Mucosal Gene Transcript Signatures in Treatment Naïve Inflammatory Bowel Disease: A Comparative Analysis of Disease to Symptomatic and Healthy Controls in the European IBD-Character Cohort

Abstract

Background

Studies of the mucosal transcriptomic landscape have given new insight into the pathogenesis of inflammatory bowel disease (IBD). Recently, the predictive biomarker potential of gene expression signatures has been explored. To further investigate the mucosal gene expression in IBD, we recruited a cohort of treatment naïve patients and compared them to both symptomatic and healthy controls.

Methods

Altogether, 323 subjects were included: Crohn’s disease (N = 75), ulcerative colitis (N = 87) and IBD unclassified (N = 3). Additionally, there were two control groups: symptomatic controls (N = 131) and healthy controls (N = 27). Mucosal biopsies were collected during ileocolonoscopy and gene expression in inflamed and non-inflamed mucosa was explored. Gene expression profiling was performed using Agilent G3 Human Gene Expression 860K v3 One-Color microarray. We recorded information about treatment escalation to anti-TNF agents or surgery, and anti-TNF response, to explore predictive opportunities of the mucosal transcriptome.

Results

Gene expression profiles in symptomatic controls in whom IBD had been excluded resembled that of IBD patients and diverged from that of healthy controls. In non-inflamed Crohn’s disease and ulcerative colitis, gene set enrichment analysis revealed dysregulation of pathways involved in basic cellular biological processes. Mitochondria-associated pathways were dysregulated both in non-inflamed and inflamed Crohn’s disease and ulcerative colitis (>2.6 normalized enrichment scores <−1.8). Gene expression signatures of Crohn’s disease and ulcerative colitis did not predict time for treatment escalation (p = 0.175). No significant association was found between gene expression signatures and anti-TNF response.

Conclusion

Non-inflamed samples are probably superior to inflamed samples when exploring gene expression signatures in IBD and might reveal underlying mechanisms central for disease initiation. The gene expression signatures of the control groups were related to if they were symptomatic or not, which may have important implications for future study designs.

Keywords:

• Crohn’s disease
• healthy controls
• mitochondria
• mucosal transcriptome
• non-inflamed
• prediction
• symptomatic controls
• ulcerative colitis

Abbreviations

CD, Crohn’s disease; DEFB4A, defensin, beta 4A; DEG, differentially expressed gene; FDR, false discovery rate; FOX03, forkhead box 03; GO, gene ontology; GSEA, gene set enrichment analysis; HBI, Harvey-Bradshaw Index; HC, healthy controls; HLA-B, human leucocyte antigen B; IBD, inflammatory bowel disease; IBD-U, inflammatory bowel disease unclassified; IBS, irritable bowel syndrome) IGFBP1, insulin-like growth factor binding protein 1; IGFBP3, insulin-like growth factor binding protein 3; PCK1, phosphoenolpyruvate carboxykinase 1; UC, ulcerative colitis; SC, symptomatic controls.

Data Transparency

Clinical and descriptive data of the cohort, analytic methods, and microarray raw data can be shared on request to the corresponding author ([email protected]) with permission from the IBD Character data access committee.

Acknowledgments

The authors thank the IBD-Character Consortium for contributions in study conception and design: Elaine R Nimmo, Hazel E Drummond, Ray K Boyapati, Nicholas T Ventham, Nicholas A Kennedy, David C Wilson, Charles W Lees, Colin L Noble, Ian D Arnott, Gwo-Tzer Ho, Alan G Shand, Kate R O’Leary, Anna Frengen, Panpan You, Janne Sølvernes, Fredrik A Dahl, Gunn S Ekeland, Haldor Husby, Johan D Söderholm, Henrik Hjortswang, Mauro D’Amato, Leif Törkvist, Christina Casén, Magdalena K Karlsson, Fredrik Hjelm, Mats Gullberg, Niklas Nordberg, Anette Ocklind, Erik Pettersson, Daniel Ekman, Mikael Sundell, Eddie Modig, Anne-Clémance Veillard, Renaud Schoemans, Dominique Poncelet, Céline Sabatel, Ivo G Gut, Marta Gut, Simon Heath, Monica Bayes, Angelika Merkel, and Ferdinando Bonfiglio.

Disclosure

Prof. Dr. Stephan Brackmann reports personal fees from Athna/Pharmanovia, personal fees from Augere medical, outside the submitted work. Dr Daniel Bergemalm reports grants from EU FP7 grant, during the conduct of the study; personal fees from Pfizer, personal fees from Janssen, personal fees from Ferring, outside the submitted work. Professor Fernando Gomollon reports grants, personal fees from TAKEDA, grants and personal fees from JANSSEN, grants, personal fees from ABBVIE, personal fees from PFIZER, outside the submitted work. Dr Trond Espen Detlie reports personal fees from Ferring, personal fees from Tillotts, personal fees from Pharmacosmos, personal fees from Vifor Pharma, outside the submitted work. Prof. Dr. Jonas Halfvarson reports grants from EU, during the conduct of the study; grants, personal fees from Janssen, grants, personal fees from Takeda, grants, personal fees from MSD, personal fees from AbbVie, personal fees from Aqilion, personal fees from Celgene, personal fees from Celltrion, personal fees from Ferring, personal fees from Gilead, personal fees from Index Pharma, personal fees from Lincs, personal fees from Novartis, non-financial support from Olink Proteomics, personal fees from Pfizer, personal fees from Prometheus Laboratories Inc., personal fees from Sandoz, personal fees from Shire, personal fees from Thermo Fisher Scientific, personal fees from Tillotts Pharma, personal fees from Vifor Pharma, outside the submitted work. The authors declare no other conflicts of interest to this work.

Additional information

Funding

The study was funded by the following EU FP7 grant: IBD-CHARACTER (contract # 2858546). PR and SV were funded by South-Eastern Norway Regional Health Authority (project numbers 2014011 and 2018001).