Cansu Karakas

All Publications

• A Validation Study of an Expanded Description of Glandular (Acinar)/Tubule Formation for the Use of Nottingham Grading System for Invasive Breast Carcinomas Demonstrates Improvement in Concordance for Breast Pathologists and Trainees in Pathology. Archives of pathology & laboratory medicine Karakas, C., Aldrees, R. A., Mohamed, A., Ellis, I. O., Fineberg, S. A., Ngo, M. H., Schnitt, S. J., Lester, S. C. 2025

  Abstract

  The Nottingham grading system, developed by Elston and Ellis, is the recommended method for grading invasive breast carcinoma. A previous study demonstrated the mean concordance for 35 breast pathologists in classifying 58 images as glandular (acinar)/tubule formation (G/TF) based on the World Health Organization definition was only 64%.To determine if an expanded description of G/TF according to the original definition and current use of the Nottingham grading system would improve recognition of G/TF among breast pathologists and pathologists in training.Fifty-eight images with one structure circled were classified as G/TF or non-G/TF by Dr Ian Ellis. Images were sent as a PowerPoint (Microsoft) file to the breast pathologists who participated in the original study and to 21 trainees. Participants were asked to classify the structures based on the expanded description and were also provided with the 58 images from the first study with annotation.Among the participating 28 of the original 35 breast pathologists, the mean concordance increased from 64% (range, 40%-97%) to 94% (range, 86%-100%). Trainees had a mean concordance of 90% (range, 52%-100%).The expanded description assisted in the recognition of G/TF for both breast pathologists and trainees. The most important impact on grading will likely be for carcinomas with complex cribriform patterns or micropapillary patterns with "inverted tubules." Participants endorsed that the expanded description of G/TF and the annotated images would be helpful reference material for pathologists.

  View details for DOI 10.5858/arpa.2025-0280-OA

  View details for PubMedID 41187113

• Low-Molecular Weight Cyclin E Confers a Vulnerability to PKMYT1 Inhibition in Triple-Negative Breast Cancer. Cancer research Li, M., Lulla, A. R., Wang, Y., Tsavaschidis, S., Wang, F., Karakas, C., Nguyen, T. D., Bui, T. N., Pina, M. A., Chen, M. K., Mastoraki, S., Multani, A. S., Fowlkes, N. W., Sahin, A., Marshall, C. G., Hunt, K. K., Keyomarsi, K. 2024; 84 (22): 3864-3880

  Abstract

  Cyclin E is a regulatory subunit of CDK2 that mediates S phase entry and progression. The cleavage of full-length cyclin E (FL-cycE) to low-molecular weight isoforms (LMW-E) dramatically alters substrate specificity, promoting G1-S cell cycle transition and accelerating mitotic exit. Approximately 70% of triple-negative breast cancers (TNBC) express LMW-E, which correlates with poor prognosis. PKMYT1 also plays an important role in mitosis by inhibiting CDK1 to block premature mitotic entry, suggesting it could be a therapeutic target in TNBC expressing LMW-E. In this study, analysis of tumor samples of patients with TNBC revealed that coexpression of LMW-E and PKMYT1-catalyzed CDK1 phosphorylation predicted poor response to neoadjuvant chemotherapy. Compared with FL-cycE, LMW-E specifically upregulates PKMYT1 expression and protein stability, thereby increasing CDK1 phosphorylation. Inhibiting PKMYT1 with the selective inhibitor RP-6306 (lunresertib) elicited LMW-E-dependent antitumor effects, accelerating premature mitotic entry, inhibiting replication fork restart, and enhancing DNA damage, chromosomal breakage, apoptosis, and replication stress. Importantly, TNBC cell line xenografts expressing LMW-E showed greater sensitivity to RP-6306 than tumors with empty vector or FL-cycE. Furthermore, RP-6306 exerted tumor suppressive effects in LMW-E transgenic murine mammary tumors and patient-derived xenografts of LMW-E-high TNBC but not in the LMW-E null models examined in parallel. Lastly, transcriptomic and immune profiling demonstrated that RP-6306 treatment induced interferon responses and T-cell infiltration in the LMW-E-high tumor microenvironment, enhancing the antitumor immune response. These findings highlight the LMW-E/PKMYT1/CDK1 regulatory axis as a promising therapeutic target in TNBC, providing the rationale for further clinical development of PKMYT1 inhibitors in this aggressive breast cancer subtype. Significance: PKMYT1 upregulation and CDK1 phosphorylation in triple-negative breast cancer expressing low-molecular weight cyclin E leads to suboptimal responses to chemotherapy but sensitizes tumors to PKMYT1 inhibitors, proposing a personalized treatment strategy.

  View details for DOI 10.1158/0008-5472.CAN-23-4130

  View details for PubMedID 39186665

  View details for PubMedCentralID PMC11567801

• Neutrophil Elastase Remodels Mammary Tumors to Facilitate Lung Metastasis. Molecular cancer therapeutics Lulla, A. R., Akli, S., Karakas, C., Caruso, J. A., Warma, L. D., Fowlkes, N. W., Rao, X., Wang, J., Hunt, K. K., Watowich, S. S., Keyomarsi, K. 2024; 23 (4): 492-506

  Abstract

  Metastatic disease remains the leading cause of death due to cancer, yet the mechanism(s) of metastasis and its timely detection remain to be elucidated. Neutrophil elastase (NE), a serine protease secreted by neutrophils, is a crucial mediator of chronic inflammation and tumor progression. In this study, we used the PyMT model (NE+/+ and NE-/-) of breast cancer to interrogate the tumor-intrinsic and -extrinsic mechanisms by which NE can promote metastasis. Our results showed that genetic ablation of NE significantly reduced lung metastasis and improved metastasis-free survival. RNA-sequencing analysis of primary tumors indicated differential regulation of tumor-intrinsic actin cytoskeleton signaling pathways by NE. These NE-regulated pathways are critical for cell-to-cell contact and motility and consistent with the delay in metastasis in NE-/- mice. To evaluate whether pharmacologic inhibition of NE inhibited pulmonary metastasis and phenotypically mimicked PyMT NE-/- mice, we utilized AZD9668, a clinically available and specific NE inhibitor. We found AZD9668 treated PyMT-NE+/+ mice showed significantly reduced lung metastases, improved recurrence-free, metastasis-free and overall survival, and their tumors showed similar molecular alterations as those observed in PyMT-NE-/- tumors. Finally, we identified a NE-specific signature that predicts recurrence and metastasis in patients with breast cancer. Collectively, our studies suggest that genetic ablation and pharmacologic inhibition of NE reduces metastasis and extends survival of mouse models of breast cancer, providing rationale to examine NE inhibitors as a treatment strategy for the clinical management of patients with metastatic breast cancer.

  View details for DOI 10.1158/1535-7163.MCT-23-0414

  View details for PubMedID 37796181

  View details for PubMedCentralID PMC10987287

• In ER-Positive, HER2-Negative Breast Cancers, HER2 mRNA Levels Correlate Better with Clinicopathologic Features and Oncotype DX Recurrence Score than HER2 Immunohistochemistry. Laboratory investigation; a journal of technical methods and pathology Tyburski, H., Karakas, C., Finkelman, B. S., Turner, B. M., Zhang, H., Hicks, D. G. 2024; 104 (3): 100309

  Abstract

  With the approval of trastuzumab deruxtecan for treating advanced human epidermal growth factor receptor-2 (HER2) low breast cancer (BC), it has become increasingly important to develop more accurate and reliable methods to identify HER2-low BC. In addition, HER2 immunohistochemistry (IHC) has limitations for quantification of HER2. We explored the relationship between HER2 IHC and mRNA levels and evaluated whether HER2 IHC scores and mRNA levels are associated with clinicopathologic features and Oncotype DX Recurrence Score (RS) in estrogen receptor (ER)-positive, HER2-negative BCs. A total of 750 BCs sent for Oncotype DX (ODX) testing were included in this study, and 559 with HER2 mRNA levels were available. There were no statistically significant differences between HER2 0 and HER2-low BC in clinicopathologic variables or ODX RS using HER2 IHC. There was a significant difference in median HER2 mRNA values between HER2 0 and HER2-low (8.7 vs 9.3, P < .001); however, the HER2 mRNA distribution had substantial overlap between these 2 groups with a suboptimal area under the receiver operating characteristic curve (area under the receiver operating characteristic curve = 0.68). A HER2 mRNA value of 9.2 was generated as the optimal cutoff for distinguishing HER2 0 and HER2-low BC. Comparing ER+ BCs with HER2 mRNA high (>9.2) and low (≤9.2) revealed a statistically significant difference in most clinicopathologic variables and ODX RS. From this large cohort of ER-positive, HER2-negative BC, our results demonstrated that HER2 mRNA levels correlated better with clinicopathologic features and recurrence risk as assessed by ODX RS than HER2 IHC scores. Our findings suggest that HER2 mRNA-detecting methods could potentially serve as a quantitative and reliable method for identifying a biologically meaningful group of HER2-low BC. Further study is needed to determine whether HER2 mRNA levels could be more reliable than IHC for identifying which patients will be most likely to benefit from trastuzumab deruxtecan.

  View details for DOI 10.1016/j.labinv.2023.100309

  View details for PubMedID 38135156

• Validation and interpretation of Pan-TRK immunohistochemistry: a practical approach and challenges with interpretation. Diagnostic pathology Karakas, C., Giampoli, E. J., Love, T., Hicks, D. G., Velez, M. J. 2024; 19 (1): 10

  Abstract

  Actionable, solid tumor activating neurotrophic receptor tyrosine kinase (NTRK) fusions are best detected via nucleic acid-based assays, while Pan-TRK immunohistochemistry (IHC) serves as a reasonable screening modality. We describe a practical and cost-effective approach to validate pan-TRK and discuss challenges that may be encountered.Pan-TRK Clone EPR17341 was validated in accordance with the 2014 consensus statements set forth by the College of American Pathologists. Confirmation of IHC results were guided by the European Society of Medical Oncology recommendations for standard methods to detect NTRK fusions.Within 36 samples, ETV6-NTRK3 (n = 8) and TPM4-NTRK3 (n = 1) fusions were confirmed. ETV6-NTRK3 fusion positive cases revealed cytoplasmic and nuclear staining. A TPM4-NTRK3 fusion positive high grade malignant peripheral nerve sheath tumor revealed diffuse cytoplasmic staining. A high grade ovarian serous carcinoma revealed focal punctate staining and revealed a non-actionable NTRK1 truncation at intron 2. Diffuse cytoplasmic staining was observed in a case of fusion-negative polymorphous adenocarcinoma. Wild-type expression of TRK in pulmonary meningothelial-like nodules was discovered following a false-positive IHC interpretation.Pan-TRK IHC shows some utility as a diagnostic and surrogate marker for NTRK screening however, physiologic or non-specific expression may lead to false-positive results.

  View details for DOI 10.1186/s13000-023-01426-5

  View details for PubMedID 38200576

  View details for PubMedCentralID PMC10777531

• HER2 categorical changes after neoadjuvant chemotherapy: A study of 192 matched breast cancers with the inclusion of HER2-Low category. Human pathology Karakas, C., Tyburski, H., Turner, B. M., Weiss, A., Akkipeddi, S. M., Dhakal, A., Skinner, K., Hicks, D. G., Zhang, H. 2023; 142: 34-41

  Abstract

  Understanding the changes of HER2 expression after neoadjuvant chemotherapy (NAC) in breast cancer (BC) is more important than ever, since it may allow more patients to access the effective therapeutic drugs targeting HER2-low BC. 192 matched pre- and post-NAC BCs were analyzed. HER2 immunohistochemistry (IHC) was re-evaluated with consensus according to the current ASCO/CAP guidelines. Tumors were categorized into HER2-0 (IHC0+), HER2-low (IHC1+ or IHC2+/ISH-) and HER2-positive (IHC3+ or IHC2+/ISH+) subgroups. 55 (28.6 %) patients achieved pathologic complete response (pCR). HER2-low BC accounted for 75/192 (39.1 %) baseline tumors, and 48/133 (36.1 %) residual tumors. In the non-pCR cohort, 53 (39.9 %) patients had HER2 categorical change after NAC, most commonly converting from HER2-low to HER2-0 (20.3 %, n = 27). Among patients with residual tumor, 25.6 % (11/43) of patients with baseline HER2-0 expression experienced a categorical change to HER2-low after NAC, significantly higher (p < 0.05) in the hormone receptor (HR) positive (9/23, 39.1 %) compared to the HR negative tumors (10 %, 2/20). Exploratory analysis failed to reveal a statistically significant difference in disease free survival and overall survival in non-pCR patients with or without HER2 change. Our results suggest that a substantial number of patients may experience HER2 categorical change after NAC, supporting re-testing of HER2 status in post-NAC residual tumors. Retesting HER2 status may be particularly important for evaluating post-NAC HER2-low status, in order to better assess which patients will more likely benefit from therapeutic drugs targeting HER2-low BC.

  View details for DOI 10.1016/j.humpath.2023.11.003

  View details for PubMedID 37979952

• Interobserver and Interantibody Reproducibility of HER2 Immunohistochemical Scoring in an Enriched HER2-Low-Expressing Breast Cancer Cohort. American journal of clinical pathology Karakas, C., Tyburski, H., Turner, B. M., Wang, X., Schiffhauer, L. M., Katerji, H., Hicks, D. G., Zhang, H. 2023; 159 (5): 484-491

  Abstract

  We assessed the interobserver and interantibody reproducibility of HER2 immunohistochemical scoring in an enriched HER2-low-expressing breast cancer cohort.A total of 114 breast cancer specimens were stained by HercepTest (Agilent Dako) and PATHWAY anti-HER2 (4B5) (Ventana) antibody assays and scored by 6 breast pathologists independently using current HER2 guidelines. Level of agreement was evaluated by Cohen κ analysis.Although the interobserver agreement rate for both antibodies achieved substantial agreement, the average rate of agreement for HercepTest was significantly higher than that for the 4B5 clone (74.3% vs 65.1%; P = .002). The overall interantibody agreement rate between the 2 antibodies was 57.8%. Complete interobserver concordance was achieved in 44.7% of cases by HercepTest and 45.6% of cases by 4B5. Absolute agreement rates increased from HER2 0-1+ cases (78.1% by HercepTest and 72.2% by 4B5; moderate agreement) to 2-3+ cases (91.9% by HercepTest and 86.3% by 4B5; almost perfect agreement).Our results demonstrated notable interobserver and interantibody variation on evaluating HER2 immunohistochemistry, especially in cases with scores of 0-1+, although the performance was much more improved among breast-specialized pathologists with the awareness of HER2-low concept. More accurate and reproducible methods are needed for selecting patients who may benefit from the newly approved HER2-targeting agent on HER2-low breast cancers.

  View details for DOI 10.1093/ajcp/aqac184

  View details for PubMedID 36856777

• Sequential Targeting of Retinoblastoma and DNA Synthesis Pathways Is a Therapeutic Strategy for Sarcomas That Can Be Monitored in Real Time. Cancer research Nguyen, T. D., Wang, Y., Bui, T. N., Lazcano, R., Ingram, D. R., Yi, M., Vakulabharanam, V., Luo, L., Pina, M. A., Karakas, C., Li, M., Kettner, N. M., Somaiah, N., Hougton, P. J., Mawlawi, O., Lazar, A. J., Hunt, K. K., Keyomarsi, K. 2023; 83 (6): 939-955

  Abstract

  Treatment strategies with a strong scientific rationale based on specific biomarkers are needed to improve outcomes in patients with advanced sarcomas. Suppression of cell-cycle progression through reactivation of the tumor suppressor retinoblastoma (Rb) using CDK4/6 inhibitors is a potential avenue for novel targeted therapies in sarcomas that harbor intact Rb signaling. Here, we evaluated combination treatment strategies (sequential and concomitant) with the CDK4/6 inhibitor abemacicib to identify optimal combination strategies. Expression of Rb was examined in 1,043 sarcoma tumor specimens, and 50% were found to be Rb-positive. Using in vitro and in vivo models, an effective two-step sequential combination strategy was developed. Abemaciclib was used first to prime Rb-positive sarcoma cells to reversibly arrest in G1 phase. Upon drug removal, cells synchronously traversed to S phase, where a second treatment with S-phase targeted agents (gemcitabine or Wee1 kinase inhibitor) mediated a synergistic response by inducing DNA damage. The response to treatment could be noninvasively monitored using real-time positron emission tomography imaging and serum thymidine kinase activity. Collectively, these results show that a novel, sequential treatment strategy with a CDK4/6 inhibitor followed by a DNA-damaging agent was effective, resulting in synergistic tumor cell killing. This approach can be readily translated into a clinical trial with noninvasive functional imaging and serum biomarkers as indicators of response and cell cycling.An innovative sequential therapeutic strategy targeting Rb, followed by treatment with agents that perturb DNA synthesis pathways, results in synergistic killing of Rb-positive sarcomas that can be noninvasively monitored.

  View details for DOI 10.1158/0008-5472.CAN-22-2258

  View details for PubMedID 36603130

  View details for PubMedCentralID PMC10023441

• Histopathologic Aspects of Malignancy-Associated Granuloma Annulare: A Single Institution Experience. Dermatopathology (Basel, Switzerland) Bagci, B., Karakas, C., Kaur, H., Smoller, B. R. 2023; 10 (1): 95-103

  Abstract

  Granuloma annulare (GA) is a benign, self-limiting granulomatous inflammatory disease that exhibits different histologic patterns. Infrequently, granuloma annulare can be associated with malignancy, the so-called malignancy-associated granuloma annulare (MGA). In this study, we aimed to compare the clinical and histopathological differences between GA and MGA. We retrospectively reviewed patient charts and identified 35 patients diagnosed with GA and concurrent hematological or solid organ malignancies as a case group. Additionally, we identified 33 patients without any known solid organ or hematological malignancy as a control group. MGA is commonly seen in the seventh decade of life, while GA affects the younger population. MGA is most commonly presented in the extremities of the body. The most common malignancy associated with MGA was chronic lymphocytic leukemia. Prostate cancer was the most common type of solid organ malignancy that was associated with MGA. The most common histopathological pattern seen in MGA was interstitial, comprising half of the cases. Multinucleated giant cells were present in half of the MGA cases and in most of the control group. In the literature, there are no established features that distinguish MGA from GA. Although MGA and GA have overlapping features, in our series, we found that the interstitial pattern was more common in MGA, while the necrobiotic pattern was more common in GA.

  View details for DOI 10.3390/dermatopathology10010015

  View details for PubMedID 36975384

  View details for PubMedCentralID PMC10047897

• Diffuse pulmonary meningotheliomatosis with pan-TRK expression by immunohistochemistry: a novel finding and potential pitfall. Diagnostic pathology Karakas, C., Nead, M. A., Velez, M. J. 2023; 18 (1): 22

  Abstract

  Pulmonary meningothelial-like nodules (PMNs) are benign proliferations of unclear clinical significance. They are mainly asymptomatic lesions that are usually discovered during the pathologic evaluation of resected pulmonary specimens or following post-mortem examination. Diffuse pulmonary meningotheliomatosis (DPM), which presents as bilateral multiple PMNs throughout the lungs, has been described less frequently. DPMs are benign lesions associated with both neoplastic and non-neoplastic pulmonary conditions.We report the case of a 59-year-old female patient who presented with a history of cough. Computerized tomography (CT) imaging revealed multiple subcentimeter bilateral pulmonary nodules. transbronchial biopsies were obtained which revealed foci of nodular interstitial proliferations composed of epithelioid to spindled cells in a vague whorled pattern. Immunohistochemical stains were diffusely positive for EMA and progesterone receptor. Furthermore, pan-TRK exhibited strong and diffuse membranous expression in the lesional cells. INSM1 was negative for expression. RNA-based next-generation sequencing for the detection of NTRK fusions was performed and was negative for gene rearrangements involving NTRK1, NTRK2, and NTRK3.Here, we report a rare case of DPM and report pan-TRK expression in PMNs which has not been described. We provide a brief review of the literature and provide insight into the potential physiologic nature of PMNs. Lastly, we emphasize the recognition of pan-TRK immunoexpression in PMNs to avoid potential diagnostic errors.

  View details for DOI 10.1186/s13000-023-01292-1

  View details for PubMedID 36782261

  View details for PubMedCentralID PMC9926707

• HER2-low breast cancers: Current insights and future directions. Seminars in diagnostic pathology Zhang, H., Karakas, C., Tyburski, H., Turner, B. M., Peng, Y., Wang, X., Katerji, H., Schiffhauer, L., Hicks, D. G. 2022; 39 (5): 305-312

  Abstract

  In light of the significant clinical benefits of novel HER2-targeting antibody-drug conjugates in advanced HER2-low expressing breast cancers in recent phases I and III clinical trials, particularly trastuzumab-deruxtecan (T-Dxd), the new "HER2-low" category in breast cancers (breast cancer with a HER2 IHC score of 1+, or 2+ without gene amplification) has gained increasing attention. In the past year, "HER2-low" breast cancers have been under active investigation by both oncologists and pathologists. In this current review, we update the recent cutting-edge research on HER2-low breast cancers, with a focus on the biology of HER2-low breast cancers, the issues on the identification of HER2-low breast cancers by immunohistochemistry in current practice of pathology, and the future directions in this emerging category in breast cancers.

  View details for DOI 10.1053/j.semdp.2022.07.003

  View details for PubMedID 35872032

• Umbilical Appendix Masquerading as a Patent Omphalomesenteric Duct in a Neonate. Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society Karakas, C., Katzman, P. J., Wakeman, D. S., Chacon, M. 2022; 25 (4): 474-478

  Abstract

  The umbilicus is the site of a number of well-recognized and unusual abnormalities. Well-known neonatal umbilical abnormalities include umbilical hernias, granulomas/polyps, and congenital remnants of development. In this article, we describe a rare case of an appendix draining through the umbilicus of a neonate. In the literature, there are only 15 cases with possible umbilical appendix. We describe this rare case along with a review of the literature and discuss the underlying pathophysiology.

  View details for DOI 10.1177/10935266221078500

  View details for PubMedID 35344403

• Subepidermal Calcified Nodule in a Child With Neurofibromatosis Type 1. Cureus Bagci, B., Karakas, C., Gokden, M. 2022; 14 (3): e23261

  Abstract

  Calcinosis cutis (CC) is characterized by calcium deposition in the subcutaneous tissues. Subepidermal calcified nodule (SCN) is a variant of idiopathic calcinosis most commonly seen in the head and neck region of children and adolescents as a single, small, painless, yellow-white papule. A 13-year-old boy with a medical history of neurofibromatosis type 1 (NF1) presented with a firm 0.3 cm white papule in the lower eyelid. He also had neurofibromas of the left forearm and spinal cord, and a malignant peripheral nerve sheath tumor of the right forearm. The eyelid lesion showed hyperkeratotic epidermis, papillomatosis, and elongated rete ridges, with a radial arrangement at the periphery of the well-circumscribed lesion comprising many dystrophic calcifications, histiocytes, and foreign body giant cell reactions. To our knowledge, this is the first case of SCN reported in the context of NF1 or any other systemic disease in the English literature. Although a coincidence is likely, rare observations of the parathyroid gland and calcium metabolism disorders in association with NF1 may provide an explanation that requires further investigation.

  View details for DOI 10.7759/cureus.23261

  View details for PubMedID 35449679

  View details for PubMedCentralID PMC9013239

• Cytoplasmic Cyclin E Expression Predicts for Response to Neoadjuvant Chemotherapy in Breast Cancer. Annals of surgery Karakas, C., Francis, A. M., Ha, M. J., Wingate, H. F., Meena, R. A., Yi, M., Rasaputra, K. S., Barrera, A. M., Arun, B., Do, K. A., Sahin, A., Keyomarsi, K., Hunt, K. K. 2021; 274 (2): e150-e159

  Abstract

  Pathologic complete response (pCR) has been shown to be associated with favorable outcomes in breast cancer. Predictors of pCR could be useful in guiding treatment decisions regarding neoadjuvant therapy. The objective of this study was to evaluate cyclin E as a predictor of response to neoadjuvant chemotherapy in breast cancer.Patients (n = 285) with stage II-III breast cancer were enrolled in a prospective study and received neoadjuvant chemotherapy with anthracyclines, taxanes, or combination of the two. Pretreatment biopsies from 190 patients and surgical specimens following chemotherapy from 192 patients were available for immunohistochemical analysis. Clinical and pathologic responses were recorded and associated with presence of tumor infiltrating lymphocytes, cyclin E, adipophilin, programmed cell death-ligand 1, and elastase staining and other patient, tumor and treatment characteristics.The pCR rate was significantly lower in patients with cytoplasmic cyclin E staining compared with those who had no cyclin E expression (16.1% vs 38.9%, P = 0.0005). In multivariable logistic regression analysis, the odds of pCR for patients who had cytoplasmic negative tumors was 9.35 times (P value < 0.0001) that compared with patients with cytoplasmic positive tumors after adjusting for ER, PR, and HER2 status. Cytoplasmic cyclin E expression also predicts long-term outcome and is associated with reduced disease free, recurrence free, and overall survival rates, independent of increased pretreatment tumor infiltrating lymphocytes.Cyclin E independently predicted response to neoadjuvant chemotherapy. Hence, its routine immunohistochemical analysis could be used clinically to identify those breast cancer patients expected to have a poor response to anthracycline/taxane-based chemotherapy.

  View details for DOI 10.1097/SLA.0000000000003551

  View details for PubMedID 31436549

  View details for PubMedCentralID PMC7031042

• LMW cyclin E and its novel catalytic partner CDK5 are therapeutic targets and prognostic biomarkers in salivary gland cancers. Oncogenesis Lulla, A. R., Akli, S., Karakas, C., Ha, M. J., Fowlkes, N. W., Mitani, Y., Bui, T., Wang, J., Rao, X., Hunt, K. K., Meijer, L., El-Naggar, A. K., Keyomarsi, K. 2021; 10 (5): 40

  Abstract

  Salivary gland cancers (SGCs) are rare yet aggressive malignancies with significant histological heterogeneity, which has made prediction of prognosis and development of targeted therapies challenging. In majority of patients, local recurrence and/or distant metastasis are common and systemic treatments have minimal impact on survival. Therefore, identification of novel targets for treatment that can also be used as predictors of recurrence for multiple histological subtypes of SGCs is an area of unmet need. In this study, we developed a novel transgenic mouse model of SGC, efficiently recapitulating the major histological subtype (adenocarcinomas of the parotid gland) of human SGC. CDK2 knock out (KO) mice crossed with MMTV-low molecular weight forms of cyclin E (LMW-E) mice generated the transgenic mouse models of SGC, which arise in the parotid region of the salivary gland, similar to the common site of origin seen in human SGCs. To identify the CDK2 independent catalytic partner(s) of LMW-E, we used LMW-E expressing cell lines in mass spectrometric analysis and subsequent biochemical validation in pull down assays. These studies revealed that in the absence of CDK2, LMW-E preferentially binds to CDK5. Molecular targeting of CDK5, using siRNA, resulted in inhibition of cell proliferation of human SGCs overexpressing LMW-E. We also provide clinical evidence of significant association of LMW-E/CDK5 co-expression and decreased recurrence free survival in human SGC. Immunohistochemical analysis of LMW-E and CDK5 in 424 patients representing each of the four major histological subtypes of human salivary cancers (Aci, AdCC, MEC, and SDC) revealed that LMW-E and CDK5 are concordantly (positive/positive or negative/negative) expressed in 70% of these patients. The co-expression of LMW-E/CDK5 (both positive) robustly predicts the likelihood of recurrence, regardless of the histological classification of these tumors. Collectively, our results suggest that CDK5 is a novel and targetable biomarker for the treatment of patients with SGC presenting with LMW-E overexpressing tumors.

  View details for DOI 10.1038/s41389-021-00324-z

  View details for PubMedID 33990543

  View details for PubMedCentralID PMC8121779

• Targeting Replicative Stress and DNA Repair by Combining PARP and Wee1 Kinase Inhibitors Is Synergistic in Triple Negative Breast Cancers with Cyclin E or BRCA1 Alteration. Cancers Chen, X., Yang, D., Carey, J. P., Karakas, C., Albarracin, C., Sahin, A. A., Arun, B. K., Guray Durak, M., Li, M., Kohansal, M., Bui, T. N., Ha, M. J., Hunt, K. K., Keyomarsi, K. 2021; 13 (7)

  Abstract

  The identification of biomarker-driven targeted therapies for patients with triple negative breast cancer (TNBC) remains a major clinical challenge, due to a lack of specific targets. Here, we show that cyclin E, a major regulator of G1 to S transition, is deregulated in TNBC and is associated with mutations in DNA repair genes (e.g., BRCA1/2). Breast cancers with high levels of cyclin E not only have a higher prevalence of BRCA1/2 mutations, but also are associated with the worst outcomes. Using several in vitro and in vivo model systems, we show that TNBCs that harbor either mutations in BRCA1/2 or overexpression of cyclin E are very sensitive to the growth inhibitory effects of AZD-1775 (Wee 1 kinase inhibitor) when used in combination with MK-4837 (PARP inhibitor). Combination treatment of TNBC cell lines with these two agents results in synergistic cell killing due to induction of replicative stress, downregulation of DNA repair and cytokinesis failure that results in increased apoptosis. These findings highlight the potential clinical application of using cyclin E and BRCA mutations as biomarkers to select only those patients with the highest replicative stress properties that may benefit from combination treatment with Wee 1 kinase and PARP inhibitors.

  View details for DOI 10.3390/cancers13071656

  View details for PubMedID 33916118

  View details for PubMedCentralID PMC8036262

• Corrigendum to "Immunohistochemistry in the workup of bladder biopsies. Frequency, variation and utility of use at an academic center" [Ann. Diagn. Pathol. 41(2019) 124-128]. Annals of diagnostic pathology McIntire, P., Khan, R., Kilic, I., Adams, D., Karakaş, C., Wojcik, E. M., Pambuccian, S. E., Barkan, G. A. 2020; 46: 151513

  View details for DOI 10.1016/j.anndiagpath.2020.151513

  View details for PubMedID 32330661

• Cytoplasmic Cyclin E Is an Independent Marker of Aggressive Tumor Biology and Breast Cancer-Specific Mortality in Women over 70 Years of Age. Cancers Johnston, S. J., Syed, B. M., Parks, R. M., Monteiro, C. J., Caruso, J. A., Green, A. R., Ellis, I. O., Hunt, K. K., Karakas, C., Keyomarsi, K., Cheung, K. L. 2020; 12 (3)

  Abstract

  Multi-cohort analysis demonstrated that cytoplasmic cyclin E expression in primary breast tumors predicts aggressive disease. However, compared to their younger counterparts, older patients have favorable tumor biology and are less likely to die of breast cancer. Biomarkers therefore require interpretation in this specific context. Here, we assess data on cytoplasmic cyclin E from a UK cohort of older women alongside a panel of >20 biomarkers. Between 1973 and 2010, 813 women ≥70 years of age underwent initial surgery for early breast cancer, from which a tissue microarray was constructed (n = 517). Biomarker expression was assessed by immunohistochemistry. Multivariate analysis of breast cancer-specific survival was performed using Cox's proportional hazards. We found that cytoplasmic cyclin E was the only biological factor independently predictive of breast cancer-specific survival in this cohort of older women (hazard ratio (HR) = 6.23, 95% confidence interval (CI) = 1.93-20.14; p = 0.002). At ten years, 42% of older patients with cytoplasmic cyclin E-positive tumors had died of breast cancer versus 8% of negative cases (p < 0.0005). We conclude that cytoplasmic cyclin E is an exquisite marker of aggressive tumor biology in older women. Patients with cytoplasmic cyclin E-negative tumors are unlikely to die of breast cancer. These data have the potential to influence treatment strategy in older patients.

  View details for DOI 10.3390/cancers12030712

  View details for PubMedID 32197318

  View details for PubMedCentralID PMC7140020

• Dedifferentiated gastrointestinal stromal tumor: Recent advances. Annals of diagnostic pathology Karakas, C., Christensen, P., Baek, D., Jung, M., Ro, J. Y. 2019; 39: 118-124

  Abstract

  Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal lesions of the gastrointestinal tract. A small minority of GISTs exhibit morphologic and phenotypic changes and differentiate into an unusual phenotype through the process of dedifferentiation. Dedifferentiation can occur either de novo or after prolonged treatment with imatinib, a selective tyrosine kinase inhibitor. GISTs can present with various morphologies including rhabdomyosarcoma, angiosarcoma, or undifferentiated pleomorphic sarcoma. The unusual histologic and immunohistochemical characteristics of these tumors can be diagnostically challenging. Therefore, it is essential that the pathologists recognize GISTs with unusual morphology and be aware of the dedifferentiation process. This review aims to provide an overview of the morphologic and molecular features of dedifferentiated GISTs. Additionally, we discuss diagnostic dilemmas and recent immunohistochemical markers that are useful in distinguishing dedifferentiated GISTs from other gastrointestinal tumors.

  View details for DOI 10.1016/j.anndiagpath.2018.12.005

  View details for PubMedID 30661742

• Cyclin E Overexpression Sensitizes Triple-Negative Breast Cancer to Wee1 Kinase Inhibition. Clinical cancer research : an official journal of the American Association for Cancer Research Chen, X., Low, K. H., Alexander, A., Jiang, Y., Karakas, C., Hess, K. R., Carey, J. P., Bui, T. N., Vijayaraghavan, S., Evans, K. W., Yi, M., Ellis, D. C., Cheung, K. L., Ellis, I. O., Fu, S., Meric-Bernstam, F., Hunt, K. K., Keyomarsi, K. 2018; 24 (24): 6594-6610

  Abstract

  Poor prognosis in triple-negative breast cancer (TNBC) is due to an aggressive phenotype and lack of biomarker-driven targeted therapies. Overexpression of cyclin E and phosphorylated-CDK2 are correlated with poor survival in patients with TNBC, and the absence of CDK2 desensitizes cells to inhibition of Wee1 kinase, a key cell-cycle regulator. We hypothesize that cyclin E expression can predict response to therapies, which include the Wee1 kinase inhibitor, AZD1775.Mono- and combination therapies with AZD1775 were evaluated in TNBC cell lines and multiple patient-derived xenograft (PDX) models with different cyclin E expression profiles. The mechanism(s) of cyclin E-mediated replicative stress were investigated following cyclin E induction or CRISPR/Cas9 knockout by a number of assays in multiple cell lines.Cyclin E overexpression (i) is enriched in TNBCs with high recurrence rates, (ii) sensitizes TNBC cell lines and PDX models to AZD1775, (iii) leads to CDK2-dependent activation of DNA replication stress pathways, and (iv) increases Wee1 kinase activity. Moreover, treatment of cells with either CDK2 inhibitors or carboplatin leads to transient transcriptional induction of cyclin E (in cyclin E-low tumors) and result in DNA replicative stress. Such drug-mediated cyclin E induction in TNBC cells and PDX models sensitizes them to AZD1775 in a sequential treatment combination strategy.Conclusions: Cyclin E is a potential biomarker of response (i) for AZD1775 as monotherapy in cyclin E-high TNBC tumors and (ii) for sequential combination therapy with CDK2 inhibitor or carboplatin followed by AZD1775 in cyclin E-low TNBC tumors.

  View details for DOI 10.1158/1078-0432.CCR-18-1446

  View details for PubMedID 30181387

  View details for PubMedCentralID PMC6317865

• Synthetic Lethality of PARP Inhibitors in Combination with MYC Blockade Is Independent of BRCA Status in Triple-Negative Breast Cancer. Cancer research Carey, J. P., Karakas, C., Bui, T., Chen, X., Vijayaraghavan, S., Zhao, Y., Wang, J., Mikule, K., Litton, J. K., Hunt, K. K., Keyomarsi, K. 2018; 78 (3): 742-757

  Abstract

  PARP inhibitors (PARPi) benefit only a fraction of breast cancer patients. Several of those patients exhibit intrinsic/acquired resistance mechanisms that limit efficacy of PARPi monotherapy. Here we show how the efficacy of PARPi in triple-negative breast cancers (TNBC) can be expanded by targeting MYC-induced oncogenic addiction. In BRCA-mutant/sporadic TNBC patients, amplification of the MYC gene is correlated with increased expression of the homologous DNA recombination enzyme RAD51 and tumors overexpressing both genes are associated with worse overall survival. Combining MYC blockade with PARPi yielded synthetic lethality in MYC-driven TNBC cells. Using the cyclin-dependent kinase inhibitor dinaciclib, which downregulates MYC expression, we found that combination with the PARPi niraparib increased DNA damage and downregulated homologous recombination, leading to subsequent downregulation of the epithelial-mesenchymal transition and cancer stem-like cell phenotypes. Notably, dinaciclib resensitized TBNC cells, which had acquired resistance to niraparib. We found that the synthetic lethal strategy employing dinaciclib and niraparib was also highly efficacious in ovarian, prostate, pancreatic, colon, and lung cancer cells. Taken together, our results show how blunting MYC oncogene addiction can leverage cancer cell sensitivity to PARPi, facilitating the clinical use of c-myc as a predictive biomarker for this treatment.Significance: Dual targeting of MYC-regulated homologous recombination and PARP-mediated DNA repair yields potent synthetic lethality in triple-negative breast tumors and other aggressive tumors characterized by MYC overexpression. Cancer Res; 78(3); 742-57. ©2017 AACR.

  View details for DOI 10.1158/0008-5472.CAN-17-1494

  View details for PubMedID 29180466

  View details for PubMedCentralID PMC5811386

• Cytoplasmic Cyclin E Mediates Resistance to Aromatase Inhibitors in Breast Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research Doostan, I., Karakas, C., Kohansal, M., Low, K. H., Ellis, M. J., Olson, J. A., Suman, V. J., Hunt, K. K., Moulder, S. L., Keyomarsi, K. 2017; 23 (23): 7288-7300

  Abstract

  Purpose: Preoperative aromatase inhibitor (AI) therapy has demonstrated efficacy in hormone receptor (HR)-positive postmenopausal breast cancer. However, many patients have disease that is either intrinsically resistant to AIs or that responds initially but develops resistance after prolonged exposure. We have shown that patients with breast tumors expressing the deregulated forms of cyclin E [low molecular weight forms (LMW-E)] have poor overall survival. Herein, we hypothesize that LMW-E expression can identify HR-positive tumors that are unresponsive to neoadjuvant AI therapy due to the inability of AIs to induce a cytostatic effect.Experimental Design: LMW-E was examined in breast cancer specimens from 58 patients enrolled in the American College of Surgeons Oncology Group Z1031, a neoadjuvant AI clinical trial. The mechanisms of LMW-E-mediated resistance to AI were evaluated in vitro and in vivo using an inducible model system of cyclin E (full-length and LMW-E) in aromatase-overexpressing MCF7 cells.Results: Breast cancer recurrence-free interval was significantly worse in patients with LMW-E-positive tumors who received AI neoadjuvant therapy, compared with those with LMW-E negative tumors. Upon LMW-E induction, MCF7 xenografts were unresponsive to letrozole in vivo, resulting in increased tumor volume after treatment with AIs. LMW-E expression overcame cell-cycle inhibition by AIs in a CDK2/Rb-dependent manner, and inhibition of CDK2 by dinaciclib reversed LMW-E-mediated resistance, whereas treatment with palbociclib, a CDK4/6 inhibitor, did not.Conclusions: Collectively, these findings suggest that cell-cycle deregulation by LMW-E mediates resistance to AIs and a combination of CDK2 inhibitors and AIs may be an effective treatment in patients with HR-positive tumors that express LMW-E. Clin Cancer Res; 23(23); 7288-300. ©2017 AACR.

  View details for DOI 10.1158/1078-0432.CCR-17-1544

  View details for PubMedID 28947566

  View details for PubMedCentralID PMC5768442

• Molecular mechanisms involving prostate cancer racial disparity. American journal of clinical and experimental urology Karakas, C., Wang, C., Deng, F., Huang, H., Wang, D., Lee, P. 2017; 5 (3): 34-48

  Abstract

  Prostate cancer (PCa) is the second leading cause of cancer-related deaths in the United States. The African (AA) descent has greater incidence and mortality rates of PCa as compared to Caucasian (CA) men. While socioeconomic differences across racial groups contribute to disparity in PCa, increasing evidence points that genetic and molecular alterations play important roles in racial disparities associated with PCa. In this review, we focus on genetic and molecular influences that contribute to racial disparity between AA and CA men including: androgen and estrogen receptor signaling pathways, growth factors, apoptotic proteins, genetic, genomic and epigenetic alterations. Future translational studies will identify prognostic and predictive biomarkers for AA PCa and assist in the development of new targeted-therapies specifically for AA men with PCa.

  View details for PubMedID 29181436

  View details for PubMedCentralID PMC5698597

• CDK4/6 and autophagy inhibitors synergistically induce senescence in Rb positive cytoplasmic cyclin E negative cancers. Nature communications Vijayaraghavan, S., Karakas, C., Doostan, I., Chen, X., Bui, T., Yi, M., Raghavendra, A. S., Zhao, Y., Bashour, S. I., Ibrahim, N. K., Karuturi, M., Wang, J., Winkler, J. D., Amaravadi, R. K., Hunt, K. K., Tripathy, D., Keyomarsi, K. 2017; 8: 15916

  Abstract

  Deregulation of the cell cycle machinery is a hallmark of cancer. While CDK4/6 inhibitors are FDA approved (palbociclib) for treating advanced estrogen receptor-positive breast cancer, two major clinical challenges remain: (i) adverse events leading to therapy discontinuation and (ii) lack of reliable biomarkers. Here we report that breast cancer cells activate autophagy in response to palbociclib, and that the combination of autophagy and CDK4/6 inhibitors induces irreversible growth inhibition and senescence in vitro, and diminishes growth of cell line and patient-derived xenograft tumours in vivo. Furthermore, intact G1/S transition (Rb-positive and low-molecular-weight isoform of cyclin E (cytoplasmic)-negative) is a reliable prognostic biomarker in ER positive breast cancer patients, and predictive of preclinical sensitivity to this drug combination. Inhibition of CDK4/6 and autophagy is also synergistic in other solid cancers with an intact G1/S checkpoint, providing a novel and promising biomarker-driven combination therapeutic strategy to treat breast and other solid tumours.

  View details for DOI 10.1038/ncomms15916

  View details for PubMedID 28653662

  View details for PubMedCentralID PMC5490269

• Cytoplasmic Cyclin E Predicts Recurrence in Patients with Breast Cancer CLINICAL CANCER RESEARCH Hunt, K. K., Karakas, C., Ha, M., Biernacka, A., Yi, M., Sahin, A. A., Adjapong, O., Hortobagyi, G. N., Bondy, M. L., Thompson, P. A., Cheung, K., Ellis, I. O., Bacus, S., Symmans, W., Kim-Anh Do, Keyomarsi, K. 2017; 23 (12): 2991–3002

  Abstract

  Purpose: Low molecular weight cyclin E (LMW-E) detected by Western blot analysis predicts for reduced breast cancer survival; however, it is impractical for clinical use. LMW-E lacks a nuclear localization signal that leads to accumulation in the cytoplasm that can be detected by IHC. We tested the hypothesis that cytoplasmic staining of cyclin E can be used as a predictor of poor outcome in different subtypes of breast cancer using patient cohorts with distinct clinical and pathologic features.Experimental Design: We evaluated the subcellular localization of cyclin E in breast cancer specimens from 2,494 patients from 4 different cohorts: 303 from a prospective study and 2,191 from retrospective cohorts [NCI, MD Anderson Cancer Center (MDA), and the United Kingdom (UK)]. Median follow-up times were 8.0, 10.1, 13.5, and 5.7 years, respectively.Results: Subcellular localization of cyclin E on IHC was associated with full-length (nuclear) and low molecular weight isoforms (cytoplasmic) of cyclin E on Western blot analysis. In multivariable analysis, cytoplasmic cyclin E staining was associated with the greatest risk of recurrence compared with other prognostic factors across all subtypes in three (NCI, MDA, and UK) of the cohorts. In the MDA cohort, cytoplasmic cyclin E staining outperformed Ki67 and all other variables as prognostic factors.Conclusions: Cytoplasmic cyclin E identifies patients with the highest likelihood of recurrence consistently across different patient cohorts and subtypes. These patients may benefit from alternative therapies targeting the oncogenic isoforms of cyclin E. Clin Cancer Res; 23(12); 2991-3002. ©2016 AACR.

  View details for DOI 10.1158/1078-0432.CCR-16-2217

  View details for Web of Science ID 000403330000016

  View details for PubMedID 27881578

  View details for PubMedCentralID PMC5441976

• Cyclin E overexpression as a biomarker for combination treatment strategies in inflammatory breast cancer ONCOTARGET Alexander, A., Karakas, C., Chen, X., Carey, J. P. W., Yi, M., Bondy, M., Thompson, P., Cheung, K., Ellis, I. O., Gong, Y., Krishnamurthy, S., Alvarez, R. H., Ueno, N. T., Hunt, K. K., Keyomarsi, K. 2017; 8 (9): 14897–911

  Abstract

  Inflammatory breast cancer (IBC) is a virulent form of breast cancer, and novel treatment strategies are urgently needed. Immunohistochemical analysis of tumors from women with a clinical diagnosis of IBC (n = 147) and those with non-IBC breast cancer (n = 2510) revealed that, whereas in non-IBC cases cytoplasmic cyclin E was highly correlated with poor prognosis (P < 0.001), in IBC cases both nuclear and cytoplasmic cyclin E were indicative of poor prognosis. These results underscored the utility of the cyclin E/CDK2 complex as a novel target for treatment. Because IBC cell lines were highly sensitive to the CDK2 inhibitors dinaciclib and meriolin 5, we developed a high-throughput survival assay (HTSA) to design novel sequential combination strategies based on the presence of cyclin E and CDK2. Using a 14-cell-line panel, we found that dinaciclib potentiated the activity of DNA-damaging chemotherapies treated in a sequence of dinaciclib followed by chemotherapy, whereas this was not true for paclitaxel. We also identified a signature of DNA repair-related genes that are downregulated by dinaciclib, suggesting that global DNA repair is inhibited and that prolonged DNA damage leads to apoptosis. Taken together, our findings argue that CDK2-targeted combinations may be viable strategies in IBC worthy of future clinical investigation.

  View details for DOI 10.18632/oncotarget.14689

  View details for Web of Science ID 000396013700056

  View details for PubMedID 28107181

  View details for PubMedCentralID PMC5362453

• Cytoplasmic Cyclin E and Phospho-Cyclin-Dependent Kinase 2 Are Biomarkers of Aggressive Breast Cancer. The American journal of pathology Karakas, C., Biernacka, A., Bui, T., Sahin, A. A., Yi, M., Akli, S., Schafer, J., Alexander, A., Adjapong, O., Hunt, K. K., Keyomarsi, K. 2016; 186 (7): 1900-1912

  Abstract

  Cyclin E and its co-activator, phospho-cyclin-dependent kinase 2 (p-CDK2), regulate G1 to S phase transition and their deregulation induces oncogenesis. Immunohistochemical assessments of these proteins in cancer have been reported but were based only on their nuclear expression. However, the oncogenic forms of cyclin E (low molecular weight cyclin E or LMW-E) in complex with CDK2 are preferentially mislocalized to the cytoplasm. Here, we used separate nuclear and cytoplasmic scoring systems for both cyclin E and p-CDK2 expression to demonstrate altered cellular accumulation of these proteins using immunohistochemical analysis. We examined the specificity of different cyclin E antibodies and evaluated their concordance between immunohistochemical and Western blot analyses in a panel of 14 breast cell lines. Nuclear versus cytoplasmic staining of cyclin E readily differentiated full-length from LMW-E, respectively. We also evaluated the expression of cyclin E and p-CDK2 in 1676 breast carcinoma patients by immunohistochemistry. Cytoplasmic cyclin E correlated strongly with cytoplasmic p-CDK2 (P < 0.0001), high tumor grade, negative estrogen/progesterone receptor status, and human epidermal growth factor receptor 2 positivity (all P < 0.0001). In multivariable analysis, cytoplasmic cyclin E plus phosphorylated CDK2 (as one variable) predicted breast cancer recurrence-free and overall survival. These results suggest that cytoplasmic cyclin E and p-CDK2 can be readily detected with immunohistochemistry and used as clinical biomarkers for aggressive breast cancer.

  View details for DOI 10.1016/j.ajpath.2016.02.024

  View details for PubMedID 27182644

  View details for PubMedCentralID PMC4929404

• Cyclin E Associates with the Lipogenic Enzyme ATP-Citrate Lyase to Enable Malignant Growth of Breast Cancer Cells. Cancer research Lucenay, K. S., Doostan, I., Karakas, C., Bui, T., Ding, Z., Mills, G. B., Hunt, K. K., Keyomarsi, K. 2016; 76 (8): 2406-18

  Abstract

  Cyclin E is altered in nearly a third of invasive breast cancers where it is a powerful independent predictor of survival in women with stage I-III disease. Full-length cyclin E is posttranslationally cleaved into low molecular weight (LMW-E) isoforms, which are tumor-specific and accumulate in the cytoplasm because they lack a nuclear localization sequence. We hypothesized that aberrant localization of cytosolic LMW-E isoforms alters target binding and activation ultimately contributing to LMW-E-induced tumorigenicity. To address this hypothesis, we used a retrovirus-based protein complementation assay to find LMW-E binding proteins in breast cancer, identifying ATP-citrate lyase (ACLY), an enzyme in the de novo lipogenesis pathway, as a novel LMW-E-interacting protein in the cytoplasm. LMW-E upregulated ACLY enzymatic activity, subsequently increasing lipid droplet formation, thereby providing cells with essential building blocks to support growth. ACLY was also required for LMW-E-mediated transformation, migration, and invasion of breast cancer cells in vitro along with tumor growth in vivo In clinical specimens of breast cancer, the absence of LMW-E and low expression of adipophilin (PLIN2), a marker of lipid droplet formation, associated with favorable prognosis, whereas overexpression of both proteins correlated with a markedly worse prognosis. Taken together, our findings establish a novel relationship between LMW-E isoforms of cyclin E and aberrant lipid metabolism pathways in breast cancer tumorigenesis, warranting further investigation in additional malignancies exhibiting their expression. Cancer Res; 76(8); 2406-18. ©2016 AACR.

  View details for DOI 10.1158/0008-5472.CAN-15-1646

  View details for PubMedID 26928812

  View details for PubMedCentralID PMC4873469

• Determination-of apoptosis and cell cycle modulators (p16, p21, p27, p53, BCL-2, Bax, BCL-xL, and cyclin D1) in thyroid follicular carcinoma, follicular adenoma, and adenomatous nodules via a tissue microarray method. Turkish journal of medical sciences Temiz, P., Akkaş, G., Neşe, N., Uğur Duman, F., Karakaş, C., Erhan, Y. 2015; 45 (4): 865-71

  Abstract

  To identify the role of gene products associated with apoptosis and cell cycle in the pathogenesis of thyroid follicular neoplasm.Thirty follicular adenomas (FAs), 16 follicular carcinomas (FCs), and 20 adenomatous nodules (ANs) were investigated with immunohistochemical staining of p16, p21, p27, p53, Bcl-2, Bax, Bcl-xL, and cyclin D1 via a tissue microarray method.Bcl-2 showed a significant difference between the benign groups (AN and FA) and the malignant group (FC). Bax was significantly higher in the FC group. p53 was lowest in the AN group and highest in the FC group with significant differences between the groups. p16 was significantly higher in the FC group than in the other groups. There was a significant difference between the AN group and neoplastic lesions in terms of p21 staining. The number of cases with positive p27 was lower in the AN group than the neoplastic groups. There was no significant difference in terms of Bcl-xL and cyclin D1.Cell cycle modulators, led by the Bcl-2 family, played an important role in the pathogenesis of thyroid follicular neoplasm, and p53, p16, and p21 in particular played a role in the carcinogenesis of FC.

  View details for DOI 10.3906/sag-1406-48

  View details for PubMedID 26422859

• A phase 1 study with dose expansion of the CDK inhibitor dinaciclib (SCH 727965) in combination with epirubicin in patients with metastatic triple negative breast cancer. Investigational new drugs Mitri, Z., Karakas, C., Wei, C., Briones, B., Simmons, H., Ibrahim, N., Alvarez, R., Murray, J. L., Keyomarsi, K., Moulder, S. 2015; 33 (4): 890-4

  Abstract

  Low molecular weight cyclin E (LMW-E) isoforms, overexpressed in a majority (~70 %) of triple-negative breast cancers (TNBC), were found in preclinical models to mediate tumorigenesis through binding and activation of CDK2. CDK1/CDK2 inhibitors, such as dinaciclib, combined with anthracyclines, were synergistic in decreasing viability of TNBC cell lines. Based on this data, a phase 1 study was conducted to determine the maximum tolerated dose of dinaciclib in combination with epirubicin in patients with metastatic TNBC.Cohorts of at least 2 patients were treated with escalating doses of dinaciclib given on day 1 followed by standard dose of epirubicin given on day 2 of a 21 day cycle. No intra-patient dose escalation was allowed. An adaptive accrual design based upon toxicity during cycle 1 determined entry into therapy cohorts. The target acceptable dose limiting toxicity (DLT) to advance to the next treatment level was 30 %.Between 9/18/2012 and 7/18/2013, 9 patients were enrolled and treated at MD Anderson Cancer Center. DLTs included febrile neutropenia (grade 3, n = 2), syncope (grade 3, n = 2) and vomiting (grade 3, n = 1). Dose escalation did not proceed past the second cohort due to toxicity. After further accrual, the first dose level was also found to be too toxic. No treatment responses were noted, median time to progression was 5.5 weeks (range 3-12 weeks). Thus, accrual was stopped rather than explore the -1 dose level.The combination of dinaciclib and epirubicin is associated with substantial toxicities and does not appear to be an effective treatment option for TNBC.

  View details for DOI 10.1007/s10637-015-0244-4

  View details for PubMedID 25947565

• Elafin is downregulated during breast and ovarian tumorigenesis but its residual expression predicts recurrence (vol 16, 3417, 2014) BREAST CANCER RESEARCH Caruso, J. A., Karakas, C., Zhang, J., Yi, M., Albarracin, C., Sahin, A., Bondy, M., Liu, J., Hunt, K. K., Keyomarsi, K. 2015; 17: 87

  View details for DOI 10.1186/s13058-015-0572-5

  View details for Web of Science ID 000356774300001

  View details for PubMedID 26108797

  View details for PubMedCentralID PMC4480452

• Elafin is downregulated during breast and ovarian tumorigenesis but its residual expression predicts recurrence BREAST CANCER RESEARCH Caruso, J. A., Karakas, C., Zhang, J., Yi, M., Albarracin, C., Sahin, A., Bondy, M., Liu, J., Hunt, K. K., Keyomarsi, K. 2014; 16 (6): 3417

  Abstract

  Elafin is an endogenous serine protease inhibitor. The majority of breast cancer cell lines lack elafin expression compared to human mammary epithelial cells. In this study, we hypothesized that elafin is downregulated during breast and ovarian tumorigenesis.We examined elafin expression by immunohistochemistry (IHC) in specimens of normal breast tissue (n = 24), ductal carcinoma in situ (DCIS) (n = 54), and invasive breast cancer (n = 793). IHC analysis of elafin expression was also performed in normal fallopian tube tissue (n = 20), ovarian cystadenomas (n = 9), borderline ovarian tumors (n = 21), and invasive ovarian carcinomas (n = 216). To understand the significance of elafin in luminal breast cancer cell lines, wild-type or M25G elafin (lacking the protease inhibitory function) were exogenously expressed in MCF-7 and T47D cells.Elafin expression was downregulated in 24% of DCIS and 83% of invasive breast tumors when compared to elafin expression in the normal mammary epithelium. However, the presence of elafin-positive cells in invasive breast tumors, even at low frequency, correlated with poor recurrence-free survival (RFS), reduced overall survival (OS), and clinicopathological markers of aggressive tumor behavior. Elafin-positive cells were an especially strong and independent prognostic marker of reduced RFS in IHC-defined luminal A-like tumors. Elafin was also downregulated in 33% of ovarian cystadenomas, 43% of borderline ovarian tumors, and 86% of invasive ovarian carcinomas when compared to elafin expression in the normal fallopian tube. In ovarian tumors, elafin-positive cells were correlated with reduced RFS, OS and disease-specific survival (DSS) only in stage I/II patients and not in stage III/IV patients. Notably, exogenous expression of elafin or elafin M25G in the luminal breast cancer cell lines MCF-7 and T47D significantly decreased cell proliferation in a protease inhibitory domain-independent manner.Elafin predicts poor outcome in breast and ovarian cancer patients and delineates a subset of endocrine receptor-positive breast cancer patients susceptible to recurrence who could benefit from more aggressive intervention. Our in vitro results suggest that elafin arrests luminal breast cancer cells, perhaps suggesting a role in tumor dormancy.

  View details for DOI 10.1186/s13058-014-0497-4

  View details for Web of Science ID 000349885800034

  View details for PubMedID 25551582

  View details for PubMedCentralID PMC4326485

• Liver cyst hydatid fistulated into duodenum European Journal of General Medicine ((ISSN 1304-3889) Okus, A., Ay, S., Karakas, C., Mustafa, M., Eryilmaz, M. 2012; 9 (1): 53-55
• Paget's disease of the breast. Journal of carcinogenesis Karakas, C. 2011; 10: 31

  Abstract

  Paget's disease of the breast is a rare type of cancer of the nipple-areola complex and that is often associated with an underlying in situ or invasive carcinoma. This article provides an overview and we review the main clinicopathological and therapeutic features of mammary Paget's disease.

  View details for DOI 10.4103/1477-3163.90676

  View details for PubMedID 22279416

  View details for PubMedCentralID PMC3263015