Host cell DNA methylation markers for the detection of high-grade anal intraepithelial neoplasia and anal cancer

Background: High-grade anal intraepithelial neoplasia (AIN2/3; HGAIN) is highly prevalent in HIV+ men who have sex with men (MSM), but only a minority will eventually progress to cancer. Currently the cancer risk cannot be established, and therefore all HGAIN are treated, resulting in overtreatment. We assessed the potential of host cell DNA methylation markers for detecting HGAIN and anal cancer. Methods: Tissue samples of HIV+ men with anal cancer (n=26), AIN3 (n=24), AIN2 (n=42), AIN1 (n=22) and controls (n=34) were analyzed for DNA methylation of nine genes using quantitative methylation-specific-PCR. Univariable and LASSO logistic regression, followed by leave-one-out-cross-validation (LOOCV) were used to determine the performance for the detection of AIN3 and cancer. Results: Methylation of all genes increased significantly with increasing severity of disease (p 0.85). The most potent marker, ZNF582 (AUC=0.89), detected all cancers and 54% of AIN3 at 93% specificity. Slightly better performance (AUC=0.90) was obtained using a marker panel including five markers. Conclusions: DNA methylation is significantly associated with anal carcinogenesis. A methylation marker panel, including ZNF582, can identify anal cancer and HGAIN with a cancer-like methylation pattern. Validation studies are warranted to verify their potential for the screening and management of HIV+ MSM at risk for anal cancer.