Ileal Transcriptomic Analysis in Paediatric Crohn's Disease Reveals IL17- and NOD-signalling Expression Signatures in Treatment-naïve Patients and Identifies Epithelial Cells Driving Differentially Expressed Genes

J Crohns Colitis. 2021 May 4;15(5):774-786. doi: 10.1093/ecco-jcc/jjaa236.


Background and 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: In all, 27 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, nor 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 with controls [p = 2.61 x 10-15 and p = 9.13 x 10-14, 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.

Conclusions: 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.

Keywords: IBD; crohn’s disease; paediatric; transcriptomics.

MeSH terms

  • Adolescent
  • Biopsy
  • Child
  • Crohn Disease / drug therapy
  • Crohn Disease / genetics*
  • Epithelial Cells / metabolism*
  • Female
  • Gastrointestinal Agents / therapeutic use
  • Gene Expression Profiling / methods*
  • Humans
  • Ileum / metabolism*
  • Interleukin-17 / genetics*
  • Male
  • Nod2 Signaling Adaptor Protein / genetics*
  • Signal Transduction
  • Th17 Cells / metabolism


  • Gastrointestinal Agents
  • Interleukin-17
  • NOD2 protein, human
  • Nod2 Signaling Adaptor Protein

Supplementary concepts

  • Pediatric Crohn's disease