Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis

Zi-An Chen; Yu-Feng Sun; Quan-Xu Wang; Hui-Hui Ma; Zhi-Zhao Ma; Chuan-Jie Yang

doi:10.3389/fgene.2021.697514

Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Ulcerative Colitis

Front Genet. 2021 Jul 9:12:697514. doi: 10.3389/fgene.2021.697514. eCollection 2021.

Authors

Zi-An Chen¹, Yu-Feng Sun¹, Quan-Xu Wang¹, Hui-Hui Ma¹, Zhi-Zhao Ma², Chuan-Jie Yang¹

Affiliations

¹ Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
² Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China.

Abstract

Background: Ulcerative colitis (UC) is a chronic, complicated, inflammatory disease with an increasing incidence and prevalence worldwide. However, the intrinsic molecular mechanisms underlying the pathogenesis of UC have not yet been fully elucidated. Methods: All UC datasets published in the GEO database were analyzed and summarized. Subsequently, the robust rank aggregation (RRA) method was used to identify differentially expressed genes (DEGs) between UC patients and controls. Gene functional annotation and PPI network analysis were performed to illustrate the potential functions of the DEGs. Some important functional modules from the protein-protein interaction (PPI) network were identified by molecular complex detection (MCODE), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG), and analyses were performed. The results of CytoHubba, a plug for integrated algorithm for biomolecular interaction networks combined with RRA analysis, were used to identify the hub genes. Finally, a mouse model of UC was established by dextran sulfate sodium salt (DSS) solution to verify the expression of hub genes. Results: A total of 6 datasets met the inclusion criteria (GSE38713, GSE59071, GSE73661, GSE75214, GSE87466, GSE92415). The RRA integrated analysis revealed 208 significant DEGs (132 upregulated genes and 76 downregulated genes). After constructing the PPI network by MCODE plug, modules with the top three scores were listed. The CytoHubba app and RRA identified six hub genes: LCN2, CXCL1, MMP3, IDO1, MMP1, and S100A8. We found through enrichment analysis that these functional modules and hub genes were mainly related to cytokine secretion, immune response, and cancer progression. With the mouse model, we found that the expression of all six hub genes in the UC group was higher than that in the control group (P < 0.05). Conclusion: The hub genes analyzed by the RRA method are highly reliable. These findings improve the understanding of the molecular mechanisms in UC pathogenesis.

Keywords: GEO database; differentially expressed genes; microarray; robust rank aggregation; ulcerative colitis.