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Background 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. Methods 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. Results 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. Conclusion 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.

Background In inflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), CD4+ T cell-responses to unknown microbial antigens drive intestinal inflammation. Both hypo- or hyperactive anti-microbial innate immunity may underlie these pathogenic T-cell responses. Previously, IgG and T-cell responses to Lachnospiraceae flagellins were detected in spontaneously colitic mice with an innate immune defect and adult CD patients with complicated disease. However, whether these IgG responses occur in therapy-naïve pediatric patients and whether they relate to hypo- or hyperresponsiveness is unknown. We hypothesize that, at diagnosis, a subgroup of pediatric CD patients has elevated anti-Lachnospiraceae flagellin IgG and concomitant inflammatory flagellin-specific T-cell responses associating with insufficient anti-microbial innate immunity. Methods Plasma IgG reactivity to 20 flagellins from Lachnospiraceae that colonize mouse and human gut was measured in therapy-naïve pediatric IBD patients (CD n=49; UC n=16), non-IBD (n=12) and age-matched healthy controls (HC n=17). CD patients were divided in two groups: ‘flagellin-hi’ (elevated IgG to 11-20 flagellins) and ‘flagellin-lo’ (elevated IgG to 0-10 flagellins), whose immunological and clinical profiles were compared. Results The proportion of flagellin-hi patients was higher in CD (41%) compared to UC (6%), non-IBD (8%) and HC (6%). In CD patients, clinical disease activity score, CRP and ESR did not relate to flagellin reactivity. Compared to flagellin-lo patients, flagellin-hi patients had increased frequencies of inflammatory gut-homing (CD38+CD62Lneg) circulating CD4+ T cells. Crucially, flagellin-hi patients had high frequencies of circulating flagellin-specific CD4+ T cells. Although high anti-flagellin IgG reactivity associated with increased flagellin-specific- and gut-homing- T-cell frequencies in the circulation, it associated with very limited immune cell infiltration, epithelial damage and phosphorylated NFκB in colonic biopsies on histology. Moreover, the plasma concentration of EN-RAGE, a neutrophil-derived protein, was decreased in flagellin-hi compared -lo patients. Conclusion In sum, a subgroup of pediatric therapy-naïve CD patients has high IgG responses to Lachnospiraceae-derived flagellins. While these flagellin-hi patients have higher frequencies of circulating gut-homing and flagellin-specific CD4+ T cells, they have lower colonic histological disease activity and NFκB activation, possibly suggesting insufficient innate immune cell activation and/or infiltration. Together, our data raise the question whether the enhanced anti-Lachnospiraceae adaptive immune response in a subgroup of CD patients may be driven by insufficient local innate immunity.

Background Crohn’s disease (CD) is a chronic disease driven by inflammatory memory CD4+ T cells. Deciphering heterogeneity in underlying immune disease is required for predicting the individual patients’ disease course. We have shown that analysis of circulating CD38+ memory CD4+ T cells, which are enriched for gut-homing, identifies therapy-naïve pediatric CD patients with a more severe disease course. At diagnosis, these patients have increased frequencies of circulating CD38+ memory T cells that do not express TIGIT (TIGITneg). TIGIT (T-cell immunoreceptor with immunoglobulin and ITIM domains), is a coinhibitory receptor selectively induced on CD4+ T cells with a memory phenotype. In healthy controls, TIGIT+CD38+ memory T cells have an inhibitory function while TIGITnegCD38+ memory T cells are enriched in inflammatory cells. In our cohort of CD patients, circulating inflammatory TIGITnegCD38+ memory T cells had increased frequencies of pathogenic IFNγ +IL-17+-double-producing or Th1* cells. We hypothesize that in these severe CD patients, CD-related inflammatory cytokines selectively increase frequencies of Th1* TIGITnegCD38+ memory T cells. Methods We cultured peripheral blood memory CD4+ T cells from healthy individuals in vitro with TCR- and co-stimulation together with different cocktails of CD-related inflammatory cytokines during 72h. Results Of all cytokines tested, only cocktails containing IL-12p70 increased TIGITneg cell frequencies within gut-homing CD38+ memory T cells, but not CD38neg memory T cells that are enriched in skin-homing. As hypothesized, IL-12p70-stimulated cultures contained higher frequencies of Th1* cells, expressing both hallmark transcription factors T-bet and RORgt, in TIGITnegCD38+ T cells but not within TIGIT+CD38+ T cells. This selective IL-12p70 responsiveness in TIGITneg cells agreed with the higher expression of the IL-12 receptor b2 subunit in TIGITnegCD38+ compared to TIGIT+CD38+ memory T cells. These data argue that IL12p70 initiates reprogramming of the TIGITnegCD38+ memory T cells to the Th1* phenotype. To assess whether IL-12p70 causes expansion of TIGITnegCD38+ cells or downregulates TIGIT expression on TIGIT+CD38+ cells, we traced fluorescently-labelled TIGIT+ cells during culture. TIGIT+ cells did not downregulate TIGIT, indicating that IL-12p70 increased proliferation of TIGITnegCD38+ cells. Conclusion The finding that IL-12p70 drives expansion of TIGITnegCD38+ memory T cells with a pathogenic Th1* phenotype argues that this cytokine may enforce chronic inflammation in these severe CD patients. These analyses pave the way toward deciphering key actors involved in CD inflammation at an individual patient level, needed to tailor novel IL-12/IL-23 targeting therapeutic strategies.

Background Inflammatory bowel disease, comprising Crohn’s disease (CD) and ulcerative colitis (UC), is driven by aberrant host-microbial immune interactions. Disease heterogeneity and severity hamper effective treatment, thus new therapeutic strategies tailored to the patient’s underlying immune defect are required. In mice, upon epithelial barrier breach and microbiota driven inflammation, colonic intestinal epithelial cells increase Secretory Leukocyte Protease Inhibitor (SLPI) expression. SLPI can exert anti-microbial activity and inhibit NF-kB activation. Therefore, we hypothesized that SLPI expression is increased in the intestine of IBD patients and may differentiate a subgroup of patients with a distinctive underlying immune disease. Methods Intestinal biopsies and plasma from therapy-naive pediatric patients (age 6-18) with CD (n=41), UC (n=22) or IBD-negative controls (n=15) were collected. Intestinal SLPI protein was detected by immunohistochemistry (IHC), scored semi-quantitatively, and patients were dichotomized into ‘SLPI-high’ and ‘SLPI-low’ groups. RNA sequencing and quantitative PCR (qPCR) were performed. Plasma protein concentrations were assessed with Olink technology®. Results We observed increased SLPI mRNA and protein expression in intestinal tissue of CD and UC patients, compared to IBD-negative controls. Expression was the strongest in macroscopically inflamed tissue and more dominant in colon than in small intestinal ileum. Colonic SLPI expression was associated with endoscopic severity of inflammation, with histologic disease activity, and with clinical disease activity in CD and UC patients. Furthermore, high epithelial SLPI expression associated with abundant neutrophil infiltration and calprotectin expression. RNA-seq revealed that biopsies of SLPI-high patients had a signature of inflammatory neutrophilic inflammation including the genes OSM, IL-1B, and CXCL8, which have been associated with severe disease progression and resistance to anti-TNF treatment. Most notably, biopsies of SLPI-high patients had a signature of increased IL-17 signaling, which was supported by IHC detection of high frequencies of IL-17 producing cells in the paired biopsies and higher plasma concentrations of CCL20, MMP10 and IL-17A. Conclusion Together, these results demonstrate that intestinal SLPI expression identifies severe IBD patients with high intestinal SLPI expression and immune features of therapy resistance, who have increased IL-17A responses and subsequent neutrophilic inflammation compared to SLPI-low patients. As such, epithelial SLPI expression is a histological parameter that could support tailored treatment strategies in pediatric IBD patients at the time of diagnosis.

Background Early intervention with biologic therapy, especially with anti-Tumor Necrosis Factor-a, is very effective and now more commonly used to prevent disease progression and complications in Crohn’s disease (CD). However, a rational approach to decide which patient should be treated First-line Infliximab (FL-IFX) is lacking. In this study, using serum from a randomized control trial, we assessed how changes in immune profiles prior to therapy and after the first standardized induction treatment with either FL-IFX or conventional treatment (CONV) related to maintaining disease remission at week 52. Methods Serum samples from therapy naive moderate to severe CD patients from the TISKIDS study1 were used at time of diagnosis and at 10–14 weeks after induction therapy with FL-IFX (n=48) and CONV (n=43). FL-IFX consisted of 5 IFX infusions (5 mg/kg) combined with azathioprine (AZA) maintenance. CONV consisted of induction therapy with Exclusive Enteral Nutrition or oral prednisolone combined with AZA maintenance. Concentrations of 92 inflammatory proteins were determined with Olink Proteomics®. Significant differences in mean protein NPX after FDR adjustment with log2fold > 0.5 were considered meaningful. Results After 10–14 weeks of induction therapy, FL-IFX suppressed a larger number inflammatory proteins and induced stronger suppression compared to CONV. Of the 30 significantly modulated FL-IFX target proteins 18 were differentially regulated by FL-IFX only. Hierarchical clustering of patients based on their baseline profiles of the 30 IFX-modulated proteins revealed 2 patient clusters, a CD-hi cluster with significantly higher baseline clinical disease activity, CRP and blood neutrophil concentrations compared to the CD-lo cluster. The CD-hi cluster had an increased abundance of 23/30 proteins amongst which Oncostatin-M, TNFSF14, HGF and TGF-alpha compared to the CD-lo cluster (Figure 1A). Of the CD-lo patients treated with FL-IFX, 58% reached clinical disease remission without treatment escalation at week 52, while this was only 24% for CD-hi patients treated with FL-IFX. Only 20% of the CD-lo patients treated with CONV reached remission while this was only 6% for the CONV treated patients in the CD-hi group (Figure 1B). Strikingly, similar clustering using the immune profiles after 10–14 weeks induction therapy did not predict remission at week 52. Conclusion FL-IFX achieves stronger reduction and modulates more inflammatory serum immune protein concentrations than CONV. Stratification of patients according to profiles of IFX-modulated proteins prior to therapy identifies patients with a lower chance of reaching clinical remission without treatment escalation at week 52. Reference 1. Jongsma MME et al. Gut. 2020 Dec; DOI:10.1136/ PMID:33384335

Background Fatigue is a common and clinically challenging symptom in patients with inflammatory bowel diseases (IBD). While fatigue occurs most often in patients with active disease, up to 50% of patients with quiescent disease still report significant fatigue of unknown aetiology. Here, we aimed to investigate whether fatigue in patients with quiescent IBD is reflected by circulating inflammatory proteins, that in turn might reflect ongoing subclinical inflammation. Methods Ninety-two (92) different inflammation-related proteins were measured in plasma of 350 patients with quiescent IBD (188 Crohn’s disease [CD]; 162 ulcerative colitis [UC]). Quiescent IBD was defined as clinical (Harvey-Bradshaw Index [HBI] Results None of the analysed plasma proteins were differentially abundant between mildly (1st quartile, Q1) or severely (4th quartile, Q4) fatigued patients under a false discovery rate of 10%. Considering nominal significance (P Conclusion Fatigue in patients with IBD is not clearly reflected by distinct circulating inflammatory protein signatures, which suggests that subclinical immune activation as defined by the studied panel of inflammatory proteins could not be detected. Reduced shedding of the LIF-R protein could be related to fatigue in IBD through modification of the oncostatin-M (OSM) signaling pathway, or through induction of pro-inflammatory phenotypes of T-cells, macrophages, or neural cells. Future studies are warranted to investigate other proteomic or metabolic markers that may accurately reflect fatigue in quiescent IBD, which might represent alternative pathophysiological pathways.

Background Chronicity of inflammatory bowel disease (IBD) is driven by reactivation of inflammatory memory CD4+ T helper (Th) cells which activate an inflammatory cascade involving innate immune cells and structural intestinal tissue cells. Because of disease heterogeneity, novel treatment strategies tailored to more precisely target the patient’s individual immune defect are required to prevent disease reactivation. We hypothesize that analysis of changes in circulating inflammatory protein abundance combined with phenotyping of circulating Th cells allow to dissect underlying immune pathogenesis and aim to stratify pediatric IBD patients accordingly. Methods We performed plasma analysis of 92 inflammatory proteins in a cohort of pediatric IBD patients (CD: n=62; UC/IBD-U: n=20), patients with suspicion of IBD but negative diagnosis (n=13) and age-matched healthy controls (HC: n=30). Peripheral blood was obtained at diagnosis and after induction treatment (t=10–14 weeks). Plasma protein concentrations were assessed with Olink Proximity Extension Assay technology® and Th cells were analyzed with flow cytometry. Results Thirty-six plasma proteins discriminated pediatric IBD patients from HC. CD and UC/IBD-U patients shared increased abundance of 17 proteins amongst which interleukin-6 and oncostatin-M. Increased abundance of the Th1 cytokine interferon-γ was strictly associated with CD while Th17-associated interleukin-17A was significantly more abundant in UC/IBD-U. Hierarchical clustering of plasma protein profiles discriminated 2 clusters of UC patients with different clinical disease activity and disease extent. In CD, three patient clusters were identified. CD#3 patients had lower clinical disease activity, lower C-reactive protein and higher blood albumin concentrations, while clusters CD#1 and CD#2 had comparable clinical parameters. CD#1 patients had higher abundance of 14 proteins associated with neutrophil function and interferon-γ signaling while CD#2 patients had a marked increase in frequencies of activated (HLA-DR+) memory Th cells. The three CD clusters responded differently to therapy with CD#1 patients exhibiting more modulated proteins and greater fold changes, CD#2 patients showing intermediate modulation and CD#3 patients exhibiting only a few changes. Conclusion Combined plasma immune protein and circulating Th cell profiling combined with in depth clinical monitoring discriminates subgroups of pediatric IBD patients during active disease which differ in their response to induction therapy. Abbreviations: CD: Crohn’s disease; UC: ulcerative colitis; IBD-U: IBD-unclassified.

Background Crohn’s disease (CD) and ulcerative colitis (UC) are characterized by intestinal infiltration of pathogenic effector CD4+ T cells. The defects driving loss of T-cell regulation vary between patients and remain undefined. Previously, we have shown that in human intestine, 20–40% of effector (CD62LnegCD4+) T cells express TIGIT (T cell immunoglobulin and ITIM domain), an inhibitory receptor modulating dendritic cell and T-cell function. TIGIT expression is enriched in circulating gut-homing CD38+ effector T cells in healthy controls while in a subgroup of IBD patients with active intestinal inflammation, frequencies of inhibitory TIGIT+CD38+ effector T cells are decreased and associated with earlier relapse of disease. Here we hypothesized that gut-homing effector T cells lacking TIGIT (TIGITneg) are pathogenic mediators of intestinal inflammation in IBD and assessed whether patients with low frequencies have a distinctive disease immunotype. Methods In the Rotterdam PIBD-SETQuality cohort of newly diagnosed pediatric IBD patients (CD: n=50; UC: n=25), patients with suspicion of IBD but negative diagnosis (n=17) and age-matched healthy controls (HC: n=22), we monitored TIGIT+ and TIGITnegCD38+ effector T cells in peripheral blood, collected plasma at diagnosis and during therapy and phenotyped intestinal T cells. Results At diagnosis, 50% of CD patients had strongly reduced frequencies of inhibitory TIGIT+CD38+ effector T cells compared to UC patients and HC. CD patients with reduced frequencies of inhibitory TIGIT+CD38+ effector T cells had higher plasma IFN-γ concentrations and 53% of them experienced a disease relapse by 1 year versus 25% for CD patients with normal TIGIT+CD38+effector frequencies. In keeping with our hypothesis that TIGITneg gut-homing effector T cells are pathogenic, absence of TIGIT expression identified CD38+ effector T cells enriched in recent proliferation and having high expression of chemokine receptors associated with inflammatory non-classical T helper-1 IFNγ highIL-17Alow producing (Th1*) cells. Moreover, intestinal TIGITnegCD4+ T cells of CD patients contained higher frequencies of IFNγ and IL-17A producing cells than TIGIT+CD4+ T cells. In order to identify the factors that drive differentiation of the pathogenic Th1* cells, inhibitory TIGIT+CD38+ effector T cells from HC were exposed to an array of IBD-associated cytokines in vitro. Only IL-12p70, a known driver of IFNγ, could convert inhibitory TIGIT+CD38+ effector T cells into their TIGITneg proinflammatory counterpart. Conclusion We identify TIGITneg gut-homing effector T cells, enriched in Th1* cells, as potential drivers of intestinal inflammation in a subgroup of CD, but not UC patients, with a more severe disease course.

Uncontrolled interferon γ (IFNγ)-mediated T-cell responses to commensal microbiota are a driver of inflammatory bowel disease (IBD). Interleukin-10 (IL-10) is crucial for controlling these T-cell responses, but the precise mechanism of inhibition remains unclear. A better understanding of how IL-10 exerts its suppressive function may allow identification of individuals with suboptimal IL-10 function among the heterogeneous population of IBD patients. Using cells from patients with an IL10RA deficiency or STAT3 mutations, we demonstrate that IL-10 signaling in monocyte-derived dendritic cells (moDCs), but not T cells, is essential for controlling IFNγ-secreting CD4+ T cells. Deficiency in IL-10 signaling dramatically increased IL-1β release by moDCs. IL-1β boosted IFNγ secretion by CD4+ T cells either directly or indirectly by stimulating moDCs to secrete IL-12. As predicted a signature of IL-10 dysfunction was observed in a subgroup of pediatric IBD patients having higher IL-1β expression in activated immune cells and macroscopically affected intestinal tissue. In agreement, reduced IL10RA expression was detected in peripheral blood mononuclear cells and a subgroup of pediatric IBD patients exhibited diminished IL-10 responsiveness. Our data unveil an important mechanism by which IL-10 controls IFNγ-secreting CD4+ T cells in humans and identifies IL-1β as a potential classifier for a subgroup of IBD patients.

Breach of tolerance to gluten leads to the chronic small intestinal enteropathy celiac disease. A key event in celiac disease development is gluten-dependent infiltration of activated cytotoxic intraepithelial lymphocytes (IELs), which cytolyze epithelial cells causing crypt hyperplasia and villous atrophy. The mechanisms leading to gluten-dependent small intestinal IEL infiltration and activation remain elusive. We have demonstrated that under homeostatic conditions in mice, gluten drives the differentiation of anti-inflammatory T cells producing large amounts of the immunosuppressive cytokine interleukin-10 (IL-10). Here we addressed whether this dominant IL-10 axis prevents gluten-dependent infiltration of activated cytotoxic IEL and subsequent small intestinal enteropathy. We demonstrate that IL-10 regulation prevents gluten-induced cytotoxic inflammatory IEL infiltration. In particular, IL-10 suppresses gluten-induced accumulation of a specialized population of cytotoxic CD4

The term oral (or mucosal) tolerance has been classically defined as the suppression of T- and B-cell responses to an antigen by prior administration of the antigen by the oral route. In recent years, it has become clear that both innate and acquired regulatory immune responses are essential for the development of oral tolerance. As such, mucosal microenvironmental factors such as transforming growth factor- β, prostaglandins but also dietary vitamin A create conditioning of an adaptive regulatory T-cell response that suppresses subsequent antigen-specific responses. Particular resident subsets of antigen presenting dendritic cells are pivotal to convey conditioning signals next to the presentation of antigen. This review discusses the primary mechanisms of adaptive regulatory T-cell induction to ingested soluble protein antigen. However, we also discuss the limitations of our knowledge with respect to understanding the very common food hypersensitivity Celiac disease caused by an aberrant adaptive immune response to the food protein gluten.

Mice with a secondary Listeria monocytogenes infection eliminate the bacteria much faster and more efficiently from their organs than mice with a primary infection. During the course of a secondary infection, serum concentrations of interferon-gamma (IFN-gamma) and tumour necrosis factor-alpha (TNF) are higher than during a primary infection. The aim of the present study was to determine whether these cytokines are involved in the acquired resistance to L. monocytogenes during a secondary infection in mice. In order to neutralize cytokines, alginate-encapsulated cells, which form anti-cytokine monoclonal antibodies, were injected into the nuchal region of mice during a Listeria infection. Mice recovered from a sublethal primary Listeria infection, which acquired cell-mediated immunity, received a subcutaneous injection of anti-IFN-gamma-forming cells, or anti-TNF-forming cells, and 4 days later received an intravenous injection with 10 50% lethal dose (LD50) L. monocytogenes. The number of bacteria recovered from the liver and spleen of immune mice treated with anti-IFN-gamma-forming cells was slightly larger (approximately 1 log10) than that found for immune mice treated with anti-beta-galactosidase-forming cells, called immune control mice. The organs of immune mice treated with anti-TNF-forming cells yielded significantly more (approximately 4 log10) bacteria than those of immune control mice, more than those of immune mice treated with anti-IFN-gamma-forming cells, and comparable numbers to those of non-immune mice. Taken together, these results demonstrate that TNF is essential in acquired resistance to L. monocytogenes during a secondary infection in mice, while IFN-gamma plays a minor role.