Methylation of HPV and a tumor suppressor gene reveals anal cancer and precursor lesions

// Attila T. Lorincz 1 , Mayura Nathan 2 , Caroline Reuter 1 , Rhian Warman 1 , Mohamed A. Thaha 4, 5 , Michael Sheaff 3 , Natasa Vasiljevic 1 , Amar Ahmad 1 , Jack Cuzick 1 and Peter Sasieni 1 1 Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Queen Mary University of London, EC1M 6BQ, UK 2 Homerton Anal Neoplasia Service, Homerton University Hospital NHS Foundation Trust, London E9 6SR, UK 3 Cellular Pathology, Barts Health NHS Trust, London E1 2ES, UK 4 National Bowel Research Centre, Blizard Institute, Queen Mary University of London, London E1 2AT, UK 5 Barts Anal Neoplasia Centre, Department of Colorectal Surgery, Surgery and Cancer CAG, The Royal London Hospital, Barts Health NHS Trust, Whitechapel, London E1 1BB, UK Correspondence to: Attila T. Lorincz, email: a.lorincz@qmul.ac.uk Keywords: anal cancer, intraepithelial neoplasia, DNA methylation, high-risk human papillomavirus, HPV genotyping Received: February 10, 2017      Accepted: May 06, 2017      Published: May 18, 2017 ABSTRACT We studied DNA methylation patterns of human papillomavirus (HPV) and tumor suppressor gene EPB41L3 in 148 anal and perianal biopsies to determine whether high levels of methylation would be associated with anal intraepithelial neoplasia (AIN). The most prevalent HPV type was HPV16, detected in 54% of the 30 benign biopsies, 33% of the 43 low-grade AIN (lgAIN), 82% of the 59 high grade AIN (hgAIN) and 4 of the 5 anal cancers. A methylation score was developed (0.561*HPV16me+0.439* EPB41L3 ) which had increasing values with severity of disease: the mean was 8.1% in benign, 13.2% in lgAIN, 22.3% in hgAIN and 49.3% in cancers ( p < 0.0001). The methylation score as a triage classifier at a cut-off of 8.8 gave a sensitivity of 90.6% (95% CI: 82.8, 96.9), specificity of 50.7% (95% CI: 39.7, 61.6) and area under the curve of 0.82 (95% CI: 0.75–0.89) for separating hgAIN and cancer from benign and lgAIN biopsies. We conclude that methylation of HPV16 and EPB41L3 show highly significant association with increasing severity of AIN and cancer and may be useful as biomarkers in anal disease.