Inflammatory Bowel Diseases

Objective Vedolizumab (VDZ) is effective in ulcerative colitis (UC), but its onset of action may be relatively slow during induction therapy. VSL#3TM, a high-potency multi-strain probiotic, may provide synergistic effects through microbiota modulation and immune regulation. This preliminary real-world study aimed to evaluate the efficacy and safety of VSL#3TM combined with VDZ in patients with UC. Methods Clinical data were retrospectively collected from patients with active UC who received VSL#3TM combined with VDZ for at least 12 weeks at the Second Affiliated Hospital of Zhejiang University School of Medicine in China between January 2023 and December 2024. The primary endpoints were clinical response rates at weeks 6 and 12. Secondary endpoints included clinical remission, changes in inflammatory bowel disease questionnaire (IBDQ) scores, safety assessment. Results Using PRO2 criteria, clinical response rates were 82.4% (14/17) at 6 weeks and 100.0% (17/17) at week 12, with clinical remission in 58.8% (10/17) at week 12. By Full Mayo Score, clinical response and remission at week 12 were 68.8% (11/16) and 50.0% (8/16), respectively. These response rates appeared numerically higher than those reported in published historical VDZ monotherapy studies, although direct comparisons are limited by the single-arm design. Mean IBDQ score improved from 157.3 at baseline to 174.5 at week 12 (p<0.001). The combination was well-tolerated with no serious adverse events. Fatigue, borborygmus, and arthralgia were reported in 1/17 (5.9%), 2/17 (11.8%), and 1/17 (5.9%) patients, respectively. Notably, all 3 patients with baseline history of Clostridioides difficile (CDI) positivity tested negative for both toxin and antigen at 12 weeks; one toxin-positive patient had received anti-CDI antibiotic therapy. Conclusions This preliminary real-world study suggests that VSL#3TM may enhance early clinical outcomes in patients receiving VDZ for active UC. The observed benefits may be related to complementary effects on the gut microbiota and intestinal immune responses, although these mechanisms were not directly assessed. Further larger prospective randomized controlled trials are warranted to confirm these findings.

Background and Aims: Fibrostenotic stricture is a severe complication of Crohn's disease (CD) that affect up to 50% of patients over their lifetime, causing irreversible narrowing of the intestinal lumen and bowel obstruction, but the molecular programs that distinguish stenotic from non-stenotic inflammation and the relative contributions of fibrosis and smooth-muscle remodeling remain incompletely characterized. We aimed to dissect bowel-wall compartment-specific and histology-defined remodeling programs in fibrostenotic CD. Methods: Matched full-thickness terminal ileal tissues from 4 patients with fibrostenotic CD were sampled from stenotic stricture (SS), non-stenotic inflamed bowel (NS), and non-inflamed bowel (NI). Histomorphology-guided NanoString GeoMx whole-transcriptome profiling was performed across mucosa, muscularis mucosae, submucosa, and muscularis propria. GeoMx data were processed by standard software provided by GeoMx platform. DESeq2 models included patient identity as a blocking factor, and the analysis was performed in 74 histologically valid regions of interest (ROIs) representing full spectrum of CD histopathologies. DEGs were defined as adjusted P < .05 and |log2FC| >= 1.0. Results: Out of 18,677 genes analyzed in each of the ROIs, direct SS-versus-NS comparison identified 0 significant DEGs in mucosa, 18 in muscularis mucosae, 43 in submucosa, and 0 in muscularis propria. NS-versus-NI submucosa showed 132 DEGs (131 increased, 1 decreased), dominated by humoral/plasma-cell genes with a modest stromal-remodeling component. SS-versus-NI submucosa showed 144 DEGs (138 increased, 6 decreased) with coordinated contractile, extracellular-matrix/remodeling and cell-matrix adhesion programs. Muscularized versus fibrotic SS submucosa showed 219 DEGs, with marked enrichment of contractile and remodeling genes in muscularized regions. Excluding 5 follicle-containing submucosal ROIs markedly altered the NS comparison but not the core SS fibromuscular program. Exploratory follicular-niche analyses showed that lymphoid follicle-rich (LFR) submucosa was lymphoid/B-cell enriched relative to lymphoid follicle-null (LFN) areas; SS-LFR nevertheless acquired a stronger fibroblast/ECM program relative to NS-LFR, while CCL19 was the only significant LFR-versus-LFN DEG within SS. Conclusions: Fibrostenotic CD is characterized by spatially concentrated submucosal fibromuscular remodeled inflammatory program. Non-stenotic submucosa is heterogeneous and may already show regional stromal remodeling, whereas established stenosis displays a broader and more robust ECM-contractile-adhesion phenotype with molecularly distinct fibrotic and muscularized niches.

Background and Aims: Fibroblast-neutrophil interactions are implicated in ulcerative colitis (UC) treatment resistance, but whether fibroblasts modify neutrophil inflammatory activity remains unclear. We investigated responses to fibroblast exposure, stromal depletion, and 5{beta}1-directed treatment. Methods: We integrated human and mouse colonic single-cell RNA sequencing (scRNA-seq), spatial protein profiling (CODEX), fibroblast-neutrophil coculture, and dextran sulfate sodium (DSS) mouse colitis with fibroblast activation protein (FAP) ablation or 5{beta}1-directed treatment. Readouts included cellular representation and protein fluorescence via flow cytometry, neutrophil extracellular trap (NET)-associated elastase activity, RNA programs and epithelial responses using scRNA-seq. Results: Inflamed UC tissue contained higher fractions of inflammatory fibroblasts and oncostatin M (OSM)- and CXCR4-associated neutrophils. Inflammatory fibroblasts had higher FAP-5{beta}1 module scores, and proximity to FAP-high fibroblasts was associated with higher neutrophil OSM and CXCR4 fluorescence. UC fibroblasts increased neutrophil OSM, CXCR4 and myeloperoxidase (MPO) fluorescence and NET-associated elastase activity relative to control fibroblasts, while 5{beta}1-directed treatment attenuated these responses. Both mouse FAP ablation and 5{beta}1 blockade in DSS colitis reduced histologic inflammation and overall neutrophil frequency. Ablation broadly reduced recovered neutrophil representation, whereas blockade increased OSM-positive and PADI4-positive percentages within neutrophils despite lower MPO fluorescence within these subsets. Both interventions were associated with lower epithelial chemokine scores but distinct absorptive and mucus/secretory responses. Conclusions: Fibroblast exposure modifies neutrophil inflammatory phenotype and effector-associated activity, identifying candidate therapeutic pathways in UC. Evaluating these responses alongside neutrophil representation and tissue inflammation could inform pharmacodynamic assessment of stromal-directed therapies.

Environmental enteropathy (EE) is a chronic, subclinical disorder of the small intestine common in low- and middle-income countries (LMICs), where access to sanitation and exposure to enteric pathogens vary greatly by socioeconomic status (SES). Systemic immune cell activation by enteric microbial exposure is a suspected but poorly characterized driver of EE severity. We hypothesised that adults from Low-SES communities would have more severe EE than adults from High-SES communities and that this would be associated with distinct circulating immune cell phenotypes. We enrolled clinically healthy adults from High- (n=26) and Low-SES (n=76) communities in Lusaka, Zambia. Duodenal biopsies from these adults were used for microscopic morphometry assessments, while plasma and stool biomarkers of epithelial damage, intestinal inflammation, microbial translocation, and systemic inflammation were measured by ELISA. Circulating monocyte, neutrophil and T cell phenotypes were characterised in buffy coat cells by flow cytometry. Compared with the High-SES group, adults from Low-SES communities had higher duodenal villus width and crypt depth and lower epithelial surface area, indicative of more severe EE pathology, and higher levels of plasma biomarkers associated with microbial translocation and systemic inflammation. The Low-SES group also had higher expression of activation markers (CD86 and TLR4) and lower expression of HLA-DR on circulating classical monocytes and neutrophils, higher percentages of gut-homing (4{beta}7+) and activated/exhausted (PD-1+) T cells, including gut-homing (4{beta}7+) regulatory T cells. Principal Component Analysis identified key patterns of immune cell phenotypes across SES groups. Confounder-adjusted linear regression models showed that Principal Component 1 (monocyte/neutrophil activation) was inversely associated with duodenal villus height and epithelial surface area across SES groups. These findings indicate that EE severity varies by SES within LMIC and suggest that monocyte and neutrophil activation is linked to greater duodenal remodelling in adults with EE.

BACKGROUND & OBJECTIVE Tofacitinib, a Janus kinase (JAK) inhibitor, is approved for ulcerative colitis (UC). We investigated baseline and longitudinal transcriptomics and proteomics in intestinal biopsies, peripheral blood, and serum from UC patients starting tofacitinib to characterise treatment-associated effects and identify which molecular compartment harbours the most predictive response-associated biomarkers. METHODS In this prospective, open-label study, patients with moderately to severely active UC started tofacitinib 10 mg BID for eight weeks. Clinical, biochemical, endoscopic, and histological data were collected at baseline and week 8. The primary outcome, histo-endoscopic mucosal improvement (HEMI), was defined as endoscopic Mayo subscore [&le;]1 with histologic remission (Robarts Histopathology Index [&le;]3, no mucosal neutrophils). Mucosal biopsies and peripheral blood were collected at baseline and week 8 for bulk RNA-sequencing (RNA-seq); biopsies and serum underwent proteomic profiling using Olink Explore 384 (Cardiometabolic, Inflammation, Neurology, Oncology panels). RESULTS In total, 127 paired multi-omic samples were collected longitudinally from 40 UC patients: 15 (38%) achieved HEMI at week 8 (responders), 13 (32.5%) were late responders, and 12 (30%) were non-responders. Pretreatment mucosal biopsies from future responders showed elevated interferon, IL-6-family, IL-2/common-{gamma}-chain, and T-cell-receptor signalling gene expression, which declined on treatment only in responders. A responder-specific JAK-STAT-dependent mechanism spanned interferon, cytokine-receptor, T-cell-receptor, and NF-{kappa}B signalling, with concordant gene- and protein-level reductions. Compared with a public infliximab dataset, JAK-STAT/interferon downregulation was shared and response-independent, while non-canonical NF-{kappa}B downregulation was tofacitinib-specific. In blood, shared pathway labels reflected distinct genes from mucosal effectors. CONCLUSION Response to tofacitinib depends on a JAK-tractable mucosal pathway absent in non-responders, suggesting a pretreatment biomarker for predicting treatment response.

Background Endoscopic resection is used for the management of dysplasia in ulcerative colitis (UC), but a subset of patients develop subsequent advanced neoplasia (AN), i.e., high-grade dysplasia and/or colorectal cancer, despite apparently complete resection with histologically clear margins. Current risk stratification relies predominantly on histopathological and procedural features, which does not capture underlying genomic field cancerization of morphologically normal mucosa. Objective To determine whether genomic alterations within histologically non-dysplastic resection margins are associated with subsequent neoplastic progression following endoscopic resection of UC-associated dysplasia. Design We analysed a retrospective cohort of 51 UC patients, who underwent endoscopic resection of dysplastic lesions at a tertiary referral centre, with a median follow-up of 1947 days. 11 of these had local progression. We performed low-coverage whole genome sequencing (lcWGS) of 56 dysplastic lesions and 91 adjacent histologically non-dysplastic margins. Somatic copy number alteration (CNA) burden and phylogenetic analysis were correlated with progression to AN . Results Histologically non-dysplastic margins from lesions that subsequently progressed to AN demonstrated significantly higher CNA burden compared with non-progressors. In multivariate analysis high margin CNA burden was independently associated with local progression, whereas histologically clear resection margins and en bloc excisions were not. Conclusion Histological clearance does not necessarily indicate clearance of the cancerised field in UC-associated dysplasia. Genomic detection of field cancerisation within histologically non-dysplastic resection margins identifies patients at increased risk of subsequent neoplasia and provides a potential biomarker for biologically informed post-resection surveillance.

Clostridioides difficile is a major cause of healthcare associated infections. C. difficile infection (CDI) is a toxin-mediated disease driven by the secretion of two large protein toxins, Toxin A (TcdA) and Toxin B (TcdB). TcdA and TcdB cause neurogenic inflammation that can contribute to intestinal inflammation in rat and mouse models. Substance P (SP), a potent vasoactive neuropeptide, is a major contributor to C. difficile toxin induced inflammation in animal models. SP acts on multiple receptors including the high affinity receptor NK1-R, and lower affinity receptors (Mrgprb2 and NK2-R). Through in vivo mouse infection models, we confirmed the effects of SP in hypervirulent C. difficile are largely mediated by the neurokinin-1 receptor (NK1-R), the high affinity receptor for SP. Through genetic mice that lack mast cells (cKitW-sh) we determined that mast cells which respond to SP in certain kinds of neurogenic inflammation appear dispensable for inflammation caused by C. difficile infection. We explored the role of NK1-R antagonists in a retrospective study of a large clinical cohort. We determined that, after propensity matching, NK1-R antagonists were associated with a significant survival benefit and that patients treated with NK1-R antagonists showed evidence of reduced vascular inflammation (increased serum albumin). Together these data suggest blocking SP activity through antagonism of NK1-R with small molecule inhibitors may be a useful strategy for adjunctive treatment during C. difficile infection.

The aim of this study was to determine whether the frequency of metabolic dysfunction-associated steatotic liver disease (MASLD) and the severity profile of inflammatory bowel disease (IBD) differ across body mass index (BMI) categories. A retrospective analysis was performed using 400 inpatient medical records from 2023-2024 with verified ulcerative colitis or Crohn's disease and sufficient information on anthropometry, hepatic status, and intestinal disease activity. The cohort comprised 118 patients with normal BMI, 176 with overweight, and 106 with obesity. MASLD status was reconstructed from routine clinical documentation and required hepatic steatosis in the appropriate cardiometabolic context. Ultrasonography was the principal source of evidence for steatosis; laboratory findings, non-invasive indices, and elastography were considered supportive when available. Ulcerative colitis activity was assessed with the Mayo Score and Crohn's disease activity with the Crohn's Disease Activity Index; disease-specific results were harmonized into mild, moderate, and severe categories for pooled comparisons. MASLD was identified in 181 of 400 patients (45.3%). Its frequency increased from 20.3% in the normal-BMI group to 49.4% in the overweight group and 66.0% in the obesity group (chi2=49.29; p<0.001). The largest absolute increase, 29.1 percentage points, occurred between normal BMI and overweight. The proportion of severe IBD rose in the same order, from 6.8% to 14.8% and 32.1% across the three BMI strata (chi2=39.45; p<0.001). In unadjusted pairwise comparisons, the odds of MASLD were higher with overweight than with normal BMI (OR=3.83; 95% CI 2.24-6.55) and higher with obesity than with normal BMI (OR=7.62; 95% CI 4.17-13.91); obesity also differed from overweight (OR=1.99; 95% CI 1.21-3.28). These findings demonstrate an ordered BMI-related pattern in which MASLD becomes more frequent and severe IBD represents a larger share of cases. However, MASLD was still documented in approximately one fifth of patients with normal BMI, indicating that BMI is useful for clinical prioritization but not for excluding steatotic liver disease. Because the study was retrospective, liver assessment reflected routine care, and the effect estimates were not adjusted for treatment exposure, disease duration, or other metabolic covariates, the observed relationships should be interpreted as associations rather than causal effects.

Background and aimsCrohns disease (CD) is a highly heterogeneous disease. Patients with similar characteristics at baseline may end up on very different therapeutic and surgical paths. We aimed to identify disease-course trajectory phenotypes from a mix of clinical, treatment, surgical and comorbidity variables, and evaluate whether information already available at diagnosis could anticipate which trajectory a patient would follow. MethodsWe analysed a retrospective cohort of 98 unique CD patients enrolled at the IRCCS Ca Granda Policlinico Hospital, Milan. Factor analysis of mixed data (FAMD) was applied to 30 disease-course variables spanning demographic and Montreal descriptors, extra-intestinal manifestation burden, individual advanced-therapy drug exposures, surgical burden and comorbidity/symptom burden; clusters were then ranked by treatment burden using a line-weighted therapy score built separately from drug line positions and therapeutic-class weights. Clustering itself was carried out in the retained FAMD coordinate space, and cluster robustness was checked with silhouette metrics and bootstrap Jaccard stability. Baseline-associated variables were assessed separately, while advanced-therapy episodes were reconstructed from the therapy timeline. ResultsThree trajectory phenotypes emerged: C1 (n=56), C2 (n=31) and C3 (n=11). C3 was characterised by younger age at diagnosis, a heavier extra-intestinal manifestation burden, more intensive and prolonged therapy, greater biologic exposure and a higher cumulative number of surgeries, with comorbidity burden rising across the gradient. Montreal behaviour and comorbidity burden emerged as the strongest baseline correlate of trajectory membership, ahead of age at diagnosis and extra-intestinal manifestation burden; penetrating (B3) behaviour, notably, was actually more common in C1 than in C3. A model built on the diagnosis-available variables independently linked to trajectory membership (age at diagnosis, disease location and Montreal behaviour) showed moderate discrimination for the C3 trajectory (area under the curve, AUC=0.80, 95% CI 0.67-0.93). A sensitivity analysis that also added extra-intestinal manifestation count and comorbidity burden, whose timing relative to diagnosis we could not confirm, pushed discrimination to AUC=0.90. ConclusionsFAMD-space clustering identified stable, clinically interpretable CD-course trajectory phenotypes, including a small, high-burden C3 subgroup. This C3 trajectory, small, early-onset and treatment-refractory, shares clinical features that overlap with the difficult-to-treat CD phenotype, though C3 was derived by unsupervised clustering rather than validated against that frameworks own criteria; variables available at or near diagnosis showed exploratory discrimination for the high-burden C3 trajectory, though external validation and careful timing verification are needed before any clinical use.

BACKGROUND & AIMS: Inflammatory bowel disease (IBD) is often diagnosed months to years after symptoms begin, and diagnostic delay is associated with complications. We tested whether longitudinal machine learning using electronic health record (EHR) data can identify incident IBD before diagnosis, and quantified lead time and deployment burden. METHODS: We studied adults with an IBD-compatible symptom, sign, or finding at UCSF (2012-2024). Incident cases were confirmed by structured filtering and validated large language model note review. We trained a state space model (Mamba) and comparators on pre-diagnostic EHR data, excluding diagnostic-workup features, and assessed discrimination at 6- and 12-month landmarks. We externally tested Mamba without recalibration at ZSFG, a safety-net hospital serving a demographically and socioeconomically distinct population, and simulated diagnosis-code-only deployment at UCSF. RESULTS: Six months after presentation, among patients still undiagnosed (67% of UCSF test cases), Mamba achieved an AUROC of 0.969 (95% CI, 0.928-0.999) at UCSF and 0.965 (0.952-0.976) at ZSFG. Median lead time was 20 months at UCSF and 15 months at ZSFG. Among future cases with an initially normal colonoscopy (N=32) or a histological finding of acute inflammation without chronicity (N=63), the model flagged 84% and 89% of these patients, respectively, before those procedures, indicating the potential for pre-diagnostic detection. Among 358,886 symptomatic patients not used for training (60 incident cases), the diagnosis-code-only model achieved an AUROC of 0.926; reviewing 20 alerts/month identified 34 cases (PPV, 1.09%; 64-fold above baseline). CONCLUSIONS: Longitudinal machine learning can identify increased IBD risk months to years before diagnosis and may define a population for prospective studies of early IBD biology. Prospective evaluation should determine whether earlier identification reduces diagnostic delay.

Background and aims. Inflammatory Bowel Disease (IBD) is a complex immune-mediated condition with a strong genetic contribution. The genetics of IBD are highly complex, with inflammation, autoimmunity, and mucosal immunity pathways involved in its pathogenicity. GenePy is a gene-level disease burden metric. The integration of clinical and genetic data and the application of machine learning methods can aid patient stratification for personalised care. Methods. Lists of consensus IBD pathway genes were curated. GenePy scores were computed from whole exome sequencing data. A K-Means algorithm was optimised using clustering quality and stability metrics on the GenePy scores of genes in each IBD pathway, and the results replicated in three independent IBD cohorts (SPARC IBD, MSCCR IBD, and Southampton IBD). Chi-square tests assessed the association between cluster assignment and phenotypic features, and were multiple test corrected via Benjamini-Hochberg FDR. Results. A strong association was replicated for NOD signalling genes driving IBD subtype, Crohns disease behaviour, and IBD surgery across all cohorts, as well as granuloma in Southampton IBD. This was mainly driven by NOD2. Similar genetic clustering patterns were observed across all cohorts, with additional phenotypic enrichment in clusters driven by NLRP1 (surgery in MSCCR IBD), and nominally significant enrichment for disease behaviour linked to BIRC2 (B2 in Southampton IBD and B2B3 in SPARC IBD). Conclusions. This analysis identified a common genetic architecture across NOD signalling genes across IBD cohorts, replicated a signal for NOD2 as a monogenic driver of disease with a strong phenotypic enrichment, and identified other putative genetic drivers of IBD, such as the NLRP1 gene.

Using an analysis pipeline that combines machine learning-based feature selection with classical statistical modelling, we aimed to predict incident inflammatory bowel disease (IBD) and to identify candidate proteins associated with disease development. We used UK Biobank data in an observational cohort study of 52,331 participants with proteomics data and without a history of IBD. The cohort was split into an 80/20 train/test dataset, and three separate extreme gradient boosting models were trained on the training dataset. Using Shapley values, we ranked the predictive importance of 2,912 proteins for incident IBD, Crohn's disease (CD), and ulcerative colitis (UC). The top 20 proteins per outcome served as features in multivariate Cox models predicting 350 incident cases over 14 years. All three proteomics Cox models showed moderate discrimination in the test dataset, with the UC model performing the best (C-index: 0.68), followed by IBD (C-index: 0.65), and CD (C-index: 0.60). All proteomics models outperformed clinical models. Smoking remained the only significant clinical predictor in the combined proteomics + clinical model. 48 unique proteins were identified across the three models, with 16 reaching statistical significance (p< 0.05). Machine learning-based feature selection with statistical survival modelling identifies plasma proteins that predict incident IBD and highlight biologically plausible, potentially targetable pathways in the preclinical phase of IBD.

Background: Patients receiving anti-TNF treatment for chronic inflammatory disease display impaired antibody responses, but it remains unclear how immune memory formation is affected. We evaluated antibody responses and memory B cells (Bmem) after COVID-19 booster vaccination in inflammatory bowel disease (IBD) patients receiving anti-TNF treatment. Methodology: Blood was sampled at baseline, 1, and 6 months after WH1/BA.5 bivalent or XBB.1.5 monovalent vaccination from 27 IBD patients receiving intravenous anti-TNF and 44 controls. Neutralizing antibodies were measured using an infectious virus assay. SARS-CoV-2 spike receptor binding domain (RBD)-specific serum IgG was quantified by ELISA, and RBD-specific Bmem were immunophenotyped by flow cytometry using recombinant proteins from ancestral, Omicron BA.1, BA.5, XBB.1.5, and JN.1 variants. Results: Serum IgG to vaccine RBD and neutralizing antibodies in patients increased pre to 1 month post-vaccination, but were lower than controls. Ancestral-, BA.5- and XBB.1.5-specific Bmem increased after vaccination but were significantly lower in patients than controls. Within RBD-specific Bmem, frequencies of recently activated CD21lo cells were increased after vaccination, and were higher in patients than controls. Fewer antigen-specific Bmem in patients expressed IgG4, and more expressed IgG3 or IgD following vaccination. Following vaccination, more RBD-specific Bmem recognized multiple viral variants. However, patients had fewer Bmem that could bind to subvariants than controls. Conclusion: Antibody and Bmem responses to COVID-19 booster vaccination in anti-TNF-treated IBD patients displayed reduced capacity, durability and cross-reactivity, suggesting impaired immune memory for protection against breakthrough infection. This supports the recommendation for annual booster vaccination to prevent severe disease and viral spread.

Intestinal epithelial barrier is a key feature of the healthy gut, and disruption of this barrier is a driver of mucosal inflammation. Integrity of the intestinal epithelial barrier is controlled by tight junctions (TJs) and adherens junctions (AJs) associated with the underlying actin cytoskeleton. Posttranslational modifications of actins affect the cytoskeletal assembly and dynamics, however whether such modifications regulate epithelial barriers remains unknown. SETD3 methyltransferase methylates actins at the His73 residue, thereby enhancing filamentous (F)-actin polymerization and turnover. This study examines the role of SETD3 in regulating structure and function of normal intestinal epithelial barrier, as well as its involvement in barrier disruption during mucosal inflammation. siRNA mediated knockdown of SETD3 in DLD-1 and HCA-7 human intestinal epithelial cells (IEC) resulted in several functional and morphological cell abnormalities. These include increased permeability of the IEC barrier, diminished assembly of the perijunctional F-actin belt, increased cell size, and delayed TJ reassembly during calcium switch. Consistently, SETD3 knockout (KO) mice displayed increased intestinal permeability and decreased labeling intensity of apical {beta}-actin as compared to wildtype controls. Furthermore, SETD3 KO mice showed increased cell stemness and proliferation in colonic epithelium without defects in AJ/TJ assembly and secretory cell differentiation. In addition, SETD3 KO mice developed more severe disease symptoms during dextran sodium sulfate (DSS)-induced colitis, which were accompanied by accelerated mucosal erosion and increased macrophage, T cell and neutrophil infiltration into colonic tissue. Overall, our data suggests that SETD3 acts as a novel positive regulator of the intestinal epithelial barrier and plays a protective role during intestinal mucosal damage and inflammation.

Background There are currently no available biomarkers that predict the clinical outcome of ulcerative colitis (UC) patients after anti-TNF withdrawal. Here we developed a semi-supervised machine learning framework on RNA-seq data derived from rectal biopsies to predict relapse following anti-TNF discontinuation. Methods We included UC patients (n=136) enrolled in the prospective, randomized controlled BIOSTOP trial. Patients were assigned to a withdrawal group (stopped treatment immediately) or a maintenance group (stopped treatment after 2 years). A machine learning framework was trained on gene expression data from mucosal biopsies collected at baseline from the withdrawal group and validated in the maintenance group using baseline samples (test cohort) and 2-year follow-up samples (interference cohort). Results A semi-supervised machine learning model, combining a shared UMAP manifold representation with LabelSpreading on a targeted 38-gene panel achieved an AUC of 0.794, a sensitivity of 90.3%, and a specificity of 73.1% on the test cohort, and an AUC of 0.711, a sensitivity of 82.9%, and a specificity of 42.3% on the inference cohort. Applying Shapley Additive exPlanations (SHAP) we found that IL1B, TYROBP, REG1B, S100A8, and TNF showed the highest predictive importance for relapse risk, whereas MUC2, HMGCS2, and CDKN1A displayed the highest predictive importance for sustained remission. Conclusion The high sensitivity makes the model a promising screening tool to prevent withdrawal-related relapse, though its moderate specificity underscores the need for multi-center validation in larger, more diverse cohorts before clinical deployment.

Background: Inflammatory bowel disease (IBD) has been linked to a two- to eightfold increase in colorectal cancer (CRC) risk. However, particular genes that bridge intestinal dysbiosis and oncogenic transcriptional reprogramming remain unclear. The Hippo/YAP pathway is a major regulator of intestinal epithelial homeostasis whose effector YAP is hyperactivated in CRC, but its transcriptional engagement in IBD mucosa and its link to specific cancer-risk genes has not been thoroughly mapped. Methods: Bulk RNA-seq data were integrated from two independent cohorts: GSE235236 (IBD colon mucosa; UC/CD vs. healthy controls; n = 56) and TCGA-COAD/READ (CRC tumors stratified by YAP activity; n = 592). Differential expression analysis was conducted separately within each cohort using Welch's t-test with Benjamini-Hochberg FDR correction. YAP transcriptional activity was estimated per sample as the mean row-wise Z-score of seven canonical YAP target genes, and TCGA tumors were stratified into Hippo-High (Q4) and Hippo-Low (Q1) groups. Genes showing consistent dysregulation across both cohorts were identified and ranked to define a Dysbiosis-Hippo Response (DHR) module, which was further organized into functional gene archetypes. Results: IBD mucosa showed 2,848 significantly dysregulated genes (FDR < 0.05). Comparison with the CRC cohort identified 120 genes showing concordant dysregulation, forming the DHR module. These genes were significantly enriched in TNF-alpha signaling via NF-kB (adjusted p = 0.006), inflammatory response (adjusted p = 0.013), and Myogenesis (adjusted p = 0.013). DHR gene classification revealed three functional archetypes: (i) innate immune activation (SPI1, OSM, IL11, LILRA2, SLC11A1) reflecting convergent myeloid reprogramming; (ii) epithelial-mesenchymal transition (TWIST1, SNAI1, PRRX2, MMP9) priming invasive potential before malignancy; and (iii) tumor microenvironment immune regulation (TN-FRSF4, TNFRSF18, PDCD1, VASN, SPON2) shaping immune tolerance. Interestingly, the canonical YAP target genes (CTGF, CYR61, ANKRD1, AMOTL2, and FSTL1), sharply upregulated in Hippo-High CRC, were essentially unchanged in IBD mucosa. This signifies that the shared DHR programme operates through non-canonical YAP effectors. And yet, YAP target scores are positively correlated with DHR module expression across IBD samples (Spearman rho = 0.726, p = 2.5 x 10-10). Conclusions: Our findings define a three-archetype DHR module that links gut dysbiosis to YAP-driven oncogenesis at single-gene resolution. The programme shared between IBD and CRC is driven by innate immune activation, EMT priming, and remodeling of the immune microenvironment, not by the canonical CTGF/CYR61 YAP target axis, which appears only at the CRC stage. This gene-level framework provides tractable mechanistic targets for chemoprevention and biomarker development at the inflammation-to-cancer transition.

Formation of autoantibodies to transglutaminase 2 (TG2) in celiac disease likely involves TG2-gluten complexes that allow gluten-specific CD4+ T cells to provide help to TG2-specific B cells. To investigate whether TG2 derived from intestinal epithelial cells (IECs) contributes to this process, we generated mice with inducible IEC-specific expression of TG2 fused to a deamidated gluten peptide (DGP) containing a T-cell epitope. Upon induction, the TG2-DGP fusion protein was expressed in IECs and released into the intestinal lumen. In HLA-DQ2.5 transgenic mice with activated gluten-specific CD4+ T cells and naive TG2-specific B cells, expression of TG2-DGP was immunogenic and drove the production of intestinal and systemic anti-TG2 autoantibodies. TG2-specific B cells predominantly expanded in Peyers patches, suggesting that their priming and subsequent differentiation into lamina propria TG2-specific IgA+ plasma cells occurs in gut-associated lymphoid tissues. The findings demonstrate immunogenicity of IEC-derived TG2-DGP fusion antigen supporting the notion of a pathogenic role for luminal TG2 in driving anti-TG2 autoimmunity in celiac disease.

Inflammatory bowel disease (IBD) is a heterogeneous chronic disease driven by dysregulated mucosal immunity and impaired epithelial barrier function. Although biologics have improved disease management, they are frequently associated with systemic immunosuppression and adverse effects, highlighting the need for localized therapeutic strategies that both control inflammation and promote tissue repair. Here, we developed a protein bispecific termed 7A2-IgG4-IL22, composed of a human IgG4-Fc domain displaying an antagonistic anti-human MAdCAM-1 single chain (sc)-Fv and a human interleukin (IL-)22. The anti-MAdCAM-1 scFv retained the functional activity of the parental monoclonal antibody, inhibiting T cell activation, expansion and differentiation from naive precursors. Blockade of the MAdCAM-1 signaling axis also reduced production of pro-inflammatory cytokines relevant to IBD pathogenesis, including IFN{gamma} and TNF. On the epithelial side, the IL-22 cargo induces robust signaling in epithelial cells, promoting the expression of IL-22 response genes associated with antimicrobial defense, mucosal homeostasis, as well as IL-10 and CXCL1 expression. This effect contributes to immune cell trafficking to the intestinal mucosa. Together, this bispecific provides a localized dual-mechanism strategy for restoring intestinal immune homeostasis.

Background and study aims: Endoscopic assessment of ulcerative colitis (UC) is central to clinical decision-making however remains subjective and limited in characterisation of disease distribution. Artificial intelligence (AI) enables analysis of entire endoscopic examination, rather than relying on selected views. We aimed to develop and validate a deep learning model for automated assessment of UC severity from full-length endoscopic videos, introducing spatial representation of inflammation (Continuous Disease Score, CDS), and assess histological correlation. Patients and methods: Full-length endoscopy videos from adult patients with UC undergoing colonoscopy or flexible sigmoidoscopy were analysed; isolated proctitis was excluded. Videos were segmented and annotated using Mayo Endoscopic Score (MES) and Ulcerative Colitis Endoscopic Index of Activity (UCEIS). A deep learning model was trained for frame-level quality control and severity prediction, enabling analysis of full-length videos. Performance was evaluated using quadratic weighted kappa (QWK) and Cohen's kappa, with patient-level separation between datasets. CDS was derived from UCEIS predictions to quantify cumulative inflammatory burden, spatial extent of disease and histological prediction. Results: A total of 67 videos from 59 patients were included. The model demonstrated agreement for remission classification (MES=0 {kappa} 0.76; UCEIS[&le;]1 {kappa} 0.84). CDS enabled quantification of inflammatory burden and revealed spatial heterogeneity not reflected in categorical scores. Agreement with histology was strong (AUROC 0.84-0.87). Conclusions: AI-based analysis enables automated assessment of UC activity from full-length endoscopic videos, including remission detection and estimation of histological healing. CDS provides continuous characterisation of inflammatory burden and disease extent beyond conventional categorical scores, with potential to support more standardised assessment in clinical trials and practice.

Background: Celiac Disease (CeD) is an immune-mediated enteropathy linked to gut microbiome dysbiosis driven by dietary gluten ingestion. Although most patients achieve clinical and histologic remission on a gluten-free diet (GFD), persistent symptoms and incomplete mucosal recovery are common. While gut microbiome alterations during active CeD are well documented, taxonomic and functional shifts during histologic remission remain considerably less characterized. Methods: We utilized PacBio's HiFi long-read metagenomic sequencing to profile the gut microbiome of 21 pediatric participants with histologically confirmed CeD remission on a GFD, active CeD, and non-CeD controls. Results: High-fidelity long reads enabled reconstruction of 857 high-quality metagenome-assembled genomes and high-resolution species- and pathway-level profiling. Microbial diversity analysis showed reduced alpha-diversity in remission patients compared with controls. Differential abundance analysis revealed persistent taxonomic and functional alterations in CeD remission, indicating incomplete restoration of microbiome homeostasis. Notably, remission patients showed depletion of commensals such as Alistipes finegoldii, Bifidobacterium longum, and Bacteroides uniformis, and persistence of some inflammation-associated taxa, alongside enrichment of beneficial species, including short-chain fatty acid producers, and suppression of other inflammation-associated taxa. At the functional level, pathways related to broader metabolic homeostasis were depleted in remission, while anti-inflammatory pathways such as propionate metabolism were enriched. Conclusions: Our findings suggest a distinct microbial ecosystem during histologic remission characterized by residual taxonomic dysbiosis and functional constraints, accompanied by adaptive remodeling that may promote mucosal healing. This work advances understanding of the gut microbiome in CeD after mucosal recovery and lays the groundwork for future studies of microbiome-based therapeutic interventions.