Promoter methylation of APC, P16, and WT1 genes among high-risk HPV infected women of North-Eastern states of India

BACKGROUND: Human papillomavirus (HPV) associated cervical cancer is the most prevalent gynaecological malignancy among women globally. Promoter hypermethylation of targeted genes may serve as a novel biomarker to monitor HPV infection dynamics which are likely to progress to HPV related cancers. METHODS: Cervical smear of representative 180 (90 persistent and 90 transient) HPV cases were included in the study from follow samples of eight North-Eastern states of India during June 2022 to September 2024. HPV positive DNA was detected using nested PCR and subsequently all nested PCR positive samples were subjected to High-risk HPV (hrHPV) genotyping using real-time polymerase chain reaction (PCR) targeting 16 hrHPV genotypes. Methylation status of Adenomatous Polyposis Coli (APC), P16, and Wilms' tumor gene (WT1) was assessed by bisulphite modification of DNA followed by methylation-specific PCR. RESULTS: The study included 180 women, of average age 37.85 ± 8.37 years. The highest HPV infection rate was found in women aged 31-40 years (38.88%). The hrHPV types HPV 16, 18, 56, 58 and 67/33/52/58 were most persistent. Methylation of the APC gene was observed in 15.5% (14/90) of persistent HPV cases, while P16 methylation was found in 34.4% (31/90) of persistent and 28.8% (26/90) of transient cases. WT1 methylation was higher in transient (45.5%, 41/90) than persistent (36.6%, 33/90) HPV cases. No significant methylation differences were observed across HPV types, although HPV HPV 67/33/52/58 showed higher APC and P16 methylation than unmethylated cases. CONCLUSIONS: The study highlights a notable role of APC, P16 and WT1 gene methylation in HPV persistent and clearance, which may provide crucial insights into HPV-associated cancer progression and identify potential biomarkers for early detection.