OP39 The effect of phenotype and genotype on the plasma proteome in patients with Inflammatory Bowel Disease

Bourgonje, A.R.(1);Hu, S.(1);Spekhorst, L.M.(1);Zhernakova, D.V.(2);Vich Vila, A.(1);Li, Y.(1);Voskuil, M.D.(1);van Berkel, L.A.(3);Bley Folly, B.(3);Charrout, M.(4);Mahfouz, A.(4);Reinders, M.J.T.(4);van Heck, J.I.P.(5);Joosten, L.A.B.(5);Visschedijk, M.C.(1);van Dullemen, H.M.(1);Faber, K.N.(1);Samsom, J.N.(3);Festen, E.A.M.(1);Dijkstra, G.(1);Weersma, R.K.(1)

(1)University Medical Center Groningen, Gastroenterology and Hepatology, Groningen, The Netherlands;(2)University Medical Center Groningen, Genetics, Groningen, The Netherlands;(3)Erasmus University Medical Center, Pediatrics- Division of Gastroenterology, Rotterdam, The Netherlands;(4)Delft University of Technology and Leiden University Medical Center, Delft Bioinformatics Lab and Leiden Computational Biology Center, Delft- Leiden, The Netherlands;(5)Radboud University Medical Center, Internal Medicine and Institute of Molecular Life Sciences, Nijmegen, The Netherlands


Protein profiling in patients with inflammatory bowel diseases (IBD) for diagnostic and therapeutic purposes is underexplored. Assessment of interactions between genetics and the plasma proteome could lead to identification of novel disease-associated molecular pathways. In this study, we performed the largest gene-protein association analysis thus far in patients with IBD, taking into account relevant phenotypic covariates and integrating information from multiple biological data layers.


Ninety-two (92) inflammation-related proteins were quantified in plasma of 1,028 patients with IBD (567 Crohn’s disease [CD]; 461 ulcerative colitis [UC]) and 148 healthy individuals to assess proteome-phenotype associations. Both whole-exome sequencing (WES) and global screening array (GSA) data of 919 patients with IBD were included to study associations between over 8 million genetic variants and protein levels (protein quantitative trait loci [pQTL]). Cis-pQTLs were defined within ± 1 Mb of the region of each protein-coding gene center, whereas trans-pQTLs were outside of that region. After adjusting for phenotypic covariates, a step-wise conditional analysis was used to identify all independent pQTLs in CD and UC separately, followed by a meta-analysis. Intestinal mucosal RNA sequencing and fecal metagenomic data were used for complementary analyses.


Thirty-four (34) proteins were differentially abundant between IBD and healthy individuals, of which 24 proteins independent of active inflammation. (Figure 1) Seventy-two (72) proteins were significantly associated to 14 phenotypic factors, including age, sex, medication use, and surgical history. (Figure 2) Fibroblast growth factor-19 (FGF-19) levels were decreased in CD patients with ileal disease or a history of ileocecal resection. Thirteen (13) novel cis-pQTL variants were identified and 10 replicated from previous studies, together affecting 21 different plasma proteins. One trans-pQTL variant of the FUT2 gene (rs602662) and two independent cis-pQTL variants of the CCL25 gene significantly affected plasma C-C motif chemokine ligand 25 (CCL25) levels. (Figure 3) Intestinal gene expression data revealed an overlapping cis-expression (e)QTL-variant (rs3745387) of the CCL25 gene. The FUT2 rs602662 trans-pQTL variant associated significantly with reduced abundances of multiple fecal butyrate-producing bacteria, including the genus Blautia and the species Faecalibacterium prausnitzii.


This study shows that both genotype and multiple disease phenotypes strongly associate with the plasma proteome in patients with IBD and identifies disease-associated pathways that may help to improve disease management in the future.