Comprehensive analysis based on methylation microarrays and single-cell transcriptomics in esophageal squamous cell carcinoma-Reference-Cited by-同舟云学术

Comprehensive analysis based on methylation microarrays and single-cell transcriptomics in esophageal squamous cell carcinoma

Published:2022-11-10 Issue: Volume: Page:
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Author:

Xiao Qiyu¹,Huang Qingguan²

Affiliation:

1. Huadu District People's Hospital of Guangzhou

2. Hunan Cancer Hospital/the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University

Abstract

Abstract Aberrant methylated genes (DMGs) play an important role in the etiology and pathogenesis of esophageal squamous cell carcinoma (ESCC). Single-cell transcriptome analysis of immune cells in tumors provides a way to comprehensively study these cells in a highly complex tumor microenvironment (TME). In this study, we combine methylation datasets and single cell datasets to ascertain aberrant methylated-differentially expressed genes and pathways associated with ESCC TME by comprehensive bioinformatics analysis. STRING and Cytoscape software were used to construct a protein-protein interaction (PPI) network. In total, 111 hypomethylated/high-expressed genes were identified at the screening step, and finally found six mostly changed hub genes including COL1A1, COL1A2, COL5A1, COL5A2, COL11A1 and THBS2. Pathway analysis indicated that aberrantly methylated DEGs mainly associated with extracellular matrix structural constituent and cytokine − cytokine receptor interaction. Analyzing the single cell data of ESCC, we confirmed the specific cell cluster highly expressing hub genes and predict the biological function of the cell cluster. These results can shed a light for screening and diagnosis of ESCC in future.

Publisher

Research Square Platform LLC

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