Gut

ObjectiveConflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models. Goal: Define complex interactions between resident microbes and their association in PSC patients by studying antibiotic-treated specific pathogen-free (SPF) and germ-free (GF) multi-drug-resistant 2 deficient (mdr2-/-) mice. DesignWe measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, fecal 16s rRNA gene profiling, and metabolomic endpoints in gnotobiotic and antibiotic-treated SPF mdr2-/- mice and targeted metagenomic analysis in PSC patients. ResultsGF mdr2-/- mice had exaggerated hepatic inflammation and fibrosis with 100% mortality by 8 weeks; early SPF autologous stool transplantation rescued liver-related mortality. Broad-spectrum antibiotics and vancomycin alone accelerated disease in weanling SPF mdr2-/- mice, indicating that vancomycin-sensitive resident microbiota protect against hepatobiliary disease. Vancomycin treatment selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increased cytolysin-expressing E. faecalis and E. coli liver translocation; colonization of gnotobiotic mdr2-/- mice with translocated E. faecalis and E. coli strains accelerated liver inflammation and mortality. Lachnospiraceae colonization of antibiotic pre-treated mdr2-/- mice reduced liver fibrosis, inflammation and translocation of pathobionts, while Lachnospiraceae-produced SCFA decreased fibrosis. Fecal E. faecalis/ Enterobacteriaceae was positively and Lachnospiraceae was negatively associated with PSC patients clinical severity Mayo risk scores. ConclusionsWe identified specific functionally protective and detrimental resident bacterial species in mdr2-/- mice and PSC patients with associated clinical outcomes. These insights may guide personalized targeted therapeutic interventions in PSC patients.

SummaryPrimary sclerosing cholangitis (PSC) is an inflammatory disease of the biliary tract eventually leading to bile duct destruction, liver failure, cholangiocellular adenocarcinoma and/or death. No disease modifying treatments are available1. Especially cytotoxicity of bile acids, are discussed as potential driver of disease progression2. Cholangiocytes are protected by a bicarbonate umbrella formed by the glycocalyx, a dense layer of membrane bound polyglycans extending into the extracellular space3,4. Bile of PSC patients harbors a unique microbiome5. Here we identified a new factor in the pathogenesis of PSC. The bacterial degradation of sialic acid and galactose are associated with a poor event free survival of PSC patients and could identify bacterial liberation of sialic acid as crucial element in cholangiocyte damage using cell culture experiments, individualized organoid models and liver biopsies. With this study the view on bacteria-host interactions in bile duct associated diseases is widened. Functional patterns of the bacterial community are crucial for bile duct destruction in PSC patients. This opens a new field of diagnostic tools, disease modifying treatment options and identification of patients at risk.

Inflammatory bowel disease (IBD) is a group of chronic diseases, affecting different parts of the gastrointestinal tract, that mainly comprises Crohns Disease (CD) and Ulcerative Colitis (UC). Most IBD genomic research to date has involved genome-wide association studies (GWAS) of common genetic variants, mostly in Europeans, resulting in the identification of over 200 risk loci. The incidence of IBD in Ashkenazi Jews (AJ) is particularly high compared to other population groups and rare protein-coding variants are significantly enriched in AJ. These variants are expected to have a larger phenotypic effect and are hypothesized to complement the missing heritability that cannot be fully addressed by GWAS in IBD. Therefore, we genetically identified 4,974 AJs IBD cases and controls from whole exome sequencing (WES) data from the NIDDK IBD Genetics Consortium (IBDGC). We selected credible rare variants with high predicted impact, aggregated them into genes, and performed gene burden and pathway enrichment analyses to identify 7 novel plausible IBD-causing genes:NCF1, CES1, ICAM1, INPP5D, ABCB1, IL33 and TLR4. We further perform bulk and single-cell RNA sequencing, demonstrating the likely relatedness of the novel genes to IBD. Importantly, we demonstrate that the rare and high impact genetic architecture of AJ adult IBD displays a significant overlap with very early onset IBD (VEOIBD) genetics. At the variant level, we performed Phenome-wide association studies (PheWAS) in the UK Biobank to replicate risk sites in IBD and reveal shared risk sites with other diseases. Finally, we showed that a polygenic risk score (PRS) has high power to differentiate AJ IBD cases from controls when using rare and high impact variants.

Background & AimsHeterozygous inactivating mutations of Serine Threonine Kinase 11 (STK11)/Liver Kinase B1 (LKB1) are causative to the Peutz-Jeghers syndrome (PJS), a hereditary disease characterized by gastrointestinal hamartomatous polyposis and increased cancer susceptibility. While LKB1 loss-induced polyp formation has been ascribed to non-epithelial tissues, how LKB1 deficiency increases cancer risk of patients by altering the phenotypical landscape and hierarchical organization of epithelial tissues remains poorly understood. MethodsUsing CRISPR/Cas9, we generated heterozygous and homozygous Lkb1-deficient mouse small intestinal and human colon organoids. These organoids were characterized by an integrated approach that combines imaging, bulk and single-cell RNA sequencing and growth factor dependency assays. Our findings were validated in human PJS-derived tissues using immunohistochemistry and linked to colorectal cancer profiles using the TCGA cancer database. ResultsOur results reveal that heterozygous Lkb1 loss is sufficient to push intestinal cells into a premalignant transcriptional program associated with serrated colorectal cancer, which is further amplified by loss-of-heterozygosity. This altered epithelial growth state associates with persistent features of regeneration and enhanced EGFR ligand and receptor expression, conferring niche-independent growth properties to Lkb1-deficient organoids. Moreover, our newly generated LKB1-mutant signature is enriched in sporadic serrated colorectal cancer, and synergistic cooperation of Lkb1-deficiency with mutant Kras was experimentally confirmed by assessing organoid growth properties and transcriptomes. ConclusionsHeterozygous loss of LKB1 pushes intestinal cells into a chronic regenerative state which is amplified upon loss-of-heterozygosity. Lkb1-deficiency thereby generates fertile ground for serrated colorectal cancer formation in the intestine, potentially explaining the increased cancer risk observed in PJS.

Background & AimsHepatocellular carcinoma (HCC) is the third top cause of cancer death globally, often arising on a background of cirrhosis. Here, we aimed to establish novel genetic drivers of HCC across ancestries at a population level through a large meta-analysis of all-cause HCC. Approach & ResultsWe included 15 cohorts comprising 17,329 HCC cases and 2,424,298 controls in this meta-analysis. We found 15 genome-wide significant (P < 5x10-8) germline loci, 6 novel in/near GCKR, MTTP, ADH5, MYC, MAP3K9, and GABPB2. MAP3K9, TERT, and GABPB2 variants act independently of cirrhosis on both co-localisation analysis and sensitivity analyses. There was significant ancestral heterogeneity in 6 loci including variants in the HLA locus that had divergent effects on HCC risk between East Asian and European ancestries. Fine-mapping identified 11 potentially causal coding variants, including p.Leu446Pro in GCKR and p.Asp418Glu in MEN1. MEN1, MYC, and TERT are all involved in the beta-catenin pathway transactivation complex. Transcriptome-wide analysis identified enrichment of germline-encoded DHRS1 in HCC. Regulome-wide analysis replicated the germline signal for EPHA2 and found a novel chromatin accessible region containing genes ZNF367 and HABP4. Finally, we demonstrated that population-level genetic architecture for HCC overlaps with steatotic and viral liver disease, and individuals with genetic risk for lower BMI have higher risk of HCC. ConclusionsGenetic risk for HCC is determined by germline susceptibility to beta-catenin pathway activation and cirrhosis. HCC is driven by both heterogenous and homogenous genetic factors across ancestries, which require further ancestral diversity in liver GWAS to fully dissect.

BackgroundCurrent British Society of Gastroenterology (BSG) guidelines misclassify metachronous lesion risk after polypectomy in approximately 40% of patients. Building on evidence that immune exclusion drives progression of adenomas to colorectal cancer, this study examined immune profiles in screen-detected adenomas as a predictive biomarker for metachronous lesion risk. MethodsPatients undergoing polypectomy within the Scottish Bowel Screening Programme, with surveillance colonoscopy between 6 months and 6 years were included. Chromogenic immunohistochemistry (IHC; n=2642), 6-plex multiplex immunofluorescence (mIF; n=334), and spatially resolved 6000-plex single cell transcriptomics (n=7) were applied to adenoma microarrays. Cell density and location were measured using QuPath. Hierarchical then K-means clustering was used to define immune cell density-based clusters, which were compared to future lesion events using Kaplan-Meier curves and the log rank test. ResultsAfter adjustment for age, sex, site, size and dysplasia, adenoma CD3+ T cell density was significantly associated with future colorectal neoplasia (HR 1.43, 95% CI 1.19-1.71, p<0.001). Using mIF three immune cell density clusters were identified; 1) high T cell density, low macrophage density, 2) low T cell density, low macrophage density, and 3) high T cell, macrophage and SMA density, with significant differences in future lesion risk (Cluster 1: 22%, Cluster 2: 41%, Cluster 3: 36%, p=0.032). Bulk RNAseq and spatial transcriptomic analysis revealed significant variation in T cell and macrophage co-location and gene expression profiles between clusters. ConclusionAdenoma immune contexture emerges as a determinant of future metachronous lesion risk, offering a novel biomarker to refine surveillance and reduce disease burden. SummaryWhat is already known on this topic: O_LIPost-polypectomy surveillance is currently recommended to patients with high-risk pathological features to detect metachronous lesions and cancer. However current guidelines misclassify risk in a proportion of patients, leading to unnecessary surveillance for some, whilst falsely reassuring others. C_LI What this study adds: O_LIAnalysis of this large post-polypectomy surveillance cohort reveals that adaptive immune responses within removed index adenomas predicts low risk of metachronous lesions, while an immune excluded phenotype signals higher risk, independent of pathological characteristics, and patient risk factors. C_LI How this study might affect research, practice or policy: O_LIDefining immune cell spatial distributions and interactions that drive future adenoma and cancer risk will enable more precise risk stratification for surveillance, informing surveillance guidelines and shaping targeted colorectal cancer prevention strategies. C_LI

BackgroundInfliximab is an effective therapy for pediatric inflammatory bowel disease (IBD), but a substantial proportion of patients experience primary non-response or relapse. Tissue eosinophilia has been implicated in treatment resistance, yet its predictive value in pediatric populations remains unclear. MethodsWe conducted a retrospective nested case-control study including 80 pediatric IBD patients treated with infliximab at CHU Sainte-Justine between 2014 and 2023 Relapse cases (n = 42) were defined by an increase in the short Pediatric Crohns Disease Activity Index (sPCDAI) [&ge;]10, and compared with non-relapse controls (n = 38). Tissue eosinophil counts were quantified from diagnostic biopsies by blinded reviewers. Primary non-response was defined as a lack of clinical improvement before treatment change. Logistic regression and receiver operating characteristic (ROC) analyses were performed to assess associations between eosinophil counts and treatment outcomes. Results80 patients were included in the study. Median age at diagnosis was 14.4 years (interquarile range [IQR] 3.65). Forty patients had a diagnosis of ulcerative colitis (UC, 50%) and the other half had a diagnosis of Crohns disease (CD). Baseline eosinophil counts were not associated with subsequent relapse (odds ratio [OR] 1.02, 95% CI 0.98-1.06, p = 0.31), and ROC analysis demonstrated poor discrimination (AUC 0.57). In contrast, higher eosinophil counts were associated with primary non-response in ulcerative colitis patients (OR 1.08, 95% CI 1.01-1.16, p = 0.03). A cutoff of a median of [&ge;] 36 eosinophils per high-power field among all segments yielded 85% sensitivity and 80% specificity for predicting primary non-response (AUC 0.82). ConclusionTissue eosinophil counts do not predict relapse in pediatric IBD patients treated with infliximab. However, elevated counts may identify ulcerative colitis patients at risk of primary non-response, suggesting a role for histological stratification in guiding the selection of biologics. Prospective validation in larger cohorts is warranted.

Background & AimsMultisystem inflammatory syndrome in children (MIS-C) is a rare, but severe complication of coronavirus disease 2019, commonly involving the gastrointestinal tract. Some children with MIS-C undergo appendectomy before the final diagnosis. There are several hypotheses explaining pathomechanism of MIS-C, with the central role of the viral antigen persistence in the gut, associated with lymphocyte exhaustion and immune system dysregulation. We aimed to examine appendectomy specimens obtained from MIS-C patients and analyze the pathological features of the disease and the presence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antigens in the appendix. MethodsIn this cross-sectional study we included 21 children with MIS-C who underwent appendectomy before the final diagnosis. MIS-C patients were recruited from the Polish national registry of inflammatory syndromes in children. The control group included 21 sex- and age-matched children with acute appendicitis (AA) unrelated to SARS-CoV-2 infection. Histological evaluation involved hematoxylin and eosin staining and immunohistochemical identification of lymphocyte subpopulations, programmed cell death protein 1, and SARS-CoV-2 nucleocapsid antigen. ResultsAppendices of MIS-C patients lacked neutrophilic infiltrate of muscularis propria typical for AA (14 vs 95%, p<0.001). The proportion of CD20+ to CD5+ cells was higher in patients with MIS-C (p 0.04), as well as the proportion of CD4+ to CD8+ (p <0.001). We found no proof of SARS-CoV-2 antigen presence, nor lymphocyte exhaustion, in the appendices of MIS-C patients. ConclusionsOur findings describe pathomorphological features of the appendix in MIS-C and argue against the central role of SARS-CoV-2 persistence in the gut and concomitant lymphocyte exhaustion as the major triggers of MIS-C.

Background and AimsPrimary sclerosing cholangitis (PSC) is a liver disease without medical therapy that significantly increases the risk of malignancies, acute cholangitis and cirrhosis. Approximately 2-7% of patients with inflammatory bowel disease (IBD) develop PSC. No drug has been shown to prevent de novo PSC in patients with IBD. Statin use, however, has been associated with increased liver transplant-free survival. Yet, the impact of statins on development of new PSC among those with IBD is unknown. MethodsWe conducted a retrospective cohort study of patients diagnosed with IBD with and without statin exposure using a large, representative national database. Patients were followed from the date of diagnosis of IBD. Patient demographics, co-morbidities, medications, and type of IBD were extracted. Unmatched and propensity score-matched Cox regression analyses were performed. ResultsOur analysis included 33,813 patients with IBD of whom 8,813 were exposed to statins. PSC developed in 181 patients over a median follow-up of 3.7 years. Only nine patients (0.1%) who were exposed to statins developed PSC compared to 173 (0.69%) in the non-exposed population. In propensity score-matched analysis, statin therapy was associated with an 86% lower risk of developing PSC (HR 0.14; 95% CI 0.06-0.33, p<0.001). The findings were consistent when accounting for unmeasured confounders (E-value) in sensitivity analyses, including stratification by age group, duration of statin use, and type of statin. ConclusionIn a propensity score-matched analysis, statin use was associated with an 86% risk reduction in new PSC diagnosis among patients with known IBD, suggesting a potential benefit as a prophylactic agent. These findings warrant prospective validation.

Background and aimsRare, pathogenic variants can cause severe liver disease, requiring transplantation in childhood, but it is unclear how common variants in the same genes affect adults. Here, we aimed to establish population-level genetic evidence for whether monogenic diseases are associated with liver injury in adulthood. MethodsWe identified 99 genes where pathological mutations cause significant liver disease in children. For each, we used data from over 1.8 million adults to identify associations with biomarkers of liver injury. Observations were validated in multiple cohorts of adults with clinical liver disease and transcriptomics. Finally, we illustrated the importance of the JAG1-NOTCH pathway on the ductular reaction using immunohistochemistry. ResultsMost genes (56% (55/99)) had at least moderate evidence of association with liver-related traits at a population level. We identified 82 genome-wide (p<5x10-8) associations with markers of liver injury in 41% (41/99) of genes. Loss of function variants in these genes had a ten-fold greater effect on liver enzymes and well-established variants in PNPLA3 had a three-fold greater effect. Variants in ABCC2, ASL, BCS1L, HFE, and SERPINA1 were linked with presence of clinical liver disease in adults. Aggregated effects of 35 variants as polygenic risk score (PRS) was associated with 0.6% lower prevalence of MASLD between highest and lowest PRS groups. Transcriptional expression of 30% of genes was associated with severity of MASLD. Expression of JAG1-NOTCH2 pathway was associated with severity of PSC. JAG1 and NOTCH2 were expressed in injured bile ducts but not adjacent unaffected ducts. ConclusionsOnset and severity of liver disease in adulthood is influenced by genes that also cause severe monogenic liver disease in children.

IntroductionHereditary diffuse gastric cancer (HDGC) associated with CDH1 germline pathogenic variants (GPV), carries a high lifetime risk of signet ring cell carcinoma (SRCC). Currently, there is uncertainty regarding to whom and when to recommend prophylactic total gastrectomy (PTG). We hypothesise a small number of early SRCC lesions correlates with low risk of progression to clinical gastric cancer. This study aimed to identify predictors of early SRCC burden and provide evidence to inform best surveillance intervals. MethodsWe analyzed data from 53 CDH1-GPV carriers who underwent PTG prospectively recruited between Aug 2004 and Aug 2024 (PTG dataset) and a separate cohort of 94 CDH1 CDH1-GPV carriers with [&ge;]2 surveillance endoscopies (endoscopy dataset). Targeted biopsies (TB) and systematic random biopsies (RB) were obtained using the Cambridge protocol. Multivariable negative binomial regression was used to assess the association of clinical (age, family history, CDH1 variant type) and endoscopic factors (mean number of positive TB and RB per endoscopy) with SRCC burden in PTG specimens. A logistic regression model with significant predictors was trained to classify patients into low and high SRCC burden. Temporal trends in biopsy findings were analyzed using linear mixed-effects models, and pathological outcomes at 6-, 12- and 24-month intervals were compared in endoscopy dataset. ResultsOf the 53 patients, 89% had early-stage cancer (pT1aN0M0) and 11% had no cancer (pT0N0M0). The number of SRCC foci ranged from 0 to 273 (median 33, IQR 2-37). The number of positive targeted (P = 0.003) and random biopsies (P < 0.001) during endoscopy surveillance were independent predictors of SRCC burden in the PTG specimen, whereas age, CDH1 mutation type (truncating vs. non-truncating), number of 1st and 2nd degree relatives (SDRs) were not significantly associated. In the endoscopy surveillance cohort, the number of positive biopsies remained largely stable over time, showing fluctuations rather than consistent progression; no significant temporal increase in biopsy positivity was detected over time (P = 0.177) with stable number of SRCC foci at follow-up. Extending surveillance intervals from 6 to 12 or 24 months did not significantly alter progression detection rates. ConclusionEndoscopic surveillance using targeted and random biopsies by experienced endoscopists provides a reliable estimate of SRCC burden in HDGC. Our findings suggest that extending surveillance intervals in patients with low early SRCC burden is clinically safe.

BackgroundPatients with cirrhosis are highly susceptible to infections due to immune dysfunction and gut barrier impairment. Non-bloodstream infections frequently trigger decompensation and mortality, yet the global distribution of antimicrobial resistance (AMR) in these infections is poorly characterized. MethodsWe performed a systematic review and meta-analysis of studies reporting AMR in non-bloodstream bacterial infections among patients with cirrhosis. PubMed, Embase, and Web of Science were searched up to 15 September 2025. Pooled prevalence estimates of multidrug-resistant (MDR) and key resistant pathogens were calculated using random-effects models. Subgroup analyses were performed by country income, continent, and bacterial species. ResultsThirty-one studies including 3,162 infections were analysed. Spontaneous bacterial peritonitis predominated (79%), followed by colonisation (12%) and urinary tract infections (7%). Gram-negative bacteria accounted for 60% of infections (Escherichia coli 29%, Klebsiella pneumoniae 11%), while Gram-positive pathogens represented 39% (Enterococcus spp. 14%, Staphylococcus aureus 6%). Overall pooled MDR prevalence was 29%, with higher burdens in lower-middle-income countries (MDR 47% vs. 22-41%; ESBL 24% vs. 10%; VRE 21% vs. 3%; CRE 32% vs. 1%). Genotypic data identified 436 resistance genes with marked continental differences. ConclusionCirrhosis-associated non-bloodstream infections are dominated by Gram-negative bacteria and show high MDR, particularly in lower-middle-income countries. These findings highlight the need for integrated phenotypic and genomic surveillance of resistance patterns in these settings to guide empiric therapy.

Background & AimsMetabolic dysfunction-associated steatohepatitis (MASH) is a leading cause of liver fibrosis, morbidity, and mortality. It is characterized by the accumulation of fat in hepatocytes causing cell death followed by stromal cell activation and scar deposition at later disease stages. While a marked accumulation of cytotoxic CD8 T cells is observed in MASH in humans and mice, the role of adaptive immune cells in fibrosis progression remains debated. MethodsTranscriptional data were curated from human datasets and preclinical mouse models, including mice deficient in TCR{beta} T cells (Tcrb-/-), which lack conventional CD4 helper and CD8 cytotoxic T cells, in diet-induced fibrosing MASH for single-cell RNA-sequencing. Specific human and mouse liver transcriptomic immune signatures were corroborated by flow cytometry and immunofluorescence. ResultsxMASH was associated with the expansion of lymphocytes and myeloid cells. Auto-aggressive CXCR6+PD1+FASLG+ CD8 T cells were enriched in livers of high-fat-diet-fed mice and correlated with MASH and fibrosis. Notably, Tcrb-deficient mice in a chemical and dietary preclinical MASH model developed fibrosis to the same extent as wild-type mice and exhibited exacerbated pro-fibrotic type 3 inflammation. Loss of conventional CD8 T cells neither impacted myeloid cell number nor phenotype within the fibrotic niche. Neutrophil- and non-conventional lymphocyte-derived GM-CSF and IL-17A were central drivers in the fibrotic niche composed of pathogenic macrophages and activated myofibroblasts. Furthermore, myeloid cells were identified as the main source of CXCL16 in diseased livers, retaining auto-aggressive CD8 T cells to the scar and contributing to their accumulation. Thus, non-adaptive cells, including scar-associated macrophages (SAMs) and myofibroblasts, are sufficient for MASH-driven fibrosis in this model. ConclusionsTargeting myeloid cells and fibroblasts should be prioritized as anti-fibrotic therapies for MASH. Graphical abstractThe immunopathological niche in fibrosis O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/694415v3_ufig1.gif" ALT="Figure 1000"> View larger version (47K): org.highwire.dtl.DTLVardef@122a24org.highwire.dtl.DTLVardef@8ca28borg.highwire.dtl.DTLVardef@103907borg.highwire.dtl.DTLVardef@10280e3_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsAdaptive and innate immune cells localize to the human MASH fibrotic niche CD8 T cells increase with MASH severity while MHC-II+ cells accumulate with fibrosis CXCR6+FASLG+ CD8 auto-aggressive T cells accumulate at the scar CXCL16+ scar-associated macrophages retain CD8 T cells in the fibrotic MASH niche Liver injury, inflammation and fibrosis persist in the absence of conventional T cells Impact and implicationsMetabolic dysfunction-associated steatohepatitis (MASH) is a progressive liver disease in which fibrosis is a key determinant of patient outcomes and survival. This study demonstrates that fibrosis in MASH can develop independent of conventional T cell immunity, driven by myeloid cells including scar-associated macrophages (SAMs) and neutrophils within a localized hepatic niche in mice and humans. This highlights the need to prioritize innate immune mechanisms as key drivers of chronic (late-stage) liver disease for researchers and clinicians developing anti-fibrotic therapies.

MessageThe COVID-19 pandemic has severely curtailed the practice of endoscopy (as an exemplar for outpatient diagnostic procedures) worldwide. Restart and recovery processes will be influenced by the need to protect patients and staff from disease transmission, but data on the risk of COVID-19 transmission after endoscopy are sparse. This is of particular importance in later pandemic phases when the risk of harm from delayed or missed significant diagnoses is likely to far outweigh the risk of infection. The British Society of Gastroenterology (BSG) guidance for restarting endoscopy included stratification of diagnostic procedures according to aerosol generation or assessment of infectious risk as well as pragmatic guidance on the use of personal protective equipment (PPE). We sought to document the risk of COVID-19 transmission after endoscopy in this "COVID-minimised" environment. Prospective data were collected from 18 UK centres for n=6208 procedures. Pre-endoscopy, 3/2611 (0.11% [95% CI: 0.00-0.33%]) asymptomatic patients tested positive for SARS-CoV-2 on nasopharyngeal swab. Based on follow-up telephone symptom screening of patients at 7 and 14 days, no cases of COVID-19 were detected by any centre after endoscopy in either patients or staff. While these data cannot determine the relative contribution of each component of a COVID-minimised pathway, they provide clear support for such an approach. The rational use of PPE and infection control policies should be continued and will aid planning for outpatient diagnostics in the COVID-19 recovery phase.

Biliary atresia (BA) is the most common obstructive cholangiopathy in neonates, often progressing to end-stage cirrhosis. BA pathogenesis is believed to be multifactorial, but the genetic contribution remains poorly defined. We conducted exome sequencing on 89 nonsyndromic BA trios. In 31.5% of the patients, rare and deleterious de novo, homozygous recessive and/or compound heterozygous variants were detected in liver-expressed ciliary genes of diverse ciliary functions. Enrichment of deleterious mutations in liver-expressed ciliary geneset was significant compared to 148 control trios (OR 2.58, 95% CI 1.15-6.07). KIF3B, PCNT and TTC17 are essential for ciliogenesis. Reduced ciliary proteins expression were detected in the BA livers with KIF3B and TTC17 mutations. CRISPR/Cas9-engineered zebrafish knockouts of KIF3B, PCNT and TTC17 displayed reduced biliary flow. Our findings support a larger genetic contribution to nonsyndromic BA risk than expected. Ciliary gene mutations leading to cholangiocyte cilia malformation and dysfunction could be a key biological mechanism in BA pathogenesis.

Esophageal adenocarcinoma (EAC), a highly aggressive cancer with limited therapeutic options, often arises in the backdrop of a molecularly-complex esophageal metaplasia disorder, Barretts Esophagus (BE). Using transcriptomics and systems biology analyses of treatment-naive malignant/pre-malignant biopsy tissues, we found Eph receptor B2 (EphB2) tyrosine kinase signaling to be frequently hyperactivated during early stages of EAC development, and across the BE-EAC continuum. Functional studies revealed EphB2 to be an upstream post-translational regulator of c-MYC activity and as a key molecular dependency in BE/EAC. Single-cell transcriptomics in a porcine esophageal 3D spheroid model showed enhanced EphB2 and MYC activity to be significantly associated with BE-like cell fate. shRNA-based knockdown of EphB2 or small molecule inhibitors of MEK, that modulate MYC protein stability, proved effective in suppressing EAC tumor growth in vivo. These findings point to EphB2-MYC axis as an early promoter of EAC and a novel therapeutic vulnerability in this increasingly-prevalent esophageal malignancy. STATEMENT OF SIGNIFICANCEWe identify EphB2 signaling as a potential master regulator and early promoter of esophageal adenocarcinoma, and the proto-oncogene MYC as a key downstream effector of EphB2 function. Targeting the EphB2-MYC axis could be a promising therapeutic strategy for these often refractory and lethal EAC tumors.

Faecal incontinence (FI) is a frequent and debilitating sequela of surgical repair of anorectal malformations (ARMs). The rectoanal inhibitory reflex (RAIR), an enteric nervous system (ENS)-mediated circuit essential for continence, is often absent or impaired in these children post-surgically. However, the biological cascade linking surgery to this reflex failure remains unknown. To identify the mechanistic pathways underlying post-surgical FI, we performed a multi-omics case-control study of 31 post-ARM children (12 incontinent, 20 continent), integrating stool 16S rRNA sequencing with untargeted serum metabolomics by liquid chromatography-mass spectrometry (LC-MS). Incontinent children exhibited greater microbial richness yet distinct communities, marked by depletion of butyrate-producing Faecalibacterium and expansion of mucin-degrading Ruminococcus along with Proteobacteria. These ecological shifts coincided with signatures of impaired fatty acid oxidation, and elevated levels of neurotoxic and inflammatory compounds such as trimethylamine and kynurenines. These findings suggest that surgical trauma destabilizes microbial and metabolic homeostasis, compromising ENS circuits. These results raise the possibility that microbial and metabolic restoration could restore faecal continence after surgical repair. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/25338825v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@908faforg.highwire.dtl.DTLVardef@c9537borg.highwire.dtl.DTLVardef@187d27eorg.highwire.dtl.DTLVardef@c6692_HPS_FORMAT_FIGEXP M_FIG C_FIG

PurposeUsing a real-world database with matched genomic-transcriptomic molecular data, we sought to characterize the distinct molecular correlates underlying clinical differences between young-onset pancreatic cancer (YOPC; <50-yrs.) and average-onset pancreatic cancer (AOPC; [&ge;]70-yrs.) patients. MethodsWe analyzed matched whole-transcriptome and DNA sequencing data from 2430 patient samples (YOPC, n=292; AOPC, n=2138) from the Caris Life Sciences database (Phoenix, AZ). Immune deconvolution was performed using the quanTIseq pipeline. Overall survival (OS) data was obtained from insurance claims (n=4928); Kaplan-Meier estimates were calculated for age-and molecularly-defined cohorts. Significance was determined as FDR-corrected P-values (Q)<0.05. ResultsYOPC patients had higher proportions of mismatch repair-deficient (dMMR)/microsatellite instability-high (MSI-H), BRCA2-mutant, and PALB2-mutant tumors compared with AOPC patients, but fewer SMAD4-, RNF43-, CDKN2A-, and SF3B1-mutant tumors. Notably, YOPC patients demonstrated significantly lower incidence of KRAS mutations compared with AOPC patients (81.3% vs. 90.9%; Q=0.004). In the KRAS-wildtype subset (n=227), YOPC tumors demonstrated fewer TP53 mutations and were more likely driven by NRG1 and MET fusions, while BRAF fusions were exclusively observed in AOPC patients. Immune deconvolution revealed significant enrichment of natural killer (NK) cells, CD8+ T cells, monocytes, and M2 macrophages in YOPC patients relative to AOPC patients, which corresponded with lower rates of HLA-DPA1 homozygosity. There was an association with improved OS in YOPC patients compared with AOPC patients with KRAS-wildtype tumors (median 16.2 [YOPC-KRASWT] vs. 10.6 [AOPC-KRASWT] months; P=0.008) but not KRAS-mutant tumors (P=0.084). ConclusionIn this large, real-world multi-omic characterization of age-stratified molecular differences in PDAC, YOPC is associated with a distinct molecular landscape that has prognostic and therapeutic implications.

Background & AimsPatients with acute decompensation (AD) of cirrhosis are at a high risk of developing acute-on-chronic liver failure (ACLF), a syndrome characterized by multi-organ failure and high short-term mortality. Prospective studies addressing the cellular mechanisms that drive the transition from AD to ACLF are lacking. In this study, we aimed to determine whether peripheral immune cell subsets at hospital admission predict the progression from AD to ACLF and to delineate underlying molecular mechanisms. Approach & ResultsWe prospectively enrolled 63 patients with AD and 15 healthy donors across five European centers, with a 90-day follow-up. Single-cell RNA sequencing was performed on peripheral blood mononuclear cells (PBMCs) from 16 patients with distinct trajectories and 4 controls. Progression to ACLF was associated with expansion of classical monocytes, particularly subcluster "C2", which specifically displayed impaired energy metabolism with reduced oxidative phosphorylation. Genes encoding respiratory chain Complex IV were markedly downregulated. A C2-derived gene signature was enriched in two large international whole-blood cohorts (PREDICT, n=689; ACLARA, n=521), particularly in patients with bacterial infections, those developing ACLF, and non-survivors. Functional validation by respirometry in an independent AD cohort confirmed declining monocyte Complex IV-dependent oxygen consumption in patients with pre-ACLF. ConclusionsWe identified and validated a distinct monocyte subpopulation with defective energy metabolism in patients with AD with poor outcomes, suggesting a mechanistic link to ACLF development.

IntroductionObesity and related cardiometabolic comorbidities, including hypertension, dyslipidemia, diabetes, metabolic dysfunction-associated steatotic liver disease (MASLD), and atherosclerotic cardiovascular disease (ASCVD), are increasingly prevalent among individuals with inflammatory bowel disease (IBD). These conditions influence disease activity, therapeutic response, surgical outcomes, and overall quality of life, yet evidence remains fragmented. The Modulate Obesity and relateD metabolic complIcations For Yielding improvements in IBD outcomes (MODIFY-IBD) initiative aims to synthesize evidence and generate consensus recommendations to guide practice and future research in this area. Methods and analysisWe will conduct a structured evidence review organized into three domains: (1) the impact of obesity on IBD outcomes (2) burden of cardiometabolic complications in IBD, and (3) management of obesity and cardiometabolic comorbidities in IBD. Draft clinical statements will be generated and evidence summaries prepared using the GRADE (Grading of Recommendations, Assessment, Development and Evaluation) framework, with certainty of evidence rated where applicable. In the assessment of those statements where GRADE is not feasible, a multidisciplinary international panel of gastroenterologists, surgeons, endocrinologists, hepatologists, cardiologists, and dietitians will assess each statement using the RAND/UCLA Appropriateness Method. Panelists will rate the appropriateness of each statement (only those that fall into their area of expertise) on a 1-9 scale (1-3 = inappropriate, 4-6 = uncertain, 7-9 = appropriate), with medians rounded up (e.g., 6.5 = appropriate). Agreement will be assessed using the RAND Disagreement Index (DI <1.0 = agreement). Ethics and disseminationThis study will not involve direct patient participation, as it is based on evidence synthesis and expert consensus; therefore, formal Research Ethics Committee approval will not be required. Patient representatives will contribute to the consensus process to provide contextual perspectives, but no identifiable data will be collected. Findings will be disseminated through publication in peer-reviewed journals, presentation at major gastroenterology and IBD conferences, and communication with professional societies. A lay summary and patient-friendly infographic will also be developed to facilitate translation of recommendations into clinical practice. PROSPERO registration numberCRD420251178843: A systematic review of the impact of obesity on inflammatory bowel disease outcomes CRD420251178799: A Systematic Review of Cardiometabolic Complications in Inflammatory Bowel Disease CRD420251174653: Management of Overweight, Obesity, and Cardiometabolic Comorbidities in Inflammatory Bowel Disease: A Systematic Review Strengths and limitationsO_LIIntegrates systematic evidence synthesis with both GRADE and RAND/UCLA methods, an approach not previously applied to obesity and cardiometabolic comorbidities in IBD. C_LIO_LIInternational, multidisciplinary panel (gastroenterology, surgery, endocrinology, cardiology, dietetics, radiology) ensures broad expertise. C_LIO_LIAnonymous scoring and iterative re-rating reduce bias while enabling structured discussion. C_LIO_LIPatient and public involvement will inform priorities and dissemination, although RAND scoring remains expert-only. C_LIO_LIEvidence is largely observational and rapidly evolving (e.g., Glucagon-Like Peptide-1 Receptor Agonists [GLP-1Ras], endobariatric therapies), necessitating future updates. C_LI