Hypermethylation and global remodelling of DNA methylation is associated with acquired cisplatin resistance in testicular germ cell tumours

Testicular germ cell tumours (TGCTs) respond well to cisplatin-based therapy. However, cisplatin resistance and poor outcomes do occur. It has been suggested that a shift towards DNA hypermethylation mediates cisplatin resistance in TGCT cells, although there is little direct evidence to support this claim. Here we utilized a series of isogenic cisplatin-resistant cell models and observed a strong association between cisplatin resistance in TGCT cells and a net increase in global CpG and non-CpG DNA methylation spanning regulatory, intergenic, genic and repeat elements. Hypermethylated loci were significantly enriched for repressive DNA segments, CTCF and RAD21 sites and lamina associated domains, suggesting that global nuclear reorganization of chromatin structure occurred in resistant cells. Hypomethylated CpG loci were significantly enriched for EZH2 and SUZ12 binding and H3K27me3 sites. Integrative transcriptome and methylome analyses showed a strong negative correlation between gene promoter and CpG island methylation and gene expression in resistant cells and a weaker positive correlation between gene body methylation and gene expression. A bidirectional shift between gene promoter and gene body DNA methylation occurred within multiple genes that was associated with upregulation of polycomb targets and downregulation of tumour suppressor genes. These data support the hypothesis that global remodelling of DNA methylation is a key factor in mediating cisplatin hypersensitivity and chemoresistance of TGCTs and furthers the rationale for hypomethylation therapy for refractory TGCT patients.

Regulation of cellular sterol homeostasis by the oxygen responsive noncoding RNA lincNORS

We hereby provide the initial portrait of lincNORS, a spliced lincRNA generated by the MIR193BHG locus, entirely distinct from the previously described miR-193b-365a tandem. While inducible by low O₂ in a variety of cells and associated with hypoxia in vivo, our studies show that lincNORS is subject to multiple regulatory inputs, including estrogen signals. Biochemically, this lincRNA fine-tunes cellular sterol/steroid biosynthesis by repressing the expression of multiple pathway components. Mechanistically, the function of lincNORS requires the presence of RALY, an RNA-binding protein recently found to be implicated in cholesterol homeostasis. We also noticed the proximity between this locus and naturally occurring genetic variations highly significant for sterol/steroid-related phenotypes, in particular the age of sexual maturation. An integrative analysis of these variants provided a more formal link between these phenotypes and lincNORS, further strengthening the case for its biological relevance.

Epigenetic Attire in Ovarian Cancer: The Emperor's New Clothes

Ovarian cancer is an aggressive epithelial tumor that remains a major cause of cancer morbidity and mortality in women. Epigenetic alterations including DNA methylation and histone modifications are being characterized in ovarian cancer and have been functionally linked to processes involved in tumor initiation, chemotherapy resistance, cancer stem cell survival, and tumor metastasis. The epigenetic traits of cancer cells and of associated tumor microenvironment components have been shown to promote an immunosuppressive tumor milieu. However, DNA methylation and histone modifications are reversible, and therapies targeting the epigenome have been implicated in potential reinvigoration of the antitumor immunity. In this review, we provide an overview specifically of DNA methylation and histone modifications as "clothes of the ovarian cancer genome" in relationship to their functional effects and highlight recent developments in the field. We also address the clinical implications of therapeutic strategies to remove or alter specific articles of genomic "clothing" and restore normal cellular function. As the clothes of the genome continue to be deciphered, we envision that the epigenome will become an important therapeutic target for cancer.

EZH2-Mediated Downregulation of the Tumor Suppressor DAB2IP Maintains Ovarian Cancer Stem Cells

The majority of women diagnosed with epithelial ovarian cancer eventually develop recurrence, which rapidly evolves into chemoresistant disease. Persistence of ovarian cancer stem cells (OCSC) at the end of therapy may be responsible for emergence of resistant tumors. In this study, we demonstrate that in OCSC, the tumor suppressor disabled homolog 2-interacting protein (DAB2IP) is silenced by EZH2-mediated H3K27 trimethylation of the DAB2IP promoter. CRISPR/Cas9-mediated deletion of DAB2IP in epithelial ovarian cancer cell lines upregulated expression of stemness-related genes and induced conversion of non-CSC to CSC, while enforced expression of DAB2IP suppressed CSC properties. Transcriptomic analysis showed that overexpression of DAB2IP in ovarian cancer significantly altered stemness-associated genes and bioinformatic analysis revealed WNT signaling as a dominant pathway mediating the CSC inhibitory effect of DAB2IP. Specifically, DAB2IP inhibited WNT signaling via downregulation of WNT5B, an important stemness inducer. Reverse phase protein array further demonstrated activation of noncanonical WNT signaling via C-JUN as a downstream target of WNT5B, which was blocked by inhibiting RAC1, a prominent regulator of C-JUN activation. Coadministration of EZH2 inhibitor GSK126 and RAC1 inhibitor NSC23766 suppressed OCSC survival in vitro and inhibited tumor growth and increased platinum sensitivity in vivo. Overall, these data establish that DAB2IP suppresses the cancer stem cell phenotype via inhibition of WNT5B-induced activation of C-JUN and can be epigenetically silenced by EZH2 in OCSC. Targeting the EZH2/DAB2IP/C-JUN axis therefore presents a promising strategy to prevent ovarian cancer recurrence and has potential for clinical translation. SIGNIFICANCE: These findings show that combining an epigenetic therapy with a noncanonical WNT signaling pathway inhibitor has the potential to eradicate ovarian cancer stem cells and to prevent ovarian cancer recurrence.

Abstract 1403: HOTAIR functions through NF-κB pathway in regulating ovarian cancer stem cells

Ovarian cancer (OC) is the fifth leading cause of cancer-related death among American women. Persistence of OC stem cells (OCSCs) is believed to contribute to resistance to platinum-based chemotherapy and disease relapse. Long non-coding RNA HOXC transcript antisense RNA (HOTAIR) has been shown to be associated with chemoresistance and overexpressed in many types of cancers, including high-grade serous OC (HGSOC). Previously published work has demonstrated that NF-κB was activated by HOTAIR through I-κB inhibition via trimethylation of histone H3 lysine K27, which contributes to chemoresistance in HGSOC. NF-κB-medicated signaling pathways involved in maintaining characteristics of CSCs, such as targeting stem cell markers, CD44, CD133, and ALDH1 has been demonstrated but not well defined in OC. The goals of this study are to understand the mechanism of HOTAIR-mediated NF-κB signaling pathway in regulating OCSCs and develop novel strategies to target OCSCs and overcome OC recurrence and drug resistance. Quantitative RT-PCR analysis revealed that HOTAIR was overexpressed in OCSCs compared to non-OCSCs. In order to produce loss-of-function phenotypes of HOTAIR and investigate the function of this gene, we utilized the paired CRISPR guide RNA design to delete the functional sites of HOTAIR without affecting nearby protein-coding gene. Knockout of HOTAIR re-sensitized OC cells to platinum treatment and significantly decreased (P<0.001) OCSC population and stemness-related phenotypes, including spheroid formation and colony formation ability. ALDH1A1 and expression of other stemness-related genes, including Notch3, PROM1 were significantly decreased by HOTAIR knockout. Overexpression of HOTAIR in OC cells significantly increased (P<0.05) these stem-like characteristics. Furthermore, we showed NF-κB nuclear accumulation and activation in OCSCs compared to non-OCSCs. Knockout of HOTAIR decreased (P<0.01) nuclear localization of NF-κB in OCSCs. Inhibiting NF-κB in using a commercially available pharmacological approach as well as NF-κB knockout both significantly decreased OCSC population and stemness-related phenotypes, as well as ALDH1 protein expression (P< 0.01). However, inhibition of NF-κB has no effect on OCSC characteristics in HOTAIR knockout cells, indicating that HOTAIR may function through constitutively activated NF-κB in regulating OCSCs. We suggest a better understanding of HOTAIR- NF-κB axis in regulating OCSCs will facilitate identifying the key therapeutic target to eliminate residual tumor cells after conventional chemotherapy and prevent OC recurrence and drug resistance.

Citation Format: Weini Wang, Fang Fang, Ali R. Özeş, Kenneth P. Nephew. HOTAIR functions through NF-κB pathway in regulating ovarian cancer stem cells [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1403.

Platinum-Induced Ubiquitination of Phosphorylated H2AX by RING1A Is Mediated by Replication Protein A in Ovarian Cancer

Platinum resistance is a common occurrence in high-grade serous ovarian cancer and a major cause of ovarian cancer deaths. Platinum agents form DNA cross-links, which activate nucleotide excision repair (NER), Fanconi anemia, and homologous recombination repair (HRR) pathways. Chromatin modifications occur in the vicinity of DNA damage and play an integral role in the DNA damage response (DDR). Chromatin modifiers, including polycomb repressive complex 1 (PRC1) members, and chromatin structure are frequently dysregulated in ovarian cancer and can potentially contribute to platinum resistance. However, the role of chromatin modifiers in the repair of platinum DNA damage in ovarian cancer is not well understood. We demonstrate that the PRC1 complex member RING1A mediates monoubiquitination of lysine 119 of phosphorylated H2AX (γH2AXub1) at sites of platinum DNA damage in ovarian cancer cells. After platinum treatment, our results reveal that NER and HRR both contribute to RING1A localization and γH2AX monoubiquitination. Importantly, replication protein A, involved in both NER and HRR, mediates RING1A localization to sites of damage. Furthermore, RING1A deficiency impairs the activation of the G₂-M DNA damage checkpoint, reduces the ability of ovarian cancer cells to repair platinum DNA damage, and increases sensitivity to platinum. IMPLICATIONS: Elucidating the role of RING1A in the DDR to platinum agents will allow for the identification of therapeutic targets to improve the response of ovarian cancer to standard chemotherapy regimens.

ERK5 Is Required for Tumor Growth and Maintenance Through Regulation of the Extracellular Matrix in Triple Negative Breast Cancer

Conventional mitogen-activated protein kinase (MAPK) family members regulate diverse cellular processes involved in tumor initiation and progression, yet the role of ERK5 in cancer biology is not fully understood. Triple-negative breast cancer (TNBC) presents a clinical challenge due to the aggressive nature of the disease and a lack of targeted therapies. ERK5 signaling contributes to drug resistance and metastatic progression through distinct mechanisms, including activation of epithelial-to-mesenchymal transition (EMT). More recently a role for ERK5 in regulation of the extracellular matrix (ECM) has been proposed, and here we investigated the necessity of ERK5 in TNBC tumor formation. Depletion of ERK5 expression using the CRISPR/Cas9 system in MDA-MB-231 and Hs-578T cells resulted in loss of mesenchymal features, as observed through gene expression profile and cell morphology, and suppressed TNBC cell migration. In vivo xenograft experiments revealed ERK5 knockout disrupted tumor growth kinetics, which was restored using high concentration Matrigel™ and ERK5-ko reduced expression of the angiogenesis marker CD31. These findings implicated a role for ERK5 in the extracellular matrix (ECM) and matrix integrity. RNA-sequencing analyses demonstrated downregulation of matrix-associated genes, integrins, and pro-angiogenic factors in ERK5-ko cells. Tissue decellularization combined with cryo-SEM and interrogation of biomechanical properties revealed that ERK5-ko resulted in loss of key ECM fiber alignment and mechanosensing capabilities in breast cancer xenografts compared to parental wild-type cells. In this study, we identified a novel role for ERK5 in tumor growth kinetics through modulation of the ECM and angiogenesis axis in breast cancer.

Abstract A81: Targeting EZH2/DAB2IP/Wnt axis in ovarian cancer stem cells

Ovarian cancer (OC) is the leading cause of death from gynecologic malignancies. Recent data have pointed to the persistence of quiescent ovarian cancer stem cells (OCSCs) not eliminated by chemotherapy and able to regenerate tumors as the main contributor to tumor relapse and metastasis. Downregulation of tumor suppressor DAB2IP significantly correlated with poor patient survival in OC. In the current study, we tested the hypothesis that DAB2IP is downregulated by EZH2 methylation in OC and targeting DAB2IP inhibits OCSCs, which would prevent disease recurrence. Subpopulations of CSC and non-CSC were isolated from OC cell lines by fluorescence-activated cell sorting (FACS) based on aldehyde dehydrogenase (ALDH) activity, a consistent CSC marker. Expression of DAB2IP in ALDH(+) cells was lower (P<0.05) compared to non-CSC ALDH(-) cells, which can be restored by EZH2 inhibition. Chromatin immunoprecipitation (ChIP) analysis demonstrated enrichment (P<0.05) of H3K27me3 at DAB2IP promoter loci in CSC compared to non-CSC. Furthermore, inhibiting EZH2 decreased H3K27me3 and increased (P<0.05) DAB2IP expression in OC cells, demonstrating that DAB2IP downregulation in CSC was due to EZH2. Knocking out DAB2IP using CRISPR/Cas9 system in OC cell lines upregulated (P<0.05) expression of stemness-related genes and increased (P<0.05) the percentage of ALDH(+) cells. Enforced overexpression of DAB2IP decreased (P<0.05) the number of ALDH(+) cells and inhibited (P<0.05) both spheroid and colony formation. Furthermore, elevated DAB2IP expression decreased (P<0.05) cisplatin IC50 of both OCSCs and OC cells and inhibited (P<0.05) cell migration capacity, suggesting DAB2IP plays a role in regulating OCSC function. OVCAR3 cells and DAB2IP-overexpressing OVCAR3 cells were further analyzed by RNA-sequencing and bioinformatics. Transcriptome analysis revealed that DAB2IP overexpression significantly (FDR < 0.05, fold change > 2) altered expression of 449 genes, including downregulation of ALDH1A1, LGR5, PROM1, and TWIST1, markers strongly associated with CSC phenotypes. Ingenuity Pathway Analysis for upstream regulators of differentially expressed genes revealed Wnt-signaling as a dominant pathway mediating the anti-OCSC effects of DAB2IP. Based on RNA-seq analysis, WNT5B expression decreased (P<0.05) by 3.83 fold, indicating that DAB2IP may negatively regulate Wnt signaling pathway by repressing WNT5B. Furthermore, WNT5B recombinant protein significantly increased (P<0.05) the OCSC population, and reverse phase protein array analysis demonstrated activation of JNK/c-Jun as a possible downstream target of WNT5B. Collectively, our data reveal that DAB2IP, via noncanonical Wnt-mediated signaling pathway, plays a critical role in modulating OCSC properties. Based on these novel findings, we are testing novel combination treatment strategies targeting OCSCs and with the goal of inhibiting tumor relapse and overcoming chemoresistance.

Citation Format: Xingyue Zong, Ali Ozes, Weini Wang, Kenneth P. Nephew. Targeting EZH2/DAB2IP/Wnt axis in ovarian cancer stem cells [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A81.

Abstract B63: Lysophosphatidic acid as a mediator of ovarian cancer cell stemness

Epithelial ovarian cancer (OC) is the deadliest gynecologic malignancy. Recurrence of advanced, multidrug-resistant metastatic disease after initially good response to standard lines of chemotherapy occurs in the majority of OC patients. Chemoresistant, recurrent OC is essentially fatal. Disease relapse is due to survival and expansion of a small pool of chemorefractory ovarian cancer stem cells (OCSCs). OC evolution to a platinum-resistant state is associated with aberrant epigenetic modifications, including altered DNA methylation and histone modifications. In addition, OC cells residing in the peritoneal cavity are exposed to a variety of external cues arising from the ascitic microenvironment, including the bioactive molecule lysophosphatidic acid (LPA), which potentially contribute to cell stemness and chemoresistance. LPA in the intraperitoneal fluid of OC patients has been strongly implicated in ovarian carcinogenesis and metastasis through a variety of mechanisms. However, regulation of OC cells by LPA is incompletely understood, and the role of LPA in OCSC acquisition/chemoresistance remains unclear. In the current study, we tested the hypothesis that LPA is a mediator of OCSC promotion and survival. Expression of aldehyde dehydrogenase (ALDH), an accepted functional marker of cancer stem cells, was assessed in a panel of high-grade serous ovarian cancer (HGSOC) cell lines (OVSAHO, OVCAR3, OVCAR5, PEO1, and Kuramochi) using an Aldefluor assay. Treatment of HGSOC cells with increasing (0-80uM, 72h) doses of LPA enriched the ALDH+ population in a cell line-specific dose-dependent manner. In PEO1 and Kuramochi cells, intermediate LPA doses (1-10uM) resulted in a 1.5-2.5-fold increase (P<0.05) of ALDH+ cells (from ∼4% to ∼8% in PEO1 and from ∼4% up to ∼10% in Kuramochi, respectively). However, 80uM LPA treatment was necessary to increase (P<0.05) the percentage ALDH+ cells in OVCAR3 (from ∼17% to 34%) and OVSAHO cells (from ∼10% up to 29%). In accordance with the results of the flow cytometry analysis, cancer stem cell properties after LPA treatment (0-80uM, every 72hr, up to 21 days) were enhanced (P<0.05), based on clonogenic assay. In particular, moderate (10-20uM) LPA treatment increased (P<0.05) cell clonogenic survival of PEO1 and Kuramochi, while a greater (80uM) LPA dose was needed for OVCAR3 and OVSAHO. Furthermore, LPA (0-80uM, 14 days) augmented spheroid formation ability in PEO1 cells (3-4-fold increase; P<0.05). Global transcriptomic and epigenomic assessment of altered genes/pathways induced by LPA are currently being examined to assess stemness-promoting pathways and epigenetic changes, which we believe will identify new biologic insights and potential therapeutic targets to eradicate OCSC in patients.

Citation Format: Yuliya Klymenko, Kenneth P. Nephew. Lysophosphatidic acid as a mediator of ovarian cancer cell stemness [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr B63.

In vivo modeling of metastatic human high-grade serous ovarian cancer in mice

Metastasis is responsible for 90% of human cancer mortality, yet it remains a challenge to model human cancer metastasis in vivo. Here we describe mouse models of high-grade serous ovarian cancer, also known as high-grade serous carcinoma (HGSC), the most common and deadliest human ovarian cancer type. Mice genetically engineered to harbor Dicer1 and Pten inactivation and mutant p53 robustly replicate the peritoneal metastases of human HGSC with complete penetrance. Arising from the fallopian tube, tumors spread to the ovary and metastasize throughout the pelvic and peritoneal cavities, invariably inducing hemorrhagic ascites. Widespread and abundant peritoneal metastases ultimately cause mouse deaths (100%). Besides the phenotypic and histopathological similarities, mouse HGSCs also display marked chromosomal instability, impaired DNA repair, and chemosensitivity. Faithfully recapitulating the clinical metastases as well as molecular and genomic features of human HGSC, this murine model will be valuable for elucidating the mechanisms underlying the development and progression of metastatic ovarian cancer and also for evaluating potential therapies.

Rarely does an experimental model fully replicate the clinical metastases of a human malignancy. Faithfully representing the clinical metastases of human high-grade serous ovarian cancer with complete penetrance, coupled with histopathological, molecular, and genomic similarities, these mouse models, particularly one harboring mutant p53, will be vital to elucidating the underlying pathogenesis of human ovarian cancer. In-depth understanding of the development and progression of ovarian cancer is crucial to medical advances in the early detection, effective treatment, and prevention of ovarian cancer. Also, these robust mouse models, as well as cell lines established from the mouse primary and metastatic tumors, will serve as useful preclinical tools to evaluate therapeutic target genes and new therapies in ovarian cancer.

Abstract P2-06-01: Intrinsic transcriptomic differences of luminal progenitors and mature luminal cells of the normal breast

Epithelial cells in the normal breast are organized hierarchically into stem, luminal progenitor (LP) and mature luminal cells (LC) with distinct gene expression patterns. However, whether these gene expression differences are cell-intrinsic, driven through LP-LC cell interactions or due to stromal-luminal cell interactions in the breasts of healthy women is incompletely understood. Furthermore, prior studies on these cell populations did not take genetic ancestry into consideration despite widely reported genetic ancestry-dependent differences in the normal breast biology and breast cancer susceptibility/outcome. We isolated LP and LC breast epithelial cells from core breast biopsies of healthy women representing European, African American and Latino ancestry (five each). After a brief propagation (five passages) under epithelial reprogramming assay conditions, transcriptomes and DNA methylomes were examined using RNA- and Methylcapture-sequencing. Differences in gene expression (FDR<0.05, fold change >2) in LC cells compared to LP cells were observed, with 1581 and 609 genes up- and down-regulated, respectively. These data were enriched for signaling networks associated with cell cycle control of chromosomal replication, mitotic roles of polo-like kinase (down-regulated genes), granulocyte adhesion and diapedesis and LXR/RXR signaling (up-regulated genes). Despite marked gene expression differences between LC and LP cells, only 14 upregulated genes and four down-regulated genes showed DNA hypo- and hyper-methylation, respectively, in LC cells compared to LP cells, suggesting a minimal role for DNA methylation in differential gene expression between the two cell types. Furthermore, of the 2190 differentially expressed genes, 7% (158 genes) were regulated by estrogen, suggesting that differences in hormone responsiveness contribute to differential gene expression in LP and LC cells. To determine relationships between genes differentially methylated and expressed in LC and LP cells and breast cancer, we used publicly available databases, including TCGA. Interestingly, all genes hypermethylated and expressed at lower levels in LC cells were similarly hypermethylated and expressed at lower levels in breast cancers compared to normal breast, suggesting that these genes are minimally altered in breast cancer. Furthermore, in LC compared to LP cells, of thegenes hypomethylated and expressed at higher levels, only four genes (AIM1L, PRSS27, PTK6 and UNC13D) showed a similar pattern in breast tumors compared to normal breast. Of these, PTK6 is significantly overexpressed in luminal and HER2+ breast cancers compared to basal-like breast cancers, suggesting that PTK6+ cells are the preferred cell-of origin of luminal breast cancers. Taken together, this is the first study to demonstrate that transcriptomic data of normal breast cells from healthy women can be used to further define cell-of-origin of tumors and identify cancer-specific gene expression changes in breast cancer.

Citation Format: Fang Fang, Poornima Bhat-Nakshatri, Manjushree Anjanappa, Dough Rusch, Aaron Buechlein, Dave Miller, Kenneth P Nephew, Harikrishna Nakshatri. Intrinsic transcriptomic differences of luminal progenitors and mature luminal cells of the normal breast [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P2-06-01.

A Randomized Phase II Trial of Epigenetic Priming with Guadecitabine and Carboplatin in Platinum-resistant, Recurrent Ovarian Cancer

PURPOSE

Platinum resistance in ovarian cancer is associated with epigenetic modifications. Hypomethylating agents (HMA) have been studied as carboplatin resensitizing agents in ovarian cancer. This randomized phase II trial compared guadecitabine, a second-generation HMA, and carboplatin (G+C) against second-line chemotherapy in women with measurable or detectable platinum-resistant ovarian cancer.

PATIENTS AND METHODS

Patients received either G+C (guadecitabine 30 mg/m² s.c. once-daily for 5 days and carboplatin) or treatment of choice (TC; topotecan, pegylated liposomal doxorubicin, paclitaxel, or gemcitabine) in 28-day cycles until progression or unacceptable toxicity. The primary endpoint was progression-free survival (PFS); secondary endpoints were RECIST v1.1 and CA-125 response rate, 6-month PFS, and overall survival (OS).

RESULTS

Of 100 patients treated, 51 received G+C and 49 received TC, of which 27 crossed over to G+C. The study did not meet its primary endpoint as the median PFS was not statistically different between arms (16.3 weeks vs. 9.1 weeks in the G+C and TC groups, respectively; P = 0.07). However, the 6-month PFS rate was significantly higher in the G+C group (37% vs. 11% in TC group; P = 0.003). The incidence of grade 3 or higher toxicity was similar in G+C and TC groups (51% and 49%, respectively), with neutropenia and leukopenia being more frequent in the G+C group.

CONCLUSIONS

Although this trial did not show superiority for PFS of G+C versus TC, the 6-month PFS increased in G+C treated patients. Further refinement of this strategy should focus on identification of predictive markers for patient selection.

Interferon-γ signaling is associated with BRCA1 loss-of-function mutations in high grade serous ovarian cancer

Loss-of-function mutations of the breast cancer type 1 susceptibility protein (BRCA1) are associated with breast (BC) and ovarian cancer (OC). To identify gene signatures regulated by epigenetic mechanisms in OC cells carrying BRCA1 mutations, we assessed cellular responses to epigenome modifiers and performed genome-wide RNA- and chromatin immunoprecipitation-sequencing in isogenic OC cells UWB1.289 (carrying a BRCA1 mutation, BRCA1-null) and UWB1.289 transduced with wild-type BRCA1 (BRCA1+). Increased sensitivity to histone deacetylase inhibitors (HDACi) was observed in BRCA1-null vs. BRCA1+ cells. Gene expression profiles of BRCA1-null vs. BRCA1+ cells and treated with HDACi were integrated with chromatin mapping of histone H3 lysine 9 or 27 acetylation. Gene networks activated in BRCA1-null vs. BRCA1 + OC cells related to cellular movement, cellular development, cellular growth and proliferation, and activated upstream regulators included TGFβ1, TNF, and IFN-γ. The IFN-γ pathway was altered by HDACi in BRCA1+ vs. BRCA1-null cells, and in BRCA1-mutated/or low vs. BRCA1-normal OC tumors profiled in the TCGA. Key IFN-γ-induced genes upregulated at baseline in BRCA1-null vs. BRCA1+OC and BC cells included CXCL10, CXCL11, and IFI16. Increased localization of STAT1 in the promoters of these genes occurred in BRCA1-null OC cells, resulting in diminished responses to IFN-γ or to STAT1 knockdown. The IFN-γ signature was associated with improved survival among OC patients profiled in the TCGA. In all, our results support that changes affecting IFN-γ responses are associated with inactivating BRCA1 mutations in OC. This signature may contribute to altered responses to anti-tumor immunity in BRCA1-mutated cells or tumors.

Abstract GMM-062: TARGETING OVARIAN CANCER STEM CELLS THROUGH THE TUMOR SUPPRESSOR DAB2IP-MEDIATED WNT SIGNALING PATHWAY

Ovarian cancer (OC) recurrence after tumor eradication by chemotherapy invariably heralds poor outcome. Recent data point to persistence of quiescent cancer stem cells (CSCs) not eliminated by chemotherapy and able to regenerate tumors as the main contributor to tumor relapse. Downregulation of tumor suppressor gene (TSG) DAB2IP, a member of the Ras GTPase-activating protein family, significantly correlated with poor patient survival in high-grade serous (HGS) OC. Furthermore, loss of DAB2IP in prostate and colon cancer enriched CSC population, suggesting a key role for DAB2IP in modulating cancer stemness. In the current study, we tested the hypothesis that targeting DAB2IP would inhibit CSCs in OC and prevent disease recurrence. Subpopulations of CSC and non-CSC were isolated from Kuramochi, OVCAR3 and COV362 HGSOC cell lines by fluorescence-activated cell sorting (FACS) based on aldehyde dehydrogenase (ALDH) activity, a consistent CSC marker. It was previously demonstrated by us and others that ALDH(+) cells share characteristics of normal stem cells such as the ability to form anchorage-independent multicellular aggregates (spheroids), undergo membrane efflux, express stem cell restricted transcription factors, and generate tumors in vivo. DAB2IP was examined in the FACS-sorted cells using qPCR and western blot. Expression of DAB2IP in ALDH(+) cells was lower (P<0.05) compared to non-CSC ALDH(-) cells. Chromatin immunoprecipitation (ChIP) analysis revealed greater (P<0.05) enrichment of H3K27me3 at DAB2IP promoter loci in CSC than non-CSC, suggesting that DAB2IP downregulation in CSC is caused by EZH2 methylation. Enforced overexpression of DAB2IP decreased (P<0.05) the number of ALDH(+) cells, inhibited (P<0.05) the ability of these cells to form spheroids (14-day incubation under stem cell conditions) and decreased (P<0.05) colony formation. Furthermore, elevated DAB2IP expression decreased (P<0.05) cisplatin IC50 of both OCSCs and HGSOC cells and inhibited (P<0.05) cell migration capacity (Bowden chamber transwell assay), suggesting DAB2IP plays a role in regulating OCSC function. Mechanistically, decreased expression of stemness-related genes in DAB2IP-overexpressing OCSCs was also observed, indicating potential key effectors downstream of DAB2IP. Moreover, dual luciferase reporter assay showed that ALDH1A1 transcription level was significantly repressed (P<0.05) in DAB2IP-overexpressing cells. OVCAR3 cells and DAB2IP-overexpressing OVCAR3 cells were further analyzed by RNA-sequencing and bioinformatics. This transcriptome analysis revealed that DAB2IP overexpression resulted in significantly (FDR < 0.05, fold change > 2) altered expression of 449 genes, including markers strongly associated with CSC phenotypes, including down-regulation of ALDH1A1, LGR5, PROM1, TWIST1 and ATP-binding cassette transporters. Differentially expressed genes were subjected to Ingenuity Pathway Analysis (IPA) for upstream regulators. IPA identified Wnt-signaling pathways as top upstream regulators of these differentially expressed genes, suggesting that Wnt-signaling is a dominant pathway mediating the anti-OCSC effects of DAB2IP. In addition, treating cells with Wnt inhibitor decreased (P<0.05) the CSC population, colony formation ability and ALDH1 expression. Collectively, our data reveals that DAB2IP plays a critical role in modulating CSC properties via Wnt-mediated signaling pathway, suggesting novel combination treatment strategy targeting OCSCs and thus impacting tumor relapse and chemoresistance in OC.

Citation Format: Xingyue Zong, Ali R Ozes, Kenneth P Nephew. TARGETING OVARIAN CANCER STEM CELLS THROUGH THE TUMOR SUPPRESSOR DAB2IP-MEDIATED WNT SIGNALING PATHWAY [abstract]. In: Proceedings of the 12th Biennial Ovarian Cancer Research Symposium; Sep 13-15, 2018; Seattle, WA. Philadelphia (PA): AACR; Clin Cancer Res 2019;25(22 Suppl):Abstract nr GMM-062.

Incorporating DNA Methyltransferase Inhibitors (DNMTis) in the Treatment of Genitourinary Malignancies: A Systematic Review

Inhibition of DNA methyltransferases (DNMTs) has emerged as a novel treatment strategy in solid tumors. Aberrant hypermethylation in promoters of critical tumor suppressor genes is the basis for the idea that treatment with hypomethylating agents may lead to the restoration of a "normal" epigenome and produce clinically meaningful therapeutic outcomes. The aim of this review article is to summarize the current state of knowledge of DNMT inhibitors in the treatment of genitourinary malignancies. The efficacy of these agents in genitourinary malignancies was reported in a number of studies and suggests a role of induced DNA hypomethylation in overcoming resistance to conventional cytotoxic treatments. The clinical significance of these findings should be further investigated.

Glutamine Metabolism Drives Growth in Advanced Hormone Receptor Positive Breast Cancer

Dependence on the glutamine pathway is increased in advanced breast cancer cell models and tumors regardless of hormone receptor status or function. While 70% of breast cancers are estrogen receptor positive (ER+) and depend on estrogen signaling for growth, advanced ER+ breast cancers grow independent of estrogen. Cellular changes in amino acids such as glutamine are sensed by the mammalian target of rapamycin (mTOR) complex, mTORC1, which is often deregulated in ER+ advanced breast cancer. Inhibitor of mTOR, such as everolimus, has shown modest clinical activity in ER+ breast cancers when given with an antiestrogen. Here we show that breast cancer cell models that are estrogen independent and antiestrogen resistant are more dependent on glutamine for growth compared with their sensitive parental cell lines. Co-treatment of CB-839, an inhibitor of GLS, an enzyme that converts glutamine to glutamate, and everolimus interrupts the growth of these endocrine resistant xenografts. Using human tumor microarrays, we show that GLS is significantly higher in human breast cancer tumors with increased tumor grade, stage, ER-negative and progesterone receptor (PR) negative status. Moreover, GLS levels were significantly higher in breast tumors from African-American women compared with Caucasian women regardless of ER or PR status. Among patients treated with endocrine therapy, high GLS expression was associated with decreased disease free survival (DFS) from a multivariable model with GLS expression treated as dichotomous. Collectively, these findings suggest a complex biology for glutamine metabolism in driving breast cancer growth. Moreover, targeting GLS and mTOR in advanced breast cancer may be a novel therapeutic approach in advanced ER+ breast cancer.

Abstract 3685: HOTAIR regulation and functionality in ovarian cancer stem cells

Ovarian cancer (OC) is the fifth leading cause of cancer-related death among American women. Persistence of OC stem cells (OCSCs) is believed to contribute to resistance to platinum-based chemotherapy and disease relapse. We have previously shown that epigenetic changes in OCSCs play a role in post-therapy OCSC persistence and demonstrated that is it possible to target OCSC using epigenetic therapies. HOXC transcript antisense RNA (HOTAIR) has been shown to be associated with chemoresistance and to be overexpressed in many types of cancers, including high-grade serous OC (HGSOC). HOTAIR interacts with Polycomb Repressive Complex 2 (PRC2) and due to its histone methyltransferases activity plays a key role in chromatin remodeling. Because HOTAIR is a known epigenetic regulator of differentiation and developmental genes in OC and other cancers, we hypothesize that HOTAIR is a key epigenetic regulator in OCSCs and therapeutically targeting HOTAIR in OCSCs will prevent tumor relapse. The goal of this study is to understand the role of HOTAIR in regulating OCSCs and further dissect the mechanism of action of HOTAIR in OCSCs. Aldehyde dehydrogenase (ALDH) activity and FACS was used to separate OCSCs from non-OCSCs in a panel of HGSOC cell lines (OVCAR3, CAOV3, OVCAR5, Kuramochi, COV362). Quantitative RT-PCR analysis revealed that HOTAIR was overexpressed in OCSC cells compared to non-OCSC cells. Knockout of HOTAIR using CRISPR-Cas9 system significantly decreased OCSC population and stemness-related phenotypes, including spheroid formation and colony formation ability. Overexpression of HOTAIR in HGSOC cells significantly increased these stem-like characteristics. Furthermore, targeting HOTAIR using peptide nucleic acid (PNA), which blocks interaction with Enhancer of Zeste Homologue 2 (EZH2), significantly decreased the OCSC population, indicating HOTAIR functions through EZH2 in regulating OCSCs. Combining the HOTAIR-targeting PNA with other epigenetic inhibitors, including the hypomethylating agent guadecitabine and the EZH2 inhibitor GSK503, significantly decreased proliferation and colony formation ability of HGSOC cells. We suggest that a better understanding of HOTAIR will facilitate identifying epigenomic alterations and chromatin landscape that contributes to OCSC phenotypes. Targeting HOTAIR in combination with epigenetic therapies may represent a therapeutic strategy to prevent tumor relapse.

Citation Format: Weini Wang, Fang Fang, Ali Ozes, Kenneth P. Nephew. HOTAIR regulation and functionality in ovarian cancer stem 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 3685.

IL-6 mediates platinum-induced enrichment of ovarian cancer stem cells

In high-grade serous ovarian cancer (OC), chemotherapy eliminates the majority of tumor cells, leaving behind residual tumors enriched in OC stem cells (OCSC). OCSC, defined as aldehyde dehydrogenase-positive (ALDH+), persist and contribute to tumor relapse. Inflammatory cytokine IL-6 is elevated in residual tumors after platinum treatment, and we hypothesized that IL-6 plays a critical role in platinum-induced OCSC enrichment. We demonstrate that IL-6 regulates stemness features of OCSC driven by ALDH1A1 expression and activity. We show that platinum induces IL-6 secretion by cancer-associated fibroblasts in the tumor microenvironment, promoting OCSC enrichment in residual tumors after chemotherapy. By activating STAT3 and upregulating ALDH1A1 expression, IL-6 treatment converted non-OCSC to OCSC. Having previously shown altered DNA methylation in OCSC, we show here that IL-6 induces DNA methyltransferase 1 (DNMT1) expression and the hypomethylating agent (HMA) guadecitabine induced differentiation of OCSC and reduced - but did not completely eradicate - OCSC. IL-6 neutralizing antibody (IL-6-Nab) combined with HMA fully eradicated OCSC, and the combination blocked IL-6/IL6-R/pSTAT3-mediated ALDH1A1 expression and eliminated OCSC in residual tumors that persisted in vivo after chemotherapy. We conclude that IL-6 signaling blockade combined with an HMA can eliminate OCSC after platinum treatment, supporting this strategy to prevent tumor recurrence after standard chemotherapy.

Epigenetic Crosstalk between the Tumor Microenvironment and Ovarian Cancer Cells: A Therapeutic Road Less Traveled

Metastatic dissemination of epithelial ovarian cancer (EOC) predominantly occurs through direct cell shedding from the primary tumor into the intra-abdominal cavity that is filled with malignant ascitic effusions. Facilitated by the fluid flow, cells distribute throughout the cavity, broadly seed and invade through peritoneal lining, and resume secondary tumor growth in abdominal and pelvic organs. At all steps of this unique metastatic process, cancer cells exist within a multidimensional tumor microenvironment consisting of intraperitoneally residing cancer-reprogramed fibroblasts, adipose, immune, mesenchymal stem, mesothelial, and vascular cells that exert miscellaneous bioactive molecules into malignant ascites and contribute to EOC progression and metastasis via distinct molecular mechanisms and epigenetic dysregulation. This review outlines basic epigenetic mechanisms, including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNA regulators, and summarizes current knowledge on reciprocal interactions between each participant of the EOC cellular milieu and tumor cells in the context of aberrant epigenetic crosstalk. Promising research directions and potential therapeutic strategies that may encompass epigenetic tailoring as a component of complex EOC treatment are discussed.

Abstract B07: Targeting DAB2IP in ovarian cancer stem cells

Ovarian cancer is the leading cause of death from gynecologic malignancies. Failure to eliminate ovarian cancer stem cells (OCSCs) by the end of conventional chemotherapy contributes to tumor relapse and metastasis. Understanding the molecular features of OCSCs may allow for effective targeting and eradicating these cells and tumor remission. We reported tumor-initiation and expansion capacity by ALDH+ OCSCs after platinum-based treatment of ovarian cancer xenografts. In addition, loss of DAB2IP in prostate and colon cancer promoted CSC-like features, suggesting a critical role in modulating CSC maintenance. DAB2IP, a novel member of Ras GTPase-activating (GAP) protein family, was identified as a potent tumor suppressor that interfered with many aspects of cancer progression and was frequently downregulated in tumors. In the current study, we aimed to elucidate the tumor-suppressor role of DAB2IP in ovarian cancer in the context of OCSCs and explore epigenetic approaches to upregulate its expression. OCSCs and non-CSCs subpopulations were isolated from multiple high-grade serous ovarian cancer cell lines (Kuramochi, OVCAR3, and COV362). Reduced (p<0.05) DAB2IP expression in OCSCs compared to non-CSC counterparts was observed, suggesting that DAB2IP suppresses OCSC maintenance. Overexpression of DAB2IP in OCSCs derived from Kuramochi decreased (p<0.05) OCSC population, and DAB2IP overexpression inhibited stemness-related phenotypes, including reduced (P<0.05) spheroid formation ability after 14-day incubation under stem cell conditions and decreased (P<0.05) colony formation. Decreased expression of stem cell markers (Oct4, Nanog, and Twist) in DAB2IP-overexpressing cells was also observed, indicating potential key effectors downstream of DAB2IP. Furthermore, elevated DAB2IP expression in OCSCs decreased (p<0.05) cisplatin IC50 and cell migration capacity in transwell assay, suggesting DAB2IP plays a role in OCSC function. Aberrant DNA promoter methylation and histone modifications were previously shown to be two major mechanisms of DAB2IP inactivation in cancer. We treated OCSCs with next-generation DNMT inhibitor guadecitabine and EZH2 inhibitor GSK-126, either alone or in combination. Single-agent guadecitabine or GSK-126 decreased ALDH expression with greater (p<0.05) effect in combination. Single GSK-126 was sufficient to increase DAB2IP expression (p<0.05) with additional increase when combined with guadecitabine, correlating with decreased ALDH expression. Collectively, our data suggested a possible combination epigenetic therapy to eliminate OCSCs, potentially through targeting DAB2IP, an important OCSC regulator.

Citation Format: Xingyue Zong, Ali R. Ozes, Kenneth P. Nephew. Targeting DAB2IP in ovarian cancer stem cells. [abstract]. In: Proceedings of the AACR Conference: Addressing Critical Questions in Ovarian Cancer Research and Treatment; Oct 1-4, 2017; Pittsburgh, PA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(15_Suppl):Abstract nr B07.

Epigenetic Targeting of Adipocytes Inhibits High-Grade Serous Ovarian Cancer Cell Migration and Invasion

Ovarian cancer (OC) cells frequently metastasize to the omentum, and adipocytes play a significant role in ovarian tumor progression. Therapeutic interventions targeting aberrant DNA methylation in ovarian tumors have shown promise in the clinic, but the effects of epigenetic therapy on the tumor microenvironment are understudied. Here, we examined the effect of adipocytes on OC cell behavior in culture and impact of targeting DNA methylation in adipocytes on OC metastasis. The presence of adipocytes increased OC cell migration and invasion, and proximal and direct coculture of adipocytes increased OC proliferation alone or after treatment with carboplatin. Treatment of adipocytes with hypomethylating agent guadecitabine decreased migration and invasion of OC cells toward adipocytes. Subcellular protein fractionation of adipocytes treated with guadecitabine revealed decreased DNA methyltransferase 1 (DNMT1) levels even in the presence of DNA synthesis inhibitor, aphidicolin. Methyl-Capture- and RNA-sequencing analysis of guadecitabine-treated adipocytes revealed derepression of tumor-suppressor genes and epithelial-mesenchymal transition inhibitors. SUSD2, a secreted tumor suppressor downregulated by promoter CpG island methylation in adipocytes, was upregulated after guadecitabine treatment, and recombinant SUSD2 decreased OC cell migration and invasion. Integrated analysis of the methylomic and transcriptomic data identified pathways associated with inhibition of matrix metalloproteases and fatty acid α-oxidation, suggesting a possible mechanism of how epigenetic therapy of adipocytes decreases metastasis. In conclusion, the effect of DNMT inhibitor on fully differentiated adipocytes suggests that hypomethylating agents may affect the tumor microenvironment to decrease cancer cell metastasis.Implications: Epigenetic targeting of tumor microenvironment can affect metastatic behavior of ovarian cancer cells. Mol Cancer Res; 16(8); 1226-40. ©2018 AACR.

Abstract 4319: Epigenetic reprogramming associated with BRCA1 loss of function in ovarian cancer induces enhanced interferon gamma signaling

Inactivating mutations of the breast cancer type 1 susceptibility protein (BRCA1) have been implicated in breast and ovarian cancer (OC) initiation. Having observed differential response of OC cells to histone deacetylase inhibitors (HDACi) dependent on the presence of a functional BRCA1, we mapped promoters marked by acetylation of lysine 9 or lysine 27 of histone H3 (H3K9ac, H3K27ac) by ChIP-sequencing, and measured gene expression by RNA-sequencing in the isogenic OC cell lines UWB1.289 carrying an inactivating mutation of BRCA1 (BRCA1-null) and UWB1.289 cells with restored BRCA1 gene (BRCA1+). Significant differences in promoter levels of H3K9 and H3K27 acetylation were associated with marked alteration of gene expression levels between BRCA-null and BRCA1+ cells and in response to the HDACi, entinostat. Pathway analyses revealed cellular movement, cellular development, cellular growth and proliferation, TGFβ1, TNF, and INF-γ among the top cellular/molecular functions and upstream regulators enriched by the absence of BRCA1 among H3K9ac differentially marked and differentially expressed genes. Importantly, the same pathways and regulators were enriched in response to entinostat in BRCA1+ cells, indicating that changes in gene expression affecting these functions and regulators in BRCA1-null cells depend on promoter-associated histone acetylation. Integrated analyses revealed that TGFβ1 and IFN-γ were also activated in BRCA1-null/or low vs. BRCA1-normal ovarian tumors in the TCGA database. IFN-γ target genes were upregulated at baseline and responded less to IFN-γ stimulation in BRCA1-null vs. BRCA1+ cells. Binding of HDAC1 to promoters of IFN-γ target genes was increased in BRCA1-null cells. Similarly, the BRCA1-null breast cancer cell line HCC1937 responded less to IFN-γ stimulation compared with HCC1937 cells in which BRCA1 was restored. The knockdown of STAT1, the main IFN-γ signaling transduction molecule, inhibited BRCA1+ cell proliferation, but did not affect BRCA1-null cells. We conclude that the transcriptome of BRCA1-null cells and tumors is altered through changes in histone acetylation affecting cancer-related pathways, including IFN-γ cellular responses. These changes could alter tumor progression in BRCA-null OC and impact response to immunotherapy.

Citation Format: Horacio Cardenas, Jessica Thomes Pepin, Guanglong Jiang, Salvatore Condello, Kenneth P. Nephew, Yunlong Liu, Daniela Matei. Epigenetic reprogramming associated with BRCA1 loss of function in ovarian cancer induces enhanced interferon gamma signaling [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 4319.

An Effective Epigenetic-PARP Inhibitor Combination Therapy for Breast and Ovarian Cancers Independent of BRCA Mutations

Purpose: PARP inhibitors (PARPi) are primarily effective against BRCA1/2-mutated breast and ovarian cancers, but resistance due to reversion of mutated BRCA1/2 and other mechanisms is common. Based on previous reports demonstrating a functional role for DNMT1 in DNA repair and our previous studies demonstrating an ability of DNA methyltransferase inhibitor (DNMTi) to resensitize tumors to primary therapies, we hypothesized that combining a DNMTi with PARPi would sensitize PARPi-resistant breast and ovarian cancers to PARPi therapy, independent of BRCA status.Experimental Design: Breast and ovarian cancer cell lines (BRCA-wild-type/mutant) were treated with PARPi talazoparib and DNMTi guadecitabine. Effects on cell survival, ROS accumulation, and cAMP levels were examined. In vivo, mice bearing either BRCA-proficient breast or ovarian cancer cells were treated with talazoparib and guadecitabine, alone or in combination. Tumor progression, gene expression, and overall survival were analyzed.Results: Combination of guadecitabine and talazoparib synergized to enhance PARPi efficacy, irrespective of BRCA mutation status. Coadministration of guadecitabine with talazoparib increased accumulation of ROS, promoted PARP activation, and further sensitized, in a cAMP/PKA-dependent manner, breast and ovarian cancer cells to PARPi. In addition, DNMTi enhanced PARP "trapping" by talazoparib. Guadecitabine plus talazoparib decreased xenograft tumor growth and increased overall survival in BRCA-proficient high-grade serous ovarian and triple-negative breast cancer models.Conclusions: The novel combination of the next-generation DNMTi guadecitabine and the first-in-class PARPi talazoparib inhibited breast and ovarian cancers harboring either wild-type- or mutant-BRCA, supporting further clinical exploration of this drug combination in PARPi-resistant cancers. Clin Cancer Res; 24(13); 3163-75. ©2018 AACR.