HPV DNA integration is correlated with persistence or progression of cervical intraepithelial neoplasia 2 (CIN2)

OBJECTIVE(S): To determine whether identical HPV-human DNA integrations in cervical intraepithelial neoplasia grade 2 (CIN2) lesions are retained during progression to squamous cervical carcinoma (SCC) and whether such integrations can predict lesion persistence or progression. METHODS: Longitudinal cervical samples were analyzed using multiplexed DNA hybridization-capture targeting 225 HPV types, followed by short-read sequencing to identify HPV-human DNA integration junctions. Integration events were evaluated in (i) serial samples from CIN lesions that progressed to SCC and (ii) a baseline cohort of 23 patients with incident CIN2. Clinical outcomes (regression vs persistence/progression) were compared by integration status using Fisher's Exact Test and multivariable Bayesian logistic regression to estimate effect sizes in the setting of small sample size. RESULTS: Identical HPV-human DNA integrations were preserved across serial samples in seven CIN lesions that progressed to SCC, supporting their biological relevance in carcinogenesis. In the CIN2 cohort, no integrations were detected in any of the 12 patients whose lesions regressed, whereas integrations were present in four of eleven patients whose lesions persisted or progressed (p=0.04). Bayesian logistic regression estimated a 22-fold higher odds of persistence/progression when integration was detected at baseline CIN2 diagnosis. HPV16 positivity was also associated with persistence/progression, with a smaller estimated effect size (9.4-fold higher odds), consistent with prior epidemiologic observations. CONCLUSION(S): HPV DNA integrations were associated with CIN2 persistence and progression, and identical integrations were retained during evolution to SCC. Integration analysis at CIN2 diagnosis may identify lesions at highest risk for progression, providing a biomarker to refine clinical management and reduce unnecessary excisional procedures.