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Epigenetic Attire in Ovarian Cancer: the Emperor's New Clothes Daniela Matei1,2,3 and Kenneth P

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Epigenetic Attire in Ovarian Cancer: the Emperor's New Clothes Daniela Matei1,2,3 and Kenneth P Published OnlineFirst May 7, 2020; DOI: 10.1158/0008-5472.CAN-19-3837 CANCER RESEARCH | REVIEW Epigenetic Attire in Ovarian Cancer: The Emperor's New Clothes Daniela Matei1,2,3 and Kenneth P. Nephew4,5,6 ABSTRACT ◥ Ovarian cancer is an aggressive epithelial tumor that remains a targeting the epigenome have been implicated in potential major cause of cancer morbidity and mortality in women. Epige- reinvigoration of the antitumor immunity. In this review, we netic alterations including DNA methylation and histone modifica- provide an overview specifically of DNA methylation and histone tions are being characterized in ovarian cancer and have been modifications as "clothes of the ovarian cancer genome" in rela- functionally linked to processes involved in tumor initiation, tionship to their functional effects and highlight recent develop- chemotherapy resistance, cancer stem cell survival, and tumor ments in the field. We also address the clinical implications of metastasis. The epigenetic traits of cancer cells and of associated therapeutic strategies to remove or alter specific articles of genomic tumor microenvironment components have been shown to "clothing" and restore normal cellular function. As the clothes of the promote an immunosuppressive tumor milieu. However, DNA genome continue to be deciphered, we envision that the epigenome methylation and histone modifications are reversible, and therapies will become an important therapeutic target for cancer. Introduction “clothing” affect the transcriptomic program and cellular functions in the disease. Ovarian cancer, an aggressive epithelial tumor, remains a major In the context of the Greek prefix epi (“over”) implying features that cause of cancer morbidity and mortality in women, causing more are “on top of” of DNA, this review will focus on DNA methylation and deaths than any other female reproductive tract cancer in the United histone modifications in ovarian cancer as the “clothes of the epigen- States (1). The majority of patients with ovarian cancer are diagnosed ome.” However, it is important to recognize that in addition to these with advanced stage disease, and despite progress in surgical and features, epigenetic traits of tumors are initiated and sustained by chemotherapy strategies, 5-year survival rates have remained below alterations in noncoding RNAs (ncRNA) and nucleosomes (remodel- 25% (2). The most common subtype of ovarian cancer is the high grade ing and positioning)-mediated gene silencing (Fig. 1A; refs. 4–6). serous (HGS) histotype, which accounts for more than three quarter of DNA methylation, due to the transfer of a methyl group to the carbon- cases and is uniformly characterized by mutations of the tumor 5 position of cytosines, almost always within the context of cytosine- suppressor gene p53, and about half of HGS cases harbor deficiencies guanine (CpG) dinucleotides, is a covalent chemical modification of in homologous recombination DNA repair (HRD) mechanisms. DNA and the best-studied epigenetic mark in mammalian cells. DNA- Advances in genomic technologies have shown that both genetic and associated histones undergo extensive posttranslational modifications epigenetic changes accompany ovarian tumor initiation and progres- (methylation, acetylation), which tightly regulate the assembly of sion. The Tumor Cancer Genome Atlas (TCGA) project found that transcriptionally permissive or repressive (i.e., open or closed) chro- aside from TP53 and BRCA1/2, only a few genes are mutated more than matin. It is now recognized that DNA methylation and histone 1% of the time in HGS ovarian cancer, and the disease is characterized modifications are intimately linked, and these epigenome alterations, by “genomic chaos” caused by extensive chromosome instability due to which have been actively characterized in ovarian cancer, have been a myriad of copy-number abnormalities and chromosomal altera- functionally linked to processes involved in tumor initiation, chemo- tions (3). Less is known about how alterations in the epigenetic therapy resistance, cancer stem cell survival, tumor progression, and metastasis (7–9). Aside from overviewing these epigenetic alterations in ovarian cancer in relationship to their functional effects, this review will highlight therapeutic strategies to remove these epigenome-wide 1Department of Obstetrics and Gynecology, Feinberg School of Medicine, marks and restore normal cellular function on a broad scale. Northwestern University, Chicago, Illinois. 2Robert H Lurie Comprehensive Cancer Center, Chicago, Illinois. 3Jesse Brown VA Medical Center, Chicago, Illinois. 4Medical Sciences, Indiana University School of Medicine, Bloomington, Alterations in Methylation of DNA in Indiana. 5Department of Anatomy, Cell Biology and Physiology; Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, Ovarian Cancer Indiana. 6Indiana University Melvin and Bren Simon Comprehensive Cancer Typically occurring in a CpG context, DNA methylation at carbon 5 Center, Indianapolis, Indiana. of cytosines (5-methylcytosine or 5 mC) plays an important role in the Corresponding Authors: Kenneth P. Nephew, Indiana University School of regulation of gene transcription. CpG methylation is regulated by Medicine, Jordan Hall 302, 1001 East Third Street, Bloomington, IN 47405- DNA methyltransferases (DNMT), primarily by DNMT-1, which 4401. Phone: 812-855-9445; Fax: 812-855-4436; E-mail: [email protected]; mediates maintenance (one strand) methylation, and by DNMT-3A and Daniela Matei, Department of Obstetrics and Gynecology, Feinberg School de novo of Medicine, Northwestern University, 250 E Superior Street; Suite 03-2303, and -3B, which catalyze methylation (5). Many tumors, Chicago, IL 60611. E-mail: [email protected] including ovarian, show increased methylation of CpG-rich regions usually but not exclusively associated with gene promoters. CpG Cancer Res 2020;XX:XX–XX islands aberrantly methylated in ovarian tumors are associated with doi: 10.1158/0008-5472.CAN-19-3837 silencing of genes involved in control of the cell cycle, apoptosis, and Ó2020 American Association for Cancer Research. drug sensitivity, as well as tumor suppressor genes (7–10). AACRJournals.org | OF1 Downloaded from cancerres.aacrjournals.org on October 2, 2021. © 2020 American Association for Cancer Research. Published OnlineFirst May 7, 2020; DOI: 10.1158/0008-5472.CAN-19-3837 Matei and Nephew A B Tumor suppressor gene Gene promoter HMA Promoter ON TSGs Therapy response Me Me Me Me OFF HMA DNA Decitabine genes methylation Guadecitabine Vidaza Me Me Me Me IFN response ASTX727 Viral mimicry CC486 Regulation of gene HDACI expression HDACI Ac Ac Ac Belinostat Me Me Me Me Me Me Me Vorinostat Panobinostat Histone acetylation Histone ncRNAs Nucleosome modifications Oncogene BRD4 BETI BRD4 ON BETI OFF JQ1 Pol II BETi Acetylated lysine Figure 1. A, Epigenetic mechanisms contributing to gene regulation. The unique epigenetic traits of tumors are initiated and sustained by alterations in DNA methylation, histone modifications, ncRNAs, and nucleosomes (remodeling and positioning) that serve as epigenetic marks, which mediate gene silencing. As methylation of DNA is the first epigenetic mark identified and most widely studied epigenetic mechanism, it is placed at the top of the triangle. B, Epigenetic drugs and general mechanism of action. Drugs in each class have been approved by the FDA for some cancers. In ovarian cancer, these classes of drugs are currently in clinical trials in combination. BETI, bromodomain and extraterminal domain inhibitors. Global examination of DNA methylation in ovarian cancer cell lines platinum-induced DNA damage and can recruit DNMTs to the and human tumors demonstrated that ovarian tumors not only damaged sites, causing aberrant DNA methylation (19). contain a large number of hypermethylated loci but that the degree Papp and colleagues reported a comprehensive integrated genomic, of aberrant methylation (i.e., the total number of methylated genes) is methylomic, and transcriptomic analysis of 45 ovarian cancer cell directly correlated with ovarian tumor progression and recurrence and lines (20). The analysis detected new driver genes and pathways can be used to identify specific methylated loci associated with poor and predicted new therapeutic vulnerabilities. The gene methylation progression-free survival (PFS; refs. 11, 12). In this regard, our group profiles of ovarian cancer cell lines were strongly correlated with developed a model to examine DNA methylation changes associated those of ovarian tumors profiled in the TCGA, demonstrating that with the onset of drug resistance in ovarian cancer (13). By integrating ovarian cancer cell lines retain epigenetic alterations seen in patient DNA methylation and gene expression profiles, we identified a samples. The observed relationship between promoter methylation specific DNA methylation signature associated with platinum resis- and loss-of-gene expression contributed to understanding functional tance (13). Recently, homozygous methylation of the tumor sup- consequences and new therapeutic sensitivities to PARP and PI3 pressor BRCA1 measured by methylation-specific high-resolution kinase inhibitors (20). The study revealed new key genetic events melting and by methylation-sensitive droplet digital PCR was found that could affect the epigenome, such as amplifications of regions to be a robust predictor of response to a PARP inhibitor in patient- containing coding sequences for the epigenetic
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