Peripheral blood DNA methylation analysis reveals epigenetic marks associated with hereditary breast and ovarian cancer risk

Abstract Background. Only a fraction of 15-20% of hereditary breast and ovarian cancer (HBOC) patients carry pathogenic coding genetic variants. Therefore, other pathogenic molecular mechanisms could explain the etiopathology of the syndrome. Aberrant germline DNA methylation in tumor suppressors has been reported in HBOC. Methods. We aimed to discover novel methylation marks associated with HBOC risk in 231 incident cases negative for pathogenic variants and 156 healthy controls using peripheral blood DNA, through methylation analysis by targeted bisulfite sequencing (NGS-Illumina) on 18 tumor suppressor gene promoters (330 CpG sites). Results. Increased methylation levels were detected in the promoters of EPCAM (p=0.00088), ATM (p=0.0074), and RAD51C (p=0.018). Four specific sites were linked to an increased risk of HBOC, FANCI (cg89786999) OR:1.64 (95%CI:1.3-2.0), PALB2 (cg23652916) OR=1.65 (95%CI:1.4-1.9), MSH2 (cg47630224) OR:1.93 (95%CI:1.5-2.4), and EPCAM (cg47596828) OR= 2.93 (95%CI:2.1-4.1). The biomarker capacity of the four sites showed an area under the curve (AUC) of 0.758, high specificity and sensitivity. Comparison with three well-established cohorts revealed that MSH2 cg47630224 methylation was associated with 3-fold increased HBOC risk (AUC: 0.892, sensitivity: 0.90, specificity: 0.89). Conclusions. Four novel DNA methylation CpG sites were associated with HBOC risk, suggesting potential application as biomarkers in patients without detectable coding mutations.