Identification of differentially expressed genes associated with ferroptosis in Crohn's disease.

Abstract

Ferroptosis-related genes may play a critical regulatory role in the pathogenesis of Crohn's disease (CD). The purpose of the present study was to identify genes expressed in CD that are associated with ferroptosis, and to provide guidance in the diagnosis and therapy of CD. CD mRNA expression data were initially gathered from the Gene Expression Omnibus (GEO) database. GSE75214 and GSE102133 datasets were selected as the major targets and were analyzed for differentially expressed genes (DEGs). Subsequently, R software was used to analyze the common genes among the DEGs between CD and ferroptosis-related genes. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genome pathway analysis were conducted to identify related pathways and functions. Protein-protein interaction (PPI) analysis was performed to identify target genes. The DSigDB website was used to predict potential target drugs for hub genes. Reverse transcription-quantitative (RT-q) PCR was employed to detect the expression of these ferroptosis-related genes in clinical samples obtained from healthy controls and patients with CD. According to the two GEO datasets, 13 ferroptosis DEGs (11 upregulated genes and two downregulated genes) were identified in CD with thresholds of P<0.05 and |log2 fold change|>1, and were selected for further analysis. PPI analysis indicated the mutual effects among these genes and filtered out five hub genes. The top 10 potential targeted drugs were selected. The qPCR results showed that the expression levels of three genes, namely, IL-6, prostaglandin-endoperoxide synthase 2 (PTGS2) and dual oxidase 2 (DUOX2), were different between CD samples and healthy samples. This result was consistent with the results obtained from the bioinformatics analysis. In conclusion, bioinformatics analysis identified a total of 13 ferroptosis-associated genes in CD. Further verification by qPCR showed that IL-6, PTGS2 and DUOX2 may affect the process of CD by regulating ferroptosis. These findings might provide new biomarkers, diagnostic and therapeutic markers for CD.