New insights into tumor microenvironment and HPV integrations in cervical cancer pathogenesis revealed by single-cell transcriptome data

HPV infection is common among women and can result in serious illnesses. This research utilizes single-cell RNA-sequencing (scRNA-seq) to study the connection between cellular heterogeneity and HPV integrations in cervical histopathology. scRNA-seq was used to examine heterogeneity among normal patients and those in three disease stages: high-grade squamous intraepithelial lesions (HSIL), microinvasive carcinoma (MIC), and cervical squamous epithelium carcinoma cancer (CSCC) tissues. A method was developed to identify HPV integration events from scRNA-seq data. Our results indicated an increase in squamous epithelial cells and a decrease in columnar epithelial cells as the disease progressed from normal to CSCC. We discovered HPV genes that were differentially expressed across normal patients and those in the three disease stages. Notably, HPV integration events were more common in squamous epithelial cells at the single-cell level. The ratio of HPV-integrated cells increased as the disease progressed from normal tissue to CSCC, eventually stabilizing. Several genes, such as EGR1, S100A11, S100A8, KRT5, RPL34, ATP1B1, RPS4X and EEF2, were frequently integrated by HPV across patients. In contrast, genes like PAN3, BABAM2, SPEN, TCIM-SIRLNT, TEX41-PABPC1P2 and KCNV1-LINC01608 showed frequent integration events across cells. KRT5, ATP1B1, RPS4X, PAN3 and SPEN were novel recurrent HPV-integrated genes we observed at the patient or cell level in this study. Additionally, we found that HPV genes from various HPV types exhibited integration preferences in various samples and disease stages. This provides a valuable insight into the mechanism of HPV-induced cervical cancer from a single-cell standpoint, highlighting its clinical relevance.