Screening potential prognostic biomarkers of colorectal cancer based on weighted gene co-expression network analysis

doi:10.3969/j.issn.1673-8640.2023.09.004

Abstract

Abstract:

Objective To investigate hub genes related to colorectal cancer（CRC） as potential prognostic biomarkers by bioinformatics analysis. Methods The GSE33113 dataset related to CRC were obtained from Gene Expression Omnibus（GEO） database. Differentially expressed genes from CRC tissues and adjacent tissues were obtained using limma program package in R software，and Gene Ontology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） enrichment analysis of differentially expressed genes were performed with the DAVID online tool. Weighted gene co-expression network analysis（WGCNA） was used to output key module genes，and the intersection of key module genes and differentially expressed genes was taken as candidate hub genes. GEPIA database was used to verify the expression and prognostic value of hub genes in CRC. The diagnostic value of the hub genes for CRC was evaluated by receiver operating characteristic（ROC） curve. Gene set enrichment analysis（GSEA） was performed to explore the biological significance of hub genes in CRC. Human normal intestinal epithelial cell HIEC cell line，CRC cell line，HCT116 and HCT15 were used to deterimine the expression of hub genes by real-time quantitative polymerase chain reaction（RT-qPCR） and western blotting. Results GSE33113 dataset contains 90 CRC tissues and 6 adjacent tissues. A total of 1 211 differentially expressed genes were screened，including 505 up-regulated cases and 706 down-regulated cases，which were mostly distributed in extracellular space and extracellular region，regulating chemokine mediated signaling pathways，inflammatory response，cell division and so on. WGCNA analysis revealed 24 and 96 key module genes were most significantly correlated with clinical features，and 24 and 62 candidate hub genes were obtained，respectively. A total of 6 hub genes（AQP8，PBK，EXO1，CCNB1，DEPDC1B and KPNA2） were acquired after screening in GEPIA database. EXO1 was selected for validation，and its expression was up-regulated in CRC tissues of different datasets. GEPIA database analysis results showed that the expression level of EXO1 mRNA was high in CRC tissues，the expression level of EXO1 in CRC patients was correlated with overall survival（OS），and ROC curve analysis showed that EXO1 had high diagnostic value for CRC. The results of GSEA analysis suggested that EXO1 may regulate CRC by affecting cell cycle and DNA replication. RT-qPCR and western blotting results revealed that the expression of EXO1 was up-regulated in CRC cells. Conclusions Totally，6 hub genes related to CRC have been identified by WGCNA，among which EXO1 may serve as a potential prognostic biomarker for CRC.

Key words: Differentially expressed gene, Weighted gene co-expression network analysis, EXO1, Gene set enrichment analysis, Colorectal cancer

CLC Number:

R446.7

LI Liangshan, ZHAO Hu, WANG Shiwen. Screening potential prognostic biomarkers of colorectal cancer based on weighted gene co-expression network analysis[J]. Laboratory Medicine, 2023, 38(9): 825-832.

Figures/Tables 8

References 18

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