Promoter CpG island methylation of genes in key cancer pathways associates with clinical outcome in high-grade serous ovarian cancer

Abstract

Purpose: We aimed to identify DNA methylation biomarkers of progression-free survival (PFS) to platinum-based chemotherapy in high-grade serous ovarian cancer (HGSOC) within biologically relevant ovarian cancer-associated pathways.

Experimental design: Association with PFS of CpG island (CGI) promoter DNA methylation at genes in the pathways Akt/mTOR, p53, redox, and homologous recombination DNA repair was sought with PFS as the primary objective in a prospectively collected ovarian cancer cohort (n = 150). Significant loci were validated for associations between PFS, methylation, and gene expression in an independent The Cancer Genome Atlas (TCGA) data set of HGSOC (n = 311).

Results: DNA methylation at 29 CGI loci linked to 28 genes was significantly associated with PFS, independent from conventional clinical prognostic factors (adjusted P < 0.05). Of 17 out of the 28 genes represented in the TCGA data set, methylation of VEGFB, VEGFA, HDAC11, FANCA, E2F1, GPX4, PRDX2, RAD54L, and RECQL4 was prognostic in this independent patient cohort (one-sided P < 0.05, false discovery rate < 10%). A multivariate Cox model was constructed, with clinical parameters (age, stage, grade, and histologic type) and significant loci. The final model included NKD1, VEGFB, and PRDX2 as the three best predictors of PFS (P = 6.62 × 10(-6), permutation test P < 0.05). Focussing only on known VEGFs in the TCGA cohort showed that methylation at promoters of VEGFA, VEGFB, and VEGFC was significantly associated with PFS.

Conclusions: A three loci model of DNA methylation could identify two distinct prognostic groups of patients with ovarian cancer (PFS: HR = 2.29, P = 3.34 × 10(-5); overall survival: HR = 1.87, P = 0.007) and patients more likely to have poor response to chemotherapy (OR = 3.45, P = 0.012).

Figure 1. Kaplan-Meier plots of progression free survival and overall survival in SGCTG cohort.

The patients were separated into two groups with high/low level of methylation index (MI) estimated from a multivariate Cox model incorporating NKD1, VEGFB and PRDX2 promoter methylation. The cut-off was determined by the third quartile of MI across all the patients (n=150). A) Progression free survival curve; B) overall survival curve.

Figure 2. Methylation and expression of VEGFB, PRDX2, VEGFA and VEGFC in TCGA cohort.

The top 20% of the patients with high methylation level at the biomarker examined were categorised into the ‘high methylation group’, otherwise, they were included in the ‘low methylation group’. Left panel (A): methylation level of candidate biomarker; right panel (B): expression level of candidate biomarker. Mann-Whitney U test (two sided) was used to examine the significant difference between two groups. *p<0.05, **p<0.01.