Identification of Differential Intestinal Mucosa Transcriptomic Biomarkers for Ulcerative Colitis by Bioinformatics Analysis

Abstract

Background. Ulcerative colitis (UC) is a complicated disease caused by the interaction between genetic and environmental factors that affect mucosal homeostasis and triggers inappropriate immune response. The purpose of the study was to identify significant biomarkers with potential therapeutic targets and the underlying mechanisms. Methods. The gene expression profiles of GSE48958, GSE73661, and GSE59071 are from the GEO database. Differentially expressed genes (DEGs) were screened by the GEO2R tool. Next, the Database for Annotation, Visualization and Integrated Discovery (DAVID) was applied to analyze gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Then, protein-protein interaction (PPI) was visualized by Cytoscape with Search Tool for the Retrieval of Interacting Genes (STRING). Results. There were a total of 128 common DEGs genes, including 86 upregulated genes enriched in extracellular space, regulation of inflammatory response, chemokine-mediated signaling pathway, response to lipopolysaccharide, and cell proliferation, while 42 downregulated genes enriched in the integral component of the membrane, the integral component of the plasma membrane, apical plasma membrane, symporter activity, and chloride channel activity. The KEGG pathway analysis results demonstrated that DEGs were particularly enriched in cytokine-cytokine receptor interaction, TNF signaling pathway, chemokine signaling pathway, pertussis, and rheumatoid arthritis. 18 central modules of the PPI networks were selected with Cytotype MCODE. Furthermore, 18 genes were found to significantly enrich in the extracellular space, inflammatory response, chemokine-mediated signaling pathway, TNF signaling pathway, regulation of cell proliferation, and immune response via reanalysis of DAVID. Conclusion. The study identified DEGs, key target genes, functional pathways, and pathway analysis of UC, which may provide potential molecular targets and diagnostic biomarkers for UC.

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

“…However, differences in measurement platforms, lab protocols, sample sizes, and operators render gene expression levels incomparable. In recent years, several studies based on microarray technology have been published to identify effective biomarkers in UC, most of which are prone to utilizing intersecting genes from different microarrays to perform analyses (Cheng et al, 2019(Cheng et al, , 2020Shi et al, 2020;Cao et al, 2021). As shown in Table 3, these methods can be applied to fewer datasets (≤3 datasets) because more datasets represent overly strict inclusion criteria, leading to fewer DEGs.…”

“…The expression of the six hub genes was confirmed in the DSS-induced UC mouse model. In published studies, some scholars screened diagnostic biomarkers for UC from the DEGs identified from a single dataset or an overlap of two or three datasets via bioinformatics analyses (Cheng et al, 2019(Cheng et al, , 2020Shi et al, 2020;Cao et al, 2021). In contrast, the advantage of this research lies in the larger dataset obtained by combining data from six GEO datasets, which increased the sample size and ensured the stability and relative reliability of the conclusions.…”

“…In recent years, several studies based on microarray technology have been published to identify effective biomarkers in UC (Cheng et al, 2019(Cheng et al, , 2020Shi et al, 2020;Cao et al, 2021). However, differences in measurement platforms, lab protocols, sample sizes, and operators render gene expression levels incomparable.…”

Systems pharmacology and transcriptomics reveal the mechanisms of Sanhuang decoction enema in the treatment of ulcerative colitis with additional Candida albicans infection

“…Transcriptomics is a high-throughput technique to observe mRNAs with differential expression in different tissues and time points in organisms, playing a major role in the study of drug action mechanism [ 39 , 40 ]. In this study, 370 differentially expressed genes, including 151 upregulated and 219 downregulated, were screened.…”

Role of TRIM22 in ulcerative colitis and its underlying mechanisms

“…The National Center for Biotechnology Information Gene Expression Omnibus ( ) is a free public database of microarray/gene profiles, which was used to obtain the GSE59071 ( 19 ) and GSE107597 ( 20 ) in UC and normal tissue gene expression profiles ( 21 ). GEO2R (ncbi.nlm.nih.gov/geo/geo2r/) was used for data preprocessing and analyzing the expression of TRIM22 in the UC (n=6) and control (n=6) groups (GSE59071: 97 UC and 11 control samples; GSE107597: 6 UC samples and 4 control samples).…”