Methylation of high-risk human papillomavirus genomes are associated with cervical precancer in HIV-positive women

• Type of Material: Article
• Authors: Ana Gradissimo, Yeshiva University; Jessica Lam, Yeshiva University; John D. Attonito, Yeshiva University; Joel Palefsky, University of California San Francisco; L. Stewart Massad, Washington University in St. Louis; Xianhong Xie, Yeshiva University; Isam-Eldin Eltoum, University of Alabama at Birmingham; Lisa Rahangdale, Unversity of North Carolina; Margaret A. Fischl, University of Miami; Kathryn Anastos, Montefiore Medical Center; Howard Minkoff, Maimonides Medical Center; Xianan Xue, Yeshiva University; Gypsyamber D'Souza, Johns Hopkins University; Lisa Flowers, Emory University; Christine Colie, Georgetown University; Sadeep Shrestha, University of Alabama at Birmingham; Nancy A. Hessol, University of California San Francisco; Howard D. Strickler, Yeshiva University; Robert D. Burk, Yeshiva University
• Language: English
• Date: 2018-12-01
• Publisher: American Association for Cancer Research
• Publication Version: Author Accepted Manuscript (After Peer Review)
• Copyright Statement: © 2018 American Association for Cancer Research.
• Final Published Version (URL): http://dx.doi.org/10.1158/1055-9965.EPI-17-1051
• Title of Journal or Parent Work: Cancer Epidemiology Biomarkers and Prevention
• Volume: 27
• Issue: 12
• Start Page: 1407
• End Page: 1415
• Grant/Funding Information: HPV testing and the current analyses were supported by the National Cancer Institute (NCI) (grant numbers R01-CA-085178 and R01-CA-174634 to H.D. Strickler and P30-CA-013330). Data in this manuscript were collected by the Women’s Interagency HIV Study (WIHS). The contents of this publication are solely the responsibility of the authors and do not represent the official views of the National Institutes of Health (NIH). WIHS (Principal Investigators): UAB-MS WIHS (M. Saag, M.C. Kempf and D. Konkle-Parker), U01-AI-103401; Atlanta WIHS (I. Ofotokun and G. Wingood), U01-AI-103408; Bronx WIHS (K. Anastos), U01-AI-035004; Brooklyn WIHS (H. Minkoff and D. Gustafson), U01-AI-031834; Chicago WIHS (M. Cohen and A. French), U01-AI-034993; Metropolitan Washington WIHS (S. Kassaye), U01-AI-034994; Miami WIHS (M.A. Fischl and L. Metsch), U01-AI-103397; UNC WIHS (A. Adimora), U01-AI-103390; Connie Wofsy Women’s HIV Study, Northern California (R. Greenblatt, B. Aouizerat and P. Tien), U01-AI-034989; WIHS Data Management and Analysis Center (S. Gange and E. Golub), U01-AI-042590; Southern California WIHS (J. Milam), U01-HD-032632 (WIHS I – WIHS IV). The WIHS is funded primarily by the National Institute of Allergy and Infectious Diseases (NIAID) (grant number P30-AI-050410 to R. Swanstrom), with additional co-funding from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), the National Cancer Institute (NCI), the National Institute on Drug Abuse (NIDA), and the National Institute on Mental Health (NIMH). Targeted supplemental funding for specific projects is also provided by the National Institute of Dental and Craniofacial Research (NIDCR), the National Institute on Alcohol Abuse and Alcoholism (NIAAA), the National Institute on Deafness and other Communication Disorders (NIDCD), and the NIH Office of Research on Women’s Health. WIHS data collection is also supported by UL1-TR000004 (UCSF CTSA) and UL1-TR000454 (Atlanta CTSA).
• Keywords: Humans; Risk Factors; Adult; HIV Infections; Papillomavirus Infections; Case-Control Studies; Genomics; Female; Methylation
• Research Categories: Biology, Virology; Health Sciences, Immunology; Biology, Genetics

Abstract

Background: HIV-positive women are at substantial risk of HPV-associated cervical neoplasia caused by high-risk (HR) HPVs. Methylation of the HPV genome is associated with cervical intraepithelial neoplasia grade 3 (CIN3) in HIVnegative women, yet it is unknown whether this holds true for HIV-positive women. Methods: We designed a case–control study within the Women's Interagency HIV Study (WIHS) cohort comparing HIV-positive CIN3 cases (N = 72) to HIV-positive controls without detectable CIN2þ. The unit of analysis and matching was HPV-type infection. Cases with 2HR-HPV types (N=23; 32%) had a separate control for each HR-HPV type. We developed and utilized next-generation sequencing (NGS) methylation assays for 12 different HR-HPVs, focusing on CpG sites in the L1/L2 regions. Results: Significant case–control differences in individual CpG site methylation levels were observed for multiple alpha-9 (HPV16/31/35/58) and alpha-7 HPV (HPV18/39/ 45) types, based on dichotomization of tertile levels (T3 vs. T1 and T2). Analyses combining homologous CpG sites [e. g., HPV16-L1-5608/HPV31-L1-5521/HPV35-L2L1-5570; OR = 7.28; 95% confidence interval (CI): 2.75–19.3], and (e.g., HPV18-L1-7062/HPV45-L1-7066; OR = 6.94; 95% CI: 1.23–39.3) were significant in separate case–control comparisons. In cases with multiple HR-HPVs, we tested and confirmed the hypothesis that one HR-HPV type would have higher methylation than other types detected, consistent with there being a single HR-HPV causally related to a lesion. Conclusions: CIN3 is associated with elevated L1/L2 CpG methylation levels in HIV-positive women. Impact: HPV DNA CpG methylation is a promising triage option in HIV-positive women testing positive for HR-HPV types and provides risk attribution in women with multiple HPV type infections.