Innovate therapeutic targets for autoimmune diseases: insights from proteome-wide mendelian randomization and Bayesian colocalization

BACKGROUND

Despite growing knowledge regarding the pathogenesis of autoimmune diseases (ADs) onset, the current treatment remains unsatisfactory. This study aimed to identify innovative therapeutic targets for ADs through various analytical approaches.

RESEARCH DESIGN AND METHODS

Utilizing Mendelian randomization, Bayesian co-localization, phenotype scanning, and protein-protein interaction network, we explored potential therapeutic targets for 14 ADs and externally validated our preliminary findings.

RESULTS

This study identified 12 circulating proteins as potential therapeutic targets for six ADs. Specifically, IL12B was judged to be a risk factor for ankylosing spondylitis (p = 1.61E - 07). TYMP (p = 6.28E - 06) was identified as a protective factor for ulcerative colitis. For Crohn's disease, ERAP2 (p = 4.47E - 14), HP (p = 2.08E - 05), and RSPO3 (p = 6.52E - 07), were identified as facilitators, whereas FLRT3 (p = 3.42E - 07) had a protective effect. In rheumatoid arthritis, SWAP70 (p = 3.26E - 10), SIGLEC6 (p = 2.47E - 05), ISG15 (p = 3.69E - 05), and FCRL3 (p = 1.10E - 10) were identified as risk factors. B4GALT1 (p = 6.59E - 05) was associated with a lower risk of Type 1 diabetes (T1D). Interestingly, CTSH was identified as a protective factor for narcolepsy (p = 1.58E - 09) but a risk factor for T1D (p = 7.36E - 11), respectively. External validation supported the associations of eight of these proteins with three ADs.

CONCLUSIONS

Our integrated study identified 12 potential therapeutic targets for ADs and provided novel insights into future drug development for ADs.

Viruses and autophagy: bend, but don't break

Autophagy is a constitutive cellular process of degradation required to maintain homeostasis and turn over spent organelles and aggregated proteins. For some viruses, the process can be antiviral, degrading viral proteins or virions themselves. For many other viruses, the induction of the autophagic process provides a benefit and promotes viral replication. In this Review, we survey the roles that the autophagic pathway plays in the replication of viruses. Most viruses that benefit from autophagic induction block autophagic degradation, which is a 'bend, but don't break' strategy initiating but limiting a potentially antiviral response. In almost all cases, it is other effects of the redirected autophagic machinery that benefit these viruses. This rapid mechanism to generate small double-membraned vesicles can be usurped to shape membranes for viral genome replication and virion maturation. However, data suggest that autophagic maintenance of cellular homeostasis is crucial for the initiation of infection, as viruses have evolved to replicate in normal, healthy cells. Inhibition of autophagic degradation is important once infection has initiated. Although true degradative autophagy is probably a negative for most viruses, initiating nondegradative autophagic membranes benefits a wide variety of viruses.

Microbiota therapeutics for inflammatory bowel disease: the way forward

Microbiota therapeutics that transplant faecal material from healthy donors to people with mild-to-moderate ulcerative colitis have shown the potential to induce remission in about 30% of participants in small, phase 2 clinical trials. Despite this substantial achievement, the field needs to leverage the insights gained from these trials and progress towards phase 3 clinical trials and drug approval, while identifying the distinct clinical niche for this new therapeutic modality within inflammatory bowel disease (IBD) therapeutics. We describe the lessons that can be learned from past studies of microbiota therapeutics, from full spectrum donor stool to defined products manufactured in vitro. We explore the actionable insights these lessons provide on the design of near-term studies and future trajectories for the integration of microbiota therapeutics in the treatment of IBD. If successful, microbiota therapeutics will provide a powerful orthogonal approach (complementing or in combination with existing immunomodulatory drugs) to raise the therapeutic ceiling for the many non-responders and partial responders within the IBD patient population.

Associations of Eosinophilic Gastrointestinal Disorders with Other Gastrointestinal and Allergic Diseases

Eosinophilic gastrointestinal disorders (EGIDs) are becoming more common causing significant suffering and reduced quality of life. These conditions can affect different parts of the digestive system, either individually or in combination. Recognition of their link to allergic disorders or other gastrointestinal (GI) diseases has raised questions about their shared underlying mechanisms, which has had implications for diagnosis and management. The authors critically examine the current understanding of the connection between EGIDs and allergic conditions (ie, atopic dermatitis, allergic rhinitis, asthma, and food allergy) and GI diseases (ie, inflammatory bowel disease, celiac disease, gastroesophageal reflux disease, and motility disorders).

Approach to a Child with Chronic Diarrhea

Chronic diarrhea in children is challenging both with regards to etiological diagnosis and for management. Etiology and pathophysiological mechanisms vary widely from neonates to adolescents. Congenital or genetic causes are more frequent in neonates, while infections, allergy and immune-mediated mechanisms are more frequent in childhood. A thorough history and proper physical examination are required to decide for further diagnostic evaluation. The approach to a child with chronic diarrhea should be age specific and based predominantly on the pathophysiological mechanism involved. The nature of the stool like watery, bloody or fatty (steatorrhea) can suggest the probable etiology and organ system involved. After routine tests, evaluation with specific serological tests, imaging, endoscopy (gastroscopy/colonoscopy), histopathology of intestinal mucosa, breath tests or radionuclide imaging may be required to make a definitive diagnosis. Genetic evaluation is important in congenital diarrheas, monogenic inflammatory bowel disease (IBD) and immunodeficiency disorders. Management is aimed at stabilization, nutritional support and etiology specific treatment. Specific therapy can be as simple as exclusion of specific nutrient or as complicated as small bowel transplant. Evaluation and management require expertise and thus patients need to be referred in a timely fashion. This will minimise morbidity including nutritional consequences and improve outcome.

An update on dietary therapies in paediatric Crohn's disease

PURPOSE OF REVIEW

This article provides a literature update on original articles published in the past 18 months (May 2022-November 2023) in the dietary management of paediatric Crohn's disease.

RECENT FINDINGS

There is more data to support the use of exclusive enteral nutrition in the management of active Crohn's disease in children. Several food-based dietary therapies have been proposed for the management of Crohn's disease. There is an interest in precision nutritional therapy in Crohn's disease, but current data are scarce.

SUMMARY

Exclusive enteral nutrition is an effective treatment for paediatric Crohn's disease. Predictors of response to exclusive enteral nutrition include mild disease phenotype and ileal disease involvement, although data remain inconclusive. Adherence to exclusive enteral nutrition is cornerstone to its efficacy. Treatment with exclusive enteral nutrition modifies the gut microbiome, modulates bile acid metabolism and has significant effects on host immune responses. More studies are expected in which drugs need to be combined with dietary therapies and microbial therapeutics. The efficacy of Crohn's disease exclusion diet coupled with partial enteral nutrition is supported by independent studies, but tolerance remains an issue, particularly for long-term disease management. More research is anticipated in precision nutritional therapy in paediatric Crohn's disease, but currently no recommendations can be made.

Inflammatory Bowel Disease in Children

Inflammatory bowel disease is an important cause of chronic diarrhea in children, with a rising incidence, globally. The two main subtypes include Crohn's disease and ulcerative colitis. The clinical features are variable, and diagnosis requires initial first-line investigations followed by the involvement of specialist input for targeted imaging and endoscopy with biopsy, to confirm the diagnosis. Despite detailed investigation, inflammatory bowel disease may be clinically indistinguishable from chronic infections such as intestinal tuberculosis, and anti-tuberculosis treatment may be considered prior to further management considerations. The medical management of inflammatory bowel disease depends on subtype classification and severity, and may involve a step-wise approach to immunosuppressive therapies. In children, the consequences of poorly controlled disease are wide ranging, from psychosocial impacts and school non-attendance, to growth impairment and pubertal delay with subsequent impacts on bone health. In addition, an increased need for hospitalization and surgical intervention, and ultimately risk of cancer long-term. A multi-disciplinary team with expertise in inflammatory bowel disease is recommended to mitigate these risks and help to achieve the goal of sustained remission with endoscopic healing. This review focuses on updates on best clinical practice on the diagnosis and management of inflammatory bowel disease in children.

Gingerenone A Attenuates Ulcerative Colitis via Targeting IL-17RA to Inhibit Inflammation and Restore Intestinal Barrier Function

Ulcerative colitis (UC) is a complicated and recurrent intestinal disease. Currently available drugs for UC treatment are scarce, therefore, novel therapeutic drugs for the UC are urgently to be developed. Gingerenone A (GA) is a phenolic compound known for its anti-inflammatory effect, but its effect on UC remains unknown. Here, it is shown that GA protects mice against UC, which is closely associated with inhibiting intestinal mucosal inflammation and enhancing intestinal barrier integrity in vivo and in vitro. Of note, RNA sequencing analysis demonstrates an evident correlation with IL-17 signaling pathway after GA treatment, and this effect is further corroborated by Western blot. Mechanistically, GA directly interacts with IL-17RA protein through pull-down, surface plasmon resonance analysis and molecular dynamics simulation. Importantly, lentivirus-mediated IL-17RA/Act1 knock-down or GA co-treatment with brodalumab/ixekizumab significantly impairs the protective effects of GA against DSS-induced inflammation and barrier dysfunction, suggesting a critical role of IL-17RA signaling for GA-mediated protection against UC. Overall, these results indicate that GA is an effective agent against UC mainly through the direct binding of IL-17RA to inhibit inflammatory signaling activation.

Impaired reprogramming of the autophagy flux in maturing dendritic cells from crohn disease patients with core autophagy gene-related polymorphisms

Crohn disease (CD) is an inflammatory bowel disease whose pathogenesis involves inappropriate immune responses toward gut microbiota on genetically predisposed backgrounds. Notably, CD is associated with single-nucleotide polymorphisms affecting several genes involved in macroautophagy/autophagy, the catabolic process that ensures the degradation and recycling of cytosolic components and microorganisms. In a clinical translation perspective, monitoring the autophagic activity of CD patients will require some knowledge on the intrinsic functional status of autophagy. Here, we focused on monocyte-derived dendritic cells (DCs) to characterize the intrinsic quantitative features of the autophagy flux. Starting with DCs from healthy donors, we documented a reprogramming of the steady state flux during the transition from the immature to mature status: both the autophagosome pool size and the flux were diminished at the mature stage while the autophagosome turnover remained stable. At the cohort level, DCs from CD patients were comparable to control in term of autophagy flux reprogramming capacity. However, the homozygous presence of ATG16L1 rs2241880 A>G (T300A) and ULK1 rs12303764 (G/T) polymorphisms abolished the capacity of CD patient DCs to reprogram their autophagy flux during maturation. This effect was not seen in the case of CD patients heterozygous for these polymorphisms, revealing a gene dose dependency effect. In contrast, the NOD2 rs2066844 c.2104C>T (R702W) polymorphism did not alter the flux reprogramming capacity of DCs. The data, opening new clinical translation perspectives, indicate that polymorphisms affecting autophagy-related genes can differentially influence the capacity of DCs to reprogram their steady state autophagy flux when exposed to proinflammatory challenges.Abbreviation: BAFA1: bafilomycin A1, CD: Crohn disease; DC: dendritic cells; HD: healthy donor; iDCs: immature DCs; IL: interleukin; J: autophagosome flux; LPS: lipopolysaccharide; MHC: major histocompatibility complex; nA: autophagosome pool size; SNPs: single-nucleotide polymorphisms; PCA: principal component analysis; TLR: toll like receptor; τ: transition time; TNF: tumor necrosis factor.

Inflammatory bowel disease: recent developments

Paediatric-onset inflammatory bowel disease (IBD) is a complex and heterogenous condition. Incidence of disease in those aged <18 years has doubled over the last 25 years, with concurrent increased prevalence and no decrease in disease severity. The tools available at diagnosis for investigation have developed over the last 10 years, including better utilisation of faecal calprotectin, improved small bowel imaging and video capsule endoscopy. Alongside this, management options have increased and include biological and small molecule therapies targeting alternative pathways (such as interleukin 12/23, integrins and Janus kinase/signal transducers and activators of transcription, JAK-STAT pathways) and better understanding of therapeutic drug monitoring for more established agents, such as infliximab. Dietary manipulation remains an interesting but contentious topic.This review summarises some of the recent developments in the diagnosis, investigation and management of IBD in children and young people. IBD is increasingly recognised as a continuum of disease, with a proportion of patients presenting with classical Crohn's disease or ulcerative colitis phenotypes. Future implementation of personalisation and stratification strategies, including clinical and molecular biomarkers, implementation of predictors of response and outcome and use of additional therapies, will continue to require working within clinical networks and multiprofessional teams.

Vimentin filaments integrate low-complexity domains in a complex helical structure

Intermediate filaments (IFs) are integral components of the cytoskeleton. They provide cells with tissue-specific mechanical properties and are involved in numerous cellular processes. Due to their intricate architecture, a 3D structure of IFs has remained elusive. Here we use cryo-focused ion-beam milling, cryo-electron microscopy and tomography to obtain a 3D structure of vimentin IFs (VIFs). VIFs assemble into a modular, intertwined and flexible helical structure of 40 α-helices in cross-section, organized into five protofibrils. Surprisingly, the intrinsically disordered head domains form a fiber in the lumen of VIFs, while the intrinsically disordered tails form lateral connections between the protofibrils. Our findings demonstrate how protein domains of low sequence complexity can complement well-folded protein domains to construct a biopolymer with striking mechanical strength and stretchability.

Defining predictors of responsiveness to advanced therapies in Crohn's disease and ulcerative colitis: protocol for the IBD-RESPONSE and nested CD-metaRESPONSE prospective, multicentre, observational cohort study in precision medicine

INTRODUCTION

Characterised by chronic inflammation of the gastrointestinal tract, inflammatory bowel disease (IBD) symptoms including diarrhoea, abdominal pain and fatigue can significantly impact patient's quality of life. Therapeutic developments in the last 20 years have revolutionised treatment. However, clinical trials and real-world data show primary non-response rates up to 40%. A significant challenge is an inability to predict which treatment will benefit individual patients.Current understanding of IBD pathogenesis implicates complex interactions between host genetics and the gut microbiome. Most cohorts studying the gut microbiota to date have been underpowered, examined single treatments and produced heterogeneous results. Lack of cross-treatment comparisons and well-powered independent replication cohorts hampers the ability to infer real-world utility of predictive signatures.IBD-RESPONSE will use multi-omic data to create a predictive tool for treatment response. Future patient benefit may include development of biomarker-based treatment stratification or manipulation of intestinal microbial targets. IBD-RESPONSE and downstream studies have the potential to improve quality of life, reduce patient risk and reduce expenditure on ineffective treatments.

METHODS AND ANALYSIS

This prospective, multicentre, observational study will identify and validate a predictive model for response to advanced IBD therapies, incorporating gut microbiome, metabolome, single-cell transcriptome, human genome, dietary and clinical data. 1325 participants commencing advanced therapies will be recruited from ~40 UK sites. Data will be collected at baseline, week 14 and week 54. The primary outcome is week 14 clinical response. Secondary outcomes include clinical remission, loss of response in week 14 responders, corticosteroid-free response/remission, time to treatment escalation and change in patient-reported outcome measures.

ETHICS AND DISSEMINATION

Ethical approval was obtained from the Wales Research Ethics Committee 5 (ref: 21/WA/0228). Recruitment is ongoing. Following study completion, results will be submitted for publication in peer-reviewed journals and presented at scientific meetings. Publications will be summarised at www.ibd-response.co.uk.

TRIAL REGISTRATION NUMBER

ISRCTN96296121.

Formula modifications to the Crohn's disease exclusion diet do not impact therapy success in paediatric Crohn's disease

OBJECTIVES

The Crohn's disease exclusion diet (CDED) + partial enteral nutrition (PEN) is an emerging diet used to induce clinical remission in children with active Crohn's disease (CD). This study aims to determine the effectiveness of using the CDED+PEN to induce clinical remission in an Australian group of children with active CD using different PEN formulas and incorporating patient dietary requirements.

METHODS

We retrospectively collected data from children (both newly diagnosed and with existing CD while on therapy) with active CD (Paediatric Crohn's Disease Activity Index [PCDAI] ≥10) and biochemical evidence of active disease (elevated C-reactive protein [CRP], erythrocyte sedimentation rate [ESR] or faecal calprotectin [FC]) who completed at least phase 1 (6 weeks) of the CDED+PEN to induce clinical remission. Data were collected at baseline, Week 6 and Week 12. The primary endpoint was clinical remission at Week 6 defined as PCDAI < 10.

RESULTS

Twenty-four children were included in phase 1 analysis (mean age 13.8 ± 3.2 years). Clinical remission at Week 6 was achieved in 17/24 (70.8%) patients. Mean PCDAI, CRP, ESR and FC decreased significantly after 6 weeks (p < 0.05). Formula type (cow's milk based, rice based, soy based) did not affect treatment efficacy. A greater than 50% decrease in FC was achieved in 14/21 (66.7%) patients who completed phase 1 and 12/14 (85.7%) patients who completed phase 2 of the CDED+PEN.

CONCLUSIONS

Formula modifications to the CDED+PEN do not impact the expected treatment efficacy in Australian children with active luminal CD.

Enhancing prediction accuracy of coronary artery disease through machine learning-driven genomic variant selection

Machine learning (ML) methods are increasingly becoming crucial in genome-wide association studies for identifying key genetic variants or SNPs that statistical methods might overlook. Statistical methods predominantly identify SNPs with notable effect sizes by conducting association tests on individual genetic variants, one at a time, to determine their relationship with the target phenotype. These genetic variants are then used to create polygenic risk scores (PRSs), estimating an individual's genetic risk for complex diseases like cancer or cardiovascular disorders. Unlike traditional methods, ML algorithms can identify groups of low-risk genetic variants that improve prediction accuracy when combined in a mathematical model. However, the application of ML strategies requires addressing the feature selection challenge to prevent overfitting. Moreover, ensuring the ML model depends on a concise set of genomic variants enhances its clinical applicability, where testing is feasible for only a limited number of SNPs. In this study, we introduce a robust pipeline that applies ML algorithms in combination with feature selection (ML-FS algorithms), aimed at identifying the most significant genomic variants associated with the coronary artery disease (CAD) phenotype. The proposed computational approach was tested on individuals from the UK Biobank, differentiating between CAD and non-CAD individuals within this extensive cohort, and benchmarked against standard PRS-based methodologies like LDpred2 and Lassosum. Our strategy incorporates cross-validation to ensure a more robust evaluation of genomic variant-based prediction models. This method is commonly applied in machine learning strategies but has often been neglected in previous studies assessing the predictive performance of polygenic risk scores. Our results demonstrate that the ML-FS algorithm can identify panels with as few as 50 genetic markers that can achieve approximately 80% accuracy when used in combination with known risk factors. The modest increase in accuracy over PRS performances is noteworthy, especially considering that PRS models incorporate a substantially larger number of genetic variants. This extensive variant selection can pose practical challenges in clinical settings. Additionally, the proposed approach revealed novel CAD-genetic variant associations.

Shared genetic architecture between autoimmune disorders and B-cell acute lymphoblastic leukemia: insights from large-scale genome-wide cross-trait analysis

BACKGROUND

To study the shared genetic structure between autoimmune diseases and B-cell acute lymphoblastic leukemia (B-ALL) and identify the shared risk loci and genes and genetic mechanisms involved.

METHODS

Based on large-scale genome-wide association study (GWAS) summary-level data sets, we observed genetic overlaps between autoimmune diseases and B-ALL, and cross-trait pleiotropic analysis was performed to detect shared pleiotropic loci and genes. A series of functional annotation and tissue-specific analysis were performed to determine the influence of pleiotropic genes. The heritability enrichment analysis was used to detect crucial immune cells and tissues. Finally, bidirectional Mendelian randomization (MR) methods were utilized to investigate the casual associations.

RESULTS

Our research highlighted shared genetic mechanisms between seven autoimmune disorders and B-ALL. A total of 73 pleiotropic loci were identified at the genome-wide significance level (P < 5 × 10-8), 16 of which had strong evidence of colocalization. We demonstrated that several loci have been previously reported (e.g., 17q21) and discovered some novel loci (e.g., 10p12, 5p13). Further gene-level identified 194 unique pleiotropic genes, for example IKZF1, GATA3, IKZF3, GSDMB, and ORMDL3. Pathway analysis determined the key role of cellular response to cytokine stimulus, B cell activation, and JAK-STAT signaling pathways. SNP-level and gene-level tissue enrichment suggested that crucial role pleiotropic mechanisms involved in the spleen, whole blood, and EBV-transformed lymphocytes. Also, hyprcoloc and stratified LD score regression analyses revealed that B cells at different developmental stages may be involved in mechanisms shared between two different diseases. Finally, two-sample MR analysis determined causal effects of asthma and rheumatoid arthritis on B-ALL.

CONCLUSIONS

Our research proved shared genetic architecture between autoimmune disorders and B-ALL and shed light on the potential mechanism that might involve in.

Trans-eQTL mapping in gene sets identifies network effects of genetic variants

Nearly all trait-associated variants identified in genome-wide association studies (GWASs) are noncoding. The cis regulatory effects of these variants have been extensively characterized, but how they affect gene regulation in trans has been the subject of fewer studies because of the difficulty in detecting trans-expression quantitative loci (eQTLs). We developed trans-PCO for detecting trans effects of genetic variants on gene networks. Our simulations demonstrate that trans-PCO substantially outperforms existing trans-eQTL mapping methods. We applied trans-PCO to two gene expression datasets from whole blood, DGN (N = 913) and eQTLGen (N = 31,684), and identified 14,985 high-quality trans-eSNP-module pairs associated with 197 co-expression gene modules and biological processes. We performed colocalization analyses between GWAS loci of 46 complex traits and the trans-eQTLs. We demonstrated that the identified trans effects can help us understand how trait-associated variants affect gene regulatory networks and biological pathways.

Clinical effectiveness and safety of ustekinumab in youth with refractory inflammatory bowel disease: A retrospective cohort study

BACKGROUND

Inflammatory bowel disease (IBD) incidence and prevalence has been increasing worldwide. Limited data exists on the effectiveness of ustekinumab (UST) in children. We aimed to describe the effectiveness and safety of UST in pediatric patients with IBD.

METHODS

A single-center retrospective study was conducted between January 2017 and February 2022. The study included patients ≤16 years of age who were treated with UST and followed up for ≥1 year. Clinical remission was defined as a score of the Pediatric Crohn's Disease (CD) and Pediatric Ulcerative Colitis (UC) Activity Indices ≤10 at week 52.

RESULTS

Thirteen patients who had failed anti-tumor necrosis factor-α (anti-TNFα) therapy were included, eight (61.5%) with CD and five (38.5%) with UC. The median age was 13 years (interquartile range [IQR]: 11.5 to 14). UST treatment was initiated at a median age of 3 years (IQR: 2.3 to 7) after diagnosis. Ten patients (76.9%) achieved clinical remission. There were no statistically significant differences in characteristics between patients who achieved and did not achieve clinical remission. Biochemical remission (BioR) was achieved in six patients (46.2%). Body mass index (BMI) significantly improved, C-reactive protein (CRP) significantly decreased, and the need for corticosteroids significantly decreased in the remission group. Endoscopy conducted post-treatment in seven patients confirmed remission in six patients. Adverse events included two cases of infection and one of headache.

CONCLUSIONS

UST was effective as a secondary biologic therapy for the induction and maintenance of remission in patients with anti-TNFα refractory IBD. At one year, 84% of patients remained on UST with no severe adverse reactions reported.

Interferon Regulatory Factor 6 Determines Intestinal Epithelial Cell Development and Immunity

Intestinal epithelial cell (IEC) responses to interferon (IFN) favor antiviral defense with minimal cytotoxicity, but IEC-specific factors that regulate these responses remain poorly understood. Interferon regulatory factors (IRFs) are a family of nine related transcription factors, and IRF6 is preferentially expressed by epithelial cells, but its roles in IEC immunity are unknown. In this study, CRISPR screens found that Irf6 deficiency enhanced IFN-stimulated antiviral responses in transformed mouse IECs but not macrophages. Furthermore, KO ofIrf6in IEC organoids resulted in profound changes to homeostasis and immunity gene expression. Irf6 KO organoids grew more slowly, and single-cell RNA sequencing indicated reduced expression of genes in epithelial differentiation and immunity pathways. IFN-stimulated gene expression was also significantly different inIrf6KO organoids, with increased expression of stress and apoptosis-associated genes. Functionally, the transcriptional changes in Irf6 KO organoids were associated with increased cytotoxicity upon IFN treatment or inflammasome activation. These data indicate a previously unappreciated role for IRF6 in IEC biology, including regulation of epithelial development and moderation of innate immune responses to minimize cytotoxicity and maintain barrier function.

NOD2 and Crohn's Disease Clinical Practice: From Epidemiology to Diagnosis and Therapy, Rewired

Crohn's disease (CD) is a chronic inflammatory bowel disease with a multifactorial pathogenesis involving environmental and genetic factors. Since the late 20th century, the discovery of the first susceptibility gene (NOD2, previously referred to as CARD15) for CD has paved the way for further investigations into the correlations between clinical features and genetics, and its potential impact on clinical practice has fueled the research in the last 2 decades. Recent therapeutic advancements involving novel biologic drugs and small molecules have shifted inflammatory bowel disease management from a disease-centered to a patient-centric approach. To date, the role of NOD2 has not been fully understood yet. Recent data suggest that its clinical impact may be greater than currently recognized. This review overviews the most common NOD2 variants' role in real-life clinical practice. These genetic variants increase the risk of developing the disease and can aid in tailoring diagnosis and treatment. They are associated with the stricturing phenotype and ileal involvement and increase the risk of steroid refractoriness. In the meantime, limited and inconclusive evidence exists regarding their predictive role in response to azathioprine, biologic drugs, and small molecules. Eventually, their role in increasing the risk for surgery is evident, especially in those with the L1007fs variant. If further trials will support the initial evidence reported so far, NOD2 genetic variants will emerge as possible candidates for developing precision medicine in CD.

Intestinal Stromal Cells in the Turmoil of Inflammation and Defective Connective Tissue Remodeling in Inflammatory Bowel Disease

In steady state, intestinal subepithelial myofibroblasts form a thin layer below the basement membrane. Unlike the rest of the stromal cells in the lamina propria, they express tensile proteins, guide epithelial regeneration, and sense luminal microbiota. Upon inflammation in inflammatory bowel disease (IBD), they express activation markers, accept trophic signaling by infiltrating neutrophils and macrophages, and are activated by cytokines from helper T cells to produce a narrow spectrum of cytokines and a wider spectrum of chemokines, attract cells of innate and adaptive immunity, orchestrate inflammatory responses, and qualitatively and quantitatively modify the extracellular matrix. Thus, beyond being structural tissue components, they assume active roles in the pathogenesis of complicated IBD. Discrimination between myofibroblasts and fibroblasts may be an oversimplification in light of single-cell sequencing data unveiling the complexity of multiple phenotypes of stromal cells with distinct roles and plasticity. Spatial transcriptomics revealed distinct phenotypes by histologic localization and, more intriguingly, the assembly of mucosal neighborhoods that support spatially distinct functions. Current IBD treatments target inflammation but fail in fibrostenotic or fistulizing disease. Baseline and recent findings on stromal cells, molecules, and pathways involved in disrupted extracellular matrix homeostasis are reviewed to provide relevant pharmacologic targets.

Disruption of epithelium integrity by inflammation-associated fibroblasts through prostaglandin signaling

Inflammation-associated fibroblasts (IAFs) are associated with progression and drug resistance of chronic inflammatory diseases such as inflammatory bowel disease (IBD), but their direct impact on epithelial cells is unknown. Here, we developed an in vitro model whereby human colon fibroblasts are induced by specific cytokines and recapitulate key features of IAFs in vivo. When cocultured with patient-derived colon organoids (colonoids), IAFs induced rapid colonoid expansion and barrier disruption due to swelling and rupture of individual epithelial cells. Colonoids cocultured with IAFs also show increased DNA damage, mitotic errors, and proliferation arrest. These IAF-induced epithelial defects are mediated by a paracrine pathway involving prostaglandin E2 and its receptor EP4, leading to protein kinase A -dependent activation of the cystic fibrosis transmembrane conductance regulator. EP4-specific chemical inhibitors effectively prevented IAF-induced colonoid swelling and restored normal proliferation and genome stability. These findings reveal a mechanism by which IAFs could promote and perpetuate IBD and suggest a therapeutic avenue to mitigate inflammation-associated epithelial injury.

Shaping immunity: The influence of natural selection on population immune diversity

Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.

Higher incidence of paediatric inflammatory bowel disease by increasing latitude in Norway, but stable incidence by age

AIM

To examine possible geographical and temporal differences in the incidence of childhood-onset inflammatory bowel disease (IBD) in Norway, motivated by previous research indicating relevant environmental factors explaining changing epidemiology.

METHODS

We analysed data from children born in Norway from 2004 to 2012 (n = 541 036) in a registry-based nationwide study. After validating registry diagnoses against medical records, we defined IBD as ≥2 entries of International Classification of Diseases, 10th revision (ICD-10) codes K50, K51 and K52.3 in the Norwegian Patient registry. We estimated hazard ratios (HR) for IBD across four geographical regions with a south-to-north gradient and the incidence by period of birth.

RESULTS

By the end of follow-up on 31 December 2020, 799 IBD diagnoses were identified (Crohn's disease: n = 465; ulcerative colitis, n = 293, IBD: unclassified, n = 41). Compared to children in the southernmost region, there was almost a two-fold HR for IBD in children in the most Northern region (HR = 1.94, 95% Cl = 1.47-2.57; Mid region: HR = 1.68, 95% CI = 1.29-2.19, ptrend <0.001). These estimates remained largely unchanged after adjustment for potential confounding factors. The cohorts born in 2004-2006 and 2010-2012 had comparable cumulative incidences, with a slightly higher incidence for those born in 2007-2009.

CONCLUSION

We observed an increase in the risk of IBD by increasing latitude which may suggest that environmental factors influence the development of IBD, although non-causal explanations cannot be ruled out.

Patients with STAT1 Gain-of-function Mutations Display Increased Apoptosis which is Reversed by the JAK Inhibitor Ruxolitinib

INTRODUCTION

The signal transducer and activator of transcription (STAT1) gain-of-function (GOF) syndrome accounts for most cases of chronic mucocutaneous candidiasis but is characterized by a broader clinical phenotype that may include bacterial, viral, or invasive fungal infections, autoimmunity, autoinflammatory manifestations, vascular complications, or malignancies. The severity of lymphopenia may vary and influence the infectious morbidity.

METHODS

In our cohort of seven STAT1-GOF patients, we investigated the mechanisms that may determine T lymphopenia, we characterized the interferon gene signature (IGS) and analyzed the effect of ruxolitinib in reverting the immune dysregulation.

RESULTS

STAT1-GOF patients exhibited increased T lymphocyte apoptosis that was significantly augmented in both resting conditions and following stimulation with mitogens and IFNα, as evaluated by flow cytometry by Annexin V/ Propidium iodide assay. The JAK inhibitor ruxolitinib significantly reduced the IFNα-induced hyperphosphorylation of STAT1 and reverted the stimulation-induced T-cell apoptosis, in vitro. In two adult STAT1-GOF patients, the JAKinib treatment ameliorated chronic mucocutaneous candidiasis and lymphopenia. Most STAT1-GOF patients, particularly those who had autoimmunity, presented increased IGS that significantly decreased in the two patients during ruxolitinib treatment.

CONCLUSION

In STAT1-GOF patients, T lymphocyte apoptosis is increased, and T lymphopenia may determine higher risk of severe infections. The JAKinib target therapy should be evaluated to treat severe chronic candidiasis and lymphopenia, and to downregulate the IFNs in patients with autoinflammatory or autoimmune manifestations.

Probiotics for inflammatory bowel disease: Is there sufficient evidence?

Inflammatory bowel disease (IBD) refers to chronic inflammatory disorders of the gut. Ulcerative colitis (UC) and Crohn's disease (CD) are two subtypes of IBD. Evidence suggests that the intestinal microbiota plays a role in the pathogenesis of IBD, so probiotics have garnered a lot of interest as a potential treatment or prevention for IBD. However, clinical evidence of the efficacy of probiotics is still debatable. We performed a literature review. An advanced search considered clinical studies on probiotic for IBD from inception to 2023 in PubMed, Embase, Cochrane Library, and Web of Science. In the treatment of UC with probiotics, only Escherichia coli Nissle 1917 for maintenance treatment of UC in remission, and Bifidobacterium and VSL#3 for induction of remission in patients with mild to moderately active UC have shown strong evidence. Currently, there are no definitive conclusions regarding the effectiveness of probiotics in CD. The mechanism of probiotic treatment for IBD may be related to reducing oxidative stress, repairing the intestinal barrier, regulating intestinal flora balance, and modulating intestinal immune response. Differences in the benefits of probiotics between CD and UC may be attributable to the different lesion extent and immune-mediated pathophysiology. More robust randomized clinical trials are required to validate the efficacy and safety of diverse probiotic strains in IBD.

The association of cigarette smoking with DNA methylation and gene expression in human tissue samples

Cigarette smoking adversely affects many aspects of human health, and epigenetic responses to smoking may reflect mechanisms that mediate or defend against these effects. Prior studies of smoking and DNA methylation (DNAm), typically measured in leukocytes, have identified numerous smoking-associated regions (e.g., AHRR). To identify smoking-associated DNAm features in typically inaccessible tissues, we generated array-based DNAm data for 916 tissue samples from the GTEx (Genotype-Tissue Expression) project representing 9 tissue types (lung, colon, ovary, prostate, blood, breast, testis, kidney, and muscle). We identified 6,350 smoking-associated CpGs in lung tissue (n = 212) and 2,735 in colon tissue (n = 210), most not reported previously. For all 7 other tissue types (sample sizes 38-153), no clear associations were observed (false discovery rate 0.05), but some tissues showed enrichment for smoking-associated CpGs reported previously. For 1,646 loci (in lung) and 22 (in colon), smoking was associated with both DNAm and local gene expression. For loci detected in both lung and colon (e.g., AHRR, CYP1B1, CYP1A1), top CpGs often differed between tissues, but similar clusters of hyper- or hypomethylated CpGs were observed, with hypomethylation at regulatory elements corresponding to increased expression. For lung tissue, 17 hallmark gene sets were enriched for smoking-associated CpGs, including xenobiotic- and cancer-related gene sets. At least four smoking-associated regions in lung were impacted by lung methylation quantitative trait loci (QTLs) that co-localize with genome-wide association study (GWAS) signals for lung function (FEV1/FVC), suggesting epigenetic alterations can mediate the effects of smoking on lung health. Our multi-tissue approach has identified smoking-associated regions in disease-relevant tissues, including effects that are shared across tissue types.

Diagnosis and classification of portosystemic shunts: a machine learning retrospective case-control study

Diagnosis of portosystemic shunts (PSS) in dogs often requires multiple diagnostic tests, and available clinicopathologic tests have limitations in sensitivity and specificity. The objective of this study was to train and validate a machine learning model (MLM) that can accurately predict the presence of a PSS utilizing routinely collected demographic data and clinicopathologic features. Dogs diagnosed with PSS or control dogs tested for PSS but had the condition ruled out (non-PSS) were identified. Dogs were included if a complete blood count and serum chemistry panel were available from PSS diagnostic testing. Dogs with a PSS were subcategorized as having a single intrahepatic PSS, a single extrahepatic PSS, or multiple extrahepatic PSS. An extreme gradient boosting (XGboost) MLM was trained with data from 70% of the cases, and MLM performance was determined on the test set, comprising the remaining 30% of the case data. Two MLMs were created. The first was designed to predict the presence of any PSS (PSS MLM), and the second to predict the PSS subcategory (PSS SubCat MLM). The trained PSS MLM had a sensitivity of 94.3% (95% CI 90.1-96.8%) and specificity of 90.5% (95% CI 85.32-94.0%) for dogs in the test set. The area under the receiver operator characteristic curve (AUC) was 0.976 (95% CI; 0.964-0.989). The mean corpuscular hemoglobin, lymphocyte count, and serum globulin concentration were most important in prediction classification. The PSS SubCat MLM had an accuracy of 85.7% in determining the subtype of PSS of dogs in the test set, with variable sensitivity and specificity depending on PSS subtype. These MLMs have a high accuracy for diagnosing PSS; however, the prediction of PSS subclassification is less accurate. The MLMs can be used as a screening tool to increase or decrease the index of suspicion for PSS before confirmatory diagnostics such as advanced imaging are pursued.

Pre-Diagnosis Diet Predicts Response to Exclusive Enteral Nutrition and Correlates with Microbiome in Pediatric Crohn Disease

Exclusive enteral nutrition (EEN) is effective in inducing remission in pediatric Crohn disease (CD). EEN alters the intestinal microbiome, but precise mechanisms are unknown. We hypothesized that pre-diagnosis diet establishes a baseline gut microbiome, which then mediates response to EEN. We analyzed prospectively recorded food frequency questionnaires (FFQs) for pre-diagnosis dietary patterns. Fecal microbiota were sequenced (16SrRNA) at baseline and through an 18-month follow-up period. Dietary patterns, Mediterranean diet adherence, and stool microbiota were associated with EEN treatment outcomes, disease flare, need for anti-tumor necrosis factor (TNF)-α therapy, and long-term clinical outcomes. Ninety-eight patients were included. Baseline disease severity and microbiota were associated with diet. Four dietary patterns were identified by FFQs; a "mature diet" high in fruits, vegetables, and fish was linked to increased baseline microbial diversity, which was associated with fewer disease flares (p < 0.05) and a trend towards a delayed need for anti-TNF therapy (p = 0.086). Baseline stool microbial taxa were increased (Blautia and Faecalibacterium) or decreased (Ruminococcus gnavus group) with the mature diet compared to other diets. Surprisingly, a "pre-packaged" dietary pattern (rich in processed foods) was associated with delayed flares in males (p < 0.05). Long-term pre-diagnosis diet was associated with outcomes of EEN therapy in pediatric CD; diet-microbiota and microbiota-outcome associations may mediate this relationship.

Blood-testis barrier: a review on regulators in maintaining cell junction integrity between Sertoli cells

The blood-testis barrier (BTB) is formed adjacent to the seminiferous basement membrane. It is a distinct ultrastructure, partitioning testicular seminiferous epithelium into apical (adluminal) and basal compartments. It plays a vital role in developing and maturing spermatocytes into spermatozoa via reorganizing its structure. This enables the transportation of preleptotene spermatocytes across the BTB, from basal to adluminal compartments in the seminiferous tubules. Several bioactive peptides and biomolecules secreted by testicular cells regulate the BTB function and support spermatogenesis. These peptides activate various downstream signaling proteins and can also be the target themself, which could improve the diffusion of drugs across the BTB. The gap junction (GJ) and its coexisting junctions at the BTB maintain the immunological barrier integrity and can be the "gateway" during spermatocyte transition. These junctions are the possible route for toxicant entry, causing male reproductive dysfunction. Herein, we summarize the detailed mechanism of all the regulators playing an essential role in the maintenance of the BTB, which will help researchers to understand and find targets for drug delivery inside the testis.

Shared genetic basis and causality between schizophrenia and inflammatory bowel disease: evidence from a comprehensive genetic analysis

BACKGROUND

The comorbidity between schizophrenia (SCZ) and inflammatory bowel disease (IBD) observed in epidemiological studies is partially attributed to genetic overlap, but the magnitude of shared genetic components and the causality relationship between them remains unclear.

METHODS

By leveraging large-scale genome-wide association study (GWAS) summary statistics for SCZ, IBD, ulcerative colitis (UC), and Crohn's disease (CD), we conducted a comprehensive genetic pleiotropic analysis to uncover shared loci, genes, or biological processes between SCZ and each of IBD, UC, and CD, independently. Univariable and multivariable Mendelian randomization (MR) analyses were applied to assess the causality across these two disorders.

RESULTS

SCZ genetically correlated with IBD (rg = 0.14, p = 3.65 × 10−9), UC (rg = 0.15, p = 4.88 × 10−8), and CD (rg = 0.12, p = 2.27 × 10−6), all surpassed the Bonferroni correction. Cross-trait meta-analysis identified 64, 52, and 66 significantly independent loci associated with SCZ and IBD, UC, and CD, respectively. Follow-up gene-based analysis found 11 novel pleiotropic genes (KAT5, RABEP1, ELP5, CSNK1G1, etc) in all joint phenotypes. Co-expression and pathway enrichment analysis illustrated those novel genes were mainly involved in core immune-related signal transduction and cerebral disorder-related pathways. In univariable MR, genetic predisposition to SCZ was associated with an increased risk of IBD (OR 1.11, 95% CI 1.07–1.15, p = 1.85 × 10−6). Multivariable MR indicated a causal effect of genetic liability to SCZ on IBD risk independent of Actinobacteria (OR 1.11, 95% CI 1.06–1.16, p = 1.34 × 10−6) or BMI (OR 1.11, 95% CI 1.04–1.18, p = 1.84 × 10−3).

CONCLUSIONS

We confirmed a shared genetic basis, pleiotropic loci/genes, and causal relationship between SCZ and IBD, providing novel insights into the biological mechanism and therapeutic targets underlying these two disorders.

The association between tea consumption and non-malignant digestive system diseases: A Mendelian randomized study

BACKGROUND

Tea consumption might be closely related to non-malignant digestive diseases. Nevertheless, this correlation remains inadequately comprehended. Therefore, our objective was to elucidate the essence of these connections.

METHODS

This study employed a Mendelian randomization approach to investigate the impact of tea consumption on specific digestive disorders. Genetic data associated with tea consumption were obtained from the UK Biobank (UKB), encompassing 447,485 participants. We chose a gene-wide association study with no sample overlap and UKB as our data source for all outcomes. The primary analytical method utilized was inverse variance weighting, and multiple analytical models were employed to enhance the analysis's reliability and ensure robust results.

RESULT

Our investigation revealed that tea consumption was linked to an elevated susceptibility to gastroesophageal reflux disease (GERD). However, there was a lack of substantial evidence suggesting an association between tea intake and Crohn's disease (CD), ulcerative colitis (UC), or non-alcoholic fatty liver disease (NAFLD).

CONCLUSIONS

Our study suggests that the excessive consumption of tea may heighten the likelihood of GERD. These results hold potential significance in guiding dietary pattern modifications for individuals with GERD. Furthermore, there may be value in implementing GERD monitoring and preventive measures in populations with elevated tea consumption.

Mechanistic insight: Linking cardiovascular complications of inflammatory bowel disease

Cardiovascular diseases (CVD) are the leading cause of mortality worldwide despite an aggressive reduction of traditional cardiovascular risk factors. Underlying inflammatory conditions such as inflammatory bowel disease (IBD) increase the risk of developing CVD. A broad understanding of the underlying pathophysiological processes between IBD and CVD is required to treat and prevent cardiovascular events in patients with IBD. This review highlights the commonality between IBD and CVD, including dysregulated immune response, genetics, environmental risk factors, altered gut microbiome, stress, endothelial dysfunction and abnormalities, to shed light on an essential area of modern medicine.

ASSESSING THE CAUSAL RELATIONSHIP BETWEEN SEPSIS AND AUTOIMMUNE: A MENDELIAN RANDOMIZATION STUDY

ABSTRACT

Objective : Numerous epidemiological studies have identified a potential link between sepsis and a variety of autoimmune disorders. The primary objective of this study is to delve deeper into this connection, investigating the potential causal relationship between sepsis and autoimmune disorders through the application of Mendelian randomization (MR). Methods : To assess the potential genetic impact on sepsis risk relating to susceptibility toward immune-related outcomes, we used summary data from the largest European genome-wide association studies (GWAS) on these conditions using a two-sample MR framework. Single nucleotide polymorphisms-which had strong associations with the nine traits-were extracted from the GWAS and examined their effects in an extensive European sepsis GWAS (486,484 cases and 474,841 controls). We used inverse-variance weighted MR, weighted median, and MR Egger for analyses, supplementing these with sensitivity analyses and assessing level pleiotropy using MR methodologies. We also executed a reverse MR analysis to test sepsis' causal effects on the designated autoimmune traits. Results : With primary sclerosing cholangitis being the exception, our MR analysis suggests that susceptibility toward most autoimmune diseases does not affect sepsis risks. The reverse MR analysis did not validate any influence of sepsis susceptibility over other autoimmune diseases. Our primary inverse-variance weighted MR analysis outcomes found general confirmation through our sensitivity MR examinations. Variance in the exposures, as dictated by the single nucleotide polymorphism sets used as MR instruments, ranged between 4.88 × 10 -5 to 0.005. Conclusion : Our MR research, centered on a European population, does not validate a correlation between susceptibility to the majority of autoimmune disorders and sepsis risk. Associations discerned in epidemiological studies may owe partly to shared biological or environmental confounders. The risk susceptibility for primary sclerosing cholangitis does relate to sepsis risk, opening doors for personalized precision treatments in the future.

Multicenter registry of pediatric inflammatory bowel disease from a developing country

BACKGROUND

Despite the rising incidence of pediatric inflammatory bowel disease (PIBD) globally, multicenter collaborative studies of PIBD children among developing countries remain sparse. We therefore aimed to define the initial presentation and short-term outcomes of Thai children with PIBD from a multicenter registry.

METHODS

Four teaching hospitals participated in this study. A diagnosis of PIBD requires gastrointestinal endoscopy and histopathology in children aged < 19 years. Besides demographics, we collected clinical information and treatment with the data at 1-year follow up.

RESULTS

We included 35 Crohn's disease (CD), one IBD-unclassified, and 36 ulcerative colitis (UC) children (total n = 72 with 60.6% males). The mean age at diagnosis was 7.9 years (SD 4.1) with 38% being very early onset IBD (VEO-IBD). When compared with UC, the CD children were more likely to exhibit fever (42.3 vs. 13.9%), weight loss/failure to thrive (68.6 vs. 33.3%), and hypoalbuminemia (62.9 vs. 36.1%) but less likely to have bloody stools (51.4 vs. 91.7%) (all P < 0.05). No significant differences in demographics, clinical data and medications used with regards to VEO-IBD status. At 1 year after diagnosis (n = 62), 30.7% failed to enter clinical remission and 43.7% remained on systemic corticosteroids. Diarrhea (OR 9.32) and weight issues (OR 4.92) at presentation were independent predictors of failure to enter clinical remission; and females (OR 3.08) and CD (vs. UC) (OR 3.03) were predictors of corticosteroids use at 1-year follow-up.

CONCLUSIONS

A high proportion of VEOIBD is noted, and CD was more likely to present with significant inflammatory burden. Diarrhea and weight issues at presentation were independent predictors of failure to enter clinical remission; and females and CD (vs. UC) were predictors of corticosteroids use at 1-year follow-up.

Preventative and therapeutic potential of nutrition for inflammatory bowel diseases: A narrative review

Diet strongly shapes the gut microbiome and metabolome, which in turn influence intestinal inflammation in patients with inflammatory bowel disease (IBD). Separate from inflammation and malnutrition, diet's direct interactions with the gastrointestinal system can also provoke or attenuate a host of nonspecific gastrointestinal symptoms. Given these multifaceted effects of diet on inflammation and symptoms, nutrition has been investigated for its potential roles in the prevention and treatment of IBD. This review presents epidemiological, observational cohort, and clinical trial evidence that underlie our current understanding of nutrition for prevention and treatment of IBD.

Epithelial regulation of microbiota-immune cell dynamics

The mammalian gastrointestinal tract hosts a diverse community of trillions of microorganisms, collectively termed the microbiota, which play a fundamental role in regulating tissue physiology and immunity. Recent studies have sought to dissect the cellular and molecular mechanisms mediating communication between the microbiota and host immune system. Epithelial cells line the intestine and form an initial barrier separating the microbiota from underlying immune cells, and disruption of epithelial function has been associated with various conditions ranging from infection to inflammatory bowel diseases and cancer. From several studies, it is now clear that epithelial cells integrate signals from commensal microbes. Importantly, these non-hematopoietic cells also direct regulatory mechanisms that instruct the recruitment and function of microbiota-sensitive immune cells. In this review, we discuss the central role that has emerged for epithelial cells in orchestrating intestinal immunity and highlight epithelial pathways through which the microbiota can calibrate tissue-intrinsic immune responses.

Role of pH-sensing receptors in colitis

Low pH in the gut is associated with severe inflammation, fibrosis, and colorectal cancer (CRC) and is a hallmark of active inflammatory bowel disease (IBD). Subsequently, pH-sensing mechanisms are of interest for the understanding of IBD pathophysiology. Tissue hypoxia and acidosis-two contributing factors to disease pathophysiology-are linked to IBD, and understanding their interplay is highly relevant for the development of new therapeutic options. One member of the proton-sensing G protein-coupled receptor (GPCR) family, GPR65 (T-cell death-associated gene 8, TDAG8), was identified as a susceptibility gene for IBD in a large genome-wide association study. In response to acidic extracellular pH, GPR65 induces an anti-inflammatory response, whereas the two other proton-sensing receptors, GPR4 and GPR68 (ovarian cancer G protein-coupled receptor 1, OGR1), mediate pro-inflammatory responses. Here, we review the current knowledge on the role of these proton-sensing receptors in IBD and IBD-associated fibrosis and cancer, as well as colitis-associated cancer (CAC). We also describe emerging small molecule modulators of these receptors as therapeutic opportunities for the treatment of IBD.

Reverse-engineered exclusive enteral nutrition in pediatric Crohn's disease: A pilot trial

BACKGROUND

In pediatric Crohn's disease (CD), commercial formulas used as exclusive enteral nutrition (EEN) are effective at inducing remission. This study aims to assess the impact of a whole-food blended smoothie as EEN on CD activity and the intestinal microbiome.

METHODS

A 4-week prospective trial assessed the impact of EEN with a whole-food smoothie on newly diagnosed mild-to-moderate active pediatric CD. The smoothie with a multivitamin were developed to meet age-appropriate nutritional requirements. Assessment over 4 weeks included Pediatric Crohn's Disease Activity Index (PCDAI), serum laboratories, fecal calprotectin (FCP), and stool collection for metagenomic shotgun sequencing and microbiota composition analysis. Clinical remission was defined as PCDAI ≤ 10 at week 4.

RESULTS

Ten participants were enrolled with median age 14.5 years, and 8 completed the trial. Baseline mean PCDAI was 26.3 ± 9.1 and mean FCP 1149 ± 718 µg/g. At week 4, 80% of participants achieved clinical remission. FCP decreased by over half in 60% of participants, with FCP below 250 µg/g in 60% and below 100 µg/g in 40%. Microbiome analysis showed a significant increase in species richness over 4 weeks (p = 0.01). Compared to baseline, the relative abundance at week 2 and at week 4 was significantly increased for Bifidobacterium and Streptococcus and decreased for Blautia (p < 0.05 for all).

CONCLUSION

A whole-food blended smoothie was effective for inducing clinical remission and decreasing FCP in pediatric CD similar to commercial EEN formulas. Further research may give insight into data-driven whole-food dietary approaches for CD management.

CLINICALTRIALS

gov NCT03508193.

The role of goblet cells in Crohn' s disease

The prevalence of Crohn's disease (CD), a subtype of inflammatory bowel disease (IBD), is increasing worldwide. The pathogenesis of CD is hypothesized to be related to environmental, genetic, immunological, and bacterial factors. Current studies have indicated that intestinal epithelial cells, including columnar, Paneth, M, tuft, and goblet cells dysfunctions, are strongly associated with these pathogenic factors. In particular, goblet cells dysfunctions have been shown to be related to CD pathogenesis by direct or indirect ways, according to the emerging studies. The mucus barrier was established with the help of mucins secreted by goblet cells. Not only do the mucins mediate the mucus barrier permeability and bacterium selection, but also, they are closely linked with the endothelial reticulum stress during the synthesis process. Goblet cells also play a vital role in immune response. It was indicated that goblet cells take part in the antigen presentation and cytokines secretion process. Disrupted goblet cells related immune process were widely discovered in CD patients. Meanwhile, dysbiosis of commensal and pathogenic microbiota can induce myriad immune responses through mucus and goblet cell-associated antigen passage. Microbiome dysbiosis lead to inflammatory reaction against pathogenic bacteria and abnormal tolerogenic response. All these three pathways, including the loss of mucus barrier function, abnormal immune reaction, and microbiome dysbiosis, may have independent or cooperative effect on the CD pathogenesis. However, many of the specific mechanisms underlying these pathways remain unclear. Based on the current understandings of goblet cell's role in CD pathogenesis, substances including butyrate, PPARγagonist, Farnesoid X receptor agonist, nuclear factor-Kappa B, nitrate, cytokines mediators, dietary and nutrient therapies were all found to have potential therapeutic effects on CD by regulating the goblet cells mediated pathways. Several monoclonal antibodies already in use for the treatment of CD in the clinical settings were also found to have some goblet cells related therapeutic targets. In this review, we introduce the disease-related functions of goblet cells, their relationship with CD, their possible mechanisms, and current CD treatments targeting goblet cells.

Gut metabolome and microbiota signatures predict response to treatment with exclusive enteral nutrition in a prospective study in children with active Crohn's disease

BACKGROUND

Predicting response to exclusive enteral nutrition (EEN) in active Crohn's disease (CD) could lead to therapy personalization and pretreatment optimization.

OBJECTIVES

This study aimed to explore the ability of pretreatment parameters to predict fecal calprotectin (FCal) levels at EEN completion in a prospective study in children with CD.

METHODS

In children with active CD, clinical parameters, dietary intake, cytokines, inflammation-related blood proteomics, and diet-related metabolites, metabolomics and microbiota in feces, were measured before initiation of 8 wk of EEN. Prediction of FCal levels at EEN completion was performed using machine learning. Data are presented with medians (IQR).

RESULTS

Of 37 patients recruited, 15 responded (FCal < 250 μg/g) to EEN (responders) and 22 did not (nonresponders). Clinical and immunological parameters were not associated with response to EEN. Responders had lesser (μmol/g) butyrate [responders: 13.2 (8.63-18.4) compared with nonresponders: 22.3 (12.0-32.0); P = 0.03], acetate [responders: 49.9 (46.4-68.4) compared with nonresponders: 70.4 (57.0-95.5); P = 0.027], phenylacetate [responders: 0.175 (0.013-0.611) compared with nonresponders: 0.943 (0.438-1.35); P = 0.021], and a higher microbiota richness [315 (269-347) compared with nonresponders: 243 (205-297); P = 0.015] in feces than nonresponders. Responders consumed (portions/1000 kcal/d) more confectionery products [responders: 0.55 (0.38-0.72) compared with nonresponders: 0.19 (0.01-0.38); P = 0.045]. A multicomponent model using fecal parameters, dietary data, and clinical and immunological parameters predicted response to EEN with 78% accuracy (sensitivity: 80%; specificity: 77%; positive predictive value: 71%; negative predictive value: 85%). Higher taxon abundance from Ruminococcaceae, Lachnospiraceae, and Bacteroides and phenylacetate, butyrate, and acetate were the most influential variables in predicting lack of response to EEN.

CONCLUSIONS

We identify microbial signals and diet-related metabolites in feces, which could comprise targets for pretreatment optimization and personalized nutritional therapy in pediatric CD.

Clinical utility of C-reactive protein-to-albumin ratio in the management of patients with inflammatory bowel disease

Background and Aim

C-reactive protein (CRP)-to-albumin ratio (CAR) is a novel score with prognostic value in inflammatory conditions. This study assessed the performance of CAR as an objective marker of disease activity and prediction of subtherapeutic infliximab trough levels in patients with inflammatory bowel disease (IBD).

Methods

A retrospective study was conducted on three different patient cohorts with IBD: patients who had (i) fecal calprotectin (FC) measurements; (ii) Mayo Endoscopic Scores; and (iii) infliximab trough levels available. The relative performances of CAR, albumin, and CRP were compared in predicting disease activity (based on FC or Mayo Endoscopic Score) and infliximab trough levels.

Results

In both the FC (n = 289) and endoscopy (n = 65) cohorts, albumin and CAR correlated with objective disease activity. CAR (area under the curve [AUC] 0.70) was only marginally better at detecting active disease, measured by FC, compared to CRP (AUC 0.68). A CAR >0.15 was able to detect Mayo 3 disease (AUC 0.83, sensitivity 81%, specificity 89%). Albumin (r = 0.38) and CAR (r = -0.42) correlated with infliximab trough levels (n = 204). The optimal CAR for detecting subtherapeutic infliximab trough levels was >0.08 (AUC 0.70, sensitivity 66%, specificity 64%). Both albumin and CAR were independent predictors of subtherapeutic infliximab trough levels but correlated poorly with infliximab trough levels longitudinally in the same patient.

Conclusion

CAR was only a modest discriminator of subtherapeutic infliximab levels and offers little more than CRP in detecting active disease. CAR has potential to detect severe Mayo 3 disease and could be calculated in patients admitted with suspected acute severe ulcerative colitis.

Sialylated glycoproteins and sialyltransferases in digestive cancers: Mechanisms, diagnostic biomarkers, and therapeutic targets

Sialic acid (SA), as the ultimate epitope of polysaccharides, can act as a cap at the end of polysaccharide chains to prevent their overextension. Sialylation is the enzymatic process of transferring SA residues onto polysaccharides and is catalyzed by a group of enzymes known as sialyltransferases (SiaTs). It is noteworthy that the sialylation level of glycoproteins is significantly altered when digestive cancer occurs. And this alteration exhibits a close correlation with the progression of these cancers. In this review, from the perspective of altered SiaTs expression levels and changed glycoprotein sialylation patterns, we summarize the pathogenesis of gastric cancer (GC), colorectal cancer (CRC), pancreatic ductal adenocarcinoma (PDAC), and hepatocellular carcinoma (HCC). Furthermore, we propose potential early diagnostic biomarkers and prognostic indicators for different digestive cancers. Finally, we summarize the therapeutic value of sialylation in digestive system cancers.

Fragility index analysis for randomized controlled trials of approved biologicals and small molecule drugs in inflammatory bowel diseases

INTRODUCTION

Biologics and small molecules have been increasingly applied in Crohn's disease (CD) and ulcerative colitis (UC). But the robustness of their trials has not been evaluated.

METHODS

We initially collected all the approved biologics or small molecules for CD or UC up to December 1, 2022. Databases were then queried by keywords in chemical name and CD or UC. Randomized controlled trials (RCTs) in the two-arm, 1:1 design were included. Fragility index (FI) and fragility quotient (FQ) were subsequently calculated.

RESULTS

We included twenty-eight RCTs, including nine pivotal trials listed in approval labels, nineteen non-pivotal trials not included in the labels. The median sample size was 99 [IQR, 60-262] and the median number of loss-of-follow-up (LFU) was 14 [IQR, 8-43]. Pivotal trials in the labels had the median FI of 8 [IQR, 4-14, n = 6] that was marginally higher than non-pivotal trials (3 [IQR, 2-4], p = 0.08). The median FQ was 0.0330 [IQR, 0.1220-0.0466] and 0.0310 [IQR, 0.0129-0.0540] for pivotal and non-pivotal trials, respectively (p = 1.0). The sample size and FI were significantly correlated (Spearman correlation coefficient [r] = 0.56, 95 %CI 0.21-0.78, p = 0.003). The number of total events was also significantly correlated with FI (r = 0.53, 95 %CI 0.17-0.77, p = 0.006). Study p-values were significantly associated with FI (p = 0.01): trials with p-values < 0.001 had the highest median FI of 10 [IQR, 6-17]. No factor was found strongly correlated with FQ.

CONCLUSION

Results from trials assessing administration-approved biologics or small molecules for treating CD or UC were vulnerable to small changes by measuring FI or FQ. Pivotal studies contributing to regulatory approvals exhibited a relatively higher degree of resilience compared to non-pivotal trials.

Updates on the management of inflammatory bowel disease from periconception to pregnancy and lactation

Inflammatory bowel disease (IBD) affects reproductive planning due to psychological effects and mechanical problems related to surgery. Children of people with IBD have an increased risk of about 10% if one parent has IBD and up to 33% if both parents have IBD. The fertility of people with IBD is similar to the general population, but fertility might be reduced in individuals with active IBD, ileal pouch-anal anastomosis, or perianal Crohn's disease. Flaring disease during pregnancy increases complications, such as preterm birth. Thus, disease management with appropriate medications can optimise outcomes. As most medications have minimal fetal risks, people with IBD should be informed about the risks of stopping medications and the importance of maintaining remission. A period of disease remission is advisable before pregnancy and could reduce the risks for both the pregnant person and the fetus. Flexible endoscopy, intestinal ultrasound, and gadolinium-free magnetic resonance enterography are safe during pregnancy. We provide state-of-the-art knowledge on the basis of the latest evidence to ensure successful pregnancy outcomes in controlled IBD.

Epigenetic regulation of innate immune dynamics during inflammation

Innate immune cells play essential roles in modulating both immune defense and inflammation by expressing a diverse array of cytokines and inflammatory mediators, phagocytizing pathogens to promote immune clearance, and assisting with the adaptive immune processes through antigen presentation. Rudimentary innate immune "memory" states such as training, tolerance, and exhaustion develop based on the nature, strength, and duration of immune challenge, thereby enabling dynamic transcriptional reprogramming to alter present and future cell behavior. Underlying transcriptional reprogramming are broad changes to the epigenome, or chromatin alterations above the level of DNA sequence. These changes include direct modification of DNA through cytosine methylation as well as indirect modifications through alterations to histones that comprise the protein core of nucleosomes. In this review, we will discuss recent advances in our understanding of how these epigenetic changes influence the dynamic behavior of the innate immune system during both acute and chronic inflammation, as well as how stable changes to the epigenome result in long-term alterations of innate cell behavior related to pathophysiology.

Pediatric stricturing Crohn's disease

Crohn's disease (CD) is a chronic inflammatory disease of the digestive tract. The incidence of pediatric CD is increasing and is currently 2.5-11.4 per 100000 world-wide. Notably, approximately 25% of children with CD develop stricturing CD (SCD) that requires intervention. Symptomatic stricturing diseases refractory to pharmacological management frequently require non-pharmacological interventions. Non-pharmacological therapeutic strategies include endoscopic balloon dilatation, stricturoplasty, and surgical resection of the strictured segment. However, strictures tend to recur postoperatively regardless of treatment modality. The lifetime risk of surgery in patients with childhood SCD remains at 50%-90%. Thus, new and emerging strategies, advanced diagnostic tools, and minimally invasive approaches are under investigation to improve the outcomes and overall quality of life of pediatric patients with SCD.

Is There Evidence of Crohn's Disease Exclusion Diet (CDED) in Remission of Active Disease in Children and Adults? A Systematic Review

Crohn's disease (CD) is an inflammatory bowel disease. Previous research has explored the impact of diet on CD, as specific dietary components can influence gut microbiota and immune responses, contributing to damage in the gastrointestinal tract. The Crohn's Disease Exclusion Diet (CDED) is based on an exclusion diet; it is a recent dietary approach that is often used alongside partial enteral nutrition (PEN) and aims to induce disease remission by excluding certain dietary components. This study assesses the current evidence for the effectiveness of the CDED + PEN in achieving remission in both children and adults with active CD. Our systematic review followed PRISMA recommendations and was registered in PROSPERO with CRD number 42022335076. The searched databases were PubMed/MEDLINE, Cochrane Library, Scopus, and Web of Science. The included studies were analyzed using Rayyan software, and the risk of bias was assessed with Cochrane RevMan 5.0 software. The primary assessed outcome was clinical remission, evaluated with validated questionnaire scores such as PCDAI, CDAI, or HBI. All analyzed papers yielded promising results. Notably, the CDED + PEN demonstrated better tolerance than exclusive enteral nutrition (EEN), resulting in higher adherence rates. Therefore, the CDED + PEN appears to be a viable alternative for induction remission in active disease for both children and adults with CD.

Associations Between ABO Blood Groups and Diseases in the Digestive System and Vein

Purpose

The ABO blood type system is crucial for human blood transfusions. However, the relationships between ABO blood groups and diseases in the digestive system and vein have not been elucidated. We investigated the relationships between ABO blood groups and diseases in the digestive system and vein in this study.

Patients and Methods

A retrospective study on a Chinese population, including 1432 Crohn's disease (CD), 416 ulcerative colitis (UC), 1140 stomach cancer (SC), 841 colorectal cancer (CRC), 384 pancreatic cancer (PC), 520 liver cancer (LC), and 563 venous thrombosis (VT) patients, was performed. Furthermore, 896 healthy subjects were enrolled as normal controls (NC) in this study. The demographic characteristics of patients and NC were compared using the unpaired t-test and χ2 test. Multivariate logistic regression model was used to evaluate the association between ABO blood groups and CD and VT.

Results

ABO blood groups distributions in UC, SC, CRC, PC, and LC patients did not differ from that of NC, but CD and VT patients had significant difference of ABO blood group distribution from that of NC (p = 0.015 and p = 0.002, respectively). Patients with CD and VT had considerably lower rates of type O blood (p = 0.011 and p = 0.001, respectively) and significantly higher rates of type AB blood (p = 0.013 and p = 0.022, respectively) than those with NC. Multivariate logistic regression analysis showed the association of CD and VT with non-O blood types was still significant with a higher risk than with blood group O after adjusting for age and gender (OR = 1.355, 95% CI = 1.100-1.670, p = 0.004 and OR = 1.465, 95% CI = 1.131-1.903, p = 0.004, respectively).

Conclusion

ABO blood groups distributions in CD and VT patients significantly differed from that of NC. Non-O blood group could be a new predictor for CD and VT.

Polygenic risk score for ulcerative colitis predicts immune checkpoint inhibitor-mediated colitis

Immune checkpoint inhibitor-mediated colitis (IMC) is a common adverse event of treatment with immune checkpoint inhibitors (ICI). We hypothesize that genetic susceptibility to Crohn's disease (CD) and ulcerative colitis (UC) predisposes to IMC. In this study, we first develop a polygenic risk scores for CD (PRSCD) and UC (PRSUC) in cancer-free individuals and then test these PRSs on IMC in a cohort of 1316 patients with ICI-treated non-small cell lung cancer and perform a replication in 873 ICI-treated pan-cancer patients. In a meta-analysis, the PRSUC predicts all-grade IMC (ORmeta=1.35 per standard deviation [SD], 95% CI = 1.12-1.64, P = 2×10-03) and severe IMC (ORmeta=1.49 per SD, 95% CI = 1.18-1.88, P = 9×10-04). PRSCD is not associated with IMC. Furthermore, PRSUC predicts severe IMC among patients treated with combination ICIs (ORmeta=2.20 per SD, 95% CI = 1.07-4.53, P = 0.03). Overall, PRSUC can identify patients receiving ICI at risk of developing IMC and may be useful to monitor patients and improve patient outcomes.

Correlation of Socioeconomic and Environmental Factors With Incidence of Crohn Disease in Children and Adolescents: Systematic Review and Meta-Regression

BACKGROUND

The worldwide incidence of Crohn disease (CD) in childhood and adolescence has an increasing trend, with significant differences between different geographic regions and individual countries. This includes an increase in the incidence of CD in countries and geographic regions where CD was not previously prevalent. In response to the increasing incidence, the pediatric care landscape is facing growing challenges.

OBJECTIVE

This systematic review and meta-analysis were undertaken to comprehensively delineate the incidence rates of CD in pediatric populations across different countries and to explore potential influencing factors.

METHODS

We performed a systematic review of PubMed and Embase (via Ovid) for studies from January 1, 1970, to December 31, 2019. In addition, a manual search was performed in relevant and previously published reviews. The results were evaluated quantitatively. For this purpose, random effects meta-analyses and meta-regressions were performed to investigate the overall incidence rate and possible factors influencing the incidence.

RESULTS

A qualitative synthesis of 74 studies was performed, with 72 studies included in the meta-analyses and 52 in the meta-regressions. The results of our meta-analysis showed significant heterogeneity between the individual studies, which cannot be explained by a sample effect alone. Our findings showed geographical differences in incidence rates, which increased with increasing distance from the equator, although no global temporal trend was apparent. The meta-regression analysis also identified geographic location, UV index, and Human Development Index as significant moderators associated with CD incidence.

CONCLUSIONS

Our results suggest that pediatric CD incidence has increased in many countries since 1970 but varies widely with geographic location, which may pose challenges to the respective health care systems. We identified geographic, environmental, and socioeconomic factors that contribute to the observed heterogeneity in incidence rates. These results can serve as a basis for future research. To this end, implementations of internationally standardized and interoperable registries combined with the dissemination of health data through federated networks based on a common data model, such as the Observational Medical Outcomes Partnership, would be beneficial. This would deepen the understanding of CD and promote evidence-based approaches to preventive and interventional strategies as well as inform public health policies aimed at addressing the increasing burden of CD in children and adolescents.

TRIAL REGISTRATION

PROSPERO International prospective register of systematic reviews CRD42020168644; https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=168644.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

RR2-10.1136/bmjopen-2020-037669.