Whole-genome bisulfite sequencing reveals the alteration of DNA methylation during malignant transformation of oral mucosal cells

Abstract

Background According to recent researches, the overall malignant transformation rate of oral potentially malignant disorders (OPMDs) is among 7.9%, and the probability of malignant transformation of OPMDs with severe epithelial dysplasia to oral squamous cell carcinoma (OSCC) is as high as 57%. In recent years, more and more studies have confirmed that abnormal DNA methylation, especially hypermethylation of the promoter CpG islands, is closely related to the occurrence and malignant transformation of OPMDs. Hypermethylation of certain tumor suppressor genes can be used as a key indicator for diagnosing early OSCC and judging the prognosis of OPMDs. There is an urgent need to expand the understanding of DNA methylation alterations occurred in OPMDs and OSCC at the cellular level. Methods and results We used the Illumina sequencing platform to perform the whole-genome bisulfite sequencing （WGBS）on dysplastic oral keratinocyte (DOK) and CAL-27 cell lines, which respectively represents epithelial dysplasia and carcinogenesis. Then we compared the results with trends in human gingival fibroblasts (HGFs) to identify differentially methylated regions (DMRs). Gene Oncology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to further explore the biological functions and signaling pathways related to the observed differences. Compared with those in HGFs, respectively 4,149 and 2,863 genes were abnormally hypermethylated in DOK and CAL-27 cells in the promoter CG context. GO and KEGG analyses showed that the identified differentially methylated genes were involved in system development, transcriptional regulation, cell differentiation, and other pathways (e.g., autophagy, mitophagy, and cAMP signaling). Conclusions Our results expand on the knowledge of DNA methylation alterations associated with OPMDs and OSCC at the cellular level. The key genes and pathways involved in the regulatory mechanisms of DNA methylation may provide a theoretical basis for research on the malignant transformation of OPMDs as well as for the early diagnosis and treatment of oral squamous cell carcinoma.