Global DNA Hypomethylation in Epithelial Ovarian Cancer: Passive Demethylation and Association with Genomic Instability

• Main Authors: Wa Zhang, David Klinkebiel, Carter J. Barger, Sanjit Pandey, Chittibabu Guda, Austin Miller, Stacey N. Akers, Kunle Odunsi, Adam R. Karpf
• Format: Article
• Language: English
• Published: MDPI AG 2020-03-01
• Series: Cancers
• Subjects: dna hypomethylation; epithelial ovarian cancer; gene expression; repetitive elements; genomic instability; dnmts
• Online Access: https://www.mdpi.com/2072-6694/12/3/764

A hallmark of human cancer is global DNA hypomethylation (GDHO), but the mechanisms accounting for this defect and its pathological consequences have not been investigated in human epithelial ovarian cancer (EOC). In EOC, GDHO was associated with advanced disease and reduced overall and disease-free survival. GDHO (+) EOC tumors displayed a proliferative gene expression signature, including <i>FOXM1</i> and <i>CCNE1</i> overexpression. Furthermore, DNA hypomethylation in these tumors was enriched within genomic blocks (hypomethylated blocks) that overlapped late-replicating regions, lamina-associated domains, PRC2 binding sites, and the H3K27me3 histone mark. Increased proliferation coupled with hypomethylated blocks at late-replicating regions suggests a passive hypomethylation mechanism. This hypothesis was further supported by our observation that cytosine DNA methyltransferases (<i>DNMTs</i>) and <i>UHRF1</i> showed significantly reduced expression in GDHO (+) EOC after normalization to canonical proliferation markers, including <i>MKI67</i>. Finally, GDHO (+) EOC tumors had elevated chromosomal instability (CIN), and copy number alterations (CNA) were enriched at the DNA hypomethylated blocks. Together, these findings implicate a passive DNA demethylation mechanism in ovarian cancer that is associated with genomic instability and poor prognosis.