Identification of chloride channel accessory 1 as a protective factor for the prognosis of colon cancer by weighted gene co-expression network and differential gene expression analysis
10.3760/cma.j.cn311367-20200908-00538
- VernacularTitle:加权基因共表达网络分析和差异基因表达分析鉴定氯离子通道附件1基因对结肠癌预后保护作用
- Author:
Zexin ZHANG
;
Wenfeng WU
;
Jing LI
;
Xiaolan JIAN
;
Yi YU
- From:
Chinese Journal of Digestion
2021;41(5):336-343
- CountryChina
- Language:Chinese
-
Abstract:
Objective:To screen the differentially co-expressed genes in the mRNA expression profile of colon cancer by combined application of weighted gene co-expression network analysis(WGCNA) and differential gene expression analysis, and to analyze the relationship between differentially co-expressed genes and prognosis.Methods:The transcriptomics data of the cancer genome atlas (TCGA)-colon adenocarcinoma (COAD) dataset and chip expression profile data of GSE68468 dataset were downloaded from TCGA and gene expression omnibus (GEO) databases based on bioinformatics methods, and differentially expressed gene (DEG) and the most significantly related weighted gene modules between normal tissues and colon cancer tissues were screened. Then, the differentially co-expressed genes related to colon cancer were screened out according to the intersection of differential genes and weighted genes. A protein-protein interaction (PPI) network was constructed, and the top ten core differentially co-expressed genes according to the maximal clique centrality (MCC) score were screened out by MCC calculation method. The expression of core genes in normal tissues and colon cancer tissues were further verified by TCGA-COAD dataset. Kaplan-Meier survival analysis was used to investigate the correlation between core genes and overall survival time and disease-free survival time of patients. The survival-related differentially co-expressed genes were verified by immunohistochemical staining in human protein atlas (HPA) database.Results:A total of 3 481 DEG of the TCGA-COAD dataset and 7 275 DEG of the GSE68468 dataset were screened out, and totally 237 differentially co-expressed genes were obtained. Ten core differentially co-expressed genes were obtained by the MCC calculation method of the PPI network, which were chloride channel accessory 1 ( CLCA1), mitogen-activated protein kinase 3, glucagon ( GCG), solute carrier family 26 member 3 ( SLC26 A3), nuclear receptor subfamily 1 group H member 4 ( NR1 H4), fatty acid binding protein 1 ( FABP1), guanylate cyclase activator 2A ( GUCA2 A), uridine diphosphate glucuronosyltransferase family 2 member A3 ( UGT2 A3), carnitine palmitoyltransferase 2 ( CPT2) and membrane spanning 4-domains A12 ( MS4 A12). Compared with those of the normal tissues, CLCA1, GCG, SLC26 A3, NR1 H4, FABP1, GUCA2 A, UGT2 A3, CPT2 and MS4 A12 of colon cancer tissues of the TCGA-COAD dataset were all down-regulated (all P<0.05). Among them, the overall survival time and disease-free survival time of patients with colon cancer with high expression of CLCA1 were both longer than those with low expression (both P<0.05). The results of immunohistochemical staining also verified the accuracy of the results at the protein level. Conclusions:CLCA1 may play a key role in the development of colon cancer, and it can be used as a potential biomarker for further diagnosis and treatment.
