Genetics of IBD: the most relevant Genetics abstracts at ECCO’22

1. Discovering in depth gene functions in ileal cells in IBD

A novel approach: combined analyses of single-cell transcriptomes with IBD genetics!

OP14: M. Krzak and colleagues, from Sanger Institute, Genomics of Inflammation and Immunity, Hinxton, United Kingdom, conducted a laborious single-cell RNA-sequencing analysis of ileal biopsies obtained from 25 CD patients and 26 non-IBD controls. They differentiated and sequenced 49 different cell types and generated high-quality transcriptomes from well-preserved villus epithelial cells. They identified 797 unique genes differentially expressed between CD patients and controls, with notable expression differences in stem cell, secretory and enterocyte populations. And for the first time, genes involved in antigen presentation and interferon-gamma signalling were enriched among those most frequently dysregulated cell types. In a creative manner, Krzak and colleagues integrated results from the latest IBD GWAS into the cellular and transcriptome data and performed joint analyses. Their exciting findings showed that genes specifically expressed in Tregs, monocytes and IL10RA-negative monocyte-derived macrophages captured a significant fraction of disease heritability, strongly implicating these cell types in disease pathogenesis. Reassuringly, many confirmed IBD effector genes (from GWAS studies) were driving these enrichment signals, including NOD2, IL18RAP, IL23R, NCF4 and IL2RA. Further experiments are underway to validate this finding.

DOP08: In another complex genomic study, P. Sudhakar and colleagues, from TARGID, Leuven, Belgium, applied different supervised and unsupervised approaches (including differential expression, pathway-based data integration, latent factor-based models, regularised generalised canonical correlation analysis and co-expression networks) to interpret the differences in the gene expression of monocytes and CD4+ T cells obtained from 125 IBD (87 CD, 38 UC) patients with different disease locations based on the Montreal classification. Functional enrichment analyses were conducted. The regulatory relationships and therapeutic relevance information were retrieved from insilico open resources In addition, comparison was performed with single-cell and bulk-derived gene expression signatures from other auto-immune diseases. Sudhakar and colleagues identified highly variant disease location-associated genes in monocytes and CD4+ T cells which were known to be involved in IBD pathogenesis and/or intestinal inflammation. They found that the RAF-independent MAPK-activation pathway and the FOXO-mediated transcriptional pathway (downregulated in UC patients) in CD4+ T cells were over-represented among the features distinguishing ileal CD and UC patients. Interestingly, 12.5% of the disease location-associated co-expression modules were also annotated as IBD drug targets. Based on gene expression signatures from bulk and single-cell sources, the disease location-associated genes were found to be active in other auto-immune diseases such as rheumatoid arthritis, systemic sclerosis, Sjögren’s syndrome, type 1 diabetes and systemic lupus erythematosus, suggesting their role in mediating immune malfunctions. They concluded by stating that they had identified signalling pathways and transcription factors that could drive the expression differences observed in the circulating immune cells between ileal CD and UC patients.

Single-cell analysis combined with IBD genetics and/or disease sub phenotypes has generated strong evidence for a causal role of novel disease mechanisms that have therapeutic potential.

2. Discovering new IBD variants

Despite the identification of 250 genetic loci for IBD, the drive to explain missing heritability in IBD continues!

OP11: L. Fachal, from IBDGC, Wellcome Sanger Institute, Human Genetics, Hinxton, United Kingdom, expanded a previous IBDGC study and performed a meta-analysis of 33 cohorts totalling 54,439 IBD patients (30,574 CD and 21,193 UC) and 37,054 European controls. They identified 174 novel genome-wide significant signals (32 associated with CD, 36 with UC, 106 with IBD), of which 79 are located >1 Mb from any known GWAS loci, including two new population-specific loci. Interestingly, six new loci contain genes implicated in monogenic syndromes like colitis, including CARMIL2, DOCK8, G6PC3, HPS4, NCF1 and PIK3CD. DOK2 encodes a protein expressed in macrophages and T cells. Several new loci alter the expression of nearby genes, such as expression of VSIR in colon. Loss-of-function mutations in CARMIL2, which is involved in NF-κB signalling in both B and T cells, are associated with primary immunodeficiencies and paediatric forms of IBD. SHARPIN was the other Cd locus and is part of the linear ubiquitin chain assembly complex that modulates activation of the NF-κB pathway. Based on their findings, Fachal and colleagues proposed an interesting hypothesis that the biological overlap between Mendelian and complex forms of IBD is demonstrated by the discovery of common non-coding variants associated with complex forms of IBD that dysregulate the function of a Mendelian IBD gene.

3. Genetics and epigenomics factors in predicting drug response

Besides ongoing genetics studies, efforts are underway to identify epigenomics factors related not only to disease susceptibility but also, most interestingly, to treatment response.

OP29: V. Joustra and colleagues, from UMC-University of Amsterdam, the Netherlands, measured DNA methylation profiles and clinical and biochemical response prior to treatment and 22 weeks after treatment in 64 patients (discovery set: 16 responders/14 non-responders; validation set: 20/14). Through classification analysis at T1, they discriminated responders from non-responders with high predictive performance (25 CpGs, AUC 0.88). In patients in deep remission, they identified 23 CpGs with high predictive performance upon independent validation. Investigating the CpGs of interest implicated genes involved in endothelial cell–cell adhesion and integrin-dependent T-cell homing, corroborating vedolizumab’s mode of action. Encouragingly, they discovered two novel 25- and 23-feature panels of CpGs that accurately predict response or deep remission to vedolizumab, respectively. The EPIC-CD study is currently conducting similar analyses on infliximab, adalimumab and ustekinumab.

4. Modulation of gene function during RCTs: from functional signature to clinical endpoints!

OP30: B. Verstockt B, from University Hospitals Leuven & KU Leuven, Leuven, Belgium, aimed to provide mechanistic insights into downstream effects of upadacitinib (UPA) in the intestinal mucosa in UC patients. They by evaluatinged pharmacodynamic modulation of gene expression in colon biopsies and thereby linking molecular changes to clinical endpoints. They obtained rectosigmoid biopsies at baseline and 8 weeks after UPA treatment from a subset of UC patients who were included in the U-ACHIEVE Phase 2b trial (n=88: 15 placebo, 73 UPA). They showed that the expression of 695 gut genes was significantly modulated at week 8 compared with baseline levels and compared with the placebo set. Of these genes, ~70% (n=492) were downregulated and enriched in inflammatory pathways, including T- and B-cell effector responses, neutrophil-mediated immunity and leucocyte chemotaxis. Also, irrespective of directionality, most differentially expressed genes from baseline to week 8 in UPA-treated patients were associated with clinical response, and remission, and histological and endoscopic improvement. Modulation of genes associated with UC disease activity [OSM and S100A8/9 (calprotectin)], Th1 (TBX21, IFNG), Th2 (GATA3, IL5RA, IL13RA2), Th9 (SPI1), Th17 (IL17A, IL23A, IL21R), B-cell responses (BTK, CD40), barrier function (ESPN, VIL1, CLDN23, OCLN, MUC1/2/12/16/20) and wound repair (ANXA1/6/13, MMP7/9) were associated with clinical improvement at week 8. Clinical benefit mediated by UPA is associated with modulation of molecular biomarkers of UC disease activity, T helper cell differentiation, B cell-mediated responses, gut barrier function and wound healing.

DOP09: Q. Zhang and colleagues, from Cambridge University Hospitals, Cambridge, United Kingdom, studied phenotypic effects on drug efficacy and the shared genetic mechanism between disease susceptibility and drug efficacy, based on data from 32,199 patients in the UK IBD BioResource (combined with genome-wide genetic data for a subset of 11,536 individuals). Interestingly the known IBD risk variants showed little contribution to drug efficacy, while three genome-wide loci showed a significant association with drug efficacy; two of these loci were related to steroid response and one to thiopurines. Though a confirmatory study is currently underway, this study suggests that the genetic causes of drug efficacy and disease susceptibility are largely independent. These findings may provide opportunities for exploring the biology of drug efficacy and improving medication prioritisation in IBD patients.

Several other studies are underway to elucidate the transcriptomic factors associated with drug response in IBD (eP697) and drug immunogenicity (eP696).

I conclude my report by highlighting that while ongoing efforts are being made to link molecular signatures at the cellular level with treatment efficacy per disease sub-phenotype, clinical applicability in patient-tailored therapy is nowhere near as yet!