Inflammatory Bowel Disease Genes Research Articles

Exploring Microbial Metabolite Receptors in Inflammatory Bowel Disease: An In Silico Analysis of Their Potential Role in Inflammation and Fibrosis

Metabolites produced by dysbiotic intestinal microbiota can influence disease pathophysiology by participating in ligand–receptor interactions. Our aim was to investigate the differential expression of metabolite receptor (MR) genes between inflammatory bowel disease (IBD), healthy individuals (HIs), and disease controls in order to identify possible interactions with inflammatory and fibrotic pathways in the intestine. RNA-sequencing datasets containing 643 Crohn’s disease (CD) patients, 467 ulcerative colitis (UC) patients and 295 HIs, and 4 Campylobacter jejuni-infected individuals were retrieved from the Sequence Read Archive, and differential expression was performed using the RaNA-seq online platform. The identified differentially expressed MR genes were used for correlation analysis with up- and downregulated genes in IBD, as well as functional enrichment analysis using a R based pipeline. Overall, 15 MR genes exhibited dysregulated expression in IBD. In inflamed CD, the hydroxycarboxylic acid receptors 2 and 3 (HCAR2, HCAR3) were upregulated and were associated with the recruitment of innate immune cells, while, in the non-inflamed CD ileum, the cannabinoid receptor 1 (CNR1) and the sphingosine-1-phospate receptor 4 (S1PR4) were downregulated and were involved in the regulation of B-cell activation. In inflamed UC, the upregulated receptors HCAR2 and HCAR3 were more closely associated with the process of TH-17 cell differentiation, while the pregnane X receptor (NR1I2) and the transient receptor potential vanilloid 1 (TRPV1) were downregulated and were involved in epithelial barrier maintenance. Our results elucidate the landscape of metabolite receptor expression in IBD, highlighting associations with disease-related functions that could guide the development of new targeted therapies.

Autoimmune diseases in primary sclerosing cholangitis and their first-degree relatives.

Primary sclerosing cholangitis (PSC) is linked to inflammatory bowel disease (IBD). However, there is limited overlap between IBD and PSC risk genes, but a stronger association between PSC and other autoimmune conditions. We aimed to assess coexistence and familial association of autoimmune disorders in PSC, and the influence of autoimmune co-morbidity on severe outcomes. In a matched cohort study, 1,378 individuals with PSC and 13,549 general population comparators and their first-degree relatives were evaluated. National registries provided data on diagnoses and outcomes (liver transplantation, hepatobiliary cancer, liver related death). Odds ratio (OR) of autoimmune disease was estimated by logistic regression. Fine & Gray competing risk regression estimated hazard ratios (HRs) for severe outcomes. Prevalence of non-IBD, non-autoimmune hepatitis (AIH), autoimmune disease was 18% in PSC and 11% in comparators, OR 1.77(95%CI; 1.53-2.05). Highest odds were seen for celiac disease [OR 4.36(95%CI; 2.44-7.49)], sarcoidosis [OR 2.74(95%CI; 1.29-5.33)], diabetes type 1 [OR 2.91(95%CI; 2.05-4.05)], and autoimmune skin disease [OR 2.15(95%CI; 1.52-2.96)]. First-degree relatives of individuals with PSC had higher odds for developing IBD, AIH and any autoimmune disease than relatives of the comparators [OR 3.25 95% CI (2.68-3.91); OR 5.94 95% CI (2.82-12.02); OR 1.34 (95% CI: 1.19-1.50)]. Autoimmune co-morbidity in PSC was not associated with poorer outcome, HR 0.96 (95%CI; 0.71-1.28). Individuals with PSC and their first-degree relatives had higher odds for autoimmune disease compared to matched comparators. This finding provides validation for prior genetic discoveries at a phenotypic level. Autoimmune comorbidity did not impact severe outcome.

Crosstalk between alternative splicing and inflammatory bowel disease: Basic mechanisms, biotechnological progresses and future perspectives.

Alternative splicing (AS) is an omnipresent regulatory mechanism of gene expression that enables the generation of diverse splice isoforms from a single gene. Recently, AS events have gained considerable momentum in the pathogenesis of inflammatory bowel disease (IBD). Our review has summarized the complex process of RNA splicing, and firstly highlighted the potential involved molecules that target aberrant splicing events in IBD. The quantitative transcriptome analyses such as microarrays, next-generation sequencing (NGS) for AS events in IBD have been also discussed. Available evidence suggests that some abnormal splicing RNAs can lead to multiple intestinal disorders during the onset of IBD as well as the progression to colitis-associated cancer (CAC), including gut microbiota perturbations, intestinal barrier dysfunctions, innate/adaptive immune dysregulations, pro-fibrosis activation and some other risk factors. Moreover, current data show that the advanced technologies, including microarrays and NGS, have been pioneeringly employed to screen the AS candidates and elucidate the potential regulatory mechanisms of IBD. Besides, other biotechnological progresses such as the applications of third-generation sequencing (TGS), single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), will be desired with great expectations. To our knowledge, the current review is the first one to evaluate the potential regulatory mechanisms of AS events in IBD. The expanding list of aberrantly spliced genes in IBD along with the developed technologies provide us new clues to how IBD develops, and how these important AS events can be explored for future treatment.

CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis

This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA’s gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.

Supervised machine learning classifies inflammatory bowel disease patients by subtype using whole exome sequencing data.

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder with two main subtypes: Crohn's disease (CD) and Ulcerative Colitis (UC). Prompt subtype diagnosis enables the correct treatment to be administered. Using genomic data, we aimed to assess machine learning (ML) to classify patients according to IBD subtype. Whole exome sequencing from paediatric/adult IBD patients was processed using an in-house bioinformatics pipeline. This data was condensed into the per-gene, per-individual genomic burden score, GenePy. Data was split into training and testing datasets (80/20). Feature selection with a linear support vector classifier, and hyperparameter tuning with Bayesian Optimisation was performed (training data). The supervised ML method random forest was utilised to classify patients as CD or UC using three panels: I) all available genes, 2) autoimmune genes, 3) 'IBD' genes. ML results were assessed using AUROC, sensitivity and specificity on the testing dataset. 906 patients were included in analysis (600 CD, 306 UC). Training data included 488 patients, balanced according to the minority class of UC. The autoimmune gene panel generated the best performing ML model (AUROC=0.68), outperforming an IBD gene panel (AUROC =0.61). NOD2 was the top gene for discriminating CD and UC, regardless of the gene panel used. Lack of variation in genes with high GenePy scores in CD patients was the best classifier of a diagnosis of UC. We demonstrate promising classification of patients by subtype utilising random forest and WES data. Focussing on specific subgroups of patients, with larger datasets may result in better classification.

Intestinal Epithelial Cell PTPN2 Restricts Intestinal Permeability and Tight-Junction Remodelling Caused by Adherent-invasive E. coli in Mice

Background: Alterations in epithelial tight junction proteins can compromise the ability of the intestinal mucosa to act as a barrier between luminal contents and underlying tissues. The resulting increase in intestinal permeability can give rise to conditions such as inflammatory bowel disease (IBD). Additionally, expansion of pathobionts, such as adherent-invasive Escherichia coli (AIEC), are associated with IBD. Mice deficient in the IBD gene candidate, Ptpn2, exhibit increased intestinal permeability and a pronounced expansion of a novel murine AIEC ( mAIEC). This study aimed to investigate how PTPN2 expression in intestinal epithelial cells protects intestinal barrier properties after mAIEC infection. Methods: Tamoxifen-inducible, intestinal epithelial cell (IEC)-specific knockout mice ( Ptpn2 ΔIEC ) and control littermates ( Ptpn2 fl/fl ) were infected with either PBS, non-invasive E. coli K12, or mcherry-tagged mAIEC ( mAIEC red ). FITC-Dextran (FD4) and Rhodamine-Dextran (RD70) permeability probes were administered by oral-gavage and serum collected after 5hrs. Results: Ptpn2 ΔIEC mice exhibited intestinal region-specific higher mAIEC red - but not K12 - bacterial load compared to Ptpn2 fl/fl mice ( P=0.038). E. coli K12 increased FD4 but not RD70 permeability in Ptpn2 ΔIEC mice compared with Ptpn2 fl/fl mice ( P=0.0025). mAIEC red also had no effect on RD70, but caused an even greater increase in FD4 permeability in Ptpn2 ΔIEC vs. Ptpn2 fl/fl mice ( P< 0.0001). Ptpn2 fl/fl mice infected with mAIEC red also exhibited increased FD4 permeability compared to PBS-treated littermates ( P =0.0210). To identify if increased FD4 permeability was due to changes in expression of relevant tight-junction proteins, we performed western blot analysis on isolated IECs. Ptpn2 ΔIEC + mAIEC red mice had decreased expression of occludin ( P=0.0030) and the adherens junction protein, E-cadherin ( P=0.0142). Expression of the cation pore, claudin-2, was increased in PBS and K12-infected Ptpn2 ΔIEC vs. Ptpn2 fl/fl mice ( P=0.015). Interestingly, mAIEC red increased claudin-2 expression in Ptpn2 fl/fl mice compared to PBS controls ( P=0.0105) however, Ptpn2 ΔIEC + mAIEC red mice exhibited decreased claudin-2 levels compared to Ptpn2 fl/fl + mAIEC red mice ( P=0.0436). Immunofluorescence staining of claudin-2 confirmed reduced claudin-2 in Ptpn2 ΔIEC + mAIEC red mice. Furthermore, we observed gaps in ZO-1 membrane localization in Ptpn2 ΔIEC mice treated with PBS and K12 but not in their Ptpn2 fl/fl controls. ZO-1 membrane localization was dramatically depleted in Ptpn2 ΔIEC + mAIEC red mice compared to the Ptpn2 fl/fl + mAIEC red controls. Conclusion: Intestinal epithelial PTPN2 exhibits a major role in maintaining intestinal homeostasis by preserving intestinal barrier function and the integrity of tight-junction protein localization. Given that loss of PTPN2 in vivo also provokes expansion of adherent-invasive E. coli, these studies indicate that PTPN2 is an important mediator of host-microbiota crosstalk. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Identifying high-impact variants and genes in exomes of Ashkenazi Jewish inflammatory bowel disease patients

Inflammatory bowel disease (IBD) is a group of chronic digestive tract inflammatory conditions whose genetic etiology is still poorly understood. The incidence of IBD is particularly high among Ashkenazi Jews. Here, we identify 8 novel and plausible IBD-causing genes from the exomes of 4453 genetically identified Ashkenazi Jewish IBD cases (1734) and controls (2719). Various biological pathway analyses are performed, along with bulk and single-cell RNA sequencing, to demonstrate the likely physiological relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of Ashkenazi Jewish adult IBD displays significant overlap with very early onset-IBD genetics. Moreover, by performing biobank phenome-wide analyses, we find that IBD genes have pleiotropic effects that involve other immune responses. Finally, we show that polygenic risk score analyses based on genome-wide high impact variants have high power to predict IBD susceptibility.

GUT MICROBIAL METABOLISM OF 5-ASA IS PROSPECTIVELY ASSOCIATED WITH TREATMENT FAILURE IN PATIENTS WITH IBD

Abstract BACKGROUND Variation in clinical response to 5-aminosalicylic acid (5-ASA) has been attributed in part to its inactivation by gut microbes. Recently, in the Inflammatory Bowel Disease (IBD) Multi’omics Database (IBDMDB), a multicenter year-long cohort of 100+ participants with IBD, we identified 12 gut microbial enzymes from two protein families that convert 5-ASA to N-acetyl 5-ASA, a compound that lacks anti-inflammatory effects. Within the IBDMDB, we then found that a subset of these enzymes was cross-sectionally linked with greater risk of treatment failure, defined by corticosteroid use. The aim of this study was to prospectively associate these drug-degrading gut microbial enzymes with treatment failure and to confirm in vitro conversion of 5-ASA by these enzymes. METHODS We examined the prospective association between gut microbial acetyltransferases with risk of 5-ASA treatment failure in the ongoing “Study of a Prospective Adult Research Cohort with IBD” (SPARC IBD). We included 208 participants who at study entry 1) gave a stool sample at baseline, 2) were on 5-ASA, and 3) were steroid-free. Fecal metagenomic data was processed by the same analysis pipeline (biobakery3) as in the IBDMDB. Exposure was defined identically as in the IBDMDB as metagenomic carriage of 3-4 drug-degrading acetyltransferases compared to 0-2 acetyltransferases. We calculated odds ratios (ORs) and 95% confidence intervals (CIs) of incident steroid use using multivariable generalized estimating equations, adjusting for age and sex. For biochemical characterization, the 12 enzymes identified in the IBDMDB were heterologously expressed by E. coli. A representative enzyme was selected from each protein family for purification, and then incubated with 5-ASA and acetyl CoA for 6 hr at 37C with 1 mM of each substrate and 50 μM enzyme. Using a custom LC–MS assay, we then detected N-acetyl 5-ASA production. RESULTS Over a median follow-up of 8 months, we identified 60 cases of corticosteroid use. Consistent with data from the IBDMDB, we found that metagenomic carriage of 3 or more microbial acetyltransferase genes in SPARC IBD (compared to 2 or fewer) was associated with treatment failure (OR 2.77, 95% CI 1.03-7.43). In a random effects meta-analysis of the two cohorts, we observed a three-fold increased risk of drug failure (OR 3.12, 95% CI 1.41-6.89) (Fig 1). In vitro biochemical experiments confirmed the ability of a thiolase and an acyl-CoA N-acetyltransferase to acetylate 5-ASA, generating product at levels consistent with >25% conversion (Fig 2). CONCLUSIONS We characterized two gut microbial protein families that are directly involved in 5-ASA metabolism and, in turn, are prospectively associated with 5-ASA treatment failure. These findings advance the possibility of microbiome-based personalized medicine for patients with IBD.

Trans-ancestry, Bayesian meta-analysis discovers 20 novel risk loci for inflammatory bowel disease in an African American, East Asian and European cohort.

Inflammatory bowel disease (IBD) is an immune-mediated chronic intestinal disorder with major phenotypes: ulcerative colitis (UC) and Crohn's disease (CD). Multiple studies have identified over 240 IBD susceptibility loci. However, most studies have centered on European (EUR) and East Asian (EAS) populations. The prevalence of IBD in non-EUR, including African Americans (AAs), has risen in recent years. Here we present the first attempt to identify loci in AAs using a trans-ancestry Bayesian approach (MANTRA) accounting for heterogeneity between diverse ancestries while allowing for the similarity between closely related populations. We meta-analyzed genome-wide association studies (GWAS) and Immunochip data from a 2015 EUR meta-analysis of 38 155 IBD cases and 48 485 controls and EAS Immunochip study of 2824 IBD cases and 3719 controls, and our recent AA IBD GWAS of 2345 cases and 5002 controls. Across the major IBD phenotypes, we found significant evidence for 92% of 205 loci lead SNPs from the 2015 meta-analysis, but also for three IBD loci only established in latter studies. We detected 20 novel loci, all containing immunity-related genes or genes with other evidence for IBD or immune-mediated disease relevance: PLEKHG5;TNFSFR25 (encoding death receptor 3, receptor for TNFSF15 gene product TL1A), XKR6, ELMO1, BC021024;PI4KB;PSMD4 and APLP1 for IBD; AUTS2, XKR6, OSER1, TET2;AK094561, BCAP29 and APLP1 for CD; and GABBR1;MOG, DQ570892, SPDEF;ILRUN, SMARCE1;CCR7;KRT222;KRT24;KRT25, ANKS1A;TCP11, IL7, LRRC18;WDFY4, XKR6 and TNFSF4 for UC. Our study highlights the value of combining low-powered genomic studies from understudied populations of diverse ancestral backgrounds together with a high-powered study to enable novel locus discovery, including potentially important therapeutic IBD gene targets.

Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases.

BackgroundGenome wide association studies (GWAS) have identified and validated more than 200 genomic loci associated with the inflammatory bowel disease (IBD), although for most the causal gene remains unknown. Given the importance of myeloid cells in IBD pathogenesis, the current study aimed to uncover the role of genes within IBD genetic loci that are endogenously expressed in this cell lineage.MethodsThe open reading frames (ORF) of 42 genes from IBD-associated loci were expressed via lentiviral transfer in the THP-1 model of human monocytes and the impact of each of these on the cell’s transcriptome was analyzed using a RNA sequencing-based approach. We used a combination of genetic and pharmacologic approaches to validate our findings in the THP-1 line with further validation in human induced pluripotent stem cell (hiPSC)-derived-monocytes.ResultsThis functional genomics screen provided evidence that genes in four IBD GWAS loci (PTGIR, ZBTB40, SLC39A11 and NFKB1) are involved in controlling S100A8 and S100A9 gene expression, which encode the two subunits of calprotectin (CP). We demonstrated that increasing PTGIR expression and/or stimulating PTGIR signaling resulted in increased CP expression in THP-1.This was further validated in hiPSC-derived monocytes. Conversely, knocking-down PTGIR endogenous expression and/or inhibiting PTGIR signaling led to decreased CP expression. These analyses were extended to the known IBD gene PTGER4, whereby its specific agonist also led to increased CP expression. Furthermore, we demonstrated that the PTGIR and PTGER4 mediated control of CP expression was dependent on signaling via adenylate cyclase and STAT3. Finally, we demonstrated that LPS-mediated increases in CP expression could be potentiated by agonists of PTGIR and PTGER4, and diminished by their antagonists.ConclusionOur results support a causal role for the PTGIR, PTGER4, ZBTB40, SLC39A11 and NFKB1 genes in IBD, with all five genes regulating the expression of CP in myeloid cells, as well as potential roles for the prostacyclin/prostaglandin biogenesis and signaling pathways in IBD susceptibility and pathogenesis.

Inhibition of TLR4 Suppresses the Inflammatory Response in Inflammatory Bowel Disease (IBD) by Modulating the PDK1-Induced Metabolism Reprogramming via a m6A-Denpendent Manner.

Objective To investigate the role of TLR4 and PDK1 genes in IBD. Methods The DSS mouse model was established by inducing BALB/C with 5% DSS solution. The behavior of DSS mice was detected, and the m6A modification was detected by m6A methylation chip. At the same time, the expressions of TLR and PDK1 were detected by fluorescence real-time quantitative PCR. Results The results showed that the model of dextran sodium sulfate colitis in mice was successful, and the colon membrane of mice had obvious naked eye inflammation. Through comparison, it was found that there were differences in m6A modification between the blank group and the model group, and compared with the blank group, the expression of PKD1 in DSS group was significantly reduced and the expression of TLR4 was significantly increased. Conclusion TLR4 inhibition inhibits the inflammatory response in inflammatory bowel disease (IBD) in a m6A-dependent manner by regulating PDK1-induced metabolic reprogramming.

Monogenic inflammatory bowel disease-genetic variants, functional mechanisms and personalised medicine in clinical practice.

Over 100 genes are associated with monogenic forms of inflammatory bowel disease(IBD). These genes affect the epithelial barrier function, innate and adaptive immunity in the intestine, and immune tolerance. We provide an overview of newly discovered monogenic IBD genes and illustrate how a recently proposed taxonomy model can integrate phenotypes and shared pathways. We discuss how functional understanding of genetic disorders and clinical genomics supports personalised medicine for patients with monogenic IBD.

OP11 Expanded genome-wide association study of Inflammatory Bowel Disease identifies 174 novel loci and directly implicates new genes in disease susceptibility

Abstract Background Genome-wide association studies (GWASs) have identified 243 loci associated with inflammatory bowel disease (IBD). However, the mapping of additional disease loci and causal variants is still limited by sample size. Larger GWAS can provide further insights into causal biology. Methods We performed a GWAS meta-analysis of 33 cohorts, totalling 54,439 IBD patients (N=30,574 with Crohn’s disease (CD), 21,193 with Ulcerative Colitis (UC)) and 37,054 European controls. Genotype imputation was undertaken using the TOPMed diverse population panel and association tests were performed using REGENIE. These results were meta-analysed with summary statistics from 4 additional studies, a Danish cohort, the UK Biobank, deCODE, and FinnGen, totalling 73,030 IBD patients and 1 million controls, Fig1. Results We identified 174 novel genome-wide significant signals (32 associated with CD, 36 with UC, 106 with IBD, Fig2). Of these, 79 are located >1Mb from any known GWAS loci. We also identified two new population specific genetic associations, Fig3. Six new loci contain genes implicated in monogenic syndromes that include colitis: CARMIL2, DOCK8, G6PC3, HPS4, NCF1, PIK3CD. Several new loci alter the expression of nearby genes, suggesting that aberrant expression of these genes underpins the association. For instance, a new variant associated with decreased risk of IBD increases the expression of VSIR in colon Fig4. VSIR knockout mice have increased expression of IL23 and develop chronic inflammation in multiple tissues. Fine-mapping analyses identified likely causal missense variants at three new loci. DOK2 (ORCD=1.3, 27p=2x10-12) encodes a protein expressed in macrophages and T cells. Loss of Dok2 in mice causes severe DSS-induced colitis with reduced IL17A and IL22 expression. The same variant has been recently associated with CD in a sequencing study. SHARPIN (ORCD=1.2, p=1x10-16) is part of the linear ubiquitin chain assembly complex that modulates activation of the NF-κB pathway. Loss-of-function (LOF) mutations in other proteins in the complex are associated with immunodeficiency and systemic autoinflammation. CARMIL2 (ORUC=1.2, p=1x10-10) is required for NF-κB signalling in both B and T cells. LOF mutations are associated with primary immunodeficiencies and paediatric forms of IBD. Conclusion The greatly expanded sample size in our latest GWAS meta-analysis has enabled the identification of low frequency variants with larger effects on IBD susceptibility than the more common variants typically identified by previous GWAS. 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.

Histopathological Features of Monogenic Inflammatory Bowel Disease: Subanalysis of Systematic Review

Recent advances in genomic technology, such as next-generation sequencing, have made it possible to diagnose patients with a monogenic form of inflammatory bowel disease (IBD) where rare genetic variants appear to be driving the disease process. IBD because of variants transmitted by Mendelian inheritance patterns is described as “monogenic” IBD, as opposed to classical IBD.1Nambu R. et al.Front Pediatr. 2021; 22: 618918Crossref Scopus (2) Google Scholar We have previously reported our findings of a systematic review of monogenic IBD cases, demonstrating that monogenic IBD diagnosis and management is a challenging but important clinical problem across many age groups.2Nambu R. et al.Clin Gastroenterol Hepatol. 2022; 20: e653-e663Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar Several studies have shown that the histopathological features of monogenic IBD in very early onset are different from those of classical IBD.3Parente P. et al.Adv Anat Pathol. 2022; 29: 71-80Crossref PubMed Scopus (3) Google Scholar,4Conrad M.A. et al.J Crohns Colitis. 2019; 13: 615-625Crossref PubMed Scopus (22) Google Scholar In this study, we comprehensively reviewed histopathological features of monogenic IBD as a subanalysis of our systematic review and specifically investigated the relationship between the characteristic histopathological findings and the respective monogenic disorders that cause IBD. From 750 cases in a systematic review, we extracted only those cases in which pathologic findings were mentioned in detail (Supplementary Methods). The 315 included cases with monogenic IBD came from a total of 180 articles (Figure A1A). The cohort included 202 males, 99 females, and 14 with gender not reported. Infantile onset IBD (with disease onset less than 2 years of age) was the most common group (n = 144, 45.7%). On the other hand, 9.5% of patients (n = 30) developed IBD after 18 years of age (Figure A1B). This group covered 54 of the 75 genes known to be associated with monogenic IBD. The most reported gene was CYBB, followed by XIAP, TTC7A, IL10RA, and HPS1 (Figure A1C). The characteristic histopathological findings reported in each case of monogenic IBD are as follows (Figure and Table A1). Characteristic granuloma was reported in 100 cases with a high frequency in chronic granulomatous disease (CGD; n = 40, 72.7%; CYBB, NCF1, NCF4), followed by XIAP deficiency (n = 16, 47.1%; XIAP), Hermansky-Pudlak syndrome (HPS; n = 14, 73.7%; HPS1, HPS4), and Niemann-Pick disease type C (NP-C; n = 7, 87.5%; NPC1). Eosinophilic infiltration was shown in 61 cases and was more frequent in Loeys-Dietz syndrome (n = 4, 80%; TGFBR1, TGFBR2) and TTC7A deficiency (n = 17, 54.8%). In CGD, eosinophilic infiltration was reported in large numbers of cases but not at a high rate (n = 10, 18.1%; CYBB, NCF4). Epithelial cell apoptosis was seen in 55 patients with the highest frequency in TTC7A deficiency (n = 30, 96.7%; TTC7A). In trichohepatoenteric syndrome (n = 5, 60%; SKIV2L, TTC37), Hoyeraal-Hreidarsson syndrome (n = 8, 50%; DKC1, RTEL1), and RIPK1 deficiency (n = 3, 50%; RIPK1), epithelial cell apoptosis was reported at a high rate, whereas in XIAP deficiency (n = 6, 17.6%; XIAP) and IPEX-like syndrome (n = 5, 23.8%; LRBA, IL21, CTLA4) epithelial cell apoptosis was reported in large numbers but not at a high rate. Villous blunting was described in 30 cases with IPEX being the most frequent (n = 4, 50%; FOXP3), followed by IPEX-like syndrome (n = 10, 47.6%; LRBA, CTLA4, MALT1, STAT3 GOF). Pigmented macrophages were reported in 37 cases with CGD (n = 30, 54.5%; CYBB, NCF1) and HPS (n = 7, 36.8%; HPS1, HPS4). In this study, we define the characteristic histopathological findings that have been reported for each case of monogenic IBD by gene. Specific pathological findings may be useful in predicting the existence of monogenic disorder causing IBD when combined with clinical course and the result of molecular tests. Although some review articles have summarized the pathologic features of monogenic IBD, this is the first study to comprehensively analyze all previous reports and to clarify the gene-by-gene distribution of each monogenic IBD gene. Characteristic granuloma can be seen in the classical IBD, as Rubio et al5Rubio C.A. et al.J Clin Pathol. 2007; 60: 1268-1272Crossref PubMed Scopus (50) Google Scholar showed that 53.8% of the pediatric patients with CD had granulomas. Conrad et al4Conrad M.A. et al.J Crohns Colitis. 2019; 13: 615-625Crossref PubMed Scopus (22) Google Scholar reported that granulomas are not seen more frequently in very early onset IBD compared with older-onset pediatric IBD. In considering that monogenic IBD is more prevalent under the age of 6 years, when granuloma is seen in younger-onset IBD, molecular diagnostic tests that can differentiate CGD and XIAP deficiency, may be considered. The presence of pigmented macrophages along with granuloma further might help identify CGD (or HPS). Eosinophil infiltration is a common finding in classical IBD but appears to be more related to disease activity than IBD subtype.6Sarin S.K. et al.Dig Dis Sci. 1987; 32: 363-367Crossref PubMed Scopus (65) Google Scholar Epithelial cell apoptosis and villous blunting are generally not seen in classical IBD, but now we can say this is also a finding that can increase suspicion of monogenic IBD.7Gomez A.J. et al.Arch Pathol Lab Med. 2016; 140: 570-577Crossref PubMed Scopus (11) Google Scholar,8Kammermeier J. et al.J Crohns Colitis. 2017; 11: 60-69Crossref PubMed Scopus (82) Google Scholar Villous blunting is rarely seen in Crohn's disease but is more commonly related to celiac disease or congenital diarrhea and enteropathy.9Pallav K. et al.Aliment Pharmacol Ther. 2012; 35: 380-390Crossref PubMed Scopus (69) Google Scholar The mechanism of villous blunting seen among monogenic IBDs is unclear, although it was frequently found in IPEX or IPEX-like syndrome, implying a potential role for regulatory T lymphocytes. Interleukin (IL) 10 and IL-10-receptor-associated colitis, which has the largest number of reports in monogenic IBD, had no characteristic pathologic findings.2Nambu R. et al.Clin Gastroenterol Hepatol. 2022; 20: e653-e663Abstract Full Text Full Text PDF PubMed Scopus (6) Google Scholar,10Glocker E.O. et al.N Engl J Med. 2009; 361: 2033-2045Crossref PubMed Scopus (1022) Google Scholar In addition, pathologic findings in many monogenic IBDs have simply not been reported or have been reported in very small numbers. Although the characteristic pathologic findings increase the suspicion of a specific monogenic IBD, they cannot be used to rule out the presence of a single genetic abnormality in the case. This study is limited mostly by the nature of systematic reviews. In most reports, negative findings are not described, and histopathology reporting is a non-standardized part of disease evaluation. This can lead to reporting bias. We excluded cases in which the pathologic findings were absent or vaguely described, again leading to potential bias for reporting of highly abnormal, rare findings. If a case was described ambiguously as IBD-like or acute chronic inflammation, the rates of characteristic findings reported in this study might have been overestimated. However, we have shown that certain histopathological findings are associated with some monogenic IBD diseases and can be used to support a suspicion of genetic abnormalities. However, there does not appear to be any pathognomonic or even highly specific histopathologic features that identify specific monogenic IBD diseases. For example, infants with typical pathologic features of CD should alert the clinician to IL-10R deficiency, and infants with atresia or stricturing disease and apoptosis should be screened for TTC7A deficiency. Further case reports and prospective observational studies are still required, but this study supports the need for early next-generation sequencing in patients where monogenic IBD and characteristic pathologic features. Download .docx (.43 MB) Help with docx files Supplemental Methods, Table A1 and Figure A1

An Integrated Taxonomy for Monogenic Inflammatory Bowel Disease

Monogenic forms of inflammatory bowel disease (IBD) illustrate the essential roles of individual genes in pathways and networks safeguarding immune tolerance and gut homeostasis. To build a taxonomy model, we assessed 165 disorders. Genes were prioritized based on penetrance of IBD and disease phenotypes were integrated with multi-omics datasets. Monogenic IBD genes were classified by (1) overlapping syndromic features, (2) response to hematopoietic stem cell transplantation, (3) bulk RNA-sequencing of 32 tissues, (4) single-cell RNA-sequencing of >50 cell subsets from the intestine of healthy individuals and patients with IBD (pediatric and adult), and (5) proteomes of 43 immune subsets. The model was validated by addition of newly identified monogenic IBD defects. As a proof-of-concept, we explore the intersection between immunometabolism and antimicrobial activity for a group of disorders (G6PC3/SLC37A4). Our quantitative integrated taxonomy defines the cellular landscape of monogenic IBD gene expression across 102 genes with high and moderate penetrance (81 in the model set and 21 genes in the validation set). We illustrate distinct cellular networks, highlight expression profiles across understudied cell types (e.g., CD8+ T cells, neutrophils, epithelial subsets, and endothelial cells) and define genotype-phenotype associations (perianal disease and defective antimicrobial activity). We illustrate processes and pathways shared across cellular compartments and phenotypic groups and highlight cellular immunometabolism with mammalian target of rapamycin activation as one of the converging pathways. There is an overlap of genes and enriched cell-specific expression between monogenic and polygenic IBD. Our taxonomy integrates genetic, clinical and multi-omic data; providing a basis for genomic diagnostics and testable hypotheses for disease functions and treatment responses.

Inflammatory Bowel Disease

Crohn disease (CD) and ulcerative colitis (UC) were often considered one disease until Charles Wells first differentiated the two in 1952. This review outlines the disease features and symptoms of CD and UC. Indeterminate colitis is described, as are the epidemiology, diagnostic testing, and etiology of inflammatory bowel disease (IBD). The role of genetics in the development of IBD is discussed as well as innate immunity, the adaptive immune system, and cytokine signaling. Drugs used in the medical management of IBD and the future of surgical treatment for IBD are described. Tables detail histologic features and symptoms of CD and UC; genetic and demographic risk factors for IBD; common IBD-associated genes, including those associated with epithelial barrier dysfunction, innate immunity, antigen presentation, T cell differentiation, cytokine production, and cell signaling; the medical treatment of IBD; 5-aminosalicylate derivatives and sites of action; advantages of genetic markers in predicting disease course; surgical application of personalized medicine; and surgically relevant IBD genes. Figures show the timeline of IBD, gross CD pathologic specimens, gross UC colectomy specimens, histologic slides of CD- and UC-affected colonic tissue, genetic and environmental factors contributing to IBD, genes involved in innate and adaptive immunity of CD, three components of the gene key to bacterial recognition, typical course of CD, treatment for a hospitalized UC patient, top-down versus bottom-up treatment of IBD, and the Kono-S procedure. This review contains 12 figures, 10 tables, and 242 references.

Loss of PTPN2 in Intestinal Epithelial Cells Increases Invasion of Human Intestinal Epithelial Cells and Intestinal Permeability in Mice by Adherent‐invasive E. coli

Background : Alterations in epithelial tight junction proteins can compromise its ability to act as a barrier between luminal contents and underlying tissues, thereby increasing intestinal permeability, an early event in inflammatory bowel disease (IBD). Additionally, shifts in the gut microbiota and expansion of pathobionts such as adherent-invasive Escherichia coli (AIEC) are associated with the pathogenesis of IBD. Mice deficient in expression of the IBD gene candidate, Ptpn2,exhibit increased intestinal permeability and a pronounced expansion of a novel murine adherent-invasive Escherichia coli (mAIEC). This study aimed to investigate how PTPN2 expression in intestinal epithelial cells modifies mAIEC invasiveness and host-barrier properties after infection using in vitro and in vivo models. Methods First, we generated a fluorescent-tagged mAIEC strain — mAIECred. Caco-2BBe intestinal epithelial cells (IEC), stably expressing either scrambled shRNA or shRNA against Ptpn2, were infected with mAIECred. Tamoxifen-inducible, intestinal epithelial cell-specific knockout mice (Ptpn2∆IEC) and control littermates (Ptpn2fl/fl) were infected with either PBS, E. coli K12 or mAIECred. FITC-Dextran (FD4) and Rhodamine-Dextran (RD70) permeability probes were administered by oral-gavage. Post-necropsy, bacterial colonies were enumerated from mouse tissues. Results First we tested if PTPN2 deficiency in human IEC altered mAIECred invasion. Immunofluorescence showed that PTPN2 knockdown (KD) IECs exhibited increased bacterial invasion compared to control IECs (n=3). To confirm our results in an in vivo model, we infected Ptpn2∆IEC mice with either E. coli K12 or mAIECred or administered PBS as vehicle control. E. coli K12 increased FD4 but not RD70 permeability in Ptpn2∆IEC mice compared with Ptpn2fl/fl mice (P=0.0025; n=5-9) while mAIECred caused an even greater increase in FD4 permeability in Ptpn2∆IEC vs. Ptpn2fl/fl mice (P< 0.0001; n=6-9). Ptpn2∆IEC mice also exhibited higher mAIECred - but not K12 - bacterial load in distal colon tissue compared to Ptpn2fl/fl mice (P=0.038; n=9-12). As FD4 permeability was increased in Ptpn2∆IEC mice infected with K12 and mAIECred, we wanted to determine if this corresponded with changes in expression of relevant tight junction proteins. Western blot analysis from isolated IEC's revealed Ptpn2∆IEC mice infected with mAIECred had decreased E-cadherin (P=0.0142; n=4) and Occludin (P=0.0030; n=4). Conversely, we observed increased Claudin-2 in PBS and K12-infected Ptpn2∆IEC vs. Ptpn2fl/fl mice (P=0.015; n=4). mAIECred increased Claudin-2 levels above control(s) to comparable levels in Ptpn2fl/fl and Ptpn2∆IEC mice (P= 0.025; n=4). Conclusion Intestinal epithelial PTPN2 is critical in maintaining intestinal homeostasis by restricting bacterial invasion and preserving intestinal barrier function. Given that loss of PTPN2 in vivo also provokes expansion of AIEC, these studies indicate that PTPN2 is an important mediator of host-microbiome crosstalk.

DNA Methylation Change Profiling of Colorectal Disease: Screening towards Clinical Use.

Colon cancer remains one of the leading causes of cancer-related deaths worldwide. Transformation of colon epithelial cells into invasive adenocarcinomas has been well known to be due to the accumulation of multiple genetic and epigenetic changes. In the past decade, the etiology of inflammatory bowel disease (IBD) which is characterized by chronic inflammation of the intestinal mucosa, was only partially explained by genetic studies providing susceptibility loci, but recently epigenetic studies have provided critical evidences affecting IBD pathogenesis. Over the past decade, A deep understanding of epigenetics along with technological advances have led to identifying numerous genes that are regulated by promoter DNA hypermethylation in colorectal diseases. Recent advances in our understanding of the role of DNA methylation in colorectal diseases could improve a multitude of powerful DNA methylation-based biomarkers, particularly for use as diagnosis, prognosis, and prediction for therapeutic approaches. This review focuses on the emerging potential for translational research of epigenetic alterations into clinical utility as molecular biomarkers. Moreover, this review discusses recent progress regarding the identification of unknown hypermethylated genes in colon cancers and IBD, as well as their possible role in clinical practice, which will have important clinical significance, particularly in the era of the personalized medicine.

DUSP16 IS A NOVEL IBD GENE IMPLICATED IN THE REGULATION OF DIFFERENTIATION AND HOMEOSTASIS OF INTESTINAL EPITHELIAL CELLS

Inflammatory bowel disease (IBD) are chronic inflammatory diseases including Crohn’s disease (CD) and ulcerative colitis (UC). More than 200 genomic regions have been identified and validated (association values (5x10-8) to be associated with CD, UC or IBD. These regions may contain multiple genes and the current challenge lies in identifying the causal gene in each of these. To address this problem, we performed a functional genomic screen of 145 genes from validated IBD loci, in a relevant intestinal epithelial cell model (HT-29). The results of this transcriptome-based screening revealed that the candidate IBD gene DUSP16 (a dual specificity phosphatase targeting MAP kinases (MAPKs) phosphorylation) as well as the known IBD gene KSR1 (a scaffold protein regulating the spatiotemporal activation of the ERK) regulate the expression of genes involved in intestinal differentiation and homeostasis. They induce, among others, the expression of the PIGR gene that encodes the polymeric immunoglobulin receptor. PIGR plays a role in transporting dimeric IgA molecules from the basolateral membrane of epithelial cells to the intestinal lumen, via transcytosis, where they play an essential role in protecting the epithelium against intestinal pathogens. Our hypothesis is that DUSP16 and KSR1 modulate the activity of MAPKs in intestinal epithelial cells to induce PIGR expression, thus participating in the maintenance of homeostasis of the intestinal barrier.

Molecular Genetic Architecture of Monogenic Pediatric IBD Differs from Complex Pediatric and Adult IBD.

Inflammatory bowel disease (IBD) manifests as a complex disease resulting from gene–environment interactions or as a monogenic disease resulting from deleterious mutations. While monogenic IBD is predominantly pediatric, only one-quarter of complex IBD is pediatric. In this study, we were the first to systematically compare genetic architecture between monogenic and complex pediatric and adult IBD on genetic and molecular pathway levels. Genes reported as causal for monogenic pediatric IBD and related syndromes and as risk factors for pediatric and adult complex IBD were analyzed using CytoScape and ClueGO software tools to elucidate significantly enriched Gene Ontology (GO) terms. Despite the small overlap (seven genes) between monogenic IBD genes (85) and complex IBD loci (240), GO analysis revealed several enriched GO terms shared between subgroups (13.9%). Terms Th17 cell differentiation and Jak/STAT signaling were enriched in both monogenic and complex IBD subgroups. However, primary immunodeficiency and B-cell receptor signaling pathway were specifically enriched only for pediatric subgroups, confirming existing clinical observations and experimental evidence of primary immunodeficiency in pediatric IBD patients. In addition, comparative analysis identified patients below 6 years of age to significantly differ from complex pediatric and adult IBD and could be considered a separate entity.