Targeted Assessment of Mucosal Immune Gene Expression Predicts Clinical Outcomes in Children with Ulcerative Colitis

Kathryn Clarkston, Rebekah Karns, Anil G. Jegga, Mihika Sharma, Sejal Fox, Babajide A. Ojo, Phillip Minar, Thomas D. Walters, Anne M. Griffiths, David R. Mack, Brendan Boyle, Neal S. Leleiko, James Markowitz, Joel R. Rosh, Ashish S. Patel, Sapana Shah, Robert N. Baldassano, Marian Pfefferkorn, Cary Sauer, Subra KugathasanYael Haberman, Jeffrey S. Hyams, Lee A. Denson, Michael J. Rosen*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


Background and Aims: We aimed to determine whether a targeted gene expression panel could predict clinical outcomes in paediatric ulcerative colitis [UC] and investigated putative pathogenic roles of predictive genes. Methods: In total, 313 rectal RNA samples from a cohort of newly diagnosed paediatric UC patients (PROTECT) were analysed by a real-time PCR microfluidic array for expression of type 1, 2 and 17 inflammation genes. Associations between expression and clinical outcomes were assessed by logistic regression. Identified prognostic markers were further analysed using existing RNA sequencing (RNA-seq) data sets and tissue immunostaining. Results: IL13RA2 was associated with a lower likelihood of corticosteroid-free remission (CSFR) on mesalamine at week 52 (p=.002). A model including IL13RA2 and only baseline clinical parameters was as accurate as an established clinical model, which requires week 4 remission status. RORC was associated with a lower likelihood of colectomy by week 52. A model including RORC and PUCAI predicted colectomy by 52 weeks (area under the receiver operating characteristic curve 0.71). Bulk RNA-seq identified IL13RA2 and RORC as hub genes within UC outcome-associated expression networks related to extracellular matrix and innate immune response, and lipid metabolism and microvillus assembly, respectively. Adult UC single-cell RNA-seq data revealed IL13RA2 and RORC co-expressed genes were localized to inflammatory fibroblasts and undifferentiated epithelial cells, respectively, which was supported by protein immunostaining. Conclusion: Targeted assessment of rectal mucosal immune gene expression predicts 52-week CSFR in treatment-naïve paediatric UC patients. Further exploration of IL-13R2 as a therapeutic target in UC and future studies of the epithelial-specific role of RORC in UC pathogenesis are warranted.

Original languageEnglish
Pages (from-to)1735-1750
Number of pages16
JournalJournal of Crohn's and Colitis
Issue number11
StatePublished - 1 Nov 2022
Externally publishedYes


  • Paediatric inflammatory bowel disease
  • gene expression array
  • weighted gene co-expression network analysis


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