Integrated analysis of DNA methylation and mRNA expression profiles to identify key genes in head and neck squamous cell carcinoma

Abstract

DNA methylation has been demonstrated to play significant roles in the etiology and pathogenesis of head and neck squamous cell carcinoma (HNSCC). In the present study, methylation microarray dataset (GSE87053) and gene expression microarray dataset (GSE23558) were downloaded from GEO database and analyzed through R language. A total of 255 hypermethylated-downregulated genes and 114 hypomethylated-upregulated genes were finally identified. Functional enrichment analyses were performed and a comprehensive protein–protein interaction (PPI) network was constructed. Subsequently, the top ten hub genes selected by Cytoscape software were subjected to further analyses. It was illustrated that the expression level of CSF2, CTLA4, ETS1, PIK3CD, and CFTR was intimately associated with HNSCC. Survival analysis suggested that CTLA4 and FGFR2 could serve as effective independent prognostic biomarkers for HNSCC patients. Overall, our study lay a groundwork for further investigation into the underlying molecular mechanisms in HNSCC carcinogenesis, providing potential biomarkers and therapeutic targets for HNSCC.

Identification of Potential Genes both Differentially Expressed and Regulated by Differential Methylation Regions in Oral Squamous Cell Carcinoma

“…And microRNA663 could inhibit the progression of human Glioblastoma by targeting PIK3CD [24]. In addition, PIK3CD is also a potential gene regulated by differentially methylation sites in HNSCC [25]. In this study, we found that the PIK3CD not only regulated by the DMRs in OSCC but also differentially expressed in HNSCC.…”

Identification of Epigenetically Modified Hub Genes and Altered Pathways Associated With Retinoblastoma

“…Integrative bioinformatics analysis is currently emerging as the most explicit approach to decipher the events of the tumor microenvironment and identify the key genes and signalling pathways underlying disease pathogenesis. Hence, this approach is widely used to predict the potent biomarkers and therapeutic targets of various cancers ( Yang et al, 2017 ; Zhang et al, 2019 ; Jin 2020 ). In this study, we have integrated the expression profiles of three major domains of cancer biology including DNA methylation, mRNA, and miRNA in healthy and Rb cancer samples using individual microarray datasets available in NCBI-GEO to comprehensively understand the epigenetic consequences of Rb loss and map the key hub and common genes that play a crucial role in the development and progression of retinoblastoma tumors.…”

“…Unlike routine integrative bioinformatics analysis that involves the combination of two major domains like gene expression profiles/epigenetic profile, genome profile/clinical profile, etc. ( Yang et al, 2017 ; Zhang et al, 2019 ; Jin 2020 ), we for the first time have integrated three major domains of cancer biology including, DNA methylation, gene and microRNA expression to precisely predict the target proteins with the potential to serve as promising early diagnostic biomarkers of Rb. The results of the integrative bioinformatics analysis were further validated in vitro by performing comparative gene expression analysis between Y79, Weri Rb1 human Rb cell lines and non-tumorigenic retinal pigment epithelial cells (hTERT-RPE).…”

An epigenomic landscape of cervical intraepithelial neoplasia and cervical cancer using single‐base resolution methylome and hydroxymethylome

“…Integrated analysis of methylation and gene expression for diagnosis, treatment, or prognosis has been reported in breast cancer, lung cancer, thyroid cancer, and hepatocellular carcinoma, head and neck squamous cell carcinoma, and polycystic ovary syndrome. 11 , 12 , 13 , 14 , 15 , 16 Although CC screening programs are now carried out worldwide, many women are still diagnosed with advanced CC which the overall prognosis remains poor. To date, only a limited number of reports about biomarkers were identified in CC by multi‐omics integrated analysis.…”

“…In addition, multi‐omics integrated analysis can better illuminate the mechanism of the occurrence and development of carcinoma. Integrated analysis of methylation and gene expression for diagnosis, treatment, or prognosis has been reported in breast cancer, lung cancer, thyroid cancer, and hepatocellular carcinoma, head and neck squamous cell carcinoma, and polycystic ovary syndrome 11–16 . Although CC screening programs are now carried out worldwide, many women are still diagnosed with advanced CC which the overall prognosis remains poor.…”