Huang, Yuting

Single-cell studies have defined immune states in inflammatory bowel disease (IBD), but how adaptive receptor histories organize circulating immunity remains unclear. We generated a single-cell transcriptomic atlas of peripheral blood from 249 participants with Crohn's disease, ulcerative colitis, or non-IBD control status, including 182 with productive TCR and BCR recovery. Expanded TCR clonotypes marked inflammatory-memory and cytotoxic states, while distinct but similar paired TCRs shared inflammatory programs across participants. BCR lineage maturation linked IgA-associated mucosal and plasma B cell programs to somatic mutation and class switching, distinguishing maturation-associated biology from clonal expansion. Helper, regulatory, and cytotoxic T-cell programs covaried with B-cell states, and inferred interactions nominated reciprocal antigen-presentation and helper pathways. Repertoire-based machine learning distinguished diagnosis, inflammation, and contemporaneous six-month treatment-response status. Together, this atlas connects receptor architecture to coordinated systemic immune remodeling, establishes a foundation for repertoire-informed patient stratification, and prioritizes candidate mechanisms of IBD pathogenesis.

Abstract Background and Aims Fibroblast–neutrophil interactions are implicated in ulcerative colitis (UC) treatment resistance, but whether fibroblasts modify neutrophil inflammatory activity remains unclear. We investigated responses to fibroblast exposure, stromal depletion, and α5β1-directed treatment. Methods We integrated human and mouse colonic single-cell RNA sequencing (scRNA-seq), spatial protein profiling (CODEX), fibroblast–neutrophil coculture, and dextran sulfate sodium (DSS) mouse colitis with fibroblast activation protein (FAP) ablation or α5β1-directed treatment. Readouts included cellular representation and protein fluorescence via flow cytometry, neutrophil extracellular trap (NET)-associated elastase activity, RNA programs and epithelial responses using scRNA-seq. Results Inflamed UC tissue contained higher fractions of inflammatory fibroblasts and oncostatin M (OSM)- and CXCR4-associated neutrophils. Inflammatory fibroblasts had higher FAP–α5β1 module scores, and proximity to FAP-high fibroblasts was associated with higher neutrophil OSM and CXCR4 fluorescence. UC fibroblasts increased neutrophil OSM, CXCR4 and myeloperoxidase (MPO) fluorescence and NET-associated elastase activity relative to control fibroblasts, while α5β1-directed treatment attenuated these responses. Both mouse FAP ablation and α5β1 blockade in DSS colitis reduced histologic inflammation and overall neutrophil frequency. Ablation broadly reduced recovered neutrophil representation, whereas blockade increased OSM-positive and PADI4-positive percentages within neutrophils despite lower MPO fluorescence within these subsets. Both interventions were associated with lower epithelial chemokine scores but distinct absorptive and mucus/secretory responses. Conclusions Fibroblast exposure modifies neutrophil inflammatory phenotype and effector-associated activity, identifying candidate therapeutic pathways in UC. Evaluating these responses alongside neutrophil representation and tissue inflammation could inform pharmacodynamic assessment of stromal-directed therapies. Graphical Abstract What You Need to Know Background and Context Fibroblast–neutrophil interactions are associated with treatment resistance in ulcerative colitis. Whether fibroblast exposure modifies neutrophil inflammatory phenotype and effector activity, beyond its established recruitment role, remains unclear. New Findings UC fibroblasts increased neutrophil inflammatory proteins and NET-associated elastase activity; α5β1-directed treatment attenuated these responses. FAP ablation and α5β1-directed treatment reduced colitis and overall neutrophil frequency. α5β1-directed treatment lowered MPO within OSM-positive and PADI4-positive neutrophils despite higher marker-positive percentages. Epithelial single-cell RNA sequencing revealed reduced chemokine programs with both interventions but distinct barrier-associated and regenerative expression patterns. Limitations Cellular drug targets remain unresolved. Spatial associations and elastase activity do not establish direct contact, NET formation, or clinical efficacy. Clinical Research Relevance Fibroblast-associated pathways offer candidate therapeutic opportunities to modify neutrophil inflammatory phenotype and effector activity in UC. Coculture responses were pharmacologically modifiable, and stromal interventions reduced experimental colitis. Measuring neutrophil frequency, subset proteins, and effector activity alongside tissue inflammation could guide pharmacodynamic assessment. Clinical efficacy and treatment-selection utility require validation. Basic Research Relevance Human coculture provides experimental evidence that fibroblast exposure modifies neutrophil inflammatory proteins and NET-associated elastase activity. FAP+ stromal ablation and α5β1-directed treatment produced distinct patterns of neutrophil representation and subset proteins in colitis. Epithelial single-cell RNA sequencing revealed reduced chemokine programs with both interventions but differing barrier-associated and regenerative expression patterns. Together, these findings motivate mechanistic studies of how stromal recruitment cues, soluble signals, and matrix-associated interactions regulate neutrophil responses, and whether these changes contribute to reduced epithelial inflammation and tissue repair. Lay Summary Fibroblasts, support cells in the intestine, increased inflammatory activity in immune cells called neutrophils. Blocking a pathway involved in cell attachment reduced these responses in cultures. Targeting fibroblast-associated pathways also reduced experimental colitis, with changes in intestinal lining gene activity related to inflammation, barrier function, and repair. These findings suggest potential approaches to treating ulcerative colitis.

Ex vivo liver perfusion (EVLP) sustains human or large animal livers outside the body under near-physiological conditions, enabling functional monitoring for lactate clearance, bile production, and oxygen consumption and allowing targeted therapeutic interventions. Originally developed to optimize donor grafts for transplantation, EVLP has evolved into a powerful translational research platform bridging preclinical discovery and early clinical translation. This review discusses EVLP as a platform for gene therapy, immunotherapy, pharmacology, and personalized medicine, with particular emphasis on gene- and immune-based interventions as mechanistically mature exemplars. We consolidate advances in pharmacological testing and toxicity modeling, viral and non-viral gene delivery, genome engineering, and immunomodulation using perfused livers. We further describe emerging applications, including autologous EVLP pathways for organ-confined therapy, ex vivo liver surgery, and bioengineering strategies such as biliary organoid repair, RNA interference, and mitochondrial transfer. We highlight how these applications align with a paradigm shift in biomedical research, including the NIH’s recent initiative to prioritize human-based experimental models over animal-only studies. By leveraging transplant-declined or surgically resected organs that would otherwise be unused, ex vivo perfusion bridges the gap between pre-clinical testing and clinical practice, enabling real-time evaluation of interventions in functional human tissue. We discuss both the scientific opportunities afforded by EVLP and the technical, biosafety, and ethical challenges that must be addressed to enable responsible clinical translation.

Background: Colorectal cancer (CRC) remains one of the common causes of cancer-related morbidity and mortality in the United States. Emerging increases in early-onset CRC and persistent disparities remain major public health concerns. Objective: To characterize long-term CRC incidence and mortality trends in the United States, with particular emphasis on identifying demographic groups experiencing rising or plateauing disease burden. Methods: We conducted a population-based ecological study using CRC incidence data from the United States Cancer Statistics database (1999–2022) and mortality data from CDC WONDER (1999–2023). Temporal trends were evaluated using Joinpoint regression to estimate annual percent change (APC) and average annual percent change (AAPC), stratified by age, sex, race/ethnicity, and urbanization level. Results: Overall CRC incidence and mortality declined during the study period (both AAPC approximately −2.08%). However, incidence increased significantly among adults younger than 55 years, particularly those aged 20–24 years. Mortality also increased among younger adults aged 25–44 years and remained elevated among individuals aged 45–54 years. Non-Hispanic Black individuals consistently experienced the highest incidence and mortality rates. Mortality declines plateaued in several older age groups after 2018–2020. Conclusions: Despite overall improvements in CRC burden, increasing incidence and mortality among younger adults and persistent disparities highlight the need for risk-stratified prevention, earlier detection strategies, and tailored therapeutic approaches.

INTRODUCTION: Colonoscopies reduce colorectal cancer incidence and mortality, but challenges remain in detecting all precancerous lesions. Operator fatigue, technique variability, and subtle lesions can lead to missed adenomas, highlighting the need for tools that standardize detection quality. Computer-aided detection (CADe) systems use artificial intelligence to enhance lesion detection and improve screening colonoscopy quality. This study evaluates the impact of CADe on key quality and efficiency metrics in a clinical setting. METHODS: A single-center retrospective study at an academic tertiary center analyzed 4,028 colonoscopies from October 2022 to December 2023. The CADe system was used in 4 of 8 endoscopy suites, creating a CADe and control group. Propensity matching accounted for age, sex, indication, and physician. Primary outcomes included adenoma detection rate (ADR) and polyp detection rate (PDR). Adenomas per colonoscopy (APC) and polyps per colonoscopy (PPC) were also measured. Per-polyp analyses were performed as a tertiary outcome. RESULTS: ADR was significantly higher in the CADe group (38.6%) vs control (34.2%) (rate ratio [RR] = 1.127, P < 0.05). PDR was significantly higher in the CADe group (67.2%) vs control (59.4%) (RR = 1.130, P < 0.05). APC was significantly higher in the CADe group (M = 0.406, SD 0.637) vs control (M = 0.359, SD 0.599) (RR = 1.131, P < 0.05). PPC was significantly higher in the CADe group (M = 1.297, SD 1.188) vs control (M = 1.046, SD 1.002) (RR = 1.240, P < 0.05). The increase in polyp resection with CADe was driven predominantly by ≤5 mm lesions, with comparatively smaller differences for larger polyps. DISCUSSION: Implementing CADe in clinical practice significantly improved ADR, PDR, APC, and PPC. However, the increase in ADR seems inflated by the detection of polyps ≤5 mm, whose clinical significance in reducing colorectal cancer remains uncertain.

Abstract Objectives To comprehensively evaluate the validity of International Classification of Diseases, Tenth Revision, Clinical Modification (ICD-10-CM) codes for both prevalent diagnoses and less common diseases, and to assess the performance of a large language model (LLM)-based system in validating these codes. Materials and Methods This retrospective study analyzed hospital admissions from the Medical Information Mart for Intensive Care IV (MIMIC-IV) database. We developed a validated LLM-based system using GPT-4o, refined through iterative prompt engineering, to assess ICD-10-CM code validity. We measured the positive predictive value (PPV) of ICD-10-CM codes, PPV of principal and secondary diagnoses, and the performance of an LLM-based system in code validation. Results Among 865 079 assigned codes, the PPV was 84.6% (95% CI, 84.5%-84.6%). Principal diagnoses had a PPV of 93.9% (95% CI, 93.7%-94.1%), while secondary diagnoses had a PPV of 83.8% (95% CI, 83.7%-83.9%). The LLM system demonstrated high performance in validating ICD codes, achieving 93.6% accuracy, 95.4% sensitivity, and 85.2% specificity. Among correctly assigned secondary diagnoses, the majority (67.9%) represented historical or baseline conditions, while 32.1% reflected active conditions that deviated from baseline status; 22.3% of these emerged after hospital admission. PPV decreases with later diagnosis positions, with the largest decline occurring between principal and secondary diagnoses. Discussion and Conclusion In this large-scale evaluation, ICD-10-CM codes exhibited generally high accuracy, though variability existed by position and condition type. A validated LLM system performed comparably to physician review and offers a scalable means to improve coding accuracy. These findings support the potential for integrating LLM-based auditing into routine workflows to strengthen the quality of administrative and research data.

ABSTRACT Objective To comprehensively evaluate the validity of ICD-10-CM codes for both prevalent diagnoses and less common diseases, and to assess the performance of a large language model (LLM)-based system in validating these codes. Materials and Methods This retrospective study analyzed hospital admissions from the Medical Information Mart for Intensive Care (MIMIC-IV) database. We developed a validated LLM-based system using GPT-4o, refined through iterative prompt engineering, to assess ICD-10-CM code validity. We measured the PPV of ICD-10-CM codes, PPV of principal and secondary diagnoses, and the performance of an LLM-based system in code validation. Results Among 865,079 assigned codes, the PPV was 84.6% (95% CI, 84.5%-84.6%). Principal diagnoses had a PPV of 93.9% (95% CI, 93.7%-94.1%), while secondary diagnoses had a PPV of 83.8% (95% CI, 83.7%-83.9%). The LLM system demonstrated high performance in validating ICD codes, achieving 93.6% accuracy, 95.4% sensitivity and 85.2% specificity. Among correctly assigned secondary diagnoses, the majority (67.9%) represented historical or baseline conditions, while 32.1% reflected active conditions that deviated from baseline status; 22.3% of these emerged after hospital admission. PPV decreases with later diagnosis positions, with the largest decline occurring between principal and secondary diagnoses. Discussion and Conclusion In this large-scale evaluation, ICD-10-CM codes exhibited generally high accuracy, though variability existed by position and condition type. A validated LLM system performed comparably to physician review and offers a scalable means to improve coding accuracy. These findings support the potential for integrating LLM-based auditing into routine workflows to strengthen the quality of administrative and research data.

Abstract Background Patients with inflammatory bowel disease (IBD) are at increased risk of herpes zoster (HZ) infection due to innate immune abnormalities and use of immunosuppressive therapy. The recombinant zoster vaccine (RZV) is recommended, but its efficacy in preventing recurrent HZ among patients with IBD is not well established. Methods Using data from the TriNetX Linked Network, we conducted a retrospective cohort study of adults (≥18 years) with IBD and a prior uncomplicated HZ episode. Patients with IBD who received RZV were propensity score-matched 1:1 with those who did not. The primary outcome was subsequent HZ complications. Secondary outcomes included subtypes of HZ complications and recurrent uncomplicated HZ. Hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated via Cox proportional hazards models. Results After matching, 1260 vaccinated and 1260 unvaccinated patients with IBD were included. Compared to the unvaccinated cohort, patients receiving RZV had a significantly reduced incidence of HZ complications (7.4% vs. 14.5%; HR, 0.75; 95% CI, 0.58–0.97; P = .028). Postherpetic neuralgia was notably decreased (5.8% vs. 12.5%; HR, 0.66; P = .010), and no central nervous system involvement occurred among vaccinated patients. Protective effects were more pronounced in patients with ulcerative colitis, females, and those not receiving immunosuppressive therapy. Conclusions RZV substantially lowers the risk of HZ complications in patients with IBD, offering significant clinical benefits to those at high risk due to immunosuppression. These findings underscore the importance of RZV as part of preventive care strategies in patients with IBD.

AbstractCholecystectomy is the standard treatment for acute cholecystitis, but it may not be suitable for all patients. For those who cannot undergo surgery, a percutaneous cholecystostomy tube (PCT) and ERCP-guided transpapillary gallbladder drainage are viable options. We aimed to perform a nationwide study to assess 30-day readmission rates, adverse events (AEs), and mortality rates in these two cohorts.We conducted a nationwide cohort study using data from the Nationwide Readmissions Database (NRD) from 2016 to 2019. We identified patients with acute cholecystitis during the index admission who underwent either PCT or ERCP-guided gallbladder drainage. Propensity score matching along with multivariable regression was used to compare cohorts.During the study period, 3,592 patients (average age 63.0 years) underwent endoscopic drainage, whereas 80,372 patients (average 70.8 years) underwent Interventional Radiology drainage. Utilizing multivariate Cox regression analysis, compared with ERCP, PCT had a higher risk for 30-day readmission (adjusted hazard ratio [aHR] 1.47; 95% confidence interval [CI] 1.27 to 1.71; P < 0.001). The PCT group had a significantly higher rate of readmission for acute cholecystitis compared with the ERCP group (2.72% vs 0.86%; P < 0.005). Cox proportional hazard ratio showed a 3.41-fold increased risk (95% CI 1.99 to 5.84) for readmission in the PCT group. ERCP was consistently associated with lower rates of post-procedural AEs compared with PCT including acute hypoxemic respiratory failure (P < 0.001), acute renal failure (P < 0.001), shock (P < 0.001), and need for blood transfusions (P < 0.001).Our nationwide analysis revealed that ERCP-guided gallbladder drainage should be the preferred approach for managing acute cholecystitis when unfit for surgery.