INTEGRATING MORPHOLOGY AND MOLECULAR DIAGNOSTICS IN HPV-ASSOCIATED CUTANEOUS AND ANOGENITAL LESIONS: A SYSTEMATIC REVIEW

Abstract

Background: The pathological spectrum of human papillomavirus (HPV) extends from productive cutaneous warts to high-grade anogenital squamous neoplasia and invasive carcinoma. Morphology identifies the lesion phenotype, but etiologic assignment increasingly requires molecular evidence that distinguishes viral presence from transforming infection. Objective: To determine how histomorphology, HPV DNA/genotyping, p16, Ki-67, E4, p53, viral methylation, integration, and genomic assays can be combined to improve diagnostic classification of HPV-associated cutaneous and anogenital lesions. Methods: A PRISMA 2020-guided systematic review was undertaken for literature published from January 2008 through January 2026. Fourteen structured evidence searches identified 140 records; 18 duplicates were removed, 122 records were screened, 53 full texts were sought, one was not retrieved, 52 reports were assessed, and 36 original human studies were included. Because of major heterogeneity in anatomical site, assay platform, and diagnostic endpoint, meta-analysis was not performed. Risk of bias was assessed using five adapted Joanna Briggs Institute domains. Results: Across cutaneous lesions, assay-based studies detected HPV in 95% of wart preparations in one series, while multiple HPV infections occurred in 35% of biopsies in another. High-risk alpha-HPV was reported in 57.9% of cutaneous SCC and 38.2% of Bowen disease in one cohort, and HPV16 integration was demonstrated in 8 of 9 HPV16-positive cutaneous SCC samples in a 2025 study. In anal lesions, diffuse p16 discriminated high-grade AIN with 100% sensitivity and 84% specificity in one study; among 1,000 anal biopsies, block p16 occurred in 89% of AIN2 and 95% of AIN3. Vulvar data showed that morphology alone incompletely separated HPV-associated from HPV-independent SCC: in 1,594 tumors, 23.0% were HPV DNA+/p16+, whereas 66.5% were HPV DNA−/p16−. Newer studies demonstrated strong reproducibility of binary p53 interpretation and distinct HPV/p53 genomic groups. Penile studies identified frequent p16 pathway disruption, viral methylation/integration, and prognostic host methylation signatures. Overall risk of bias was low in 11 studies (30.6%), showed some concerns in 22 (61.1%), and was high in 3 (8.3%). Conclusion: No single test is sufficient across all anatomical sites. The most reliable diagnostic model begins with morphology and site, uses HPV DNA/genotyping for viral attribution, applies p16/Ki-67/E4/p53 to define biological pathway, and reserves E6/E7 RNA, integration, methylation, or genomic profiling for discordant lesions and risk stratification.