Journal Article

Genome-wide host methylation profiling of anal and cervical carcinoma

Abdalla, Ibrahim, Simko, Jeff P., Siegel, Erin M., Pizzolato, Joseph F., Shibata, David, Crane, Christopher H., Guerrero, Whitney, Ajidahun, Abidemi, Eschrich, Steven, Guha, Chandan, Berglund, Anders, Putney, Ryan M., Ajani, Jaffer A., Becker, Mark J., Magliocco, Anthony, Riggs, Bridget, Winter, Kathryn, Okawara, Gordon S., Brown, Kevin D.

2021

Overview

HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n = 143; 99% HPV+) and fresh frozen cervical tissues (n = 28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array. Differentially methylated regions (DMR; t test q<0.01, 3 consecutive significant CpG probes and mean Δβ methylation value>0.3) were compared between normal and cancer specimens in partial least squares (PLS) models and then used to classify anal or cervical intraepithelial neoplasia-3 (AIN3/CIN3). In AC, an 84-gene PLS signature (355 significant probes) differentiated normal anal mucosa (NM; n = 9) from AC (n = 121) while a 36-gene PLS signature (173 significant probes) differentiated normal cervical epithelium (n = 10) from CC (n = 9). The CC progression signature was validated using three independent publicly available datasets (n = 424 cases). The AC and CC progression PLS signatures were interchangeable in segregating normal, AIN3/CIN3 and AC and CC and were found to include 17 common overlapping hypermethylated genes. Moreover, these signatures segregated AIN3/CIN3 lesions similarly into cancer-like and normal-like categories. Distinct methylation changes occur across the genome during the progression of AC and CC with overall similar profiles and add to the evidence suggesting that HPV-driven oncogenesis may result in similar non-random methylomic events. Our findings may lead to identification of potential epigenetic drivers of HPV-associated cancers and also, of potential markers to identify higher risk pre-cancerous lesions.

• Publisher: Public Library of Science,Public Library of Science (PLoS)
• Subject: Adult / Aged / Anal cancer / Anus / Anus Neoplasms - genetics / Anus Neoplasms - pathology / Anus Neoplasms - therapy / Bioinformatics / Biology and life sciences / Biomarkers, Tumor - genetics / Bisulfite / Cancer / Carcinoma, Squamous Cell - genetics / Carcinoma, Squamous Cell - pathology / Carcinoma, Squamous Cell - therapy / Cervical cancer / Cervical carcinoma / Cervix / Chemoradiotherapy - methods / Clinical Trials, Phase III as Topic / Colorectal cancer / CpG islands / Deoxyribonucleic acid / DNA / DNA Methylation / DNA probes / Epidemiology / Epigenetics / Epithelium / Female / Follow-Up Studies / Gene Expression Regulation, Neoplastic / Genetic aspects / Genetic testing / Genome, Human / Genomes / Genotyping / Health aspects / Health risks / Human papillomavirus / Humans / Lesions / Male / Medical research / Medicine and Health Sciences / Methylation / Middle Aged / Mucosa / Oncology / Paraffin / Paraffins / Physical Sciences / Probes / Prognosis / Randomized Controlled Trials as Topic / Signatures / Surgery / Survival Rate / Tumorigenesis / Uterine Cervical Neoplasms - genetics / Uterine Cervical Neoplasms - pathology / Uterine Cervical Neoplasms - therapy / Young Adult