Background/Aims
Crohn’s disease (CD) arises through host-environment interaction. Abnormal gene expression results from disturbed pathway activation or response to bacteria. We aimed to determine activated pathways and driving cell types in paediatric CD.
Methods
- We employed contemporary targeted autoimmune RNA sequencing, in parallel to single-cell sequencing, to ileal tissue derived from paediatric CD and controls. Weighted-gene-co-expression-network-analysis (WGCNA) was performed and differentially expressed genes (DEGs) were determined. We integrated clinical data to determine co-expression modules associated with outcomes.
Results
- Twenty-seven treatment-naive CD (TN-CD), 26 established-CD patients and 17 controls were included. WGCNA revealed a 31-gene signature characterising TN-CD patients, but not established-CD, or controls. The CSF3R gene is a hub within this module and is key in neutrophil expansion and differentiation. Antimicrobial genes including S100A12 and the calprotectin subunit S100A9 were significantly upregulated in TN CD compared to controls (p=2.61x10 -15 and p=9.13x10 -14, respectively) and established-CD (both p=0.0055). Gene-enrichment analysis confirmed upregulation of the IL17-, NOD- and Oncostatin-M-signalling pathways in TN-CD patients, identified in both WGCNA and DEG analyses. An upregulated gene-signature was enriched for transcripts promoting Th17-cell differentiation and correlated with prolonged time to relapse (correlation-coefficient-0.36, p=0.07).Single-cell sequencing of TN-CD patients identified specialised epithelial cells driving differential expression of S100A9. Cell groups, determined by single-cell gene-expression, demonstrated enrichment of IL17-signalling in monocytes and epithelial cells.
Conclusion
- Ileal tissue from treatment naïve paediatric patients is significantly upregulated for genes driving IL17-, NOD- and Oncostatin-M-signalling. This signal is driven by a distinct subset of epithelial cells expressing antimicrobial gene transcripts.