Background: The aberrant methylation included hypermethylation and hypomethylation plays significant role in the progression of many kind of cancers but poorly investigated in oral squamous cell carcinoma (OSCC).
Methods: GSE123781 and GSE87053 were used to identify the differential methylation regions (DMRs) by R software. the targeted genes regulated by DMRs were predicted by wANNOVAR. The biological process, cellular component, molecular function and cell pathways of common targeted genes between GSE123781 and GSE87053 were analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) enrichment analysis. The hub genes in common targeted genes both associated with cancer biological process and cancer cell pathways were identified by protein to protein interaction network (PPI). Finally, the expression level of hub genes and correspondence relationship with head and neck squamous cell carcinoma (HNSCC) patient survival were confirmed by The Cancer Genome Atlas (TCGA) dataset.
Results: There are 372 common targeted genes regulated by DMRs between GSE123781 and GSE87053 and RUNX family transcript factor 1 (RUNX1), phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma (PIK3CG), phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta (PIK3CD), laminin subunit beta 1 (LAMB1), integrin subunit alpha M (ITGAM), interleukin 2 receptor subunit alpha (IL2RA), interleukin 10 (IL10), FYN proto-oncogene, Src family tyrosine kinase (FYN), cholinergic receptor muscarinic 1 (CHRM1) and C-C motif chemokine receptor 1 (CCR1) are hub genes in common targeted genes. Furthermore, RUNX1, PIK3R1, PIK3CD, LAMB1, ITGAM, IL2RA, IL10, FYN, CHRM1 and CCR1 differentially expressed in HNSCC tissues and the overexpressed genes PIK3CD, LAMB1 and IL10 could lead to the decrease of HNSCC patient survival.
Conclusions: PIK3CD, LAMB1 and IL10 both differentially expressed and regulated by DMRs are quite associated with the progression of OSCC and the survival of HNSCC patients, which has much potential to be new biomarkers in targeted therapy of OSCC.