Frontiers in Genetics (Dec 2024)
Identification of hub programmed cell death-related genes and immune infiltration in Crohn’s disease using bioinformatics
Abstract
BackgroundCrohn’s disease (CD) is an immune-mediated disorder characterized by immune cell infiltration that induces persistent chronic inflammation of the gastrointestinal tract. Programmed cell death (PCD) plays a critical role in the pathogenesis of CD. This study identified vital PCD-related genes in CD based on immune infiltration using bioinformatic analysis.MethodsWe obtained two CD datasets from the Gene Expression Omnibus (GEO) database and examined immune cell infiltration to investigate immune cell dysregulation in CD. PCD-related genes were retrieved from the GeneCards database. Based on the differentially expressed genes (DEGs) and PCD gene sets, PCD-related DEGs were identified. Candidate hub genes were identified using a protein-protein interaction (PPI) network, and their diagnostic effectiveness was predicted using receiver operating characteristic (ROC) curve analysis. Functional enrichment and immune infiltration analyses were used to assess the distinct roles of the hub genes. Finally, the miRWalk and ENCORI databases were used to predict which microRNAs (miRNAs) regulated the hub genes and to verify gene expression in CD colonic tissues via transcriptome sequencing.ResultsA total of 335 PCD-related DEGs and 3 hub genes (MMP1, SAA1, and PLAU) were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional analyses indicated the enrichment of these genes in the immune response. Infiltration analysis of immune cells showed abundant endothelial cells, plasma cells, dendritic cells, and monocytes in the CD samples. Based on the correlation analysis, the three hub genes were positively correlated with monocytes and negatively correlated with CD8 naïve T-cells. MMP1, SAA1, and PLAU correlated with the pathogenicity of CD and had good diagnostic value for CD. The three hub genes were highly expressed in the CD tissues, as confirmed using transcriptome sequencing.ConclusionThis study identified MMP1, SAA1, and PLAU as hub genes involved in PCD in patients with CD. These genes regulate immune cell function and their expression levels are closely related to immune cell infiltration. These findings provide novel insights into the mechanisms underlying CD pathogenesis. The identified PCD genes and regulatory miRNAs are potential biomarkers and therapeutic targets for CD.
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