Advances in understanding the pathogenesis of inflammatory bowel disease (IBD) point toward a key role of the gut microbiome. We review the data describing the changes in the gut microbiome from IBD case-control studies and compare these findings with emerging data from studies of the preclinical phase of IBD. What is apparent is that assessing changes in the composition and function of the gut microbiome during the preclinical phase helps address confounding factors, such as disease activity and drug therapy, which can directly influence the gut microbiome. Understanding these changes in the predisease phase provides a means of predicting IBD in high-risk populations and offers insights into possible mechanisms involved in disease pathogenesis. Finally, we discuss strategies to use this information to design interventions aimed at modulating the microbiome as a means of preventing or delaying the onset of IBD.

B cells have important functions in gut homeostasis, and dysregulated B cell populations are frequently observed in patients with inflammatory bowel diseases, including both ulcerative colitis (UC) and Crohn's disease (CD). How these B cell perturbations contribute to disease remains largely unknown. Here, we perform deep sequencing of the B cell receptor (BCR) repertoire in four cohorts of patients with CD, together with healthy controls and patients with UC. We identify BCR clones that are shared between patients with CD but not found in healthy individuals nor in patients with UC, indicating CD-associated B cell immune responses. Shared clones are present in the inflamed gut mucosa, draining intestinal lymph nodes and blood, suggesting the presence of common CD-associated antigens that drive B cell responses in CD patients.

Since its introduction in 2012, ferroptosis has garnered significant attention from researchers over the past decade. Unlike autophagy and apoptosis, ferroptosis is an atypical iron-dependent programmed cell death that falls under necrosis. It is regulated by various cellular metabolic and signaling processes, which encompass amino acid, lipid, iron, and mitochondrial metabolism. The initiation of ferroptosis occurs through iron-dependent phospholipid peroxidation. Notably, ferroptosis exhibits a dual effect and is associated with various diseases. A significant challenge lies in managing autoimmune disorders with unknown origins that stem from the reactivation of the immune system. Two contributing factors to autoimmunity are the aberrant stimulation of cell death and the inadequate clearance of dead cells, which can expose or release intracellular components that activate the immune response. Ferroptosis is distinct from other forms of cell death, such as apoptosis, necroptosis, autophagy, and pyroptosis, due to its unique morphological, biochemical, and genetic characteristics and specific relationship with cellular iron levels. Recent studies indicate that immune cells can both induce and undergo ferroptosis. To better understand how ferroptosis influences immune responses and its imbalance in disease, a molecular understanding of the relationship between ferroptosis and immunity is essential. Consequently, further research is needed to develop immunotherapeutics that target ferroptosis. This review primarily focuses on the role of ferroptosis in immune-related disorders.

Previous work on inflammatory bowel disease (IBD) revealed changes in the abundance of colonic stromal subsets during intestinal inflammation. However, it is currently unknown whether these stromal cell subset changes are also reflected in different IBD mouse models and how commonly used IBD therapies affect stromal cell subset composition.

Stromal subset markers CD55, C-X-C motif chemokine 12 (CXCL12), podoplanin (PDPN), CD90, and CD73 were analyzed by flow cytometry in 3 mouse models for IBD, namely interleukin (IL)-10 knockout (KO), dextran sulfate sodium-induced, and T-cell transfer model for colitis. Next, the effects of IBD therapies on the stromal subset composition were studied. In vitro experiments were performed to study the interaction between stromal cell subsets and epithelial/immune cells.

The colitis-induced changes in the abundance of stromal cell subsets differed considerably between the 3 colitis mouse models. Interestingly, treatment with IBD medication affected specific stromal subsets in a therapy and model-specific manner. In vitro experiments showed that specific stromal subsets affected epithelial wound healing and/or T-cell activation.

The relative abundance changes of stromal cell subsets during experimental colitis differ between 3 established colitis models. Treatment with IBD therapies influences stromal subset abundance, indicating their importance in IBD pathogenesis, possibly through affecting epithelial migration, and T-cell activation.

Inflammation can generate pathogenic Th17 cells and cause an inflammatory dysbiosis. In the context of inflammatory bowel disease (IBD), these inflammatory Th17 cells and dysbiotic microbiota may perpetuate injury to intestinal epithelial cells. However, many models of IBD like T-cell transfer colitis and IL-10-/- mice rely on the absence of regulatory pathways, so it is difficult to tell if inflammation can also induce protective Th17 cells.

We subjected C57BL6, RAG1-/-, or JH-/- mice to systemic or gastrointestinal (GI) Citrobacter rodentium (Cr). Mice were then subjected to 2.5% dextran sodium sulfate (DSS) to cause epithelial injury. Fecal microbiota transfer was performed by bedding transfer and co-housing. Flow cytometry, qPCR, and histology were used to assess mucosal and systemic immune responses, cytokines, and tissue inflammation. 16s sequencing was used to assess gut bacterial taxonomy.

Transient inflammation with GI but not systemic Cr was protective against subsequent intestinal injury. This was replicated with sequential DSS collectively indicating that transient inflammation provides tissue-specific protection. Inflammatory Th17 cells that have a tissue-resident memory (TRM) signature expanded in the intestine. Experiments with reconstituted RAG1-/-, JH-/- mice, and cell trafficking inhibitors showed that inflammation-induced Th17 cells were required for protection. Fecal microbiota transfer showed that the inflammation-trained microbiota was necessary for protection, likely by maintaining protective Th17 cells in situ.

Inflammation can generate protective Th17 cells that synergize with the inflammation-trained microbiota to provide host resiliency against subsequent injury, indicating that inflammation-induced Th17 TRM T cells are heterogenous and contain protective subsets.

Inflammatory bowel disease (IBD) is a multifactorial illness with a climbing prevalence worldwide. While biologics are commonly prescribed especially for severe cases, they may worsen patients' outcomes due to financial burden. Consequently, there has been an increased focus on biosimilars to improve overall disease outcomes by maintaining similar efficacy and safety while minimizing the cost of therapy. Infliximab-dyyb was the first biosimilar approved by US-FDA for IBD. Since that, the US-FDA approved 14 biosimilars with different mechanisms of action and different routes of administration for IBD patients (four infliximab biosimilars, nine adalimumab biosimilars, and most recently one ustekinumab biosimilar). It should be noted that more biologics are in the pipeline as golimumab and natalizumab patents are set to expire in the near future, and biosimilars are now in pre-clinical to phase 3 trials. Different studies have evaluated biologics' effectiveness and safety and concluded that the majority of available biosimilars are efficacious and have similar adverse effect profiles compared to their reference biologics. It is worth mentioningthat post-marketing surveillance reports revealed some risks associated with biosimilars which should be taken into consideration in future research and clinical trials to avoid health hazards. Most biologics and biosimilars are administered parenterally which results in several drawbacks such as raised risk of infections, hypersensitivity, autoimmunity, development of malignancies, liver toxicity as well as worsening of heart failure. Several drug delivery systems based on passive and active targeting mechanisms are under active investigation to overcome these limitations. This review sheds light on the emergence of biologics and biosimilars as alternatives in IBD management, the differences between them, challenges and risks, and future perspectives in IBD therapy and new trends in drug delivery systems.

Genomic prediction encompasses the techniques used in agricultural technology to predict the genetic merit of individuals towards valuable phenotypic traits. It is related to Genome Interpretation in humans, which models the individual risk of developing disease traits. Genomic prediction is dominated by linear mixed models, such as the Genomic Best Linear Unbiased Prediction (GBLUP), which computes kinship matrices from SNP array data, while Genome Interpretation applications to clinical genetics rely mainly on Polygenic Risk Scores.

In this article, we exploit the positive semidefinite characteristics of the kinship matrices that are conventionally used in GBLUP to propose a novel Genomic Multiple Kernel Learning method (GMKL), in which the multiple kinship matrices corresponding to Additive, Dominant, and Epistatic Inheritance Mechanisms are used as kernels in support vector machines, and we apply it to both worlds. We benchmark GMKL on simulated cattle phenotypes, showing that it outperforms the classical GBLUP predictors for genomic prediction. Moreover, we show that GMKL ranks the kinship kernels representing different inheritance mechanisms according to their compatibility with the observed data, allowing it to produce hypotheses on the normally unknown inheritance mechanisms generating the target phenotypes. We then apply GMKL to the prediction of two inflammatory bowel disease cohorts with more than 6500 samples in total, consistently obtaining results suggesting that epistasis might have a relevant, although underestimated role in inflammatory bowel disease (IBD).

We show that GMKL performs similarly to GBLUP, but it can formulate biological hypotheses about inheritance mechanisms, such as suggesting that epistasis influences IBD.

The role of particulate matter (PM) on genetic susceptibility to inflammatory bowel disease (IBD) is a controversial topic. The study aims to evaluate the causal effect of PM on IBD using Mendelian randomization (MR). PM and IBD datasets were screened for common single nucleotide polymorphisms (SNPs) based on the MR basic assumptions. Subsequently, the effect of these SNPs on genetic susceptibility to IBD was analyzed using inverse variance weighted. Finally, the heterogeneity and robustness of the results were assessed using Cochran's Q and leave-one-out sensitivity analysis, respectively. MR analysis revealed that PM2.5 was linked to a heightened genetic predisposition to (odds ratio [OR] 1.530, 95% confidence interval [CI] 1.100-2.128, p = 0.011) and ulcerative colitis (UC) (OR 1.675, 95% CI 1.129-2.485, p = 0.010), but not to Crohn's disease (CD) (OR 1.685, 95% CI 0.883-3.216, p = 0.114). PM10 was not associated with increased genetic susceptibility to IBD (OR 1.164, 95% CI 0.650-2.083, p = 0.610), UC (OR 1.439, 95% CI 0.691-2.996, p = 0.331), or CD (OR 0.825, 95% CI 0.265-2.564, p = 0.739). MR-Egger intercept did not indicate any horizontal pleiotropy (p > 0.05). Cochran's Q revealed no evidence of heterogeneity (p > 0.05). Leave-one-out sensitivity analysis confirmed the robustness of the results. The MR analysis demonstrated that PM2.5 increased genetic susceptibility to UC, while no such association was observed for CD. Furthermore, PM10 showed no association with genetic susceptibility to IBD. Therefore, implementing protective measures, such as air purifiers and anti-haze masks, may help reduce the risk of UC.

The purpose of this review is to describe the immune function of the liver, guiding the reader from the homeostatic tolerogenic status to the aberrant activation demonstrated in chronic liver disease. An extensive description of the pathways behind the inflammatory modulation of the healthy liver will be provided focusing on the complex immune cell network residing within the liver. The limit of tolerance will be presented in the context of organ transplantation, seizing the limits of homeostatic mechanisms that fail in accepting the graft, progressing eventually toward rejection. The triggers and mechanisms behind chronic activation in metabolic liver conditions and viral hepatitis will be discussed. The last part of the review will be dedicated to one of the greatest paradoxes for a tolerogenic organ, developing autoimmunity. Through the description of the three most common autoimmune liver diseases, the autoimmune reaction against hepatocytes and biliary epithelial cells will be dissected.

Inflammatory bowel disease (IBD) is an idiopathic gastrointestinal disease with drastically increasing incidence rates. Due to its multifactorial etiology, a precise investigation of the pathogenesis is extremely difficult. Although reductionist cell culture models and more complex disease models in animals have clarified the understanding of individual disease mechanisms and contributing factors of IBD in the past, it remains challenging to bridge research and clinical practice. Conventional 2D cell culture models cannot replicate complex host-microbiota interactions and stable long-term microbial culture. Further, extrapolating data from animal models to patients remains challenging due to genetic and environmental diversity leading to differences in immune responses. Human intestine organ-on-chip (OoC) models have emerged as an alternative in vitro model approach to investigate IBD. OoC models not only recapitulate the human intestinal microenvironment more accurately than 2D cultures yet may also be advantageous for the identification of important disease-driving factors and pharmacological interventions targets due to the possibility of emulating different complexities. The predispositions and biological hallmarks of IBD focusing on host-microbiota interactions at the intestinal mucosal barrier are elucidated here. Additionally, the potential of OoCs to explore microbiota-related therapies and personalized medicine for IBD treatment is discussed.

Colorectal cancer (CRC) results from the accumulation of mutations and epigenetic changes in gut epithelial cells likely due to gut microbiota dysbiosis. However, limited research has been done to explore the link between host tumour dysbiosis and disease outcome.

The mechanisms influencing outcomes of 97 colorectal cancer (CRC) patients, including 13 with Lynch syndrome, 20 with inflammatory bowel disease (IBD), and 64 sporadic cases, were analyzed using a multiomics approach. These patients were categorized into two groups: "disease-free/stable disease" and "progression disease" survival outcomes. The analysis included tumor adherent microbiota composition (16S rRNA), somatic gene mutations (WES), gene expression (RNAseq), immune markers (RNAscope), and immune infiltrate cells (immunohistochemistry).

IBD-CRC patients had worse outcomes than those with Lynch or sporadic CRC, regardless of TNM staging or treatment. Symbiotic bacteria like Lactococcus lactis were significantly reduced in IBD-CRC tissues. Patient outcomes were influenced by the abundance of virulent ( Escherichia coli ) relative to beneficial bacteria ( Lactococcus lactis ). Although no significant increase in deleterious somatic mutations was found in IBD-CRC. 16sRNA revealed increased virulent- and decreased anti-inflammatory symbiotic-bacteria correlating with the upregulation of oncogenes and downregulation of anti-oncogenes like PHLPP1. The multiplex in situ hybridization of CD8, IFNγ and PHLPP1 an anti-oncogene revealed significant decrease of immune cells with detectable PHLPP1 expression in IBD-CRC tumour tissues as compared to sporadic CRCs.

The poor outcomes in IBD-CRC patients are likely due to gut dysbiosis and immune cell alterations, possibly triggered by microbiota-related epigenetic pathways.

BACKGROUND AND CONTEXT: Colorectal cancer (CRC) is associated with gut microbiota dysbiosis. Inflammatory bowel disease-related CRC (IBD-CRC) is classified as an environment-related condition.NEW FINDINGS: In relation with patient outcomes, tumour tissues from three types of CRC (Sporadic-, IBD-, and Lynch syndrome-CRC) were analyzed using a multiomic approach. This included examining tissue adherent virulent bacteria, gene analyses, and quantifying immune cell infiltration in the mucosa. IBD-CRC patients had the worst outcomes, associated with the down regulation of PHLPP1 gene, virulent/symbiotic imbalance, and immune response failure.LIMITATIONS: Lack of animal experiments using FMT of fresh stool from IBD-CRC patients.CLINICAL AND TRANSLATIONAL RESEARCH RELEVANCE: Among the different types of CRC, IBD-CRC patients showed a greater imbalance between harmful and beneficial bacteria, along with immune response failure.Lay summary: This study compares the pathological and clinical characteristics of patients with colorectal cancer (CRC) across three distinct etiologies: sporadic CRC, inflammatory bowel disease (IBD)-associated CRC, and Lynch syndrome-associated CRC (LS-CRC). Distinct differences in tumor-adherent microbiota, gene expression and immune response profiles were observed. Notably, IBD-CRC patients demonstrated the poorest prognosis depending on microbe-host gene interaction highlighting potential biomarkers for disease prognosis and treatment strategies.

Colonic mucus forms a first line of defense against bacterial invasion while providing nutrition to support coinhabiting microbes in the gut. Mucus is composed of polymeric networks of mucin proteins, which are heavily modified post-translationally. The full compendium of enzymes responsible for these modifications and their roles in health and disease remain incompletely understood. Herein, we determine the biochemical function of NXPE1, a gene implicated in ulcerative colitis (UC), and demonstrate that it encodes an acetyltransferase that modifies mucin glycans. Specifically, NXPE1 utilizes acetyl-CoA to regioselectively modify the mucus sialic acid, 5-N-acetylneuraminic acid (Neu5Ac), at the 9-OH group to generate 9-O-acetylated Neu5Ac (Neu5,9Ac2). We further demonstrate that colonic organoids derived from donors harboring the missense variant NXPE1 G353R, which is protective against UC, exhibit severely impaired acetylation of Neu5Ac on mucins. Together, our findings support a model in which NXPE1 masks the alcohols of mucus sialoglycans via acetylation, which is important for modulating mucus barrier properties that limit interactions with commensal microbes.

More than 300 genomic loci have been associated with increased susceptibility to inflammatory bowel disease (IBD) through genome-wide association studies. A major challenge in the translation of genome-wide association studies to mechanistic insights lies in connecting noncoding variants to function. For example, single-nucleotide variants (SNVs) in the vicinity of the gene encoding the transcription factor ETS2 on human chromosome 21 are associated with the risk of developing IBD in Europeans. The peak of SNV association lies within a distal enhancer that may regulate ETS2 transcription. The interpretation of this and many other SNV associations with IBD depends on a model linking variation in transcriptional regulation to the likelihood of developing chronic intestinal inflammation. One model for the ETS2 locus is that overexpression in monocytes is causally associated with the risk allele, which in turn leads to a hyperinflammatory state. Here we summarize evidence for an alternative mechanism focused on negative regulators of monocyte-macrophage activation. We argue that IBD susceptibility arises from dysregulation of monocyte adaptation in the intestinal milieu to form resident intestinal macrophages that are anergic to inflammatory stimuli. This process depends on signals initiated by macrophage colony-stimulating factor (CSF1) binding to its receptor (CSF1R). Within this framework, ETS2 is a myeloid-specific transcription factor, expressed in pluripotent and committed progenitors and monocytes, and is down-regulated by CSF1, in common with many genes associated with IBD susceptibility, including NOD2. ETS2 is also both a downstream target and a mediator of the CSF1/CSF1R signaling pathway. Therapeutic targeting of ETS2 and its upstream regulators has the potential to prevent CSF1-dependent monocyte differentiation toward a prorepair resident macrophage phenotype and consequently exacerbate intestinal inflammation.

Ulcerative colitis (UC) is a typical type of inflammatory bowel disease, which is often recurrent and directly related with colorectal cancer. Therefore, early prevention and treatment for UC is very necessary. Therefore, it is necessary to find efficient substances to treat the UC with less side effects than drugs. Exopolysaccharides (EPSs) are important bioactive constituents of lactic acid bacteria. The study evaluated the effects of EPS1 produced by Levilactobacillus brevis M-10 on UC by determining the weight, the disease activity index (DAI) and the physiological and biochemical indexes. The pathological structures of colon were observed. The gut microbiota and the short-chain fatty acids were analyzed. The results demonstrated high dose (HD) of EPS1 (400 mg/kg-BW) that had the best effects on UC mice. The HD group restored body weight, decreased DAI and alleviated shortening of the length of the colon, recovered liver tissue, declined lipopolysaccharide, and myeloperoxidase. Also the HD group showed that the expression of tight junction proteins increased, IL-10 up-regulated, IL-6, IL-1β, and TNF-α down-regulated, and the gut microbiota dysbiosis balanced. The HD group markedly elevated the relative abundance of Lachnospiraceae_NK4A136_group, Unclassified-Lachnospiraceae, and Unclassified- Muribaculaceae. Acetic acid, propionic acid, and n-butyric acid were significantly increased in the HD group (P < 0.05). The study could provide a theoretical basis and material support for the exploration of safe functional food in alleviating and preventing UC.

The pathogenesis of inflammatory bowel diseases (IBD) involves genetic, environmental, immunological, and microbial factors; however, it remains unclear. Pro-inflammatory interleukin 8 (IL-8), encoded by the CXCL8 gene, assumes a crucial chemotactic role in leukocyte migration.

This study aimed to investigate whether an association exists between IBD and two CXCL8 variants, namely, c.-251A>T (rs4073) and c.91G>T (rs188378669), and IL-8 concentration. We analyzed the distribution of both variants among 353 Polish IBD patients and 200 population subjects using pyrosequencing, competitive allele-specific PCR and Sanger sequencing.

The c.91T stop-gained allele was significantly more frequent in IBD patients (2.12%) than in controls (0.25%) (p = 0.0121), while the c.-251T allele frequencies were similar (54% vs. 51.5%, p = 0.4955). Serum IL-8 concentrations, measured using ELISA, were higher in IBD patients with the c.91 GG genotype compared to healthy controls (mean, 70.02 vs. 51.5 pg/ml, p<0.01) and patients with c.91 GT (mean, 61.73 pg/ml). Moreover, clinical data indicated that carriers of the c.91T variant need more often corticosteroids and surgical treatment of the disease than GG homozygous IBD patients.

This suggest that the CXCL8 c.91T allele may influence IBD manifestation and the course of the disorders in Polish patients, potentially serving as a novel target for future studies and therapeutic approaches.

C1ORF106 has previously been associated with inflammatory bowel diseases (IBD) via large-scale genetic studies. Increased intestinal permeability is a hallmark of IBD and is observed in at-risk individuals prior to the appearance of clinical symptoms. C1ORF106 was previously shown to regulate intestinal barrier permeability through the regulation of adherens junction stability and through the formation of tight junctions, which impacted actin assembly. However, the downstream impact and molecular mechanisms involved in actin regulation by C1ORF106 haven't been explored. Our study aimed at identifying which pathways involved in intestinal epithelial barrier regulation and F-actin regulation are impacted by C1ORF106 and its IBD-associated variant.

We knocked down (KD) the expression of C1ORF106 in human colonic epithelial cells and characterized the function of the 333F variant in intestinal epithelial spheroid cultures obtained from patient-derived human induced pluripotent stem cell (hiPSC). We measured barrier permeability and characterized spheroid formation, actin regulation and cell migration though immunofluorescence, western blots and permeability assays.

C1ORF106 KD leads to impaired cortical actin belt dynamics and regulation of stress fiber formation, resulting in increased cell constriction, impaired barrier permeability, cell polarity and cell migration. Moreover, we demonstrated that an inhibition of ROCK rescues the actin belt and cell polarity phenotypes in C1ORF106 KD cells, demonstrating that C1ORF106 regulates these phenotypes through a ROCK-dependent mechanism. We also observed an altered nmMYO2-P localization in C1ORF106 KD cells associated with the formation of Vacuolar Apical Compartments (VACs), which are important for 3D epithelial spheroid formation. We observed a similar impact on cell polarity in intestinal epithelial spheroids obtained from hiPSC carrying the 333F variant, providing additional support that this pathway is involved in disease development.

We provide insights into the molecular mechanisms by which C1ORF106 controls actin dynamics to regulate intestinal epithelial integrity.

Genome wide association studies (GWAS) identify many risks for Crohn's disease (CD), including a site near the metabolism gene laccase domain containing 1 (LACC1). We previously found this site near LACC1 was associated with decreased LACC1 expression in T lymphocytes, yet the mechanism affecting gene expression and its links to T cell function and inflammatory disease were unknown. Here we identify variants in the promoter region that influence transcription of LACC1. Direct association of disease-risk variants with lower LACC1 pre-mRNA in human CD4+ T cells is confirmed by comparing transcripts from each allele from donors heterozygous for the LACC1 CD-risk allele. Using gene editing, we validate the function of this promoter region in LACC1 expression in T cells. Human CD4+ T cells with LACC1 gene knockdown show altered metabolism, including reduced oxygen consumption rate, and reduced in vitro regulatory T cell differentiation. Therefore, our study provides a mechanism linking these specific LACC1 variants to colitis by attributing promoter region variants to changes in T cell metabolism and function.

Polygenic severe obesity (body mass index [BMI] ≥40 kg/m2) has increased, especially in Hispanic/Latino populations, yet we know little about the underlying mechanistic pathways. We analyzed whole-blood multiomics data to identify genes differentially regulated in severe obesity in Mexican Americans from the Cameron County Hispanic Cohort. Our RNA sequencing analysis identified 124 genes significantly differentially expressed between severe obesity cases (BMI ≥40 kg/m2) and controls (BMI <25 kg/m2); 33% replicated in an independent sample from the same population. Our integrative approach identified inflammatory genes, including IL4R, ZNF438, and LILRA5. Several genes displayed transcriptomic effects on severe obesity in subcutaneous adipose tissue. We further showed that the genetic regulation of these genes is associated with several traits in a large biobank, including bone fractures, obstructive sleep apnea, and hyperaldosteronism, illuminating potential risk mechanisms. Our findings furnish a molecular architecture of the severe obesity phenotype across multiple molecular domains.

In the gut, microRNAs (miRNAs) produced by intestinal epithelial cells are secreted into the lumen and can shape the composition and function of the gut microbiome. Crosstalk between gut microbes and the host plays a key role in irritable bowel syndrome (IBS) and inflammatory bowel diseases, yet little is known about how the miRNA-gut microbiome axis contributes to the pathogenesis of these conditions. Here, we investigate the ability of miR-21, a miRNA that we found decreased in fecal samples from IBS patients, to associate with and regulate gut microbiome function. When incubated with the human fecal microbiota, miR-21 revealed a rapid internalization or binding to microbial cells, which varied in extent across different donor samples. Fluorescence-activated cell sorting and sequencing of microbial cells incubated with fluorescently labeled miR-21 identified organisms belonging to the genera Bacteroides, Limosilactobacillus, Ruminococcus, or Coprococcus, which predominantly interacted with miR-21. Surprisingly, these and other genera also interacted with a miRNA scramble control, suggesting that physical interaction and/or uptake of these miRNAs by gut microbiota is not sequence-dependent. Nevertheless, transcriptomic analysis of the gut commensal Bacteroides thetaiotaomicron revealed a miRNA sequence-specific effect on bacterial transcript levels. Supplementation of miR-21, but not of small RNA controls, resulted in significantly altered levels of many cellular transcripts and increased transcription of a biosynthetic operon for indole and L-tryptophan, metabolites known to regulate host inflammation and colonic motility. Our study identifies a novel putative miR-21-dependent pathway of regulation of intestinal function through the gut microbiome with implications for gastrointestinal conditions.

The mammalian gut represents one of the largest and most dynamic host-microbe interfaces. Host-derived microRNAs (miRNAs), released from the gut epithelium into the lumen, have emerged as important contributors to host-microbe crosstalk. Levels of several miRNAs are altered in the stool of patients with irritable bowel syndrome or inflammatory bowel disease. Understanding how miRNAs interact with and shape gut microbiota function is crucial as it may enable the development of new targeted treatments for intestinal diseases. This study provides evidence that the miRNA miR-21 can rapidly associate with diverse microbial cells form the gut and increase levels of transcripts involved in tryptophan synthesis in a ubiquitous gut microbe. Tryptophan catabolites regulate key functions, such as gut immune response or permeability. Therefore, this mechanism represents an unexpected host-microbe interaction and suggests that host-derived miR-21 may help regulate gut function via the gut microbiota.

The genetic contribution to inflammatory bowel disease (IBD), encompassing both Crohn's disease (CD) and ulcerative colitis (UC), accounts for around 20% of disease variance, highlighting the need to characterize environmental and epigenetic influences. Recently, considerable progress has been made in characterizing the adult methylome in epigenome-wide association studies.

We report detailed analysis of the circulating methylome in 86 patients with childhood-onset CD and UC and 30 controls using the Illumina Infinium Human MethylationEPIC platform.

We derived and validated a 4-probe methylation biomarker (RPS6KA2, VMP1, CFI, and ARHGEF3), with specificity and high diagnostic accuracy for pediatric IBD in UK and North American cohorts (area under the curve: 0.90-0.94). Significant epigenetic age acceleration is present at diagnosis, with the greatest observed in CD patients. Cis-methylation quantitative trait loci (meQTL) analysis identifies genetic determinants underlying epigenetic alterations notably within the HLA 6p22.1-p21.33 region. Passive smoking exposure is associated with the development of UC rather than CD, contrary to previous findings.

These data provide new insights into epigenetic alterations in IBD and illustrate the reproducibility and translational potential of epigenome-wide association studies in complex diseases.

Extraintestinal manifestations (EIMs) significantly affect the life quality of people with inflammatory bowel disease (IBD) and are crucial factors impacting occurrence rates and mortality among IBD patients. This study performed a Mendelian randomization (MR) analysis to investigate the causal relationships between genetically predicted IBD and the development of EIMs, including erythema nodosum (EN), episcleritis, scleritis, uveitis, primary sclerosing cholangitis (PSC), and spondyloarthritis. To further investigate differences between subtypes, separate analyses were conducted for ulcerative colitis (UC) and Crohn's disease (CD).

The study was conducted based on genome-wide association studies (GWAS) data. We carefully selected SNPs associated with both exposure and outcome by comparing and integrating data from GWAS and relevant literature, and prioritizing studies with large sample sizes, high quality, and as much population homogeneity as possible. The SNPs associated with IBD, UC and CD were extracted from the International Inflammatory Bowel Disease Genetics Consortium. And the SNPs associated with EIMs were extracted from the UK Biobank, the International PSC Study Group and the FinnGen study. A series of quality control steps were taken in our analysis to select eligible instrumental SNPs which were strongly associated with exposure. The causal effects were estimated using a primary analysis that employed inverse-variance weighting (IVW) and complementary analysis that utilized MR-Egger weighted by the median. A sensitivity analysis was conducted using the Cochran Q statistic, a funnel plot, the MR-Egger intercept, and a leave-one-out approach. Reverse causality analysis was also performed to ensure the robustness of the findings. Furthermore, a fixed-effects meta-analysis was employed to combine MR outcomes from various data origins, bolstering the strength and dependability of our findings.

Our findings indicated that genetically predicted IBD had a robust causal relationship with an increased risk of specific conditions, including EN (OR, 1.20; 95% CI, 1.09-1.32; p < 0.01), uveitis (OR, 1.15; 95% CI, 1.11-1.20; p < 0.01), PSC (OR, 1.21; 95% CI, 1.13-1.28; p < 0.01), and spondyloarthritis (OR, 1.19; 95% CI, 1.14-1.23; p < 0.01). In subgroup analyses, the causal effects of both UC and CD on EN, uveitis, PSC, and spondyloarthritis were also significant and robust. Additionally, no significant evidence of causality was observed between genetically predicted IBD, UC, and CD, and the occurrence of both episcleritis and scleritis. The results of reverse causality analysis indicated a robust causal association between genetically predicted PSC and the elevated risk of IBD (OR, 1.21; 95% CI, 1.15-1.29; p < 0.01), UC (OR, 1.27; 95% CI, 1.17-1.37; p < 0.01), and CD (OR, 1.10; 95% CI, 1.02-1.20; p < 0.01). Additionally, spondyloarthritis had a causal relationship with an increased risk of both IBD (OR, 1.03; 95% CI, 1.01-1.06; p < 0.01) and UC (OR, 1.05; 95% CI, 1.02-1.08; p < 0.01).

Inflammatory bowel diseases (IBD) are polygenic, with many genetic variants contributing to disease risk. Knowing the genotype of specific variants or calculating a combined genetic risk score benefits translational and functional research. To address this, we developed MIP4IBD, a flexible and cost-effective genotyping-by-sequencing assay using molecular inversion probes (MIPs).

The assay targets 463 IBD risk variants, and 77 additional relevant variants. Molecular inversion probes capture and library preparation were optimized using 15 IBD DNA samples, comparing genotypes with immunochip. A custom GitHub pipeline was created for data processing, performance testing, and genotype calling. The final design was validated on a larger scale (149 IBD patients, 104 non-IBD controls, and 3 external cell lines), incorporating post hoc quality control criteria.

The assay achieved a 3.5-day turnaround time at €15 per sample with optimal sample throughput, demonstrating a 92.6% success rate in variant capture and genotype concordance rates of 99.3% and 99.6% with Infinium Global Screening Array24 BeadChip and WGS, respectively. A downstream application involved the calculation of a weighted IBD polygenic risk score (PRS), which was significantly higher in IBD patients than controls (mean 0.42 vs -0.49, P = 1.95E-11). Individuals in the highest PRS quartile had a 15.7-fold (95% CI: 6.5-38.3) risk of developing IBD and an earlier age of onset (26 vs 37 years, P = 0.02), compared to the lowest quartile.

MIP4IBD is a validated, scalable genotyping assay targeting IBD risk loci, with an integrated bioinformatics pipeline from sequencing data to genotypes and PRS calculation. Its cost-effectiveness and flexibility for additional variants make it particularly appealing for translational and clinical applications.

70 % of the ulcerative colitis (UC) linked gene loci are associated with other autoimmune or immunodeficient diseases. The phosphatase activity of PTPN22 can regulate the development of T cells and contribute to regulate the level of inflammation in autoimmune diseases. We produced PTPN22-CS thymus-specific transgenic mice, which suppressed PTPN22 enzyme activity in the thymocytes. Overexpressed PTPN22-CS facilitated the development of the thymocytes towards CD4+T cells and resulted in an increased proportion of the Th1 and Treg cells in the UC mesenteric lymph nodes. PTPN22-CS promoted the activation of the JAK/STAT signaling pathway in the Th1 and Treg cells that localized in the colon, resulting in an excessive production of inflammatory mediators such as IL-2 and IFN-γ. Consequently, PTPN22-CS contributes to the inflammatory response of ulcerative colitis. In summary, the tyrosine phosphatase activity of PTPN22 plays a role in modulating UC by regulating T cell differentiation and modulating the JAK/STAT signaling pathway, thereby influencing the inflammatory response in colonic. These findings provide new insight into the association between PTPN22 and the pathogenesis of UC.

Appropriate cellular recognition of viruses is essential for the generation of an effective innate and adaptive immune response. Viral sensors and their downstream signaling components thus provide a crucial first line of host defense. Many of them exhibit subcellular relocalization upon activation, resulting in the expression of interferon and antiviral genes. To comprehensively identify signaling factors, we analyzed protein relocalization on a global scale during viral infection. cAMP-responsive element-binding protein (CREB)-regulated transcription coactivators 2 and 3 (CRTC2/3) exhibited early cytoplasmic-to-nuclear translocation upon infection with multiple viruses in diverse cell types. This movement was dependent on mitochondrial antiviral signaling protein (MAVS), cyclo-oxygenase proteins, and protein kinase A. A key effect of CRTC2/3 translocation is transcription of the fibro-inflammatory cytokine interleukin (IL)-11. This may be important clinically in viral infections associated with fibrosis, including SARS-CoV-2. Nuclear translocation of CRTC2/3 is, therefore, identified as an important pathway in the context of viral infection.

Current studies suggest a potential link between inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), and cardiovascular diseases, such as stroke. This study aimed to assess the risk of stroke in IBD patients compared to general population.

Systematic search was done in PubMed, Embase, CENTRAL, Scopus, and CINAHL databases for studies published till September 2023. Using a random-effects model, the hazard ratios (HRs) with 95% confidence intervals (CIs) for stroke occurrence were calculated. Subgroup analyses were done to estimate pooled HR with 95%CI for CD, UC, and overall IBD cases separately. Publication bias assessment was done by Begg's and Egger's tests.

Thirteen studies with 2,802,955 participants were included. IBD patients in general had significantly higher risk of stroke, with HR of 1.30 [95% CI 1.21-1.39]. Subgroup analysis demonstrated an HR of 1.35 [95% CI 1.22-1.49] for CD and 1.15 [95% CI 1.09-1.22] for UC. Substantial heterogeneity was detected across studies, with no substantial publication bias. Sensitivity analyses affirmed the stability of findings.

IBD in general, and Crohn's disease in particular are associated with significantly higher risk of stroke. Our findings further emphasize the importance of cardiovascular risk assessment and management strategies in IBD care.

PROSPERO, CRD42023470602.

A gene encoding the transcription factor RTF1 has been associated with an increased risk of ulcerative colitis (UC). In this study, we investigated its function in modulating T cells expressing interleukin-17A (Th17 cells), a cardinal cell type promoting intestinal inflammation. Our results indicate that Rtf1 deficiency disrupts the differentiation of Th17 cells, while leaving regulatory T cells (Treg) unaffected. Mechanistically, RTF1 facilitates histone H2B monoubiquitination (H2Bub1), which requires its histone modification domain (HMD), for supporting Th17 cell function. Impaired Th17 differentiation was also observed in cells lacking the H2Bub1 E3 ligase subunit RNF40, an enzyme known to physically interact with RTF1. Thus, our study underscores the essential role of RTF1 in H2Bub1-mediated epigenetic regulation of Th17 cell differentiation. Understanding this process will likely provide valuable insights into addressing Th17-associated inflammatory disorders. (Images were created with BioRender).

Dysfunctional NF-κB signaling is critically involved in inflammatory bowel disease (IBD). We investigated the mechanism by which RIPK1 and TRADD, two key mediators of NF-κB signaling, in mediating intestinal pathology using TAK1 IEC deficient model. We show that phosphorylation of TRADD by TAK1 modulates RIPK1-dependent apoptosis. TRADD and RIPK1 act cooperatively to mediate cell death regulated by TNF and TLR signaling. We demonstrate the pathological evolution from RIPK1-dependent ileitis to RIPK1- and TRADD-co-dependent colitis in TAK1 IEC deficient condition. Combined RIPK1 inhibition and TRADD knockout completely protect against intestinal pathology and lethality in TAK1 IEC KO mice. Furthermore, we identify distinctive microbiota dysbiosis biomarkers for RIPK1-dependent ileitis and TRADD-dependent colitis. These findings reveal the cooperation between RIPK1 and TRADD in mediating cell death and inflammation in IBD with NF-κB deficiency and suggest the possibility of combined inhibition of RIPK1 kinase and TRADD as a new therapeutic strategy for IBD.

Peptidoglycan recognition proteins (PGLYRPs) are implicated in the control of the intestinal microbiota; however, molecular requirements for peptidoglycan (PGN) binding and receptor signaling mechanisms remain poorly understood. Here we show that PGLYRP1 is a receptor for the disaccharide motif of lysine N-acetylglucosamine N-acetylmuramic tripeptide (GMTriP-K). PGLYRP1 is required for innate immune activation by GMTriP-K but not muramyl dipeptide (MDP). In macrophages, intracellular PGLYRP1 complexes with NOD2 and GEF-H1, both of which are required for GMTriP-K-regulated gene expression. PGLYRP1 localizes to the endoplasmic reticulum and interacts at the Golgi with NOD2 upon GMTriP-K stimulation. PGLYRP1 and dependent gene expression signatures are induced in both mouse intestinal inflammation and human ulcerative colitis. Importantly, PGLYRP1 activation by GMTriP-K can result in the protection of mice from TNBS-induced colitis. Mammalian PGLYRPs can function as intracellular pattern recognition receptors for the control of host defense responses in the intestine.

Innate immune cells, including dendritic cells (DCs), monocytes (Mono), macrophages (Mac), natural killer (NK), and innate lymphoid cells (ILC), contribute to chronic inflammation in lymphoid tissues. Here, we characterized the innate immune cell landscape in inflamed mesenteric lymph nodes (MLNs) of patients with inflammatory bowel diseases (IBD) at the single-cell level.

Surgically resected colonic MLNs were obtained from patients with Crohn's disease (CD; n = 3), ulcerative colitis (UC; n = 3), non-inflamed UC (n = 1), and non-IBD (n = 2). CD45+CD3-CD19- non-T/non-B cells were FACS-sorted to capture rare innate immune cells. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) was performed on the BD Rhapsody platform alongside multiparameter flow cytometry staining.

CITE-seq analysis unveiled the molecular signature of 11 Mono/Mac/DC (MMDC) and 7 NK/ILC enriched clusters in human MLNs. DC clusters included 3 newly characterized DC clusters such as CD1c/CD163/VCAN/CD64-expressing DC3; AXL-expressing DCs; and a CD103+ DC subset, expressing LTB, S100B, and IL22RA2 (encoding IL22BP). Mono/Mac clusters comprised inflammatory monocytes, which accumulated in IBD compared to non-IBD MLNs. Among NK/ILC clusters, we identified a cytotoxic ILC subset (IL7R, KLRD1, GNLY), previously not reported in MLNs, reminiscent of cytotoxic ILC1-like cells found in inflamed gut mucosa.

CITE-seq and flow-cytometry analyses of colonic MLNs from patients with active IBD reveal the molecular signature and cell distribution of previously uncharacterized DC and ILC subpopulations in human MLNs. These findings expand our understanding of immune responses during chronic inflammation in IBD.

Interleukin-10 (IL-10) is an immunomodulatory cytokine critical for intestinal immune homeostasis. IL-10 is produced by various immune cells but IL-10 receptor signaling in intestinal CX3CR1+ mononuclear phagocytes is necessary to prevent spontaneous colitis in mice. Here, we utilized fluorescent protein reporters and cell-specific targeting and found that Rorc-expressing innate lymphoid cells (ILCs) produce IL-10 in response to anti-CD40-mediated intestinal inflammation. Deletion of Il10 specifically in Rorc-expressing ILCs led to phenotypic changes in intestinal macrophages and exacerbated both innate and adaptive immune-mediated models of experimental colitis. The population of IL-10+ producing ILCs shared markers with both ILC2 and ILC3 with nearly all ILC3s being of the NCR+ subtype. Interestingly, Ccl26 was enriched in IL-10+ ILCs and was markedly reduced in IL-10-deficient ILC3s. Since CCL26 is a ligand for CX3CR1, we employed RNA in situ hybridization and observed increased numbers of ILCs in close proximity to Cx3cr1-expressing cells under inflammatory conditions. Finally, we generated transgenic RorctdTomato reporter mice that faithfully marked RORγt+ cells that could rescue disease pathology and aberrant macrophage phenotype following adoptive transfer into mice with selective Il10 deficiency in ILC3s. These results demonstrate that IL-10 production by a population of ILCs functions to promote immune homeostasis in the intestine possibly via direct effects on intestinal macrophages.

Inflammatory bowel disease (IBD) represents a group of chronic inflammatory disorders of the gastrointestinal tract. Despite substantial advances in our understanding of IBD pathogenesis, the currently available therapeutic options remain limited in their efficacy and often come with significant side effects. Therefore, there is an urgent need to explore novel approaches for the management of IBD. One promising avenue of investigation revolves around the use of histone deacetylase (HDAC) inhibitors, which have garnered considerable attention for their potential in modulating gene expression and curbing inflammatory responses. This review emphasizes the pressing need for innovative drugs in the treatment of IBD, and drawing from a wealth of preclinical studies and clinical trials, we underscore the multifaceted roles and the therapeutic effects of HDAC inhibitors in IBD models and patients. This review aims to contribute significantly to the understanding of HDAC inhibitors' importance and prospects in the management of IBD, ultimately paving the way for improved therapeutic strategies in this challenging clinical landscape.

The causal relationship between inflammatory bowel disease (IBD) and diabetes mellitus remains unclear. The aim of this study was to delve into this association and investigate the correlation between AMP-activated protein kinase (AMPK), a target gene of metformin, and the risk of developing IBD. Researchers conducted a bidirectional two-sample Mendelian randomization analysis to examine causal relationships between IBD, including ulcerative colitis and Crohn disease (CD), and diabetes mellitus, encompassing both type 1 diabetes mellitus (T1DM) and type 2 diabetes mellitus (T2DM). Additionally, this study utilized AMPK-related variants associated with HbA1c (%) as instrumental variables for the metformin target gene AMPK to further investigate their association with the risk of IBD. The inverse variance weighted method was used as the primary analytical approach. Mendelian randomization analysis revealed a suggestive association between IBD and T1DM (P = .024). CD was associated with an increased risk of T1DM (P = .011). In the reverse analysis, T1DM also increased the risk of IBD (P = .043). No causal relationship was found between IBD and T2DM in either the forward or reverse analyses. In addition, this study did not find any significant effect of AMPK on IBD. In conclusion, this study suggests a bidirectional association between IBD and T1DM, in which CD may increase the risk of T1DM. However, no causal relationship was found between IBD and T2DM. Furthermore, our findings revealed that the metformin's target gene AMPK had no significant effect on the onset of IBD.