Weighted gene co-expression network analysis and CIBERSORT screening of key genes related to m6A methylation in Hirschsprung's disease

Jiaqian Huang; Tingwei Chen; Junjie Wang; Zhiqiang Wang; Shungen Huang

doi:10.3389/fgene.2023.1183467

Weighted gene co-expression network analysis and CIBERSORT screening of key genes related to m6A methylation in Hirschsprung's disease

Front Genet. 2023 Apr 18:14:1183467. doi: 10.3389/fgene.2023.1183467. eCollection 2023.

Authors

Jiaqian Huang^{1

2}, Tingwei Chen¹, Junjie Wang², Zhiqiang Wang², Shungen Huang¹

Affiliations

¹ Pediatric Surgery, Children's Hospital of Soochow University, Suzhou, China.
² Department of Biochemistry and Molecular Biology, Medical College, Soochow University, Suzhou, China.

Abstract

Hirschsprung's disease (HSCR) is a neural crest disease that results from the failure of enteric neural crest cells (ENCCs) to migrate to the corresponding intestinal segment. The RET gene, which regulates enteric neural crest cell proliferation and migration, is considered one of the main risk factors for HSCR and is commonly used to construct HSCR mouse models. The epigenetic mechanism of m6A modification is involved in HSCR. In this study, we analyzed the GEO database (GSE103070) for differentially expressed genes (DEGs) and focused on m6A-related genes. Comparing the RNA-seq data of Wide Type and RET Null, a total of 326 DEGs were identified, of which 245 genes were associated with m6A. According to the CIBERSORT analysis, the proportion of Memory B-cell in RET Null was significantly higher than that of Wide Type. Venn diagram analysis was used to identify key genes in the selected memory B-cell modules and DEGs associated with m6A. Enrichment analysis showed that seven genes were mainly involved in focal adhesion, HIV infection, actin cytoskeleton organization and regulation of binding. These findings could provide a theoretical basis for molecular mechanism studies of HSCR.

Keywords: CIBERSORT; M6A; WGCNA; enrichment analysis; hirschsprung’s disease.

Grants and funding

The work was supported by Suzhou Key Discipline of Medicine (SZXK202105) and Suzhou Municipal Health and Family Planning Commission’s Key Diseases Diagnosis and Treatment Program (LCZX202107).