Abstract Background Intestinal tuberculosis (ITB) and ileal Crohn's disease (iCD) are common chronic granulomatous diseases of the intestine, exhibiting similarities in clinical and histopathological features, which makes differential diagnosis challenging. We aim to explore the transcriptomic signature of ITB and iCD and identify potential biomarkers for differential diagnosis. Methods We prospectively enrolled seven iCD patients, seven ITB patients, and nine healthy donors. All participants underwent laboratory tests and colonoscopies. Biopsy samples from the ulcer margins of the ileocecal region were collected for bulk transcriptome analysis. Differentially expressed genes (DEGs; P-value<0.05, fold change>2) were selected for further analysis. Results Patients with ITB and iCD showed no statistical differences in routine blood tests, inflammatory markers, or nutritional indicators. Transcriptome analysis revealed 2,690 and 1,849 differentially expressed genes (DEGs) in ITB and iCD, respectively, compared to healthy controls. KEGG pathway enrichment analysis of DEGs that changed commonly or specifically in two diseases revealed shared activation of the IL-17 signaling pathway and upregulation of cytokine-cytokine receptor interactions in the iCD and ITB groups. Distinct changes in the iCD group included upregulation of virus-related responses, neuroactive ligand-receptor interaction, efferocytosis, and downregulation of bile secretion and cholesterol metabolism. In contrast, the ITB group showed activation of chemokine signaling and complement-related pathways and downregulation of tyrosine and retinol metabolism pathways. Further comparison of inflammatory cytokines, chemokines, and extracellular matrix (ECM) related genes among the three groups revealed that ITB patients exhibited a more robust pro-inflammatory response and more pronounced ECM remodeling than iCD patients. To identify diagnostic markers for ITB and iCD, we analyzed the DEGs that changed specifically in iCD or ITB, selecting the top 20 genes with the most tremendous fold changes. We found that genes such as CCL17, PDZK1, PLA2G12B, PRRX1, and ZNF488 showed significant differences in expression between the iCD and ITB groups. Receiver Operating Characteristic (ROC) Curve analysis demonstrated strong predictive value for these five genes in distinguishing ITB from iCD patients, with AUC values of 0.8214, 0.8367, 0.8750, 0.8571, and 0.9643, respectively. Conclusion Our study advances the molecular understanding of ITB and iCD, emphasizing distinct transcriptomic responses in the mucosal tissues of these conditions. Notably, five genes—PRRX1, PDZK1, PLA2G12B, ZNF488, and CCL17—exhibited strong diagnostic potential for distinguishing ITB from iCD.
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