Integrative analysis in head and neck cancer reveals distinct role of miRNome and methylome as tumour epigenetic drivers

Head and neck cancer (HNC) is the sixth most common malignancy worldwide with a relatively low 5-year survival rate, mainly because it is diagnosed at a late stage. Current literature suggests that epigenetics is the main driving force for this type of cancer and that HPV infection plays a role in a subset of HNC. In this study, we aimed to find potential epigenetic biomarkers by integrating miRNome, methylome and transcriptome analyses. From the fresh tissue samples of HNC tumours, we selected a group for miRNome, methylome and transcriptome profiling in comparison with appropriate control samples. Bioinformatic analyses were performed in R v4.2.2. Count normalization and group differential expression for mRNA and previously obtained miRNA count data were performed (DESeq2\_v1.36). Gene set enrichment analysis was performed and visualised (gProfiler2\_v0.2.1). Identification of miRNA targets was performed by querying miRTarBase (multiMiR\_v1.18.0). For the integrative analysis, we performed kmeans clustering using 8-12 clusters and nstart 100 (stats\_v4.2.2). Transcriptome analysis divided the samples into cancer and control clusters without reference to HPV status or anatomic location. The differentially expressed genes (n=2781) were associated with signaling pathways of tumour progression. We identified a cluster of genes under the control of the transcription factor E2F that were significantly underexpressed in cancer tissue along with T-cell immunity and transcriptional regulation related genes. Among tumour overexpressed genes, we found genes related to cell cycle regulation and vasculature. In this Integrative study we showed distinct role of miRNome and methylome as epigenetic drivers in HNC. ### Competing Interest Statement The authors have declared no competing interest.