Gut

Biliary Atresia (BA) is the leading cause of pediatric liver transplantation. Given the heterogeneity of the disease, outcomes after diagnosis remain unpredictable. A multiscale atlas of BA hepatic tissue established early lymphatic dysplasia in infants that later proceed toward liver failure and transplantation (severe BA). An architecturally distorted, immature and CCL21-high lymphatic vasculature marked severe BA, along with an expanding cholangiocyte compartment pivoting toward immune-reactive MMP7/SOX9-high states. Hepatocyte-to-biliary transdifferentiation emerged broadly across BA- and non-BA-cholestatic injuries, while dedifferentiation and acute-phase-reactions were specific to severe BA. Functionally, lymphatic endothelial tissue, isolated from severe BA livers, induced an analogous LGR5- and SOX9-positive epithelial progenitor response when assembled with cholangiocytes as organoids. Further experiments revealed that lymphatic endothelium signals ectopically on liver epithelium via CCL21-CCR7-axis after BA-specific inflammatory priming. CCL21-depletion strategies mitigated the BA-specific MMP7-program. In sum, a maladaptive lymphatic endothelial dysplasia perturbs intrahepatic epithelium in severe BA and offers CCL21 as a possible target for epithelial stability.

Background: The organization of pancreatic cancer care may be associated with survival. Using health administrative claims data, we reconstructed the pathway from diagnosis to first-line therapy and examined associations of multidisciplinary team review and treatment at specialized centers with overall survival. Methods: Longitudinal historical cohort study using anonymized health administrative claims data from six Czech health insurance funds, covering approximately 17% of patients diagnosed with pancreatic cancer nationally between 2018 and 2020. Adults with an incident ICD-10 C25 record confirmed by imaging and histopathology were followed from the index date (the date of the first qualifying imaging or histopathological examination) until death, censoring, or 31 December 2021. Overall survival was analyzed using Kaplan-Meier methods and Cox regression adjusted for age and first-line therapy type. Results: Of 1,255 patients, 920 (73.3%) received first-line therapy and 266 (21.2%) died untreated. Among treated patients, 436 (47.4%) underwent multidisciplinary team review, 335 (36.4%) underwent surgery, and 667 (72.5%) were treated at a complex oncological center. Surgery was associated with longer overall survival than chemotherapy (age-adjusted hazard ratio [HR] 0.32, P < 0.001). Treatment at a complex oncological center was associated with longer overall survival (adjusted HR 0.77, 95% confidence interval [CI] 0.64-0.92, P = 0.004; crude median 532 versus 394 days). Multidisciplinary team review was not significantly associated with overall survival (adjusted HR 0.86, 95% CI 0.73-1.01, P = 0.073). Conclusions: Treatment at a complex oncological center was associated with longer survival, while fewer than half of patients had a recorded multidisciplinary team review. How care is organized, not only which therapy is delivered, is associated with outcome. The observational design and absence of key clinical covariates limit causal interpretation.

Surgical decisions for intraductal papillary mucinous neoplasms (IPMNs), precursors of pancreatic cancer, depend on distinguishing low- from high-grade dysplasia, a distinction that molecular markers could refine. We microdissected 433 tumor regions from 135 patients and integrated transcriptomics, deep-learning histology, and KRAS/GNAS RNA-called variants. RNA programs and morphological motifs separated lesions by phenotype, intestinal versus others, rather than by dysplasia grade. Along gastric IPMN trajectories, low-grade lesions recapitulated the pit-chief polarity of normal gastric glands, whereas high-grade lesions were indistinguishable from pancreatobiliary lesions in morphology, RNA programs, and driver mutations. Intestinal IPMNs arose through two routes: a canonical GNAS-associated pathway and a KRAS-associated shift from low-grade gastric features, with lesions sharing driver mutations retaining common programs across phenotypes. Resolving these phenotypic trajectories clarified distinct progression paths and enabled phenotype-specific prediction of high-grade dysplasia in mucus aspirated from 94 resected lesions. These findings support a promising fluid-based assessment of IPMN status.

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: 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.

Progressive hepatic fibrosis is the principal determinant of morbidity and mortality in metabolic dysfunction-associated steatotic liver disease and steatohepatitis (MASLD/MASH). Mitochondrial dysfunction is a hallmark of MASH, and the release of mitochondrial damage-associated molecular patterns (mito-DAMPs) from injured hepatocytes can promote fibrosis. However, how mitochondrial dynamics and quality control shape the fibrotic response in MASLD/MASH remains unclear. Here, through large-scale genomic analyses of mitochondrial genes governing mitophagy, fusion and fission in human MASLD, with a power-equivalent sample size of approximately 700,000 individuals, we identify a strong association between hepatic fibrosis and the mitochondrial fusion factor dynamin-like GTPase optic atrophy 1 (OPA1). OPA1 transcripts and protein abundance in the liver epithelium were progressively dysregulated with advancing fibrosis. In mice, hepatocyte-specific OPA1 loss alone was sufficient to induce hepatic stellate cell activation and fibrosis in zone 3, promoted the release of mito-DAMPs into the circulation and exacerbated fibrosis in experimental MASH. These findings identify OPA1 as a central regulator of the hepatic fibrotic response and connect defective mitochondrial homeostasis to mito-DAMP release, hepatic stellate cell activation and fibrosis in MASLD.

Fluid accumulates within serosal cavities in diverse disease states, where it creates biologically active and potentially pathologic niches. How these expanded microenvironments reflect and shape disease biology remains incompletely resolved. Here, we investigated human ascites fluid (n = 118), a hallmark of decompensated cirrhosis, to determine whether signatures of microbial exposure and local host response distinguish outcomes. Cirrhotic ascites was characterized by barrier remodeling, depletion of plasma cell-associated programs, and enrichment of oropharyngeal microbes. Surprisingly, detection of oropharyngeal microbes in ascites was not associated with adverse outcomes. Instead, the ascites of cirrhotic patients with poor outcomes was marked by profound plasma cell depletion and significantly reduced dimeric IgA, despite the presence of antigen-experienced B cells. Together, these findings identify local B cell dysregulation as a previously underappreciated component of cirrhosis-associated immune dysfunction. Impaired local humoral immunity, rather than microbial translocation alone, emerges as a feature of high-risk decompensated cirrhosis.

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.

Pancreatic ductal adenocarcinoma (PDAC) arises within an extensively remodeled microenvironment, yet tissue markers that distinguish invasive carcinoma from precursor lesions remain limited. Integrating four single cell RNA sequencing atlases comprising 324,662 cells from 26 patients, we identified cancer associated fibroblast expansion, accumulation of C1QA+ immunoregulatory macrophages, and depletion of a dendritic cell compartment expressing plasmacytoid markers. Fibroblasts were enriched for extracellular matrix and PI3K AKT programs and macrophages for an antigen-presentation program. We then examined the protein level correlates of these populations in a tissue proteomic reference framework of 356 samples spanning non diseased pancreas, normal-adjacent tissue, low and high grade intraductal papillary mucinous neoplasms (IPMNs), IPMN associated invasive carcinoma, and PDAC, prioritizing proteins that changed monotonically across the six histopathologic reference groups or marked tumor enriched cell types. Despite depletion of plasmacytoid dendritic cells, the principal source of type I interferon, the interferon stimulated protein ISG15, expressed by both fibroblasts and macrophages, increased monotonically toward PDAC. In exploratory cross-validated benchmarking of PDAC versus low and high grade IPMN, excluding IPMN-associated invasive carcinoma (145 versus 56 samples), CATB+EPIPL achieved an AUC of 0.98, with a sensitivity of 92% at an achieved specificity of 92%, exceeding protein abundance models of diagnostic IHC-associated markers (S100P+IMP3+maspin+MSLN, 0.79) and refitted published IPMN progression combinations (<0.91). Against non diseased pancreas, candidate and comparator panels performed similarly (AUC 0.99 1.00). These biologically informed tissue protein panels warrant independent validation, including immunohistochemical evaluation of EUS guided fine needle biopsy specimens and measurement in blood.

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.

Neutrophils infiltrate the liver as metabolic dysfunction-associated steatotic liver disease (MASLD) progresses from simple steatosis to steatohepatitis, but whether neutrophil effectors merely mark this transition or cause it is unknown. Here we show that human neutrophil peptides (HNPs), or alpha-defensins, are drivers rather than bystanders of disease. In patients surgically treated for hepatic hemangioma who displayed overt MASLD, the abundance of HNPs in their liver biopsy samples localized to diseased tissue correlates with the histological severity of steatosis. In vitro, HNPs enter hepatocytes to induce multimerization of voltage-dependent anion channel 1 (VDAC1) in the mitochondrial outer membrane, causing mitochondrial dysfunction and lipid accumulation. Under lipid overload, but not on a standard diet, HNP1-transgenic mice develop increased adiposity and steatohepatitis, which is reversed by an orally available prodrug that inhibits HNP-induced VDAC1 multimerization. These findings link neutrophil innate immunity to hepatocyte mitochondrial dysfunction, recast host-protective HNPs as pathogenic effectors when hepatocyte mitochondria are lipid-burdened, and establish the HNP-VDAC1 axis as a therapeutic target in MASLD.

Background & AimsWe previously developed multiple machine-learning and regression-based risk prediction models using retrospective electronic health records (EHR) to estimate near-term risk of pancreatic cancer (PC). This pilot study aimed to assess the feasibility of an early detection strategy combining initial EHR-based risk prediction with downstream imaging and blood-based testing. MethodsThis prospective study included adults aged 50-84 years with an estimated [&ge;]1% 18-month risk of PC, identified between January 2021 and March 2023 using four previously validated models. Patients with a history or active suspicion of PC were excluded. Participants completed cross-sectional imaging and CA19-9 labs at baseline and again at 18 months. Outcomes included enrollment rates, test completion rate, and burden of incidental findings. ResultsOf 1,251 eligible patients, 102 (8.2%) enrolled (median age 69 years [IQR 62-75]; 58% women; 48% Hispanic, 34% White, 11% Black, and 7% Asian). At baseline, 89 (87%) completed imaging and 98 (96%) completed CA19-9. At 18 months, 79% completed both imaging and CA19-9. Ten (10%) participants underwent additional clinical evaluations triggered by imaging findings. Evaluations included an endoscopic ultrasound, renal imaging, and FibroScan. CA19-9 results were normal in most participants, though 18% had elevated levels at baseline. ConclusionsReal-time EHR-based ML algorithms can be combined with blood- and imaging-based surveillance for early detection of PC with acceptable burden of incidental findings. However, improved patient engagement is a key aspect that will need to be addressed in order to successfully scale an AI-guided strategy for early detection.

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.

Hospital readmission is used in cirrhosis research as if a return to hospital meant the disease had worsened: it is a trial outcome, a quality indicator and a prediction target. We asked what those readmissions were. Sixty-one adults with alcohol-related cirrhosis, selected because they had been hospitalized more than once, contributed all 326 later admissions to one department. A clinician read each full record and classified it for acute decompensation and for admission mode, blinded to diagnostic codes and structured flags. Fewer than two in five admissions (125, 38.3%) were decompensations. One in three (114) had been booked in advance; none of these was a decompensation, yet they used 29.1% of all bed-days. Among 124 returns within 30 days, planned admissions outnumbered decompensations, 48 to 43. Counting all admissions tracked a patients decompensations only moderately (correlation 0.50) whereas counting urgent admissions tracked them closely (0.93). In crude analysis the sicker patients had fewer admissions, not more, because planned care goes to those well enough to receive it. A liver severity score, computable for 165 admissions, did not separate planned from urgent admissions or decompensations from other stays, even within one patient. Readmission was not the same thing as decompensation.

Objective: Autoimmune hepatitis (AIH) and primary biliary cholangitis (PBC) frequently present as overlap syndromes, characterized by shared sexual dimorphism and elevated intestinal Veillonella dispar (V. dispar) abundance, yet exhibiting distinct hallmark pathological manifestations. This study aimed to elucidate the shared pathogenesis, phenotypic differentiation mechanisms and sex-specific predisposition of AIH and PBC induced by V. dispar. Methods: Clean-grade and germ-free (GF) mice were employed to establish AIH and PBC models. Model induction involved oral gavage of V. dispar and intraperitoneal injection of either liver-specific antigen S100 (for AIH) or a pyruvate dehydrogenase complex E2 subunit (PDC-E2) mimetic peptide (for PBC). Single-cell RNA sequencing, metabolomics, transmission electron microscopy, western blotting, and flow cytometry were utilized to elucidate the underlying mechanisms. Results: V. dispar successfully induced autoimmune liver disease-like features in mice, characterized by significant intrahepatic B cell infiltration. Mechanistically, V. dispar caused systemic arginine reduction, leading to intrinsic apoptosis of gonadal stromal cells and a subsequent reduction in testosterone. This decreased testosterone weakened its inhibitory effect on B cell activating factor (BAFF) secretion, thereby amplifying B cell-mediated immune responses. Furthermore, in the presence of S100 or PDC-E2 mimetic peptide, V. dispar also facilitated Th17 cell activation, which guided the phenotypic differentiation into AIH or PBC, respectively. Consistent with these findings, our clinical observations revealed that patients with AIH and PBC tended to harbor enriched V. dispar, along with lower serum arginine and testosterone. In addition, elevated serum levels of BAFF and IL-17 were also observed in these patients. Conclusion: V. dispar induces reduced testosterone levels and upregulation of BAFF, leading to intrahepatic B cell expansion, which serves as the common pathogenic basis for AIH and PBC. The presence of S100 and PDC-E2 subsequently drives further maturation of these expanded B cells and promotes Th17 cell activation, thereby determining the phenotypic divergence between AIH and PBC.

The accrual of somatic copy number alterations (CNAs) in the premalignant condition Barrett's oesophagus (BO) predicts transformation to oesophageal adenocarcinoma (OAC). The dynamics of CNA evolution, namely when CNAs first appear and their rate of clonal expansion, are unknown. Here we show that CNAs typically begin to accrue in BO many decades prior to first clinical detection of BO or cancer occurrence, and in some cases during childhood. We constructed a hierarchical Bayesian methodology called CARBINE to calculate the calendar year occurrence time of CNAs from single-timepoint contemporary genetic data. We analysed data from 80 individuals who had received longitudinal endoscopic surveillance of their BO and had known cancer progression status. Loss of heterozygosity (LOH) on chromosome 9p tended to be the first CNA event and often occurred when patients were between 10-30 years old. Genome doubling (GD), known to be a strong risk factor for cancer development, also typically originated multiple decades prior to cancer develop and the GD clone expanded very slowly. Patients who progressed to OAC had an enrichment of CNAs late in life. CNA accrual dynamics were more predictive of cancer risk than CNA burden measurements alone. Analysis of 97 OAC whole genomes, of which 38 had sufficient purity for CNA timing analysis, confirmed the early-life origins of CNAs found in the cancer and indicated that the seeds of OAC exist within an increasingly cancerised BO field for many years. CNA timing shows that the malignant transformation potential of BO may be recorded within the somatic genome in the first decades of life, giving a strong rationale for the effectiveness of risk stratification in early life for Barrett's patients.

BACKGROUND Primary sclerosing cholangitis (PSC) is characterized by multifocal biliary strictures on MRI/MRCP. However,we have observed that young PSC patients often displayed a marked intrahepatic bile duct visibility,sometimes with gallbladder enlargement, before developing biliary strictures. This study aimed to evaluatewhether this imaging pattern was associated with subsequent diagnosis of PSC. PATIENTS AND METHODS This retrospective two-center study included patients younger than 21 years who had a baseline liverMRI/MRCP, without biliary strictures. The endpoint was a definite diagnosis of large duct PSC during follow-up. The association of baseline imaging findings with the endpoint was evaluated by multivariable logisticregression, Cox models, and Kaplan-Meier analyses. RESULTS Ninety-four patients were included: 54% were women, the mean age was 16.7 years, and 23% had IBD. Overa mean follow-up of 7.75 years, 21 patients were subsequently diagnosed with large duct PSC after a mediantime of 5.60 years. Marked intrahepatic bile duct visibility and gallbladder enlargement displayed goodperformance to predict the subsequent diagnosis of PSC (AUC, 0.77 and 0.69, respectively). The presence ofboth signs displayed a specificity of 1.00. In multivariable analyses, marked intrahepatic bile duct visibility andgallbladder enlargement were independently associated with subsequent PSC diagnosis (OR 17.00 (95% CI,3.10-93.24; p = 0.001) and 16.08 (95% CI, 2.29-113.02; p = 0.005) respectively) and shorter time to diagnosis(HR 9.42 (95% CI, 2.50-35.59; p < 0.001) and 7.59 (95% CI, 2.03-28.41; p = 0.003) respectively). Survivalanalyses confirmed the association between these two imaging signs and the subsequent PSC diagnosis (HR7.78 (95% CI, 2.62-23.16; p < 0.001) and 3.85 (95% CI, 1.64-9.08; p < 0.001) respectively). CONCLUSIONS In young patients without biliary strictures, marked intrahepatic bile duct visibility and gallbladder enlargementon MRI/MRCP were strongly associated with subsequent diagnosis of large duct PSC.

Deep learning (DL) applied to haematoxylin and eosin (H&E)-stained pathology images can predict microsatellite instability (MSI) in gastric cancer (GC). We evaluated its diagnostic accuracy and discriminative performance. PubMed, Embase, Cochrane Library and Web of Science were searched for studies applying DL to H&E images for MSI prediction in GC. The protocol was prospectively registered in PROSPERO (CRD420261503140). Risk of bias was assessed with QUADAS-2. Pooled sensitivity and specificity were estimated with a bivariate random-effects model, with subgroup analyses by validation strategy and data source; slide-level areas under the curve (AUCs) were pooled after logit transformation. Prespecified scenario analyses assessed robustness. Ten studies were included; seven independent datasets from six studies entered the primary synthesis. Pooled sensitivity, specificity and summary receiver operating characteristic AUC were 0.78 (95% CI 0.63-0.88), 0.85 (95% CI 0.77-0.90) and 0.89 (95% CI 0.86-0.91); nine studies contributed to the secondary AUC synthesis (pooled AUC 0.85, 95% CI 0.80-0.89). Hospital-derived cohorts showed numerically higher sensitivity (0.86) and diagnostic odds ratio (39.8) than TCGA-derived cohorts (0.71 and 11.5), but subgroup differences were limited by the small number of studies and substantial heterogeneity. DL models show good diagnostic accuracy for MSI prediction in GC, but clinical utility still requires confirmation in standardised multicentre, independent external and prospective studies.

Background: Real-world evidence on food-as-medicine programs for irritable bowel syndrome (IBS) is scarce, and single-arm evaluations overstate improvement because of regression to the mean (RTM). We estimated change in the IBS Symptom Severity Scale (IBS-SSS, 0-500) in a multi-omics personalized digital health food-as-medicine program, unadjusted and RTM-corrected. Methods: Retrospective single-arm cohort. Of 15,933 members with a valid baseline, 2,254 had a follow-up reading and 1,683 one at least 14 days after baseline. Change at 4, 12 (primary) and 26 weeks was estimated by baseline severity stratum, unadjusted and RTM-corrected by analysis of covariance. A responder fell by at least 50 points (the minimal clinically important difference benchmark). Sensitivity analyses covered equity, inverse-probability weighting and tipping-point analyses for members without a reading in each landmark window, a negative-control stratum and medication. The association of weight loss and dietary nutrient density with symptom change was evaluated within and between members. Results: At 12 weeks (n = 430) IBS-SSS fell by 43.88 points unadjusted (95% confidence interval [CI] -52.44 to -35.32; p < 0.001) and by 47.73 RTM-corrected (-55.48 to -39.98; p < 0.001); 720 of 1,339 symptomatic members (53.8%; 95% CI 51.1 to 56.4) fell by at least 50 points. Larger improvement in more severe members persisted after RTM correction (severe stratum, n = 37: unadjusted -127.43, RTM-corrected -60.71, 95% CI -97.75 to -23.68, p = 0.001). A higher meal nutrient density was associated with lower IBS-SSS within a member's own trajectory (p = 0.018) while weight change was not (p = 0.361). Improvement was similar across groups in spite of baseline differences by age and sex: RTM-corrected 12-week change did not differ by age (p = 0.458), body-mass index (p = 0.328), sex (p = 0.749), income (p = 0.486) or ethnicity (p = 0.170). Estimates were robust to weighting for members without a reading in the landmark window (RTM-corrected estimates moved by less than 2 points), and the change of those members would have had to be 39 to 73 points worse than observed before the mean change reached zero. Baseline medication use and starting a GLP-1 receptor agonist did not explain symptom changes. Conclusions: IBS-SSS fell significantly among program participants, with steeper improvement in the more severe group, even after RTM correction. The improvement was comparable across socioeconomic characteristics, age and sex and robust to the confounders and missing-data assumptions evaluated. These associations from a self-selected single-arm cohort warrant replication in independent studies.