Multi-omics analysis reveals the crosstalk of epigenetic regulatory networks in cutaneous squamous cell carcinoma progression

Cutaneous squamous cell carcinoma (cSCC) is the second most common form of non-melanoma skin cancer (NMSC), with a steadily increasing global incidence, especially in populations with prolonged ultraviolet (UV) exposure. Advanced or metastatic cSCC carries a poor prognosis, while the application of targeted therapies and immunotherapies remains in the exploratory stage, due to limited understanding of the underlying mechanisms of cSCC occurrence and progression. Epigenetic dysregulation plays important roles in the progression of cSCC. However, how multi-dimensional regulatory networks reshape the epigenetic landscape and contribute to dysregulated gene expression in cSCC remains unclear. In this study, we performed parallel RNA m6A sequencing, 850K DNA methylation arrays, whole transcriptome sequencing, and ATAC-seq chromatin accessibility profiling on samples from normal skin, actinic keratosis (AK), and cSCC. We analyzed the regulatory networks and pathways of epigenetic modifications on gene expression. We further explored the crosstalk of epigenetic regulatory networks by correlation analysis. By integrating single-cell RNA-seq data, we identified epigenetically upregulated candidate genes and confirmed their expression and functions with experimental methods. Our integrated multi-omics analysis provides a comprehensive and dynamic epigenetic map of cSCC progression. Further analysis revealed that DNA methylation and m6A modification jointly regulate gene expression through independent and synergistic ways. The identified epigenetically upregulated candidate genes IDO1, IFI6, and OAS2 were validated to be overexpressed in cSCC tissues and cell lines, and functional assays confirmed their potential key roles in regulating the processes of cell proliferation, migration and invasion in cSCC. By integrating multi-omics data, this study systematically highlights the multi-layered epigenetic alterations and regulatory mechanisms involved in cSCC development. This multi-stage, multi-omics, and multi-resolution integrated analysis provides a theoretical basis and new insights for future personalized treatment strategies for cSCC.