Journal of Cystic Fibrosis

Background and aimsGastrointestinal symptoms remain common in adults with cystic fibrosis (CF) despite cystic fibrosis transmembrane conductance regulator modulator use, suggesting persistent and heterogeneous gut dysfunction. This prospective observational study tests the hypothesis that distinct gut symptom phenotypes in CF can be observed and linked to underlying mechanisms. MethodsAdults from three UK CF centres completed the Gastrointestinal Symptom Rating Scale, Patient Assessment of Constipation Symptoms and a bowel-habit questionnaire. Latent class analysis using an ordinal logistic model was applied to 36 symptom indicators. Associations between phenotypes and demographic, clinical, and treatment variables were examined using generalised linear models. ResultsThree hundred participants completed questionnaires (54% male; median 31 years). We identified four symptom phenotypes: mild; moderate-constipation predominant; moderate-diarrhoea predominant and severe. The severe phenotype was associated with gastroesophageal reflux (RRR 2.86; 95%CI: 1.30-6.31; p=0.009), distal intestinal obstruction syndrome (RRR 2.46; 95%CI: 1.04-5.81; p=0.04), proton pump inhibitor (RRR 3.29; 95%CI 1.39-7.74; p=0.007), and laxative use (RRR 6.13; 95%CI 2.54-14.84; p<0.001). CF-related liver disease was associated with both moderate-constipation and diarrhoea phenotypes, respectively (RRR 2.08; 95%CI 1.13-3.81; p=0.018; RRR 2.11; 95%CI 1.03-4.29; p=0.04). There was a lower likelihood of long-term oral antibiotic use in the moderate-constipation phenotype (RRR 0.53; 95%CI 0.3-0.92; p=0.025) and moderate-diarrhoea phenotype (RRR 0.46; 95%CI 0.24-0.91; p=0.025). ConclusionsFour distinct symptom phenotypes were identified, independent of demographics and pancreatic status, but associated with specific complications and medication profiles. These phenotypes provide a framework for mechanistic studies within the GRAMPUS-CF cohort and precision management of CF-related gut disease.

Chronic infections in cystic fibrosis (CF) emerge from gradual ecological transitions in the airway microbiome, yet early predictive markers remain poorly defined. We developed a new autoencoder-based framework that outperforms read-based or metagenome-assembled genome-based analyses at capturing the continuum from health-associated commensals to pathogen-dominated, antibiotic-tolerant communities. This improvement is achieved by integrating taxonomic and functional data from 127 sputum and bronchoalveolar lavage metagenomes from 64 people with CF into latent "Clusters of Phylogeny and Functions" (COPFs). Coupled with gradient-boosted random forests, COPFs predicted Pseudomonas aeruginosa colonisation, multidrug resistance, and impending infection up to a year before clinical detection. The multidrug-resistant P. aeruginosa signature showed the same resistance-mechanism evolution as found in laboratory experiments. The inclusion of eukaryotic markers revealed persistent Aspergillus fumigatus signatures even during culture-negative intervals. Applying our South Australian-trained model to over 1,000 global metagenomes from 22 independent CF datasets, we achieved 94% accuracy in predicting P. aeruginosa status across platforms and geographies, validating the models universal utility. Our results demonstrate that combining datasets with deep learning reveals conserved ecological and metabolic mechanisms in disease progression, transforming metagenomics into a predictive framework for managing chronic infections.

BackgroundInnovative treatments for rare diseases often strain healthcare budgets. Precision medicine can improve care and reduce costs by guiding treatment allocation. One example is the forskolin-induced swelling (FIS) assay, which uses patient-derived organoids to predict-response to Cystic Fibrosis Transmembrane conductance Regulator (CFTR) modulators in people with Cystic Fibrosis (pwCF). However, it remains unclear when and for whom this assay adds most value. Therefore, the impact of assay accuracy and target population on health-benefits and costs needs assessment. Research questionTo quantify the impact of sensitivity, specificity and target population on health benefits and costs to inform further development of a predictive assay to guide treatment allocation in pwCF. Study design and methodsAn early economic evaluation was conducted using a decision tree and Markov model. Two strategies were compared over a 40-year horizon: (i) treat all pwCF with CFTR modulators and (ii) predict-response using the FIS assay to guide treatment. Scenario analyses varied assay sensitivity, specificity and treatment responsiveness, reflecting subpopulations of pwCF, including rare CFTR variants. Outcomes included quality-adjusted life years (QALY), false negative rates and costs. Model inputs were based on literature on pwCF with F508del mutations. ResultsThe primary analysis yielded a loss of 1.22 QALYs, with {euro}2,16 million cost-savings per patient in the predict-response strategy. Increasing assay sensitivity reduced QALY loss and false negatives while maintaining cost-savings, while specificity had limited effect on outcomes. Lower treatment responsiveness reduced QALY loss and false negatives while maintaining cost-savings. ConclusionThe assay appears most valuable in pwCF with rare CFTR variants, where treatment response is uncertain. Improving sensitivity is crucial to prevent QALY loss, especially in high-responder populations like pwCF with F508del. The model provides insights into variables impacting personalized testing and serves as a dynamic dashboard to explore scenarios once clinical data becomes available. Key pointsO_LIThis early economic evaluation provides insights in key variables affecting personalized testing to guide CFTR treatment allocation to inform further assay development. C_LIO_LIHigh assay sensitivity is crucial to prevent QALY loss in high responder CF populations, such as pwCF with F508del. C_LIO_LIThe FIS assay appears most value for pwCF with rare CFTR variants and uncertain treatment response. C_LI

Mucociliary clearance is a key component of the pathophysiology of bronchiectasis but cilia function is poorly defined. This study aims to characterize nasal ciliary function in bronchiectasis and examine associations with disease severity, infection, inflammation and outcome. Adults with bronchiectasis and healthy volunteers were recruited to the international observational study EMBARC-BRIDGE. Individuals with a known diagnosis of Primary Ciliary Dyskinesia (PCD) were excluded. Nasal respiratory epithelium was sampled by brush biopsy. Ciliary function was assessed by high-speed video microscopy in primary samples and following re-differentiation in air-liquid interface (ALI) culture. Ciliary parameters (cilia length, angle, amplitude, clearance, frequency and ciliation) were quantified and compared with disease severity, microbiology, inflammation and future risk of exacerbations. 171 participants with bronchiectasis were recruited (54% female, age 68years (59-74)). Bronchiectasis nasal brushings showed greater epithelial disruption compared to healthy volunteers (p=0.0006). Six individuals with previously undiagnosed PCD were identified and excluded. In the remaining bronchiectasis cohort, ciliary beat frequency and length were similar to healthy controls. In contrast ciliary beat amplitude, angle, amplitude per second and clearance capacity, were significantly reduced (all p<0.001). These parameters were restored following ALI culture. Regenerated epithelia from bronchiectasis donors exhibited reduced ciliated area. Ciliary dysfunction was strongly associated with future risk of severe exacerbations. The upper airway epithelium is disrupted in bronchiectasis; ciliary movement is impaired and is associated with future risk of exacerbation. Ciliary dysmotility is reversible following ALI culture. This indicates that impaired ciliary function is secondary to the airway environment and therapeutically targetable.

Background and AimMASLD affects 30-38% of Indian adults, yet the contribution of genetic risk variants to disease susceptibility and fibrosis progression remains poorly characterised. We investigated the association of 12 candidate SNPs with MASLD susceptibility and fibrosis severity in North Indian patients, benchmarking allele frequencies against IndiGenomes and global populations. MethodsSixty-nine MASLD patients (75.4% male; median BMI 29.8 kg/m{superscript 2}) from a tertiary care liver clinic in New Delhi were genotyped for 12 SNPs using Illumina custom BeadChip array and Sanger sequencing. Patients were stratified by liver stiffness measurement (LSM): significant fibrosis ([&ge;]8 kPa, n=38) versus no significant fibrosis (<8 kPa, n=31). Allele frequencies were compared with IndiGenomes ([~]1,020 Indian individuals) and 1000 Genomes populations. ResultsPNPLA3 rs738409 G allele was the strongest within-cohort predictor of significant fibrosis (allelic OR 2.89, 95% CI 1.35-6.19, P=0.006; dominant model OR 3.94, P=0.008), with carriers demonstrating higher LSM (median 15.6 vs. 7.5 kPa, P=0.005). SAMM50 rs3761472 (OR 2.12, P=0.065) and FTO rs9939609 (OR 2.08, P=0.089) showed non-significant trends. In the population-level comparison, APOC3 rs2854116 T allele was the only variant significantly enriched after Bonferroni correction (64.0% vs. 47.9%; OR 1.93, 95% CI 1.35-2.77, P<0.001), followed by PNPLA3 (33.3% vs. 24.1%, OR 1.57, P=0.019) and SAMM50 (31.2% vs. 22.6%, OR 1.55, P=0.028). Notably, APOC3 showed no association with fibrosis (OR 0.96, P=1.000), suggesting a role in susceptibility rather than progression. All SNPs were in Hardy-Weinberg equilibrium. ConclusionsThis study reveals a dissociation between genetic determinants of MASLD susceptibility and fibrosis progression in North Indian patients. APOC3 rs2854116 predisposes to MASLD at the population level, while PNPLA3 rs738409 drives fibrosis severity within established disease, underscoring the need for ancestry-specific genetic risk stratification. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/26347059v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@187f189org.highwire.dtl.DTLVardef@25d3borg.highwire.dtl.DTLVardef@13704e9org.highwire.dtl.DTLVardef@1238cce_HPS_FORMAT_FIGEXP M_FIG C_FIG

Background Short-chain fatty acids (SCFAs) are widely used as functional readouts of gut microbial activity in vivo. The growing adoption of decentralised study designs and self-collection protocols has amplified the need for reliable room-temperature storage and shipment strategies. However, SCFAs volatility and the persistence of post-collection microbial metabolism raise concerns regarding pre-analytical stability and the interpretability of measured concentrations. Methods We assessed the temporal stability of fatty acids (FAs) across intestinal and systemic matrices under room-temperature storage. Untreated stool was compared with two nucleic acid stabilisation devices (eNAT and OMNIgene-GUT), while whole blood, plasma and dried blood spots (DBS) were evaluated as minimally invasive systemic sampling strategies. Profiles were quantified using complementary GC-MS and LC-MS/MS workflows. Results Untreated stool showed fermentation-driven increases in major SCFAs, whereas immediate freezing preserved baseline profiles. eNAT maintained faecal FA stability for up to 21 days, while OMNIgene-GUT exhibited baseline and time-dependent alterations. In systemic matrices, plasma and whole blood showed upward drift, whereas DBS declined initially before stabilising after approximately 14 days. Conclusions FA measurements are highly matrix- and device-dependent. Our findings provide practical guidance for the selection of sampling strategies in microbiome-associated FA studies and emphasise the need for controlled pre-analytical conditions in decentralised microbiome studies.

AbstractO_ST_ABSRationaleC_ST_ABSIdiopathic pulmonary fibrosis (IPF) is an age-related disorder with common and rare genetic risk factors. It is unknown if the effects of PF genetic risk factors differ by chronologic age. ObjectivesTo assess age-specific effects of genetic risk factors in PF patients and their relatives. MethodsWe identified common and rare genetic risk factors using a Columbia whole genome sequencing (WGS) cohort (777 IPF, 2905 controls) and replicated findings using Trans-Omics for Precision Medicine (TOPMed, 1148 IPF, 5202 controls). We assessed age-stratified genetic risk of IPF and assessed for interaction with age across a range of cutoffs. We analyzed 313 FPF pedigrees and compared age-specific prevalence of interstitial lung disease in relatives stratified by proband genetic risk factors. Measurements and Main ResultsAdjusted odds of disease from MUC5B SNP increase with age, while odds of disease from rare variants decrease with age. The magnitude of the interaction term between age and both genetic variables was greatest in younger individuals. There were significant interactions between age <55 and the MUC5B SNP (discovery pinteraction=0.01; replication pinteraction<0.0001) and rare variants (discovery pinteraction<0.0001; replication pinteraction=0.03). Pedigree analysis showed more prevalent disease especially in younger relatives in FPF families with rare variants versus without (p<0.0001). ConclusionsAge modifies the effects of genetic risk factors in IPF. Rare variants confer greater risk in younger individuals whereas the MUC5B SNP confers greater risk in older individuals. Relatives of FPF patients with rare variants exhibit earlier prevalent disease, which has implications for preclinical disease screening.

RationaleSevere SARS-CoV-2 infection induces disrupted oropharyngeal and gut microbiota during acute disease which may persist and contribute to the development of post-acute pulmonary sequelae. To date, it is unclear whether dysbiosis following severe disease is linked to long-term pulmonary function impairment. ObjectivesTo determine associations between oropharyngeal and gut microbiota composition with lung function after severe COVID-19. Methods16S and internal transcribed spacer (ITS) rRNA amplicon sequencing were performed on oropharyngeal (16S and ITS) and rectal (16S) swabs at 3-, 6- and 12-months post-hospitalisation from 83 subjects previously admitted to the ICU with severe COVID-19 (Swiss COVIDlung study, NCT04581135). Subjects underwent 1-3 follow-up visits during which lung function testing was performed to investigate associations with microbiota composition. Measurements and Main ResultsThe oropharyngeal microbiota of subjects having suffered from COVID-19-related-severe acute non-cardiogenic hypoxemic respiratory failure with bilateral lung infiltrates (AHRF-BLI) was characterized by decreased -diversity and the presence of differentially abundant taxa. Subjects who recovered in lung function (TLC, FVC, FEV1 and DLCO >Lower Limit of Normal) had a distinct oropharyngeal and gut microbiota composition compared to those whose lung function never recovered. Fungal analysis of oropharyngeal samples revealed the presence of three distinct clusters which were characterized by distinct lung-function associated bacterial-fungal co-occurrence. ConclusionsThis study provide first insights into the role of the airway and gut microbiota in the development of long-term pulmonary sequelae after severe SARS-CoV-2 infection, shedding the light on the potential of the microbiota for preventive and therapeutic strategies in severe COVID-19.

BackgroundCrohns disease (CD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by high post-operative recurrence (POR) rates, reaching up to 90% within one year. Current clinical and endoscopic predictors show limited accuracy. ObjectiveThis study aimed to identify molecular mechanisms associated with POR at the time of surgery through integrated transcriptomic and bacteriomic analyses of ileal tissue. DesignIleal samples were obtained during surgery from 20 patients with CD and 10 inflammatory bowel disease-free controls, with an independent validation cohort of 49 patients with CD. POR was evaluated every six months using ileocolonoscopy and defined by Rutgeerts score. Host gene expression and tissue-associated microbiome profiles were integrated using correlation and pathway enrichment analyses to uncover host-microbe interactions linked to POR. ResultsIn the inflamed mucosa of patients who developed endoscopic POR, we identified a novel immune interaction involving the Porphyromonadaceae family, mainly Parabacteroides gordonii, which was slightly depleted. This depletion was associated with downregulation of epithelial barrier and tissue repair genes, including TFF1 and LSR, findings confirmed in the validation cohort. Porphyromonadaceae abundance positively correlated with short-chain fatty acid levels, particularly propionate. Additionally, omics integration revealed an association between Xanthomonadaceae and increased expression of ITGAM, a gene involved in neutrophil activation. ConclusionThese results highlight microbial-host gene interactions associated with POR. The pathogenic ITGAM-driven immune signature and the protective Porphyromonadaceae-TFF1-propionate axis supporting epithelial integrity may enable microbiome-informed prognostic tools and therapeutic strategies for CD POR. O_LIWhat is already known on this topic: Post-operative recurrence in Crohns disease is linked to microbial dysbiosis, particularly reduced diversity and expansion of Enterobacteriaceae. However, how microbial changes translate into host molecular mechanisms driving POR remains unclear. C_LIO_LIWhat this study adds: This prospective multi-omic study identifies a disrupted Porphyromonadaceae-SCFA-epithelial barrier axis and the participation of neutrophil responses in patients who develop POR at surgery time. C_LIO_LIHow this study might affect research, practice or policy: The findings provide mechanistic targets for microbiome-informed risk stratification and prevention of POR. They support development of microbial or metabolite-based interventions aimed at restoring epithelial barrier function after surgery. C_LI

BackgroundPerianal Crohns disease (PCD) represents one of the most severe and refractory forms of pediatric inflammatory bowel disease (IBD). Constipation and colonic redundancy, particularly type 1 dolichocolon (T1-DC), may increase distal rectosigmoid pressure, and exacerbate perianal pathology. We hypothesized that T1-DC is more common in children with PCD than in those with uncomplicated ileocolonic Crohns disease (CD) or non-IBD controls. MethodsWe retrospectively analyzed 20 consecutive pediatric PCD cases (penetrating [B3p] or inflammatory [B1p]) and compared them with 20 patients with non-complicated ileocolonic CD (L3/B1) and 30 non-IBD trauma controls. DC type was determined radiographically using established criteria, focusing on T1- and T2-DC. Constipation history was abstracted from medical records under IRB-approved protocols. ResultsDC was significantly more prevalent in PCD than in ileocolonic CD or controls (p < 0.001), primarily due to T1-DC. The associations persisted (p<0.03) in PCD patients without a history of constipation. ConclusionsRectosigmoid redundancy (T1-DC) may represent an underrecognized anatomic co-morbidity in pediatric PCD, contributing to increased distal pressure and susceptibility to perianal complications. Identification of T1-DC could inform surgical decision-making and postoperative management. Targeted approaches--such as segmental resection during stoma reversal, structured bowel regimens, physical activity, and pelvic-floor biofeedback--may help reduce recurrence risk. Prospective studies are needed to define the mechanistic role of colonic redundancy in the pathogenesis of PCD.

IntroductionPrevious studies have shown that Aquamin(R), a multi-mineral extract from red marine algae, enhances barrier integrity proteins in the human colon. These findings prompted further investigation into Aquamin(R)s effects on gastrointestinal barrier function and permeability. MethodsSubjects with mild or in remission ulcerative colitis (UC) and healthy controls were enrolled in an open-label trial and received Aquamin(R) capsules (800 mg calcium/day) for 90 days. Intestinal permeability was evaluated before and after the 90-day intervention by urinary mannitol excretion after ingestion of a 5 g mannitol solution, with collections across several time intervals (pre-drink, 0-2 h, 2-8 h, and 8-24 h). The primary outcome was the change in mannitol excretion. Serum samples were also collected to assess liver and renal function. ResultsIn this pilot study (NCT04855799), which included UC patients and healthy controls (n = 8 per group), baseline urine mannitol levels in the 0-2 h sample were 54% higher in UC patients compared to healthy subjects (p = 0.006). Following 90 days of Aquamin(R) supplementation, urinary mannitol levels in UC patients decreased by 28%, 26%, and 41% at the 0-2 h, 2-8 h, and 8-24 h timepoints, respectively; the reduction at the 0-2 h interval reached statistical significance (p = 0.015). Overall, Aquamin(R) supplementation reduced total post-intervention mannitol excretion by 29% (p = 0.024). Aquamin(R) was well tolerated, with no serious adverse events reported. The serum metabolic panel revealed a modest but statistically significant reduction in alkaline phosphatase levels after 90 days of intervention. ConclusionThese results provide preliminary evidence that Aquamin(R) supplementation beneficially modulates gut barrier function and supports epithelial integrity in UC patients. These findings support further investigation of Aquamin(R) as a safe and promising adjunct to current UC management strategies, with potential utility as a barrier therapy in UC. SummaryAquamin(R) supplementation for 90 days reduced intestinal permeability in ulcerative colitis patients, as measured by urinary mannitol excretion. The intervention was well tolerated, suggesting Aquamin(R) may be a safe, promising adjunct for enhancing gut barrier function in UC management.

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 and aimsPopulation screening for liver disease in high-risk groups is recommended. Community diagnosis of liver disease is a challenge due to the asymptomatic nature of disease until very advanced stages. Moreover, regional variation in testing availability can result in people with clinically significant liver disease being missed. Machine learning (ML) has been proposed as a method to reduce diagnostic error and automate screening. We present a novel machine learning derived algorithm (ID LIVER-ML) designed to predict the risk of clinically significant liver disease in a high-risk community population to identify those needing further investigations or specialist referral. MethodsUsing data from 2039 patients recruited to two UK cohorts, we created a parsimonious model using investigations that would be available in primary care using liver stiffness measurement as reference standard. The performance of ID LIVER-ML was compared against FIB-4 score in a second unseen hold out cohort (n=327). ResultsID LIVER-ML performed well at identifying patients at risk of clinically significant liver fibrosis (sensitivity 0.90, Specificity 0.43, PPV 0.54, NPV 0.86, AUC 0.83) and outperformed conventional risk scoring systems (FIB-4: AUC 0.65; NAFLD Fibrosis Score: AUC 0.66; APRI: AUC 0.53; BARD: AUC 0.58). ConclusionMachine learning derived algorithms can help screen high risk populations in a community setting for liver fibrosis. ClinicalTrials.gov ID: NCT04666402 Impact and ImplicationsThe prevalence of steatotic liver disease is rising globally and is an increasingly significant challenge for healthcare systems. Existing risk stratification scores are not validated in a real-world cohort where patients have risk factors for multiple aetiologies of liver disease. Our work shows that a machine learning model can predict the risk of clinically significant liver disease using routine primary care data, better than existing non-invasive risk stratification tools in a real-world cohort. This highlights a potential role for machine learning in the automation of fibrosis risk assessment in primary care. Highlights- Machine learning derived algorithms can predict the risk of clinically significant liver disease in an at risk community population with a mixed aetiology of liver diseases. - The performance of the ML algorithm (ID LIVER-ML) is not affected by metabolic, alcohol, or mixed aetiologies. - ID LIVER-ML outperforms traditional risk stratification scoring systems such as FIB-4 and NAFLD fibrosis scores. - Compared to the FIB-4 score, the use of Machine Learning can reduce the need for secondary care investigations by 59%.

Chronic constipation is highly prevalent, and cases refractory to treatment are particularly challenging to manage. High-resolution colonic manometry (HRM) is used to further evaluate these patients to identify cases of intrinsic motor dysfunction (underlying myopathy or neuropathy). However, HRM is invasive and resource-intensive, limiting uptake and clinical utility. This study presents Body Surface Colonic Mapping (BSCM), a non-invasive cutaneous electrical recording technique, as a clinical alternative. Simultaneous recordings from HRM (36-channel) and BSCM (8x8 electrode array) were performed in 10 patients with chronic refractory constipation. Lower gut symptom scores were also tracked patients over the duration of the recording. Motility was assessed during meal and bisacodyl challenges. We optimized BSCM signal processing specifically to detect high-amplitude propagating contractions (HAPCs) evoked by bisacodyl. Analysis included time-frequency quantification of motility indices and blinded visual assessment by domain experts to classify the presence or absence of motor responses. BSCM motility indices showed strong correlation with HRM for both meal (r = 0.86) and bisacodyl (r = 0.69) responses. Expert visual analysis yielded concordant classification between BSCM and HRM in the majority (87.5 {+/-} 9.6%) of cases. Furthermore, BSCM identified distinct, patient-specific symptom-motility associations during the meal response. BSCM accurately detects meal- and stimulant-induced increases in colonic motility with high fidelity to invasive HRM. As a non-invasive method that is easy to apply with minimal resource and time requirements, BSCM is well-positioned for clinical translation as a scalable diagnostic tool to elucidate symptom-motility associations and guide personalized management in refractory chronic constipation.

PurposeHirschsprung-associated enterocolitis remains a major postoperative complication of Hirschsprungs disease (HD), and impaired epithelial barrier integrity has been proposed as a contributing factor. In this study, we investigated whether 12-hydroxyheptadecatrienoic acid (12-HHT), an endogenous leukotriene B4 receptor 2 (BLT-2) agonist, enhances the epithelial barrier and exerts anti-inflammatory effects in patient-derived colonic organoids. MethodsNormoganglionic specimens from rectal/rectosigmoid HD at pull-through (HD-N; n = 8) and transverse colon specimens from anorectal malformation (ARM) at colostomy closure (n = 10) were used to generate colonic organoids. Epithelia were isolated using ethylenediaminetetraacetic acid and subsequently embedded in Matrigel. Baseline expression of TJP1, TJP2, F11R (encoding junctional adhesion molecule-A), JAM2, CLDN1, CLDN3, CLDN4) and LTB4R2 (encoding BLT-2) was assessed by qPCR and immunoblotting. Organoids were then treated with 12-HHT (0.4, 2, or 10 M) for 7 days, followed by qPCR. Additional experiments assessed cytokine expression (IL1B, IL6) and TJPs after 24 h with tumor necrosis factor- (TNF-, 100 ng/mL) plus phosphate buffered saline or 12-HHT. Barrier function was evaluated using FITC-dextran influx assays. ResultsHD-N and ARM organoids exhibited similar growth efficiencies. Baseline expression for F11R, JAM2, CLDN1, CLDN3, CLDN4, and LTB4R2 was significantly lower in HD-N than in ARM. TJPs were upregulated by 12-HHT at 2 and 10 M in both groups, with stronger effects in ARM. In HD-N organoids, 10 M 12-HHT suppressed TNF--induced IL1B and IL6 elevation mitigated tight junction proteins (TJPs) downregulation more effectively than 2 M. 12-HHT attenuated TNF--induced FITC-dextran influx in HD-N organoids. Conclusion12-HHT may exert anti-inflammatory effects by integrating TJPs of HD-N.

Hereditary -tryptasemia (HT), defined by increased TPSAB1 copy number and elevated basal serum tryptase, is associated with mast cell (MC)-mediated symptoms, yet its role in gastrointestinal disease remains unclear. Because intestinal MCs express the non-IgE-dependent activation receptor MRGPRX2, we investigated whether MRGPRX2 expression is altered in individuals with HT and inflammatory bowel disease (IBD). We genotyped 854 biobanked IBD samples, performed spatial transcriptomics on descending colon tissue (n = 4 HT; n = 4 non-HT), and analyzed small-intestinal biopsies by mass cytometry (CyTOF; n = 5 HT; n = 9 controls). Across these complementary platforms, HT was associated with increased gastrointestinal MC abundance and higher expression of activation markers including CD203c, LAMP-1, and SIGLEC8. Both spatial transcriptomics and ddPCR demonstrated significantly increased MRGPRX2 and SIGLEC8 transcripts in IBD samples from individuals with HT compared with matched non-HT IBD cases. These findings suggest that enhanced MRGPRX2 expression and associated MC activation may contribute to gastrointestinal symptoms in HT, particularly in the context of IBD. As interest in precision immunogenetics grows, defining MC phenotypes linked to -tryptase copy number may help refine diagnostic evaluation and identify patients who could benefit from emerging mast cell-targeted therapeutic strategies in the context of IBD.

Pulmonary arterial hypertension (PAH) is a rare, life-limiting disease where deficiency of the TGF/BMP pathways have causal roles in hereditary and idiopathic forms. It is an attractive candidate for therapeutic intervention but there is an unmet need for clinically-relevant and practical biomarkers that can measure target engagement. A major challenge has been the inaccessibility of lung tissue in disease for molecular profiling. Here we explore the surrogate capacity of peripheral blood BMP pathway-specific markers. We demonstrate that BMPR-II in flow cytometrically characterised white blood cell subsets is reduced in a proportion of patients, however proteomic analysis demonstrates pleiotropic alterations of TGF{beta}/BMP modulators. Downstream BMPR-II canonical and non-canonical signalling is impacted and measurable in whole blood. We present discovery and international replication cohorts for a transcriptomic BMPR-II signalling signature. The composite biomarker panel is repeatable, reproducible, longitudinally stable and expressed in correlated gene modules in PAH which associate with clinical outcomes. The assay performance characteristics of the biomarker panel make it feasible for early phase, target engagement clinical trials and an adaptive three arm study of two pre- clinically validated modulators of BMPR-II is underway. One Sentence SummaryThe first demonstration of clinically-relevant BMP biomarker panels validated in international populations of patients with PAH.

ObjectivesTo characterize ultra-processed food (UPF) circulating metabolic signatures associated with Crohns disease (CD) and to localize key metabolic mediators linking UPF intake to CD risk. DesignProspective cohort study. SettingTwo large multi-center cohorts (UK Biobank [UKB] and Whitehall II [WHII] study) across the UK and an Eastern multi-center cohort ONE-IBD Study from China. ParticipantsUK Biobank discovery cohort (n=10,229) for signature derivation, internal validation cohort (n=91,306), external validation cohort Whitehall-II (n=7,893), and three additional cohorts (two Western and ONE-IBD) for validation of key metabolic drivers. Main outcome measuresPrimary outcomes were UPF-related circulating metabolic signatures and their associations with CD risk; secondary outcomes included evidence supporting causal roles of candidate metabolites and genetic pathways assessed by Mendelian randomization, colocalization, and gene-environment analysis. ResultsA UPF metabolic signature of 73 metabolites was constructed and validated across cohorts (Spearman {rho}: 0.20-0.25). More pronounced UPF metabolic signature was associated with increased CD risk (HRper SD=2.65, 95% CI 1.57-4.48). WGCNA revealed a cluster enriched in fatty acids. Within this cluster, docosahexaenoic acid (DHA) emerged as the strongest, which mediated 17.1% of the UPF-CD association. External validation in ONE-IBD supported DHA as the strongest associated metabolite with UPF and CD. Mendelian randomization supported a causal protective effect of DHA on CD (OR=0.72, 95% CI 0.61- 0.83; P<0.001), with colocalization implicating rs174546 in the FADS1 gene. ConclusionThe adverse effects of UPF on CD risk may be driven by a relative deficiency of protective metabolites such as DHA, apart from additive harm to metabolic depletion. This reframes UPF-related risk and highlighting potential targets for precision nutrition in CD prevention.

BackgroundThough a normal forced vital capacity (FVC) is typically thought to imply the absence of restriction, recent data suggest that restriction may in fact be common among patients with normal spirometry. However, the clinical significance of restriction with normal spirometry is unknown. Research QuestionWhat clinical characteristics and outcomes are associated with restriction with normal spirometry? Study Design and MethodsWe interpreted pulmonary function tests (PFTs) with both static and dynamic lung volume measurements performed between 2012 and 2025 at four pulmonary diagnostic labs. We used multivariable logistic regression to identify clinical characteristics associated with restriction among patients with normal spirometry and used a Cox proportional hazards model to assess the association of restriction with survival, adjusting for age, sex, forced expiratory volume in 1 second (FEV1) z-score, FVC z-score, and FEV1/FVC z-score. ResultsWe interpreted 83,886 PFTs from 47,597 patients (mean age 58.8 years, 59.8% female, 63.6% White). The prevalence of restriction among patients with normal spirometry was 25.7% Restriction with normal spirometry was more likely in older patients (adjusted odds ratio [aOR] 1.01 per year, 95% CI 1.01-1.01), in non-White patients (aOR 1.33, 95% CI 1.26-1.41), and in patients with a diagnosis (aOR 3.65, 95% CI 3.43-3.88) or radiographic evidence (aOR 3.02, 95% CI 2.79-3.28) of interstitial lung disease (ILD). Restriction with normal spirometry was less likely among female patients (aOR 0.64, 95% CI 0.60-0.67), and patients with a diagnosis (0.74, 95% CI 0.67-0.82) or radiographic evidence (aOR 0.81, 95% CI 0.73-0.89) of chronic obstructive pulmonary disease. Restriction with normal spirometry was associated with increased all-cause mortality (adjusted hazard ratio 1.45, 95% CI 1.34-1.57) as compared to normal spirometry without restriction. InterpretationRestriction with normal spirometry is associated with ILD and with decreased survival. Clinically significant ventilatory impairments are common in patients with normal spirometry.

BackgroundSystemic infections are a leading cause of hospitalization and death among patients with cirrhosis. Timely and accurate infection identification is essential for both clinical care and the development of predictive models. However, existing methods such as ICD-10 coding are unreliable, and manual chart review is resource-intensive and difficult to scale. This study aimed to develop and validate an automated large language model (LLM)-based approach for infection classification and subtyping in patients with cirrhosis presenting to the emergency department (ED). MethodWe developed INFEHR (INfection identification and subtyping using Free-text EHR analysis), an LLM-powered pipeline utilizing Claude 3.5 Sonnet to analyze clinical notes from the first 72 hours of admission. Model outputs were compared against a physician-adjudicated gold standard in a cohort of 1,000 encounters from patients with cirrhosis who presented to the ED. Performance was benchmarked against ICD-10 code-based labeling and CDC Adult Sepsis Event criteria. ResultsINFEHR achieved 94.7% overall accuracy, with 99.5% sensitivity and 92.8% positive predictive value for identifying infection presence, outperforming ICD-10-based classification across all metrics (p < 0.0001). The model also demonstrated strong performance in classifying pathogen type and infection site. This pipeline processed notes within seconds, offering improvements in efficiency and scalability over manual review. ConclusionINFEHR offers a scalable, reproducible, and accurate method for infection phenotyping in cirrhosis. By overcoming limitations of traditional coding and manual review, it supports high-throughput infection surveillance, improves cohort construction for clinical research, and enables future integration into real-time decision-support tools in hepatology.