Multi-Cohort Transcriptomics Combined with Mendelian Randomization Identifies PPARGC1A, NAAA and GIPC2 as NLRP3...

Ulcerative Colitis (UC), a subtype of inflammatory bowel disease with unclear specific pathogenesis, was associated with recurrent inflammatory infections, genetics, and immunodeficiency. This study aimed to analyze the potential pathogenesis of NLRP3 inflammasome (NLRP3-INF)-mediated UC via transcriptomics combined with Mendelian Randomization (MR), explore the causal relationship between NLRP3-INF, related target genes and UC, and provide insights for mining UC therapeutic targets.

Gene expression data (GSE87473 as training set, GSE75214 as validation set, GSE87466 as external validation set) were obtained. Differential expression analysis and Weighted Gene Co-expression Network Analysis (WGCNA) were performed to screen differentially expressed genes (DEGs) and NLRP3-INF related genes (NLRP3-RGs) related module genes. Candidate genes were obtained by intersecting DEGs with module genes. MR analysis was conducted between candidate genes and UC. Receiver Operating Characteristic (ROC) analysis and expression validation were used to confirm key genes; immune infiltration drug prediction; and molecular dynamics (MD) simulation analyses were carried out, and the expression of key genes was further verified in the UC mouse model.

A total of 942 DEGs were screened. WGCNA identified eight modules, with the MEyellow module (813 genes) highly correlated with NLRP3-RGs. A total of 307 candidate genes were obtained. Nine candidate key genes were screened through MR analysis; after validation, PPARGC1A (Peroxisome proliferator-activated receptor gamma coactivator 1-alpha), NAAA (N-acylethanolamine acid amidase), and GIPC2 (GIPC PDZ domain containing family member 2) (significantly downregulated in UC) were confirmed as key genes. They were correlated immune cells such as M0 macrophages and activated CD4+ T cells; Molecular docking revealed a binding free energy of -8.7 kcal/mol between PPARGC1A and Rosiglitazone, indicating favorable binding affinity. Molecular dynamics simulations confirmed the binding conformation remained stable over 100 ns Animal experiments confirmed lower expression of the three key genes in the model group.

PPARGC1A, NAAA, and GIPC2 were identified through bioinformatics analyses as key genes for NLRP3-INF-mediated UC, which could serve as potential biomarkers and provide a basis for UC pathogenesis research and therapeutic target development.