Inflamm Bowel Dis. 2022 Jun 3;28(6):912-922. doi: 10.1093/ibd/izab318.

James J Ashton ^1 2, Konstantinos Boukas ³, Imogen S Stafford ^1 4 5, Guo Cheng ^1 5, Rachel Haggarty ⁵, Tracy A F Coelho ², Akshay Batra ², Nadeem A Afzal ², Anthony P Williams ^3 4, Marta E Polak ^4 6, R Mark Beattie ², Sarah Ennis ¹

Author information

¹Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, United Kingdom.

²Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, United Kingdom.

³Wessex Investigational Sciences Hub laboratory (WISH lab), University of Southampton, Faculty of Medicine, Southampton, United Kingdom.

⁴Institute for Life Sciences, University of Southampton, Southampton, United Kingdom.

⁵NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, United Kingdomand.

⁶Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, United Kingdom.

Abstract

Background: Inflammatory bowel disease may arise with inadequate immune response to intestinal bacteria. NOD2 is an established gene in Crohn's disease pathogenesis, with deleterious variation associated with reduced NFKB signaling. We hypothesized that deleterious variation across the NOD2 signaling pathway impacts on transcription.

Methods: Treatment-naïve pediatric inflammatory bowel disease patients had ileal biopsies for targeted autoimmune RNA-sequencing and blood for whole exome sequencing collected at diagnostic endoscopy. Utilizing GenePy, a per-individual, per-gene score, genes within the NOD signaling pathway were assigned a quantitative score representing total variant burden. Where multiple genes formed complexes, GenePy scores were summed to create a "complex" score. Normalized transcript expression of 95 genes within this pathway was retrieved. Regression analysis was performed to determine the impact of genomic variation on gene transcription.

Results: Thirty-nine patients were included. Limited clustering of patients based on NOD signaling transcripts was related to underlying genomic variation. Patients harboring deleterious variation in NOD2 had reduced NOD2 (β = -0.702, P = 4.3 × 10-5) and increased NFKBIA (β = 0.486, P = .001), reflecting reduced NFKB signal activation. Deleterious variation in the NOD2-RIPK2 complex was associated with increased NLRP3 (β = 0.8, P = 3.1475 × 10-8) and TXN (β = -0.417, P = 8.4 × 10-5) transcription, components of the NLRP3 inflammasome. Deleterious variation in the TAK1-TAB complex resulted in reduced MAPK14 transcription (β = -0.677, P = 1.7 × 10-5), a key signal transduction protein in the NOD2 signaling cascade and increased IFNA1 (β = 0.479, P = .001), indicating reduced transcription of NFKB activators and alternative interferon transcription in these patients.

Conclusions: Data integration identified perturbation of NOD2 signaling transcription correlated with genomic variation. A hypoimmune NFKB signaling transcription response was observed. Alternative inflammatory pathways were activated and may represent therapeutic targets in specific patients.