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BRCA1 and BRCA2 (Breast cancer susceptibility gene 1 and 2) are tumor suppressor genes that maintain genomic stability by repairing damaged DNA. The proteins coded by these genes are involved in complexes that activate the repair of double strand breaks (DSBs) and initiate homologous recombination (HR). BRCA mutations are common in various forms of human cancers, most notably breast cancer, and previously described in canine tumors. Tumors in canines and humans share many characteristics, including: inter-individual and intra-tumoral heterogeneity, biological behavior, similar tumor microenvironments, and similar genomic mutations. This study interrogates naturally-occuring cancers in dogs as a tool that can add valuable information to our understanding of similar tumors in people. A total of 667 tumors of various histologies were obtained from client-owned dogs and sequenced on the FidoCure® Next-generation sequencing (NGS) panel as part of their veterinary precision medicine platform. Mutations in BRCA1 and BRCA2 were among the 5 most common genetic mutations identified. BRCA1 or BRCA2 mutations were identified in 71.8% (479/667) of tumors overall; 36.4% (n=243) BRCA1 mutations, 33.7% (n=225) BRCA2 mutations, and 1.6% (n=11) BRCA1/2 co-mutations. Germline single-nucleotide polymorphisms (SNPs) represented 56% (136/243) and 61% (138/225) of BRCA1 and BRCA2 mutations, respectively. Removing SNPs and focusing on single-nucleotide variants (SNVs), 16.1% of cases (107/667) had BRCA1 mutations, 13.0% (87/667) had BRCA2 mutations, and 1.65% (11/667) had both BRCA1 and BRCA2 mutations. Utilizing Protein Variation Effect Analyzed (PROVEAN) and Sort Intolerant From Tolerant (SIFT) bioinformatic tools to assess the functional significance of BRCA1 and BRCA2 missense variants, 69.2% and 54.8% of mutations, respectively, were predicted as pathogenic/deleterious. Interestingly, a search of the 2017 MSK IMPACT dataset reveals a pan-cancer prevalence in humans of 2.0% BRCA1 variants (216/10,945 cases) and 3.6% BRCA2 variants (399/10,945 cases). Looking at cancer histologies in dogs, BRCA1 variants were identified in 14.1% of soft tissue sarcomas (STS), 11.4% of apocrine gland anal-sac adenocarcinomas (AGASACA), 11.1% of mast cell tumors (MCT), 10.9% of osteosarcomas (OSA), and 10% of thyroid carcinomas. BRCA2 mutations were identified in 33.3% of MCTs, 32.1% of STSs, 23.8% of histiocytic sarcomas, 17.2% of OSAs, and 16.3% of AGASACAs. This analysis of BRCA1/2 mutations in dogs highlights the value of companion animals as a model for human disease to better understand the contribution of these genes in tumorigenesis and for exploring different targeted therapeutic interventions. Further evaluation of the efficacy of PARP inhibitors, either with or without chemotherapy and/or radiotherapy, in tumors with BRCA1/2 mutations in dogs may reveal information that can then be used to benefit humans with similar malignancies. Citation Format: Benjamin Lewis, Gerry Post, Garrett Harvey, Lindsay Lambert, Aubrey Miller, Rilke Van Buren, Christina Lopes, Lucas Rodrigues. Mutational screening of BRCA1/2 genes in 667 spontaneous canine tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2991.

Cholangiocarcinoma (CCA) is an aggressive bile duct neoplasm which is typically not diagnosed until late stage. The current standard of care, resection followed by gemcitabine with or without cisplatin, is relatively ineffective. Additionally, most patients are ineligible for surgical resection, and postoperative chemotherapy rarely prolongs overall survival. No previously identified mutations (KRAS, SMAD4 and p53) have been shown to drive disease progression. We and others have shown that the proto-oncogene c-Myc is expressed at relatively high levels in CCA cells compared to uninvolved normal tissue, suggesting this oncogene as a prospective therapeutic target in CCA. To evaluate whether c-Myc inhibition affected the proliferation of CCA cells, we evaluated the efficacy of the bromodomain and extraterminal domain (BET) inhibitor JQ1 on c-Myc expression and cell proliferation of CCA cells. JQ1 functions as an acetyl lysine (K-Ac) mimetic which binds to the K-Ac binding pocket of BET protein family members (BRD2, BRD3, BRD4 and BRDT). This binding competitively inhibits the association of BET proteins with K-Ac residues of nuclear proteins and inhibits c-Myc expression. Using a patient-derived xenograft (PDX) model of CCA, we showed previously that JQ1 downregulated c-Myc expression and inhibited tumor growth. Therefore, we hypothesized that JQ1 induces CCA cell death through disruption of BET protein binding to the promoter region of the MYC locus, inducing its downregulation. Our data show that JQ1 decreased c-Myc RNA and protein expression as well as the expression c-Myc transcriptional targets CHK1 and BRCA2. JQ1 also decreased CCA cell viability, clonogenic potential and induced apoptosis of KKU-055 CCA cells in vitro. The likely mechanism of JQ1-mediated c-Myc reduction has been postulated to involve competitive inhibition of the K-Ac binding function of the BET protein BRD4. Our current chromatin immunoprecipitation (ChIP) assays indicate that BRD2 binds to the MYC transcriptional start sites (TSS) P1 and P2, while BRD4 primarily binds MYC TSS P1 in KKU-055 cells. JQ1 precludes these BET proteins from binding their respective sites. When exposed to the IC50 of JQ1, ChIP pulldown with an anti-BRD2 antibody displays a near 100% reduction in binding of BRD2 to the MYC TSS while an anti-BRD4 antibody displays a 70% reduction in binding. In addition, stable BRD2 knockdown models of KKU-055 display reduced c-Myc protein expression by 60 to 80%, while BRD4 knockdown models showed no such reduction. The data demonstrate that in addition to BRD4, BRD2 contributes to regulation of expression of c-Myc in CCA cells. Research funded by NIH/NCI R21 CA205501 Citation Format: Samuel C. Fehling, Aubrey L. Miller, Karina J. Yoon. JQ1 induces cell death and disrupts BET protein binding to the MYC locus in cholangiocarcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3837.

Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer (PC), is now the third leading cause of cancer related deaths in the US. This is a highly aggressive disease in that 80% of patients present with locally advanced or metastatic disease and their only treatment option is systemic chemotherapy. Ultimately patient tumors develop resistance to therapy and resulting in a median survival of ~6 months. Therefore, there is an imperative need to identify therapies that provide a more durable response for this patient population. The family of bromodomain and extraterminal domain (BET) proteins has recently become a target of interest for the treatment of PDAC. The BET proteins (BRD2, BRD3, BRD4, and BRDT) function to regulate transcription by recruiting positive transcriptional activators to the promoters of genes. Our lab has shown that inhibition of BET bromodomain function using the BET inhibitor JQ1 suppresses PDAC tumor growth in vivo and inhibits cell viability in vitro. Importantly, PDAC cells and tumors exposed to JQ1 show evidence of DNA damage. We hypothesized that because of the role BET proteins are known to play in regulating gene expression, that the observed JQ1-induced DNA damage may result from JQ1 inhibiting the expression of DNA repair genes whose expression are dependent on BET protein transcriptional complexes. qRT-PCR and immunoblot analysis demonstrated that treatment of the pancreatic cancer cell line BxPC3 with JQ1 inhibited the expression of two double strand break repair proteins, Ku80 and RAD51, both of which have been shown to be overexpressed in cancer including PDAC. Although it has been established that JQ1 co-occupies 99% of the genomic loci that BRD4 is known to bind to, specific gene products whose expression is dependent on BRD4 in PDAC have not been thoroughly investigated. The goal of the current study was to determine if the expression of DNA repair genes Ku80 and RAD51 were specific gene targets of BRD4 transcriptional complexes. We exposed BxPC3 cells to JQ1 for 48 hours and assessed changes in the association of BRD4 with the promoter loci of Ku80 and RAD51 using chromatin immunoprecipitation (ChIP) assays. qRT-PCR of the ChIP demonstrated that treatment with JQ1 significantly (p Citation Format: Aubrey Lynn Miller, Samuel C. Fehling, Patrick L. Garcia, Karina J. Yoon. BET inhibition decreases the expression of DNA repair enzymes in pancreatic cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5244.

Pancreatic ductal adenocarcinoma (PDAC), the most common type of pancreatic cancer, is a highly aggressive tumor with a 5-year survival of We and others document that inhibiting the function of BET bromodomain proteins suppresses PDAC tumor growth in preclinical models. The BET family of proteins is characterized by two N-terminal bromodomains, BD1 and BD2, which bind to acetylated lysine residues on specific histones. The binding of BET proteins to acetylated lysines promotes the formation of transcriptional complexes, and impacts gene transcription and chromatin structure. The literature suggests the potential specific roles for BD1 vs BD2 using pharmacological inhibitors and dominant negative mutational analyses. However, the relative importance of each bromodomain with respect to transcriptional regulation compared to chromatin structure is not well understood. Further, there is suggestion in the literature that each bromodomain function may differ in specific tumor cell types. Functional differences between BD1 and BD2 in PDAC cells have not been reported. The goal of the current study was to compare the efficacy of the BD2-specific BET inhibitor (BETi) SJ018 with the efficacy of the pan-BET inhibitor I-BET762 in PDAC cells. We exposed four PDAC cell lines (Panc1, BxPC3, MiaPaCa2, and CFPAC) to a range of concentrations of SJ018 or I-BET762 for 96 hours, and assessed cell viability using alamarBlue. Data, analyzed using GraphPad Prism 7, demonstrated that SJ018 exerted up to ~60-fold lower IC50 values across all cell lines tested compared to the pan-BET inhibitor I-BET762. Further, we recently made a novel observation that the pan-BETi JQ1 induced DNA damage and inhibits expression of the DNA repair protein Rad51 in PDAC cells. Immunoblot analysis for phosphorylated Ser-139 H2AX (γH2AX), a marker of DNA damage, demonstrated that SJ018 and I-BET762 also increased DNA damage, and that the BD2-specific SJ018 induces DNA damage to a greater extent and at a lower dose than the BD1/BD2 inhibitor I-BET762 in BxPC3 cells. The data also showed that both SJ018 and I-BET762 inhibited expression of the homologous recombination protein Rad51 in vitro. We conclude that SJ018 is more potent than I-BET762 in PDAC cells as a single agent, and that degree of potency is reflected by higher levels of DNA damage. Citation Format: Aubrey Lynn Miller, Peter J. Slavish, Brandon M. Young, Philip M. Potter, Anang A. Shelat, Karina J. Yoon. Targeting the BD2 BET bromodomain to inhibit proliferation of pancreatic ductal adenocarcinoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5794.

Cholangiocarcinoma (CCA) is an aggressive bile duct neoplasm, and the second most common primary hepatic malignancy. CCA is usually diagnosed at a late stage where the current standard of care, resection followed by gemcitabine with or without cisplatin, is not effective. Up to 90% of CCA patients are ineligible for resection and, of those eligible, postoperative chemotherapy does not significantly prolong overall survival. The limited number of CCA models hinders drug development and discovery of new therapeutic targets. Mutations have been identified in KRAS (17% of CCA tumors), p53 (44%) and SMAD4 (17%), but are not recognized as essential to CCA progression. c-Myc protein is highly expressed in 94% of CCA cases while low to undetectable in normal adult liver, suggesting c-Myc overexpression may contribute to CCA tumor progression but this hypothesis has not been tested. Toward developing novel effective therapies for CCA, we evaluated the effect of the bromodomain and extraterminal domain (BET) inhibitor JQ1 on c-Myc expression and on the proliferation of CCA cells. JQ1 inhibits c-Myc transcription by binding to the acetylated lysine (K-Ac) binding pockets of BET protein family members (BRD2, BRD3, BRD4 and BRDT), preventing their interaction with K-Ac residues on nuclear proteins, disrupting the formation of functional transcriptional complexes and inhibiting c-Myc transcription. We have shown that JQ1 inhibited tumor growth in a patient-derived xenograft (PDX) model of CCA and downregulated expression of c-Myc and its transcriptional targets BRCA2 and Chk1, both involved in DNA damage response. Our current data show that JQ1 decreased c-Myc protein expression, CCA cell viability, and clonogenic potential in KKU-055 CCA cell line. Of note, the literature suggests that tumors deficient in BRCA2 or Chk1 are relatively sensitive to PARP inhibitors (PARPi). Therefore, we hypothesize that JQ1-induced downregulation of c-Myc and its transcriptional targets BRCA2 and Chk1 would potentiate the efficacy of PARPi. We exposed CCA cell line KKU-055 with a range of JQ1 and PARPi (olaparib and veliparib) concentrations as single agent or combination therapy. Each combination of JQ1 with either PARPi was more effective than any of the three drugs as single agents. Combination indices (CI), calculated using CompuSyn 1.0, ranged from 0.05 to 0.09 which indicated strong synergy for JQ1 with olaparib or veliparib. Further, synergy with JQ1 was not dependent on a single PARPi. JQ1 with olaparib (1:1) also decreased the clonogenic potential of KKU-055 cells, compared to each drug as a single agent. These data suggest that inhibition of BET protein function sensitizes CCA cells to PARPi, coincident with downregulation of c-Myc and its transcriptional targets BRCA2 and Chk1. Research funded by NIH/NCI R21 CA205501 Citation Format: Samuel C. Fehling, Aubrey L. Miller, James E. Bradner, Karina J. Yoon. The BET inhibitor JQ1 sensitizes cholangiocarcinoma cells to PARP inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 5824.

Cholangiocarcinoma (CCA) is a lethal malignancy arising from cholangiocytes in any part of the biliary tree. The incidence of CCA has been on the rise worldwide, and the prognosis and clinical outcome have remained essentially unchanged for 30 years. The majority of patients are diagnosed at late stage, and surgery continues to be the only cure. Patients receive systemic chemotherapy with the first-line combination therapy comprising gemcitabine and cisplatin. Median survival for these patients is To determine gene products whose upregulation or downregulation is responsible for the differences in sensitivity to JQ1 among our CCA models, we generated expression profiles of tumors from vehicle control and JQ1 treated mice using NanoString technology (nCounter PanCancer Pathways panel). Our data demonstrate that JQ1 inhibited the expression of c-Myc to a greater extent in the sensitive models than in the insensitive model. Expression array data showed further that gene products involved in cell cycle and DNA repair pathways were also decreased by JQ1. Of particular interest were two transcriptional targets of c-Myc, Chk1 and BRCA2, each of which is involved in DNA damage response. Immunohistochemistry staining confirmed expression profile analyses. We conclude that the inhibition of cell cycle and DNA repair genes may contribute to the mechanism of action of JQ1 in CCA tumors. Citation Format: Aubrey L. Miller, Patrick L. Garcia, Tracy L. Gamblin, Leona N. Council, Xiangqin Cui, James E. Bradner, Eddy S. Yang, Karina J. Yoon. JQ1 sensitivity of patient-derived xenograft models of cholangiocarcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 1293.

Cholangiocarcinoma (CCA) is a lethal malignancy of the biliary epithelium that can arise in any part of the biliary tree. Surgery is the only curative treatment for CCA, but only ∼30% of patients present with resectable disease. The remaining 70% of patients present with advanced or metastatic disease and, if eligible, undergo systemic chemotherapy with the first-line combination of gemcitabine and cisplatin. This combination was shown in a phase II clinical trial to significantly increase median survival from 8.1 to 11.7 months, compared to gemcitabine alone. In order to improve on current treatment, pre-clinical evaluation of novel therapeutics is essential to improving outcome. Unfortunately, the paucity of data describing characteristics common to CCA make development of targeted therapy difficult. However, as is true for other types of solid tumors, c-Myc expression likely contributes to CCA phenotype: c-Myc expression has been observed in 95% of CCA tumors, and experimental down-regulation of c-Myc decreases the invasive potential of CCA cells in vitro. Recently it has become possible to inhibit expression of c-Myc using BET inhibitors. Therefore, we evaluated the efficacy of the bromodomain (BET) inhibitor JQ1 using in vivo models of CCA. The five patient-derived xenograft (PDX) models of CCA that we developed are the first such models to be reported. These models retain the heterogeneity, architecture and specific genetic characteristics of the primary tumors from which they were derived. We used three of these models to examine whether the BET inhibitor JQ1 inhibited CCA tumor growth and generated expression profiles of vehicle- and drug-treated tumors. We administered 50 mg/kg of JQ1 i.p. daily for 20 days and monitored tumor growth. This treatment regimen was well tolerated by tumor-bearing mice, without apparent toxicity. Our data demonstrate that JQ1 suppressed tumor growth in two of the three models, compared to vehicle control treated mice. The data also showed that JQ1-treated tumors had lower levels of c-Myc RNA (↓5-fold) and protein and of RNA encoding multiple transcriptional targets downstream of this oncogenic transcription factor. We conclude that BET inhibitors such as JQ1 warrant further investigation as potentially effective drugs for the treatment of CCA. Citation Format: Patrick L. Garcia, Aubrey L. Miller, Kelly Kreitzburg, Tracy L. Gamblin, Leona N. Council, John D. Christein, Pablo Arnoletti, Marty Heslin, Sushanth Reddy, Joseph H. Richardson, Eddy S. Yang, Jun Qi, James E. Bradner, Karina J. Yoon. Bromodomain inhibitor JQ1 inhibits cholangiocarcinoma tumor growth in patient-derived xenograft models. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1779. doi:10.1158/1538-7445.AM2015-1779