Causal Insights Into Crohn's Disease: The Role of Oxidative Stress and Genetic Variants

Crohn's disease (CD) is a chronic inflammatory condition of the gastrointestinal tract, where oxidative stress is a significant contributing factor to its pathogenesis. This study utilized multi-omics data, including RNA sequencing from the GSE216447 dataset and three genome-wide association studies (GWAS) datasets (ieu-a-10, ieu-a-11, ieu-a-13), to investigate the molecular networks related to oxidative stress in CD. Differential expression analysis was performed using DESeq2, followed by pathway enrichment analysis with clusterProfiler. Protein-protein interaction (PPI) networks were constructed using the STRING database. Mendelian Randomization (MR) analysis was conducted using TwoSampleMR and MRMix to identify causal relationships between genetic variants and CD. Quantitative real-time polymerase chain reaction (qPCR) was further applied to verify key differentially expressed genes (DEGs), including FASN, HMGCR, ASCC3, CD101, ELOVL6, PHLDA2, PHLDA3, and SCPEP1, in intestinal mucosal samples from both inactive and active CD patients. The analysis identified 64 up-regulated and 46 down-regulated differentially expressed genes (DEGs) in response to H₂O₂ intervention. Key pathways related to oxidative stress, including the p53 signalling pathway and steroid biosynthesis, were significantly enriched. Consistent with transcriptomic data, qPCR confirmed that FASN and HMGCR were significantly upregulated in inactive CD, while ASCC3, CD101, ELOVL6, PHLDA2, PHLDA3, and SCPEP1 were markedly increased in active CD (all p < 0.05). The MR analysis revealed that in the dataset ieu-a-10, ABCB9 and OSGIN1 were identified as having a significant causal relationship with CD using TwoSampleMR, while only OSGIN1 was significant in MRMix. In dataset ieu-a-11, ARL4C, CD101, HMGCR, and IL24 were found to be significantly associated with CD, with overlapping findings between TwoSampleMR and MRMix. For dataset ieu-a-13, ACTA2 and CD101 were consistently identified as significant, suggesting their potential roles in CD pathogenesis. The findings highlight the crucial involvement of oxidative stress-related molecular networks in CD and underscore the utility of Mendelian Randomization in elucidating causal genetic factors. qPCR validation confirmed persistent upregulation of lipid metabolism genes in inactive CD and significant elevation of inflammation-related genes in active CD, reinforcing the link between oxidative stress and disease activity.