S1595 Integrative Transcription Factor-Gene-Metabolite Network Analysis Reveals Mitochondrial Regulatory Nodes in Crohn’s Disease

Introduction: Mitochondrial dysfunction is a well-recognized hallmark of Crohn’s disease (CD), yet its upstream transcriptional regulation and downstream metabolic consequences remain poorly characterized. We constructed a triadic transcription factor (TF) → gene → metabolite network to uncover regulatory axes underlying mitochondrial alterations in CD. Methods: Using publicly available whole blood transcriptomic data (GSE119600), we identified differentially expressed genes (DEGs) in CD compared to controls. Upstream TFs predicted to regulate these DEGs were identified via ChEA3. Independently, stool metabolomics data (ST000923) were screened for mitochondrial-related metabolites. A directed multi-layer network was constructed by linking TFs to their target genes and genes to biochemically associated metabolites, with emphasis on mitochondrial pathways. Results: The resulting TF–gene–metabolite network highlighted mitochondrial genes such as COX5A, NDUFB8, and NDUFS4, and metabolites including lactate, fumarate, and NADH, all known to be dysregulated in CD. Notably, predicted regulators such as MTERF3 and SNAPC5, along with lesser-studied TFs like CENPX and GTF3A, were integrated into the network, suggesting novel transcriptional control points. Additionally, the inclusion of uncommon metabolites (e.g., 5-acetylamino-6-amino-3-methyluracil) expands the landscape of potentially relevant mitochondrial disruptions. Conclusion: This integrative tri-layered network approach underscores the pivotal role of mitochondrial dysfunction in CD and highlights potential regulatory nodes that bridge transcriptional and metabolic dysregulation. While several interactions align with prior findings, others-particularly those involving understudied TFs and rare metabolites-may indicate uncharacterized pathways, necessitating further experimental validation.