the relative contribution to clinical prognosis by these distinct patterns, the histology of 241 consecutive radical prostatectomy specimens with the highest Gleason grade of 4 was reviewed. The presence of poorly formed glands, fused glands, and cribriform pattern was recorded for each case, and the types of architectural patterns present were associated with patient outcome. In this population, prostatic adenocarcinomas demonstrated architectural heterogeneity, with 17% of cases exhibiting a single Gleason grade 4 pattern, and 41% of cases exhibiting all 3 morphologic patterns. Patients exhibiting all 3 architectural patterns had lower rates of biochemical disease-free survival (66% vs. 76% at 5 y; log rank P=0.006). Twenty-two of 165 patients (13.3%) with cribriform pattern adenocarcinoma developed metastasis, whereas 2 of 76 patients (2.6%) without cribriform pattern developed metastasis at a median postoperative follow-up of 10.0 years. The presence of a cribriform pattern was an independent predictor for biochemical recurrence (hazard ratio 2.41; 95% confidence interval, 1.34-4.32; P=0.003) as well as metastasis after radical prostatectomy (hazard ratio 5.62; 95% confidence interval, 1.29-24.5; P=0.02). These results suggest that the morphologic subclassification of distinct Gleason grade 4 architectural patterns provides prognostic information beyond the current Gleason classification system.

    View details for PubMedID 24145642

  • Impact on the Clinical Outcome of Prostate Cancer by the 2005 International Society of Urological Pathology Modified Gleason Grading System AMERICAN JOURNAL OF SURGICAL PATHOLOGY Dong, F., Wang, C., Farris, A., Wu, S., Lee, H., Olumi, A. F., McDougal, W., Young, R. H., Wu, C. 2012; 36 (6): 838–43

    Abstract

    The 2005 International Society of Urological Pathology (ISUP) Consensus Conference modified the Gleason grading system for prostate cancer. In the modified criteria, ill-defined glands with poorly formed lumina and large cribriform glands with smooth borders, classically described as Gleason pattern 3 adenocarcinoma, were redefined as Gleason pattern 4. To evaluate the clinical outcome of patients upgraded by the ISUP criteria, the histologic slides of 1240 consecutive radical prostatectomy specimens at a single institution were reviewed, and each case of adenocarcinoma was graded on the basis of the original and modified Gleason criteria. A total of 806 patients with prostate cancer of classical Gleason score 3+3=6 or 3+4=7 and modified Gleason score 6 to 8 were analyzed with a median overall follow-up of 12.6 years. In the study population, 34% of patients with classical Gleason score 3+3=6 prostate cancer were upgraded to modified Gleason score 7 or 8 by the ISUP criteria. Compared to patients with modified Gleason score 3+3=6 and patients with classical Gleason score 3+4=7, the upgraded patients were at intermediate risk for biochemical progression (paired log-rank P≤0.003) and metastasis (paired log-rank P≤0.04) after radical prostatectomy. The hazard ratio for upgrading was 1.60 (95% confidence interval, 1.09-2.35, P=0.02) for biochemical recurrence and 5.02 (95% confidence interval, 1.77-14.2, P=0.003) for metastasis. These results validate the prognostic value of the modified Gleason grading system and suggest that the recognition of an intermediate-risk histological pattern may be useful in the prognosis of patients with prostate cancer.

    View details for PubMedID 22592143

  • Kruppel-Like Factor 2 Regulates Endothelial Barrier Function ARTERIOSCLEROSIS THROMBOSIS AND VASCULAR BIOLOGY Lin, Z., Natesan, V., Shi, H., Dong, F., Kawanami, D., Mahabeleshwar, G. H., Atkins, G., Nayak, L., Cui, Y., Finigan, J. H., Jain, M. K. 2010; 30 (10): 1952-U181

    Abstract

    A central function of the endothelium is to serve as a selective barrier that regulates fluid and solute exchange. Although perturbation of barrier function can contribute to numerous disease states, our understanding of the molecular mechanisms regulating this aspect of endothelial biology remains incompletely understood. Accumulating evidence implicates the Kruppel-like factor 2 (KLF2) as a key regulator of endothelial function. However, its role in vascular barrier function is unknown.To assess the role of KLF2 in vascular barrier function in vivo, we measured the leakage of Evans blue dye into interstitial tissues of the mouse ear after treatment with mustard oil. By comparison with KLF2(+/+) mice, KLF2(+/-) mice exhibited a significantly higher degree of vascular leak. In accordance with our in vivo observation, adenoviral overexpression of KLF2 in human umbilical vein endothelial cells strongly attenuated the increase of endothelial leakage by thrombin and H(2)O(2) as measured by fluorescein isothiocyanate dextrans (FITC-dextran) passage. Conversely, KLF2 deficiency in human umbilical vein endothelial cells and primary endothelial cells derived from KLF2(+/-) mice exhibited a marked increase in thrombin and H(2)O(2)-induced permeability. Mechanistically, our studies indicate that KLF2 confers barrier-protection via differential effects on the expression of key junction protein occludin and modification of a signaling molecule (myosin light chain) that regulate endothelial barrier integrity.These observations identify KLF2 as a novel transcriptional regulator of vascular barrier function.

    View details for DOI 10.1161/ATVBAHA.110.211474

    View details for Web of Science ID 000281882800014

    View details for PubMedID 20651277

    View details for PubMedCentralID PMC3095948

  • The Epstein criteria predict for organ-confined but not insignificant disease and a high likelihood of cure at radical prostatectomy. European urology Lee, M. C., Dong, F., Stephenson, A. J., Jones, J. S., Magi-Galluzzi, C., Klein, E. A. 2010; 58 (1): 90-5

    Abstract

    Few reports attempt to validate the role of Epstein criteria in selecting patients for an active surveillance protocol.To determine the performance of the Epstein biopsy criteria for predicting pathologic end points and biochemical relapse-free survival (bRFS) in men with early stage prostate cancer (PCa) treated by radical prostatectomy (RP).Between October 1999 and January 2007, 746 consecutive patients were biopsied, and then underwent RP at our tertiary care institution. Two hundred sixty-eight patients met the entry criteria of Gleason 6 disease only on initial biopsy with complete pathologic information.Primary end point was insignificant disease. Insignificant disease was defined using a classical (organ-confined, Gleason score <6, and tumor volume <0.5 cm(3)) and more liberal (organ-confined, Gleason <6 tumor of any volume) formulation. Secondary end points included organ-confined disease and bRFS.One hundred thirty-six men (51%) met the Epstein biopsy criteria, and 167 (62%) had organ-confined cancer. Insignificant disease by the classical and liberal definitions was present in 68 (25%) and 92 (34%) patients, respectively. Cases meeting Epstein biopsy criteria were more likely to have insignificant disease by either definition (p<0.001) and more likely to have organ-confined tumors (p<0.001). Sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) varied widely among the end points, with sensitivity (74%) and NPV (86%) best for the classical definition of insignificant disease and specificity (74%) and PPV (92%) best for organ-confined disease. The estimated 5-yr bRFS was 100% for those meeting Epstein biopsy criteria compared to 83% for those not meeting these criteria.The Epstein biopsy criteria predict for a high likelihood of organ-confined disease and the absence of biochemical failure up to 5 yr after RP. These criteria are insufficiently robust to predict the presence of biologically insignificant disease.

    View details for DOI 10.1016/j.eururo.2009.10.025

    View details for PubMedID 19875227

  • Translating the Metastasis Paradigm from Scientific Theory to Clinical Oncology CLINICAL CANCER RESEARCH Dong, F., Budhu, A. S., Wang, X. 2009; 15 (8): 2588-2593

    Abstract

    Cancer metastasis contributes to significant morbidity and mortality. Patients with metastatic cancer, often considered incurable, are provided with either supportive care or aggressive management without curative intent. Despite decades of research toward unraveling cancer progression mechanisms, the current body of knowledge has not translated into effective antimetastasis therapies, but recent findings challenge the classic notion that metastases develop during the late stages of carcinogenesis. Here, we evaluate the scientific evidence in the context of the multistage metastasis model. The resolution of current controversies has implications on both the prognostic value of molecular technology and the future of targeted therapies for the clinical benefit of metastasis patients.

    View details for DOI 10.1158/1078-0432.CCR-08-2356

    View details for Web of Science ID 000265314600003

    View details for PubMedID 19351761

    View details for PubMedCentralID PMC2683353

  • Prostate biopsy clinical and pathological variables that predict significant grading changes in patients with intermediate and high grade prostate cancer BJU INTERNATIONAL Moussa, A. S., Li, J., Soriano, M., Klein, E. A., Dong, F., Jones, J. 2009; 103 (1): 43-48

    Abstract

    To identify the clinical and pathological variables that predict pathological changes in the significant proportion of men with prostate cancer who have an intermediate- or high-grade biopsy Gleason score (GS) of >or=7 and who are upgraded or downgraded on interpretation of radical prostatectomy (RP) pathological specimens, as GS is critical in treatment decisions.We retrospectively evaluated 1129 patients who had RP after a biopsy showing a GS of >or=7, at our institution, from 2000 to 2007. Complete relevant clinical information was available for all patients. A multivariable logistic regression analysis was used to identify predictors of pathological grading changes.The overall mean age was 61 years, with median prostate-specific antigen (PSA) level of 6 ng/mL. Of the 1129 patients, the surgical GS was upgraded in 296 (26.2%), downgraded in 210 (18.6%), and remained the same in 623 (55.2%). Factors predicting a surgical GS upgrade were a higher PSA level (P = 0.005), presence of perineural invasion (P = 0.043), absence of inflammation (P < 0.001), and absence of associated high-grade prostatic intraepithelial neoplasia (P = 0.02). In an analysis of pathological variables the number of positive cores (P = 0.033) was predictor of upgrading. Large prostate volume (P = 0.004) and low maximum percentage cancer in any core (P = 0.001) were predictors of downgrading.Men with a higher PSA level, perineural invasion and high-volume cancer at biopsy are most likely to be upgraded, while men with a large prostate volume and low-volume cancer at biopsy are more likely to be downgraded. These findings have implications for men with prostate cancer managed without confirmation by RP of their true GS.

    View details for DOI 10.1111/j.1464-410X.2008.08059.x

    View details for Web of Science ID 000261683700010

    View details for PubMedID 18782303

  • Adenoid Cystic Carcinoma of the External Auditory Canal LARYNGOSCOPE Dong, F., Gidley, P. W., Ho, T., Luna, M. A., Ginsberg, L. E., Sturgis, E. M. 2008; 118 (9): 1591-1596

    Abstract

    To describe the clinical history and outcome of patients with adenoid cystic carcinoma (ACC) of the external auditory canal (EAC).Retrospective case series.A search of our institution's tumor registry identified 22 patients with ACC of the EAC. Both clinical histories and pathology slides, when available, were reviewed.The mean age at diagnosis was 42 years (median, 38.5 years), and the most common presenting complaints were otalgia and ear canal mass. Nine patients (41%) developed recurrences at a mean of 8 years (median, 8 years) after initial diagnosis, six died of ACC, and three were living with distant metastases at their last follow-up. The mean duration of symptoms at the time of diagnosis was 7.7 years (range, 2-30 years) for patients who developed a recurrence after treatment vs. 1.2 year (range, 0-2 years) for patients who remained disease-free (P = .137). Every patient who had recurrent disease reported a duration of symptoms of >or=2 years (P = .013), and every patient with a duration of symptoms >2 years recurred (P = .002). There was a trend for more local recurrences after limited resection (P = .061).ACC of the EAC often recurs many years after definitive treatment. Although our sample size was too small to make definitive conclusions, we recommend aggressive local therapy with lateral temporal bone resection and adjuvant postoperative radiotherapy. In addition to successful local therapy, early diagnosis may be the only other effective means of preventing distant metastases.

    View details for DOI 10.1097/MLG.0b013e31817c42a8

    View details for Web of Science ID 000260662700014

    View details for PubMedID 18677277

  • Validation of pretreatment nomograms for predicting indolent prostate cancer: Efficacy in contemporary urological practice JOURNAL OF UROLOGY Dong, F., Kattan, M. W., Steyerberg, E. W., Jones, J., Stephenson, A. J., Schroeder, F. H., Klein, E. A. 2008; 180 (1): 150-154

    Abstract

    Many patients diagnosed with low grade and early stage prostate cancer have indolent disease and may not benefit from immediate therapy. In patients referred for biopsy following community screening we validated the Kattan and Steyerberg nomograms for predicting indolent disease in a contemporary urological practice.A total of 296 patients who underwent prostate biopsy and radical prostatectomy at a single institution were identified for nomogram validation. All patients had clinically localized, stage T1c or T2a and biopsy Gleason score 6 prostate cancer. Clinical and biopsy pathological information was compared to surgery pathology results for nomogram validation with indolent disease defined as surgical Gleason score 6 or less, tumor volume less than 0.5 cc and organ confined disease. Nomogram performance was assessed by the ROC curve.Of the patients 27.4% had pathologically indolent disease at prostatectomy. Based on pretreatment variables the Kattan and Steyerberg nomograms were able to predict indolent disease with similar discrimination levels (AUC 0.777 and 0.772, respectively).Two previously described nomograms performed equally well for predicting indolent disease. These data further establish the role of validated nomograms for clinical decision making for managing screening detected prostate cancer.

    View details for DOI 10.1016/j.juro.2008.03.053

    View details for Web of Science ID 000256643900036

    View details for PubMedID 18485398

  • Prostate cancer volume at biopsy predicts clinically significant upgrading JOURNAL OF UROLOGY Dong, F., Jones, J., Stephenson, A. J., Magi-Galluzzi, C., Reuther, A. M., Klein, E. A. 2008; 179 (3): 896-900

    Abstract

    A significant proportion of patients with prostate cancer with Gleason score 6 disease at biopsy is upgraded to Gleason score 7 or higher after radical prostatectomy, increasing the risk of adverse outcome. We identified clinical and pathological parameters that predict pathological upgrading in this population.A total of 268 patients with biopsy Gleason score 6 prostate cancer who underwent biopsy and radical prostatectomy between October 1999 and January 2007 were included in the study. Pretreatment characteristics were used to identify predictors of pathological upgrading. Upgrading significance was established by comparing radical prostatectomy pathology between cases that were and were not upgraded.A total of 134 patients (50%) were upgraded postoperatively to Gleason score 7 or higher. Preoperative prostate specific antigen greater than 5.0 ng/ml (p = 0.036), prostate weight 60 gm or less (p = 0.004) and more cancer volume at biopsy, defined by cancer involving greater than 5% of the biopsy tissue (p = 0.002), greater than 1 biopsy core (p <0.001) or greater than 10% of any core (p = 0.014), were associated with pathological upgrading. Upgraded patients were more likely to have extraprostatic extension and positive surgical margins at radical prostatectomy (p <0.001 and 0.001, respectively).Prostate specific antigen, prostate volume and biopsy cancer volume predict clinically significant upgrading in patients diagnosed with Gleason score 6 disease. These parameters may be valuable in the pretreatment risk assessment of this patient population.

    View details for DOI 10.1016/j.juro.2007.10.060

    View details for Web of Science ID 000253176000029

    View details for PubMedID 18207180

  • Pathologic stage migration has slowed in the late PSA era UROLOGY Dong, F., Reuther, A. M., Magi-Galluzzi, C., Zhou, M., Kupelian, P. A., Klein, E. A. 2007; 70 (5): 839-842

    Abstract

    Serum prostate specific antigen (PSA) screening has led to clinical and pathologic stage migration. We examined patients treated by radical prostatectomy between 1987 and 2005 to establish temporal trends in pathologic stage migration as assessed by the proportion of patients with nonorgan-confined disease (NOCD).Step-sectioned prostatectomy specimens of 3364 consecutively treated patients were evaluated by year. The data were modeled by joinpoint regression, and the optimal model was selected by a Bayesian information criterion.From 1987 to 2005, the population underwent pathologic stage migration toward more organ-confined tumors (P <0.0001). The proportion of patients with NOCD exhibited changes in trend at 1992 and 1995. After widespread implementation of PSA screening, stage migration accelerated between 1992 and 1995. Since 1995, stage migration has substantially slowed but continues at an annual change of -4.2% (P = 0.0027).The presence of NOCD at prostatectomy has declined substantially in the PSA era. Recent slowing in this trend suggests a diminishing effect of PSA screening on pathologic stage migration.

    View details for DOI 10.1016/j.urology.2007.09.001

    View details for Web of Science ID 000251746100001

    View details for PubMedID 18068435