Human CLIC5 as a Recurrent Hotspot of HPV 16 Integration in Cervical Cancer

Despite extensive global efforts to eradicate cervical cancer through improved screening and widespread HPV vaccination, the disease continues to claim over 350 000 lives annually. Persistent infection with high-risk HPV genotypes, primarily HPV-16 and HPV-18, is the principal etiological driver, with viral DNA integration into the host genome representing a critical event in malignant progression. In this study, HPV integration was investigated using 25 RNA-seq datasets from HPV-positive cervical cancer cell lines and 2 datasets from the HPV-negative C-33A cell line. Analysis revealed a recurrent HPV-16 integration hotspot on Chromosome 6 within the CLIC5 gene. This integration was validated by qRT-PCR and Sanger sequencing. Subsequent gene expression analysis demonstrated significant CLIC5 upregulation in HPV-16-positive cell lines, with a 21-fold increase in CaSki and a 4-fold increase in SiHa compared to HPV-negative and HPV-18-positive controls. These findings delineate a distinct HPV-16 integration pattern and its associated transcriptional impact. The identification and validation of this strain-specific integration site nominates HPV-16 integration at the CLIC5 locus as a potential biomarker for HPV-driven cervical cancer.