Segregation of HPV-positive vulvar neoplastic lesions by an anal cancer progression methylation signature

Abstract

Background: Human papillomavirus (HPV) has been implicated in the development of different cancers and has been associated with genome-wide epigenetic alterations. We have demonstrated an 86-gene methylomic signature to be associated with the progression of anal cancer (AC) from normal mucosa. The signature is also able to classify AIN3 as either cancer-like or normal-like. We sought to evaluate whether this AC signature is applicable to HPV-associated vulvar cancer (VC) progression. Methods: Our 16 formalin-fixed paraffin-embedded study specimens consisted of 8 VC, 6 VIN3, and 2 normal vulvar tissues (NV). Extracted DNA was subjected to HPV genotyping (SPF10-LiPA25 kit) as well as genome-wide methylation profiling (Illumina Methylation EPIC array). Differential methylation was defined by false discovery rate of 0.3. The AC methylation signature was applied to vulvar tissues. Results: All 16 tissues except for one VC were found to be HPV+. By principal components analysis, distinct separations between NV, VIN3 and VC were observed. Application of the AC signature to the vulvar tissues demonstrated strong separation of NV and VC cases with segregation of VIN3 cases into normal-like (n=2) and cancer-like (n=4) types. By both analyses, the HPV-negative VC case presented as a distinct outlier. Conclusions: Methylomic alterations can distinguish between HPV+ NV, VIN3 and VC. Successful segregation of vulvar lesions by an AC signature suggests that HPV-driven oncogenesis may be associated with similar methylation events across different tissue types. Our findings may have implications for development of shared early detection and prevention biomarkers.