Analysis of the associations between DNA methylation and clinical features reveals the potential oncogenic effect of CFAP52 in esophageal squamous cell cancer.

BACKGROUND: Esophageal squamous cell cancer (ESCC) is one of the most common and lethal malignancies. It is urgent to uncover the underlying mechanisms for ESCC progression. Aberrant DNA methylation is observed in ESCC. However, the precise relationship between DNA methylation alterations and clinical features of ESCC is still largely unknown. We aimed to further explore the potential role of DNA methylation in the development of ESCC. METHODS: Abnormal DNA methylation and gene expression were analyzed with TCGA ESCA cohort data. Differentially methylated CpGs were identified with Mann-Whitney U test. Differentially expressed genes (DEGs) were analyzed with limma package and student's t-test. Prognosis-related CpGs were screened by Cox regression analysis. ESCC subgroups were identified with ConsensusClusterPlus package. Epithelial-mesenchymal transition (EMT) score was calculated with epithelial and mesenchymal gene expression data. CIBERSORTx was employed to analyze immune cell infiltration. Drug sensitivity was predicted with oncoPredict package. Gene Expression Omnibus (GEO) dataset GSE53624 was used to verify CFAP52 expression in ESCC, and GSE160269 and GSE203115 were utilized to investigate the expression of CFAP52 in different cell types. Seurat package was used for single-cell RNA-seq data analysis. Western blot was used to assess CFAP52 expression. MTS, transwell, scratch wound healing, colony formation and cell cycle assays were conducted to verify the function of CFAP52. The genes affected by CFAP52 overexpression were explored via RNA-seq. Arachidonic acid level was quantified with UPLC-MS/MS system. Immunohistochemistry was used to check the protein level of CFAP52. RESULTS: 3443 differentially methylated CpGs and 43 related DEGs were identified between males and females. Besides, 1219 alcohol-related CpGs were screened, and 9 related genes were differentially expressed. 175 ESCC prognosis-related CpGs were screened, and ESCC subgroups were identified with these CpGs. Poor prognosis group had higher EMT score, and showed elevated proportion of regulatory T cells and M2 macrophages and higher estimated IC50s of cisplatin_1496, gemcitabine_135 and docetaxel_1007. CFAP52 was identified as a stage-related gene, and mainly expressed in epithelial cells, especially in malignant epithelial cells. Furthermore, CFAP52 was upregulated in ESCC cells and promoted cell proliferation and migration. CFAP52 might affect arachidonic acid metabolism in ESCC cells. CFAP52 protein level increased in ESCC tissues, and high CFAP52 was associated with poor survival of ESCC patients. Treatment with DNA methylation inhibitor downregulated CFAP52. CONCLUSIONS: Collectively, our investigations show that DNA methylation is associated with sex and alcohol consumption in ESCC. Besides, DNA methylation is linked to ESCC prognosis. Moreover, we uncover the potential oncogenic role of CFAP52 in ESCC.