The role of CRISPR-Cas9 and CRISPR interference technologies in the treatment of autoimmune diseases

Autoimmune disorders can be described as inappropriate immune responses directed against self-antigens, which account for substantial healthcare concerns around the world. Immunosuppression or immune modulation are the main therapeutic modalities for autoimmune disorders. These modalities, however, impair the ability of the immune system to fight against infections, thereby predisposing to opportunistic diseases. This review explores existing therapies for autoimmune disorders, highlighting their limitations and challenges. Additionally, it describes the potential of CRISPR-Cas9 technology as a novel therapeutic approach to address these challenges.

High Healthcare Costs in Childhood Inflammatory Bowel Disease: Development of a Prediction Model Using Linked Clinical and Health Administrative Data

BACKGROUND

The incidence of pediatric-onset inflammatory bowel disease (IBD) and the costs of caring for individuals with IBD are both increasing. We calculated the direct healthcare costs of pediatric IBD in the first year after diagnosis and developed a model to predict children who would have high costs (top 25th percentile).

METHODS

Using data from the Canadian Children IBD Network inception cohort (≤16 years of age, diagnosed between 2013 and 2019) deterministically linked to health administrative data from Ontario, Canada, we estimated direct healthcare and medication costs accrued between 31 and 365 days after diagnosis. Candidate predictors included age at diagnosis, sex, rural/urban residence location, distance to pediatric center, neighborhood income quintile, IBD type, initial therapy, disease activity, diagnostic delay, health services utilization or surgery around diagnosis, regular primary care provider, and receipt of mental health care. Logistic regression with stepwise elimination was used for model building; 5-fold nested cross-validation optimized and improved model accuracy while limiting overfitting.

RESULTS

The mean cost among 487 children with IBD was CA$15 168 ± 15 305. Initial treatment (anti-tumor necrosis factor therapy, aminosalicylates, or systemic steroids), having a mental health care encounter, undergoing surgery, emergency department visit at diagnosis, sex, and age were predictors of increased costs, while having a regular primary care provider was a predictor of decreased costs. The C-statistic for our model was 0.71.

CONCLUSIONS

The cost of caring for children with IBD in the first year after diagnosis is immense and can be predicted based on characteristics at diagnosis. Efforts that mitigate rising costs without compromising quality of care are needed.

Stromal Cell Subsets Show Model-Dependent Changes in Experimental Colitis and Affect Epithelial Tissue Repair and Immune Cell Activation

BACKGROUND

Previous work on inflammatory bowel disease (IBD) revealed changes in the abundance of colonic stromal subsets during intestinal inflammation. However, it is currently unknown whether these stromal cell subset changes are also reflected in different IBD mouse models and how commonly used IBD therapies affect stromal cell subset composition.

METHODS

Stromal subset markers CD55, C-X-C motif chemokine 12 (CXCL12), podoplanin (PDPN), CD90, and CD73 were analyzed by flow cytometry in 3 mouse models for IBD, namely interleukin (IL)-10 knockout (KO), dextran sulfate sodium-induced, and T-cell transfer model for colitis. Next, the effects of IBD therapies on the stromal subset composition were studied. In vitro experiments were performed to study the interaction between stromal cell subsets and epithelial/immune cells.

RESULTS

The colitis-induced changes in the abundance of stromal cell subsets differed considerably between the 3 colitis mouse models. Interestingly, treatment with IBD medication affected specific stromal subsets in a therapy and model-specific manner. In vitro experiments showed that specific stromal subsets affected epithelial wound healing and/or T-cell activation.

CONCLUSIONS

The relative abundance changes of stromal cell subsets during experimental colitis differ between 3 established colitis models. Treatment with IBD therapies influences stromal subset abundance, indicating their importance in IBD pathogenesis, possibly through affecting epithelial migration, and T-cell activation.

IBDome: An integrated molecular, histopathological, and clinical atlas of inflammatory bowel diseases

Multi-omic and multimodal datasets with detailed clinical annotations offer significant potential to advance our understanding of inflammatory bowel diseases (IBD), refine diagnostics, and enable personalized therapeutic strategies. In this multi-cohort study, we performed an extensive multi-omic and multimodal analysis of 1,002 clinically annotated patients with IBD and non-IBD controls, incorporating whole-exome and RNA sequencing of normal and inflamed gut tissues, serum proteomics, and histopathological assessments from images of H&E-stained tissue sections. Transcriptomic profiles of normal and inflamed tissues revealed distinct site-specific inflammatory signatures in Crohn's disease (CD) and ulcerative colitis (UC). Leveraging serum proteomics, we developed an inflammatory protein severity signature that reflects underlying intestinal molecular inflammation. Furthermore, foundation model-based deep learning accurately predicted histologic disease activity scores from images of H&E-stained intestinal tissue sections, offering a robust tool for clinical evaluation. Our integrative analysis highlights the potential of combining multi-omics and advanced computational approaches to improve our understanding and management of IBD.

Inflammation-Induced Th17 Cells Synergize with the Inflammation-Trained Microbiota to Mediate Host Resiliency Against Intestinal Injury

BACKGROUND AND AIMS

Inflammation can generate pathogenic Th17 cells and cause an inflammatory dysbiosis. In the context of inflammatory bowel disease (IBD), these inflammatory Th17 cells and dysbiotic microbiota may perpetuate injury to intestinal epithelial cells. However, many models of IBD like T-cell transfer colitis and IL-10-/- mice rely on the absence of regulatory pathways, so it is difficult to tell if inflammation can also induce protective Th17 cells.

METHODS

We subjected C57BL6, RAG1-/-, or JH-/- mice to systemic or gastrointestinal (GI) Citrobacter rodentium (Cr). Mice were then subjected to 2.5% dextran sodium sulfate (DSS) to cause epithelial injury. Fecal microbiota transfer was performed by bedding transfer and co-housing. Flow cytometry, qPCR, and histology were used to assess mucosal and systemic immune responses, cytokines, and tissue inflammation. 16s sequencing was used to assess gut bacterial taxonomy.

RESULTS

Transient inflammation with GI but not systemic Cr was protective against subsequent intestinal injury. This was replicated with sequential DSS collectively indicating that transient inflammation provides tissue-specific protection. Inflammatory Th17 cells that have a tissue-resident memory (TRM) signature expanded in the intestine. Experiments with reconstituted RAG1-/-, JH-/- mice, and cell trafficking inhibitors showed that inflammation-induced Th17 cells were required for protection. Fecal microbiota transfer showed that the inflammation-trained microbiota was necessary for protection, likely by maintaining protective Th17 cells in situ.

CONCLUSION

Inflammation can generate protective Th17 cells that synergize with the inflammation-trained microbiota to provide host resiliency against subsequent injury, indicating that inflammation-induced Th17 TRM T cells are heterogenous and contain protective subsets.

Specialized and standard nutritional formulas for the dietary management of pediatric patients with Crohn's disease: a systematic literature review

INTRODUCTION

This systematic literature review (SLR) aims to compare the clinical, humanistic, and economic outcomes associated with specialized and standard nutritional formulas for the treatment of mild-to-moderate pediatric Crohn's disease.

METHODS

Search strategies were applied across MEDLINE, Cochrane and Web of Science (January 2000-October 2023) and recent congress proceedings (January 2021-October 2023). PRISMA-P guidelines were followed. Quality assessment evaluated risk of bias.

RESULTS

Twenty-three unique studies met the inclusion criteria. Nineteen studies (754 patients) evaluated specialized formula, 10 assessed standard formula (246 patients). Mucosal healing (7 studies), induction (20 studies) and maintenance of remission (9 studies) were reported over various timeframes. High proportions of patients who received specialized formula achieved mucosal healing (63-89% 8 weeks; 25-74% 10 weeks), and remission (50-100% 8 weeks). Specialized formula sustained remission (34-62.5% 6 months and 24-87.5% 1 year). Results were not directly comparable with standard formula due to significant heterogeneity in study methodology, patient populations, and remission definition.

CONCLUSIONS

The evidence predominantly supports the benefits of specialized formula in inducing mucosal healing, remission, and sustaining positive outcomes across multiple timepoints. Direct comparison of nutritional interventions is required to further support the findings of this SLR.Protocol registration: PROSPERO CRD42023472370.

Role of noncontrast enhanced abdominal ultrasound in the diagnostic assessment of pediatric inflammatory bowel disease

OBJECTIVES

Assessment of small bowel involvement when diagnosing inflammatory bowel disease (IBD) delineates clinical subtype and disease extension. The gold standard for small bowel assessment is magnetic resonance enterography (MRE), but MRE is not always feasible for children. Standard, non-contrast enhanced abdominal ultrasound is an acceptable alternative. The study aimed to evaluate the utility of ultrasound in the diagnostic work-up of pediatric IBD to identify small bowel involvement.

METHODS

A retrospective study was conducted among children (< 18 years) who had abdominal ultrasound during assessment for IBD (2019-2023) at Christchurch Hospital, New Zealand. Descriptive analysis compares small bowel ultrasound to MRE, endoscopy and histology.

RESULTS

The cohort comprised 47 children, mean age 9.9 years (± 4.1), 23 (49%) males and 42 (89%) with Crohn's disease. All had endoscopy and histology data available for comparison, and 26 had MRE. Fourteen (30%) had no small bowel disease on ultrasound, MRE, endoscopy, or histology. Ultrasound confirmed small bowel disease diagnosed by other modalities for 12 (26%). Ultrasound identified small bowel disease for 7 (15%) that had not been seen during the diagnostic process by MRE, endoscopy or histology, possibly due to the limitations of endoscopy and time-delays between diagnosis and MRE. Small bowel disease was not picked up on ultrasound for 14 (30%) children, disease locations being duodenum (n = 6), TI (n = 5), proximal ileum (n = 3), and jejunum (n = 2).

CONCLUSIONS

Abdominal ultrasound is a valuable resource for assessing disease extent in suspected pediatric IBD. This study highlights the clinical benefit and feasibility of a multi-modal diagnostic approach.

Metagenomic and transcriptomic investigation of pediatric acute liver failure cases reveals a common pathway predominated by monocytes

In 2022, a cluster of severe childhood hepatitis was detected primarily in Europe and North America, leading to a global alert by the World Health Organization. An association with adeno-associated virus 2 (AAV2) in conjunction with human adenoviruses was found. Five percent of the cases progressed to acute liver failure, necessitating transplantation. The mechanism of disease that accounts for fulminant liver failure in these patients remains incompletely described. An upsurge was observed of in the five total cases of acute liver failure that presented to the Dutch national referral center for pediatric liver transplantation in the spring of 2022. An in-depth molecular analysis of the mechanism of pediatric acute liver failure was performed using targeted transcriptomics and metagenomics to identify any virus present in the cases, immune profile haplotypes, and differentially expressed gene groups. Explanted liver tissue and plasma samples (n = 15) were subjected to viral metagenomic and human transcriptomic profiling, targeting >600 inflammatory genes. Liver transcriptomic signatures of transplanted cases were compared with those of pediatric controls from a liver biobank (n = 6). AAV2, adenoviruses, and herpesviruses were detected in liver explant tissue and plasma samples of the cases. Epstein-Barr virus and varicella zoster virus infection with pathognomonic clinical symptomatology preceded liver failure in two respective cases. AAV2 was detected in one-third of control livers. Excessive activation of monocyte pathways was detected in liver explants from cases compared with controls. Remarkably, this signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases. Our multi-omic findings suggest a common transcriptomic profile, with an upregulation of monocyte pathways in the presented transplanted cases, which had similar severe clinical outcomes. In the cohort presented, AAV2 was not exclusively associated with acute liver failure, suggesting that other processes may have contributed to a uniform cascade of irreversible pathology.

IMPORTANCE

Since the appearance of the cluster of pediatric hepatitis of unknown origin in 2022, several groups have reported an association of adenoviruses and AAV2 in a high number of cases in contrast to controls. The adenoviruses detected were heterogeneous in both species-adenovirus C and F-and sequences. The mechanisms of disease that accounts for fulminant liver failure, occurring in 5% of pediatric hepatitis cases, remain incompletely described. The current study adds to previous data by including pediatric acute liver failure cases during the upsurge, enabling the analyses of inflammation expression profiles in cases with different viruses in relation to pediatric controls. This led to the discovery of transcriptome upregulation of monocyte pathways in liver explants from the cases. This inflammatory transcriptomic signature was comparable for AAV2, adenoviruses, and/or herpesviruses-positive transplant cases.

Real-World Treatment Patterns Among Pediatric and Adult Patients with Crohn's Disease in the United States

BACKGROUND

The advent of biologics has expanded treatment options for Crohn's disease (CD). This study assessed treatment patterns in pediatric and adult patients with CD in the United States during 1- and 3-year follow-up periods.

METHODS

This retrospective, claims-based cohort study utilized the Merative™ MarketScan® Research Databases from January 1, 2014, to December 31, 2021. The index date was the date of the first CD diagnosis during the identification period. Among pediatric and adult CD cohorts, patients were stratified into two subgroups: (a) previously diagnosed (presence of a CD claim) and (b) newly diagnosed (absence of a CD claim) in the 12-month pre-index period. Results were summarized descriptively.

RESULTS

Data from 2809 pediatric and 25,940 adult patients were analyzed at 1-year follow-up. Mean age in years was 13.5 for pediatric and 46.0 for adult patients. Combination therapies were more common in pediatric versus adult patients, especially among those newly diagnosed with CD (38.2% vs 13.9%). A higher percentage of pediatric patients were prescribed biologics than adults (35.1% vs 24.3%). Numerically shorter time from diagnosis to corticosteroid initiation was observed in pediatric versus adult patients (9.5 vs 35 days). Higher persistence to biologics was observed in pediatric versus adult patients (94.6% vs 87.1%).

CONCLUSIONS

Combination therapies with biologics were more frequent among pediatric patients than adults. Although the overall treatment pattern among pediatric and adult patients was similar, early initiation of corticosteroids and adoption of biologics were more frequently observed in pediatric than adult patients, consistent with pediatric CD presenting with more aggressive disease.

Ulcerative colitis increases the risk of atrioventricular block: evidence from a Mendelian randomized analysis

Although inflammatory bowel disease (IBD) has been linked to cardiovascular disease in a growing body of literature, the relationship between IBD and arrhythmia remains unclear. To investigate the causal relationship between inflammatory bowel disease and arrhythmia, we conducted this Mendelian randomization (MR) analysis. We identified single nucleotide polymorphisms (SNP) associated with IBD as instruments, including IBD, ulcerative colitis (UC), and Crohn's disease (CD). SNPs of two arrhythmia phenotypes as outcome data, namely atrioventricular block (AVB), and paroxysmal tachycardia (PTA). The inverse variance weighting method was used to analyze the two-sample Mendelian randomization with four other methods, including MR Egger, Weighted median, Simple mode, and Weighted mode. Sensitivity analysis involves different methods to detect and adjust for bias in results, including heterogeneity analysis, pleiotropy analysis, and leave-one-out sensitivity analysis. To ensure the rigor of the analysis results, we selected another set of exposure data sets and conducted the MR verification analysis using the same method. Results suggested UC is significantly associated with an increased risk of AVB (odds ratio, OR 1.178, 95% CI 1.070-1.297, P = 0.000828), the verification analysis results are consistent with this (OR 1.048, 95% CI 1.007-1.091, P = 0.022947). Our study suggests a potential risk increase of atrioventricular block in patients with UC. These results also provide further evidence that inflammatory bowel disease may increase the risk of developing arrhythmia.

Role of gut microbiota and mesenteric adipose tissue in the pathology of Crohn's disease: Potential therapeutic targets

This editorial comments on the article by Wu et al in the World Journal of Gastroenterology. The article explored the relationship between mesenteric adipose tissue, creeping fat, inflammation, and gut microbiota in Crohn's disease (CD). We discussed three key aspects of the interaction between gut microbiota and inflammatory bowel disease (IBD): The physiological functions of the gut microbiota, the potential role of probiotics in IBD treatment; and the effect of fecal microbiota transplantation (FMT) in combating IBD. IBD, comprising CD and ulcerative colitis (UC), is influenced by the gut microbiota. Changes in gut microbiota composition disrupt intestinal function and promote chronic inflammation, but the exact mechanisms remain unclear. Probiotics have demonstrated some efficacy in inducing remission in UC, though their effectiveness in CD is still debated. FMT shows promise in treating IBD, especially UC, by restoring gut microbiota diversity and inducing clinical remission. As for CD, FMT has potential, but more studies are needed to confirm its long-term effectiveness and safety. Dietary approaches may help manage IBD symptoms or disease activity, but patient adherence is crucial. Clinicians and researchers must recognize the importance of the gut microbiota and the need for personalized therapies targeting microbial imbalances.

Endoplasmic reticulum stress in gut inflammation: Implications for ulcerative colitis and Crohn's disease

Eukaryotic cells contain the endoplasmic reticulum (ER), a prevalent and intricate membranous structural system. During the development of inflammatory bowel disease (IBD), the stress on the ER and the start of the unfolded protein response are very important. Some chemicals, including 4μ8C, small molecule agonists of X-box binding protein 1, and ISRIB, work on the inositol-requiring enzyme 1, turn on transcription factor 6, and activate protein kinase RNA-like ER kinase pathways. This may help ease the symptoms of IBD. Researchers investigating the gut microbiota have discovered a correlation between ER stress and it. This suggests that changing the gut microbiota could help make new medicines for IBD. This study looks at how ER stress works and how it contributes to the emergence of IBD. It also talks about its possible clinical importance as a therapeutic target and looks into new ways to treat this condition.

Biosimilars versus biological therapy in inflammatory bowel disease: challenges and targeting strategies using drug delivery systems

Inflammatory bowel disease (IBD) is a multifactorial illness with a climbing prevalence worldwide. While biologics are commonly prescribed especially for severe cases, they may worsen patients' outcomes due to financial burden. Consequently, there has been an increased focus on biosimilars to improve overall disease outcomes by maintaining similar efficacy and safety while minimizing the cost of therapy. Infliximab-dyyb was the first biosimilar approved by US-FDA for IBD. Since that, the US-FDA approved 14 biosimilars with different mechanisms of action and different routes of administration for IBD patients (four infliximab biosimilars, nine adalimumab biosimilars, and most recently one ustekinumab biosimilar). It should be noted that more biologics are in the pipeline as golimumab and natalizumab patents are set to expire in the near future, and biosimilars are now in pre-clinical to phase 3 trials. Different studies have evaluated biologics' effectiveness and safety and concluded that the majority of available biosimilars are efficacious and have similar adverse effect profiles compared to their reference biologics. It is worth mentioningthat post-marketing surveillance reports revealed some risks associated with biosimilars which should be taken into consideration in future research and clinical trials to avoid health hazards. Most biologics and biosimilars are administered parenterally which results in several drawbacks such as raised risk of infections, hypersensitivity, autoimmunity, development of malignancies, liver toxicity as well as worsening of heart failure. Several drug delivery systems based on passive and active targeting mechanisms are under active investigation to overcome these limitations. This review sheds light on the emergence of biologics and biosimilars as alternatives in IBD management, the differences between them, challenges and risks, and future perspectives in IBD therapy and new trends in drug delivery systems.

Genomic prediction with kinship-based multiple kernel learning produces hypothesis on the underlying inheritance mechanisms of phenotypic traits

BACKGROUND

Genomic prediction encompasses the techniques used in agricultural technology to predict the genetic merit of individuals towards valuable phenotypic traits. It is related to Genome Interpretation in humans, which models the individual risk of developing disease traits. Genomic prediction is dominated by linear mixed models, such as the Genomic Best Linear Unbiased Prediction (GBLUP), which computes kinship matrices from SNP array data, while Genome Interpretation applications to clinical genetics rely mainly on Polygenic Risk Scores.

RESULTS

In this article, we exploit the positive semidefinite characteristics of the kinship matrices that are conventionally used in GBLUP to propose a novel Genomic Multiple Kernel Learning method (GMKL), in which the multiple kinship matrices corresponding to Additive, Dominant, and Epistatic Inheritance Mechanisms are used as kernels in support vector machines, and we apply it to both worlds. We benchmark GMKL on simulated cattle phenotypes, showing that it outperforms the classical GBLUP predictors for genomic prediction. Moreover, we show that GMKL ranks the kinship kernels representing different inheritance mechanisms according to their compatibility with the observed data, allowing it to produce hypotheses on the normally unknown inheritance mechanisms generating the target phenotypes. We then apply GMKL to the prediction of two inflammatory bowel disease cohorts with more than 6500 samples in total, consistently obtaining results suggesting that epistasis might have a relevant, although underestimated role in inflammatory bowel disease (IBD).

CONCLUSIONS

We show that GMKL performs similarly to GBLUP, but it can formulate biological hypotheses about inheritance mechanisms, such as suggesting that epistasis influences IBD.

Environmental risk factors of inflammatory bowel disease: toward a strategy of preventative health

The pathogenesis of inflammatory bowel disease (IBD) involves a complex interplay between genetic, environmental, and microbial factors. Many of these environmental determinants are modifiable, offering opportunities to prevent disease or delay its onset. Advances in the study of preclinical IBD cohorts offer the potential to identify biomarkers that predict individuals at high risk of developing IBD, enabling targeted environmental interventions aimed at reducing IBD incidence. This review summarizes findings from 79 meta-analyses on modifiable environmental factors associated with the development of IBD. Identified risk factors include smoking, Western diets, ultra-processed foods, and early life antibiotic use, while protective factors include breastfeeding, Mediterranean diets rich in fiber, plant-based foods, and fish, along with an active physical lifestyle. Despite the promise shown by observational data, interventional or randomized controlled studies evaluating the efficacy of modifying environmental risk factors remain limited and mostly focus on dietary intervention. This review aims to inform the design of higher quality interventional and randomized controlled studies for disease prevention while providing actionable guidance to healthcare providers on reducing the risk of developing IBD through environmental modifications.

Multimodal metagenomic analysis reveals microbial InDels as superior biomarkers for pediatric Crohn's disease

BACKGROUND AND AIMS

The gut microbiome is closely associated with pediatric Crohn's disease (CD), while the multidimensional microbial signature and their capabilities for distinguishing pediatric CD are underexplored. This study aims to characterize the microbial alterations in pediatric CD and develop a robust classification model.

METHODS

A total of 1175 fecal metagenomic sequencing samples, predominantly from 3 cohorts of pediatric CD patients, were re-analyzed from raw sequencing data using uniform process pipelines to obtain multidimensional microbial alterations in pediatric CD, including taxonomic profiles, functional profiles, and multi-type genetic variants. Random forest algorithms were used to construct classification models after comparing multiple machine learning algorithms.

RESULTS

We found pediatric CD samples exhibited reduced microbial diversity and unique microbial characteristics. Pronounced abundance differences in 45 species and 1357 KEGG orthology genes. Particularly, Enterocloster bolteae emerged as a pivotal pediatric CD-associated species. Additionally, we identified a vast amount of microbial genetic variants linked to pediatric CD, including 192 structural variants, 1256 insertions/deletions (InDels), and 3567 single nucleotide variants, with a considerable portion of these variants located in non-genic regions. The InDel-based model outperformed other predictive models against multidimensional microbial signatures, achieving an area under the ROC curve (AUC) of 0.982. The robustness and disease specificity were further confirmed in an independent CD cohort (AUC = 0.996) and 5 other microbiome-associated pediatric cohorts.

CONCLUSIONS

Our study provided a comprehensive landscape of microbial alterations in pediatric CD and introduced a highly effective diagnostic model rooted in microbial InDels, which contributes to the development of noninvasive diagnostic tools and targeted therapies.

Labor Market Participation and Income in Patients With Inflammatory Bowel Disease Onset Before Young Adulthood-The Role of Disease Severity and Mental Health

BACKGROUND AND AIMS

Only few studies have examined the socioeconomic consequences of being diagnosed with inflammatory bowel disease (IBD) in childhood or youth. Disease severity has been linked to lower earnings, but little attention has been paid to comorbid mental health conditions. The aim is to examine labor market participation (LMP) and income in patients with IBD onset in childhood or youth and examine how disease severity and mental health conditions affect LMP.

METHODS

In this register-based cohort study, we included patients with IBD onset before 25 years of age and matched comparators. We estimated the relative risk (RR) of having low LMP and the median yearly income from ages 26 to 30. RR of low LMP was also assessed in subgroups of patients based on disease severity (severe/nonsevere) and mental health conditions (yes/no).

RESULTS

A total of 3398 patients with IBD and 28 207 comparators were included. Overall, patients with IBD more often had low LMP (16.4% vs 14.4% in comparators), but slightly higher income (median yearly income difference at age 30: 1141 Euro [95% CI, 483-1798]). In subgroup analyses, only patients with severe IBD had a higher risk of low LMP (RR: 1.46 [95% CI, 1.23-1.72]), whereas patients with nonsevere IBD did not. Among patients with severe disease and mental health conditions, 46% had low LMP (RR: 5.03 [95% CI, 4.38-5.78]).

CONCLUSIONS

Patients with IBD more often had low LMP, but their income was not affected. The subgroup of patients with severe disease and mental health conditions had the highest risk of low LMP.

Development and validation of a risk prediction tool for the diagnosis of inflammatory bowel disease in patients presenting in primary care with abdominal symptoms

INTRODUCTION

Patients with inflammatory bowel disease (IBD) may experience delays in their diagnosis. This study aimed to develop and validate a risk prediction tool for IBD.

METHODS

A retrospective cohort study was conducted using primary care data from 2010 to 2019, including symptomatic patients aged ≥18. UK-based primary care databases linked to hospital records were utilized for model development and validation. Cox proportional hazards models were used to derive risk equations for IBD, ulcerative colitis (UC), and Crohn's disease (CD) in men and women. Candidate predictors included demographics, comorbidities, symptoms, extraintestinal manifestations, and laboratory results. Model performance was evaluated using measures of fit, discrimination, and calibration at 1, 2, 3, and 5 years after symptom onset.

RESULTS

In total, 2 054 530 patients were included in the derivation cohort and 673 320 in the validation cohort. In the derivation cohort, 0.7% were diagnosed with IBD (66.3% UC and 33.7% CD). Predictors in the final IBD model included age, smoking, body mass index, gastrointestinal symptoms, extraintestinal manifestations, comorbidities, family history of IBD, and laboratory investigations. The model demonstrated good discrimination and calibration; C-statistic 0.78 (95% confidence interval [CI], 0.77-0.79) in men and 0.78 (95% CI, 0.77-0.79) in women. In the validation cohort, the model tended to slightly overestimate IBD risk at higher risk thresholds.

CONCLUSIONS

A risk model using patient demographics, symptoms, and laboratory results accurately predicted IBD, UC, and CD at 1, 2, 3, and 5 years after symptom onset, potentially aiding in prioritizing patients for a referral or fecal calprotectin testing in primary care.

Wnt signaling pathways in biology and disease: mechanisms and therapeutic advances

The Wnt signaling pathway is critically involved in orchestrating cellular functions such as proliferation, migration, survival, and cell fate determination during development. Given its pivotal role in cellular communication, aberrant Wnt signaling has been extensively linked to the pathogenesis of various diseases. This review offers an in-depth analysis of the Wnt pathway, detailing its signal transduction mechanisms and principal components. Furthermore, the complex network of interactions between Wnt cascades and other key signaling pathways, such as Notch, Hedgehog, TGF-β, FGF, and NF-κB, is explored. Genetic mutations affecting the Wnt pathway play a pivotal role in disease progression, with particular emphasis on Wnt signaling's involvement in cancer stem cell biology and the tumor microenvironment. Additionally, this review underscores the diverse mechanisms through which Wnt signaling contributes to diseases such as cardiovascular conditions, neurodegenerative disorders, metabolic syndromes, autoimmune diseases, and cancer. Finally, a comprehensive overview of the therapeutic progress targeting Wnt signaling was given, and the latest progress in disease treatment targeting key components of the Wnt signaling pathway was summarized in detail, including Wnt ligands/receptors, β-catenin destruction complexes, and β-catenin/TCF transcription complexes. The development of small molecule inhibitors, monoclonal antibodies, and combination therapy strategies was emphasized, while the current potential therapeutic challenges were summarized. This aims to enhance the current understanding of this key pathway.

Global, regional and national disparities and temporal trends of common autoimmune disease burdens among children and adolescents from 1990 to 2019

INTRODUCTION

Previous evidence lacked a thorough review of the disparities of autoimmune diseases (AD) burdens among countries and regions, which led to an insufficient basis for developing country-specific developmental level relevant preventive measures. This study aimed to analyse disparities and trends of global, regional and national burden of common ADs in children and adolescents from 1990 to 2019 and to investigate the associations between specific ADs and varied country indexes.

METHODS

All data for four major ADs were obtained from the Global Burden of Diseases Study 2019. Age period-cohort modelling was conducted to disentangle age, period and birth cohort effects on AD incidence from 1990 to 2019. Local regression smoothing models were used to fit the correlation between AD burdens and sociodemographic index (SDI). Pearson's correlation was used to investigate varied country-level risk factors for disease burden.

RESULTS

A global increase in four common ADs incidence was observed from 1.57 million to 1.63 million between 1990 and 2019 in the 0-24 age group. The age-standardised incidence rate of overall four ADs showed substantial regional and global variation with the highest incidence in high SDI regions. The age, period and cohort distributions of AD incidence varied significantly, especially in high SDI countries. Relative to the expected level of age-standardised incidence associated with SDI, the distribution varied by regions depending on the specific ADs. Countries with higher levels of socioeconomic development, better quality of life and easier access to healthcare and the healthcare system showed lower disease burdens of ADs.

CONCLUSIONS

The incidence patterns and disease burdens of ADs varied considerably according to age, time period and generational cohort, across the world between 1990 and 2019. Incidences of ADs in children and adolescents were significantly correlated with indexes involving risks of the environment, human rights and health safety and quality of life.

Human leukocyte antigen variation is associated with cytomegalovirus serostatus in healthy individuals

Cytomegalovirus (CMV) is a common β-herpes virus worldwide with an estimated seroprevalence among the general population of 83%. Primary infection is usually benign; however, CMV can cause severe morbidity in newborns in whom it is acquired congenitally, as well as immunocompromised individuals. Understanding the role of immunogenetic variation in risk for CMV infection can provide insight into the immune control of this ubiquitous pathogen. Here, we evaluated the association of human leukocyte antigen (HLA) genetic variation with CMV seropositivity in more than 518,000 individuals from two independent cohorts. We found three HLA class II alleles (HLA-DRB1∗04:03 with risk; HLA-DRB1∗01:03 and HLA-DRB1∗07:01 with protection) to be significantly associated with CMV serostatus across both cohorts and in multiple population subgroups. Interestingly, HLA-DRB1∗04:03 and HLA-DRB1∗01:03, the alleles with the strongest observed effect, are relatively rare, while common homologous alleles show no association with CMV. We show that these differences are mediated by changes in charge and volume to two key pockets in the peptide-binding groove of the HLA molecule, providing a structural basis for the observed association. Our results provide population-scale evidence for the role of HLA in mediating infection with this ubiquitous human virus and a framework for understanding immunological conditions necessary for efficient viral control.

A Bibliometric Analysis of GWAS on Rheumatoid Arthritis from 2002 to 2024

INTRODUCTION

Rheumatoid arthritis (RA) has become a serious threat to human health and quality of life worldwide. Previous studies have demonstrated that genetic factors play a crucial role in the onset and progression of RA. Due to the rapid development of genome-wide association study (GWAS) and large-scale genetic analysis, GWAS research on RA has received widespread attention in recent years. Therefore, we conducted a comprehensive visualization and bibliometric analysis of publications to identify hotspots and future trends in GWAS research on RA.

METHODS

Literature on RA and GWAS published between 2002 and 2024 was extracted from the Web of Science Core Collection database by strategic screening. Collected data were further analyzed by using VOSviewer, CiteSpace, and Excel. The collaborations networks of countries, authors, institutions, and the co-citation networks of publications were visualized. Finally, research hotspots and fronts were examined.

RESULTS

A total of 713 publications with 45,773 citations were identified. The number of publications and citations has had a significant surge since 2007. The United States contributed the most publications globally. Okada, Yukinori, was the most influential author. The most productive institution in this field was the University of Manchester. The analysis of keywords revealed that "mendelian randomization analysis", "association", "innate", "instruments", "bias", "pathogenesis", and "genome-wide association study" are likely to be the frontiers of research in this field.

CONCLUSION

This study can be used to predict future research advances in the fields of GWAS on RA and helps to promote academic collaboration among scholars.

Shielding the immunocompromised: COVID-19 prevention strategies for patients with primary and secondary immunodeficiencies

The COVID-19 pandemic has significantly impacted immunocompromised patients, particularly those with inborn errors of immunity (IEI), transplant recipients, hematologic malignancies, and those undergoing treatment with immunosuppressive biologics and medications. These patients face an elevated risk of experiencing severe or even fatal consequences following SARS-CoV-2 infections. Vaccination is the primary defense against COVID-19; however, immune responses following immunization are often suboptimal in these patients, with variable specific humoral response rates. Despite the expedited regulatory approval and the widespread implementation of COVID-19 vaccines, the efficacy and safety for immunocompromised populations require thorough investigation. In future pandemics, including vulnerable populations (VPs) in vaccine and monoclonal antibody (mAb) trials is crucial to develop safe, effective immunization strategies, address gaps in vaccine efficacy and safety data, and create tailored guidelines for at-risk groups. This review provides a comprehensive examination of the efficacy of COVID-19 vaccines and mAbs in patients with primary and secondary immunodeficiency, with a specific focus on individuals with IEI, considering previous regulatory aspects and the necessity of including VPs in vaccine trials to enhance the quality of patient care and promote equitable health outcomes in future pandemics.

Prediction of deep remission through serum TNF-α level at 1 year of treatment in pediatric Crohn's disease

A pilot study investigated the cytokine profile (IL-6, TNF-α, IL-17 A, and IL-10) at diagnosis, affecting infliximab (IFX) trough levels (TLs) in pediatric patients with Crohn's disease (CD). In this follow-up study, we evaluated the changes in cytokine level changes after Crohn's disease treatment. Cytokines were re-measured after 1 year of treatment. infliximab trough levels and total anti-infliximab antibodies were also measured in patients who had started infliximab treatment. In total, 29 patients followed up for a year after moderate to severe Crohn's disease diagnosis from June 2020 to June 2021 were enrolled. The mean concentrations of all cytokines at one year were significantly lower than those at the time of diagnosis. IL-6, IL-17 A, and IL-10 concentrations at 1 year maintained their correlation with each other observed at diagnosis, unlike TNF-α following infliximab treatment. At 1 year, TNF-α concentration exhibited a negative correlation with infliximab trough levels (Pearson coefficient = -0.500, p = 0.009), and a positive correlation with anti-infliximab antibody titre (Pearson coefficient = 0.510, p = 0.018). The diagnostic capability of 1-year TNF-α concentration to predict achievement of deep remission had an area under the ROC of 0.802 (p = 0.008), with a TNF-α cut-off concentration set at 9.40 pg/mL. Decreased cytokine concentrations following Crohn's disease treatment reflected reduced inflammatory burden. Targeted medical intervention (infliximab) aimed at specific cytokines, such as TNF-α, led to the reduction of the corresponding cytokines. High TNF-α level post-treatment, combined with suboptimal infliximab trough levels and increased antibody formation, may contribute to deep remission failure in patients.

CARTp/GPR160 mediates behavioral hypersensitivities in mice through NOD2

ABSTRACT

Neuropathic pain is a debilitating chronic condition that remains difficult to treat. More efficacious and safer therapeutics are needed. A potential target for therapeutic intervention recently identified by our group is the G-protein coupled receptor 160 (GPR160) and the cocaine- and amphetamine-regulated transcript peptide (CARTp) as a ligand for GPR160. Intrathecal administration of CARTp in rodents causes GPR160-dependent behavioral hypersensitivities. However, the molecular and biochemical mechanisms underpinning GPR160/CARTp-induced behavioral hypersensitivities in the spinal cord remain poorly understood. Therefore, we performed an unbiased RNA transcriptomics screen of dorsal horn spinal cord (DH-SC) tissues harvested at the time of peak CARTp-induced hypersensitivities and identified nucleotide-binding oligomerization domain-containing protein 2 ( Nod2 ) as a gene that is significantly upregulated. Nucleotide-binding oligomerization domain-containing protein 2 is a cytosolic pattern-recognition receptor involved in activating the immune system in response to bacterial pathogens. While NOD2 is well studied under pathogenic conditions, the role of NOD2-mediated responses in nonpathogenic settings is still not well characterized. Genetic and pharmacological approaches reveal that CARTp-induced behavioral hypersensitivities are driven by NOD2, with co-immunoprecipitation studies indicating an interaction between GPR160 and NOD2. Cocaine- and amphetamine-regulated transcript peptide-induced behavioral hypersensitivities are independent of receptor-interacting protein kinase 2 (RIPK2), a common adaptor protein to NOD2. Immunofluorescence studies found NOD2 co-expressed with endothelial cells rather than glial cells, implicating potential roles for CARTp/NOD2 signaling in these cells. While these findings are based only on studies with male mice, our results identify a novel pathway by which CARTp causes behavioral hypersensitivities in the DH-SC through NOD2 and highlights the importance of NOD2-mediated responses in nonpathogenic settings.

Characterisation of autophagy induction by the thiopurine drugs azathioprine, mercaptopurine and thioguanine in THP-1 macrophages

Activating autophagy may be therapeutically beneficial, and we have previously shown that azathioprine (AZA), an immunomodulatory drug, induces autophagy. Here, we evaluated the induction of autophagy by the thiopurines AZA, mercaptopurine (6-MP) and thioguanine (6-TG) in THP-1 macrophages and investigated the mechanism of action in the context of this cellular process. The cytotoxicity of thiopurines was evaluated using an LDH assay. Induction of endogenous LC3 by thiopurines was evaluated using immunostaining. To confirm autophagy activation by thiopurines, a GFP-RFP-LC3 reporter plasmid was used to monitor the maturation of autophagosomes to autolysosomes. Induction of apoptosis by thiopurines was evaluated using Annexin V/PI staining, and ER stress was assessed via RT‒PCR analysis of XBP1 splicing. To gain insight into the mechanism of action of thiopurines, mTORC1 activity and eIF2α-S51 phosphorylation were evaluated by immunoblotting. Thiopurines were not cytotoxic to cells and induced strong time- and concentration-dependent autophagy. Thiopurines activate autophagy with complete progression through the pathway. Induction of autophagy by thiopurines occurred independently of apoptosis and ER stress. Immunoblotting revealed that AZA inhibited mTORC1 activity, and AZA and 6-TG increased eIF2α-S51 phosphorylation. In contrast, 6-MP had a minor effect on either signalling pathway. Thiopurines are strong inducers of autophagy, and autophagy induction should be considered among the mechanisms responsible for patient response to thiopurines.

Causal effects of various particulate matter on inflammatory bowel disease and its subtypes: insights from Mendelian randomization

The role of particulate matter (PM) on genetic susceptibility to inflammatory bowel disease (IBD) is a controversial topic. The study aims to evaluate the causal effect of PM on IBD using Mendelian randomization (MR). PM and IBD datasets were screened for common single nucleotide polymorphisms (SNPs) based on the MR basic assumptions. Subsequently, the effect of these SNPs on genetic susceptibility to IBD was analyzed using inverse variance weighted. Finally, the heterogeneity and robustness of the results were assessed using Cochran's Q and leave-one-out sensitivity analysis, respectively. MR analysis revealed that PM2.5 was linked to a heightened genetic predisposition to (odds ratio [OR] 1.530, 95% confidence interval [CI] 1.100-2.128, p = 0.011) and ulcerative colitis (UC) (OR 1.675, 95% CI 1.129-2.485, p = 0.010), but not to Crohn's disease (CD) (OR 1.685, 95% CI 0.883-3.216, p = 0.114). PM10 was not associated with increased genetic susceptibility to IBD (OR 1.164, 95% CI 0.650-2.083, p = 0.610), UC (OR 1.439, 95% CI 0.691-2.996, p = 0.331), or CD (OR 0.825, 95% CI 0.265-2.564, p = 0.739). MR-Egger intercept did not indicate any horizontal pleiotropy (p > 0.05). Cochran's Q revealed no evidence of heterogeneity (p > 0.05). Leave-one-out sensitivity analysis confirmed the robustness of the results. The MR analysis demonstrated that PM2.5 increased genetic susceptibility to UC, while no such association was observed for CD. Furthermore, PM10 showed no association with genetic susceptibility to IBD. Therefore, implementing protective measures, such as air purifiers and anti-haze masks, may help reduce the risk of UC.

Immune dysregulation in bipolar disorder

BACKGROUND

Bipolar disorder is a debilitating mood disorder associated with a high risk of suicide and characterized by immune dysregulation. In this study, we used a multi-faceted approach to better distinguish the pattern of dysregulation of immune profiles in individuals with BD.

METHODS

We analyzed peripheral blood mononuclear cells (bipolar disorder N = 39, control N = 30), serum cytokines (bipolar disorder N = 86, control N = 58), whole blood RNA (bipolar disorder N = 25, control N = 25), and whole blood DNA (bipolar disorder N = 104, control N = 66) to identify immune-related differences in participants diagnosed with bipolar disorder compared to controls.

RESULTS

Flow cytometry revealed a higher proportion of monocytes in participants with bipolar disorder together with a lower proportion of T helper cells. Additionally, the levels of 18 cytokines were significantly elevated, while two were reduced in participants with bipolar disorder. Most of the cytokines altered in individuals with bipolar disorder were proinflammatory. Forty-nine genes were differentially expressed in our bipolar disorder cohort and further analyses uncovered several immune-related pathways altered in these individuals. Genetic analysis indicated variants associated with inflammatory bowel disease also influences bipolar disorder risk.

DISCUSSION

Our findings indicate a significant immune component to bipolar disorder pathophysiology and genetic overlap with inflammatory bowel disease. This comprehensive study supports existing literature, whilst also highlighting novel immune targets altered in individuals with bipolar disorder. Specifically, multiple lines of evidence indicate differences in the peripheral representation of monocytes and T cells are hallmarks of bipolar disorder.

The liver as a central "hub" of the immune system: pathophysiological implications

The purpose of this review is to describe the immune function of the liver, guiding the reader from the homeostatic tolerogenic status to the aberrant activation demonstrated in chronic liver disease. An extensive description of the pathways behind the inflammatory modulation of the healthy liver will be provided focusing on the complex immune cell network residing within the liver. The limit of tolerance will be presented in the context of organ transplantation, seizing the limits of homeostatic mechanisms that fail in accepting the graft, progressing eventually toward rejection. The triggers and mechanisms behind chronic activation in metabolic liver conditions and viral hepatitis will be discussed. The last part of the review will be dedicated to one of the greatest paradoxes for a tolerogenic organ, developing autoimmunity. Through the description of the three most common autoimmune liver diseases, the autoimmune reaction against hepatocytes and biliary epithelial cells will be dissected.

The current state of pediatric gastroenterology in under-resourced nations

Background

Pediatric gastroenterology (GI) care in low- and middle-income countries (LMICs) faces substantial challenges due to limited healthcare infrastructure, inadequate resources, and a shortage of specialized healthcare professionals. These challenges lead to delayed diagnoses and treatment, exacerbating the morbidity and mortality associated with pediatric GI diseases, which include both infectious conditions like diarrhea and chronic conditions such as inflammatory bowel disease (IBD) and liver diseases.

Aim

The aim of this review is to examine the current state of pediatric GI care in LMICs, identify the key challenges these regions face, and propose strategies to improve healthcare outcomes for children affected by GI disorders.

Methods

This review synthesizes existing literature from a range of LMICs, analyzing factors such as the economic burden of healthcare, barriers to access, the availability of diagnostic and therapeutic services, and the state of pediatric hepatology and endoscopy. Studies included in the review were sourced from countries in sub-Saharan Africa, South Asia, and other LMIC regions, focusing on pediatric GI disorders and healthcare delivery.

Results

Economic burden: Families in LMICs face significant economic barriers in accessing pediatric GI care, with treatment costs often exceeding household income, especially in private healthcare settings. Healthcare access: Limited access to healthcare facilities, especially in rural areas, coupled with the shortage of trained pediatric gastroenterologists and necessary medical equipment, leads to delayed diagnoses and inadequate care for conditions like Helicobacter pylori infections and chronic liver diseases. Sanitation and infectious diseases: Poor sanitation and lack of access to clean water contribute to the high prevalence of diarrheal diseases, which can be reduced through better hygiene practices and improved infrastructure. Training gaps: The shortage of trained healthcare workers, particularly pediatric specialists, hinders effective care delivery, with healthcare workers often overburdened due to workforce migration and low salaries. Hepatology and endoscopy: Pediatric hepatology, especially in the context of viral hepatitis, and the availability of pediatric GI endoscopy are severely limited in LMICs, further complicating the management of liver diseases and GI conditions in children.

Conclusion

Improving pediatric GI care in LMICs requires addressing systemic challenges such as inadequate healthcare infrastructure, limited financial resources, and a shortage of trained professionals. Prevention strategies like vaccination, sanitation improvements, and public health education campaigns are crucial for reducing the prevalence of pediatric GI diseases. In addition, enhancing access to specialized training, healthcare services, and diagnostic tools will improve outcomes for children in resource-limited settings. Continued international collaboration and investment in local healthcare systems are essential for creating sustainable solutions and bridging the gap in pediatric GI care.

TYK2 :p.Pro1104Ala Variant Protects Against Autoimmunity by Modulating Immune Cell Levels

The TYK2:p.Pro1104Ala (rs34536443) hypomorph variant has been associated with protection against numerous autoimmune disorders. Thus, its mechanism of action becomes of great interest. Here, consistent with the participation of activated immune cells in autoimmunity, we show that the variant regulates the levels of immune cells at a human, general population level and is associated particularly with higher levels of T and B lymphocytes, especially the naïve (non-activated) compartment. Also, consistent with a protective function in autoimmunity, the level of regulatory CD4+ T cells was increased. Thus, this variant decreases immune activation thereby protecting from autoimmunity. Our work links the cellular mechanism regulated by the TYK2:p.Pro1104Ala variant to autoimmunity protection and supports TYK2 as a therapeutic target in autoimmunity.

Proposal and exploration of a novel score to quantify patient-perceived burden of inflammatory bowel disease under routine care

BACKGROUND

The burden of inflammatory bowel disease (IBD) is often reported on from a system or cost viewpoint. We created and explored a novel patient-perceived burden of disease (PPBoD) score in a large Australasian cohort.

AIM

To create and explore a novel patient-perceived burden of disease (PPBoD) score in a large Australasian cohort, and correlate PPBoD scores with demographics, disease and treatment factors.

METHODS

The Crohn Colitis Care Registry was interrogated in October 2023. Data from adults with IBD with an outpatient care encounter in the last 14 months among 17 centres were included. A novel PPBoD score was designed for ulcerative colitis (UC), Crohn disease (CD) and IBD-unclassified (IBDU). Correlations between PPBoD scores and demographics, disease and treatment factors were examined.

RESULTS

Of those with adequate data, 46.7% (2653/5685) had no PPBoD, 34.6% (1969/5685) had mild, 11.3% (641/5685) had moderate and 7.4% (422/5685) had significant PPBoD. New Zealanders were more likely to have higher PPBoD compared to Australians (P = 0.047). Greater PPBoD was seen in patients with CD and IBDU compared to patients with UC (P < 0.001) and females were more likely to have significant PPBoD (8.7%) than males (6.1%) (P < 0.001). People with no or mild PPBoD were more likely to be on advanced therapies (55.7% and 59.5% respectively) than those with significant PPBoD (46.3%) (P < 0.001). The proportion of people on advanced therapies in Australia was higher than in New Zealand (61.2% vs 38.5% respectively, P < 0.001). Steroid usage was significantly higher in people with greater PPBoD (significant BoD 7.1% vs no BoD 1.1%; P < 0.001).

CONCLUSION

Most of this real-world care cohort had no or mild PPBoD. Data suggest that higher PPBoD levels may be resolved by appropriate therapeutic escalations.

TGFβ links EBV to multisystem inflammatory syndrome in children

In a subset of children and adolescents, SARS-CoV-2 infection induces a severe acute hyperinflammatory shock1 termed multisystem inflammatory syndrome in children (MIS-C) at four to eight weeks after infection. MIS-C is characterized by a specific T cell expansion2 and systemic hyperinflammation3. The pathogenesis of MIS-C remains largely unknown. Here we show that acute MIS-C is characterized by impaired reactivation of virus-reactive memory T cells, which depends on increased serum levels of the cytokine TGFβ resembling those that occur during severe COVID-19 (refs. 4,5). This functional impairment in T cell reactivity is accompanied by the presence of TGFβ-response signatures in T cells, B cells and monocytes along with reduced antigen-presentation capabilities of monocytes, and can be reversed by blocking TGFβ. Furthermore, T cell receptor repertoires of patients with MIS-C exhibit expansion of T cells expressing TCRVβ21.3, resembling Epstein-Barr virus (EBV)-reactive T cell clones capable of eliminating EBV-infected B cells. Additionally, serum TGFβ in patients with MIS-C can trigger EBV reactivation, which is reversible with TGFβ blockade. Clinically, the TGFβ-induced defect in T cell reactivity correlates with a higher EBV seroprevalence in patients with MIS-C compared with age-matched controls, along with the occurrence of EBV reactivation. Our findings establish a connection between SARS-CoV-2 infection and COVID-19 sequelae in children, in which impaired T cell cytotoxicity triggered by TGFβ overproduction leads to EBV reactivation and subsequent hyperinflammation.

Leveraging Organ-on-Chip Models to Investigate Host-Microbiota Dynamics and Targeted Therapies for Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is an idiopathic gastrointestinal disease with drastically increasing incidence rates. Due to its multifactorial etiology, a precise investigation of the pathogenesis is extremely difficult. Although reductionist cell culture models and more complex disease models in animals have clarified the understanding of individual disease mechanisms and contributing factors of IBD in the past, it remains challenging to bridge research and clinical practice. Conventional 2D cell culture models cannot replicate complex host-microbiota interactions and stable long-term microbial culture. Further, extrapolating data from animal models to patients remains challenging due to genetic and environmental diversity leading to differences in immune responses. Human intestine organ-on-chip (OoC) models have emerged as an alternative in vitro model approach to investigate IBD. OoC models not only recapitulate the human intestinal microenvironment more accurately than 2D cultures yet may also be advantageous for the identification of important disease-driving factors and pharmacological interventions targets due to the possibility of emulating different complexities. The predispositions and biological hallmarks of IBD focusing on host-microbiota interactions at the intestinal mucosal barrier are elucidated here. Additionally, the potential of OoCs to explore microbiota-related therapies and personalized medicine for IBD treatment is discussed.

Exome-wide association analysis identifies novel risk loci for alcohol-associated hepatitis

BACKGROUND AND AIMS

Alcohol-associated hepatitis (AH) is a clinically severe, acute disease that afflicts only a fraction of patients with alcohol use disorder. Genomic studies of alcohol-associated cirrhosis (AC) have identified several genes of large effect, but the genetic and environmental factors that lead to AH and AC, and their degree of genetic overlap, remain largely unknown. This study aims to identify genes and genetic variations that contribute to the development of AH.

APPROACH AND RESULTS

Exome-sequencing of patients with AH (N=784) and heavy drinking controls (N=951) identified an exome-wide significant association for AH at patalin-like phospholipase domain containing 3, as previously observed for AC in genome-wide association study, although with a much lower effect size. Single nucleotide polymorphisms (SNPs) of large effect size at inducible T cell costimulatory ligand ( ICOSLG ) (Chr 21) and TOX4/RAB2B (Chr 14) were also exome-wide significant. ICOSLG encodes a co-stimulatory signal for T-cell proliferation and cytokine secretion and induces B-cell proliferation and differentiation. TOX high mobility group box family member 4 ( TOX4 ) was previously implicated in diabetes and immune system function. Other genes previously implicated in AC did not strongly contribute to AH, and the only prominently implicated (but not exome-wide significant) gene overlapping with alcohol use disorder was alcohol dehydrogenase 1B ( ADH1B ). Polygenic signals for AH were observed in both common and rare variant analysis and identified genes with roles associated with inflammation.

CONCLUSIONS

This study has identified 2 new genes of high effect size with a previously unknown contribution to alcohol-associated liver disease and highlights both the overlap in etiology between liver diseases and the unique origins of AH.

Genetic Links between Gastrointestinal Disorders and Kidney Stone Disease: Insights from a Genome-Wide Cross-Trait Analysis

Key Points

Positive genetic links and shared genetic architecture exist between gastrointestinal disorders and kidney stone disease. Ion homeostasis and response to vitamin D bridge two types of disorders. Genetically predicted irritable bowel syndrome, gastroesophageal reflux, and Crohn's disease were associated with higher risk of kidney stone disease.

Background

Epidemiological associations between kidney stone disease (KSD) and gastrointestinal disorders have been reported, and intestinal homeostasis plays a critical role in stone formation. However, the underlying intrinsic link is not adequately understood. This study aims to investigate the genetic associations between these two types of diseases.

Methods

We obtained summary statistics from large-scale genome-wide association studies of KSD and gastrointestinal diseases, including gastroesophageal reflux disease, peptic ulcer disease, inflammatory bowel disease and its subtypes, irritable bowel syndrome, and diverticular disease (N =311,254–720,199). Their overall genetic correlations were first estimated. We then detected the shared genetic architecture, including pleiotropic single nucleotide polymorphisms, loci, genes, and biological processes, through cross-trait analyses. In addition, bidirectional Mendelian randomization analysis was performed to look for their causal relationships.

Results

We found significantly positive genetic correlations between KSD and all five gastrointestinal diseases. The cross-trait analysis identified 3184 potential pleiotropic single nucleotide polymorphisms, and 33 of which were pleiotropic loci shared by the two disorders. Gene-level analyses revealed eight pleiotropic causal genes, primarily enriched in biological pathways involving ion homeostasis and response to vitamin D. In the Mendelian randomization analysis, we detected causal effects from gastroesophageal reflux disease, irritable bowel syndrome, and Crohn's disease to KSD, while no reverse causality was observed.

Conclusions

Our study demonstrated the positive genetic links between KSD and gastrointestinal diseases and reported pleiotropic variants, loci, and genes, implicating potential biological mechanisms in the pathogenesis of stone disease. These findings further support the role of the gut-kidney axis and provide a genetic basis for the prevention, coregulation, and treatment of these diseases.

Incidence of Inflammatory Bowel Disease in Children

Background

Many of the patients with inflammatory bowel disease (IBD) are children and adolescents, and the incidence of pediatric IBD is increasing. However, understanding epidemiological trends is crucial for effective prevention and treatment and reducing the local and global burden of IBD. Little data exist regarding the incidence of IBD in the child population in the Kujawsko-Pomorskie Voivodeship. The aims of this study were to evaluate the incidence of IBD in the period 2011 - 2022 and to compare the data regarding three types of IBD, namely ulcerative colitis (UC), Crohn's disease (CD), and unclassified inflammatory bowel disease (IBD-U), from the first half, i.e. 2011 - 2016, to the second half, i.e. 2017 - 2022.

Methods

This retrospective study analyzed the medical records of 118 IBD patients hospitalized at the Department of Pediatrics, Allergology and Gastroenterology from the central-northern part of Poland.

Results

Of the 118 patients diagnosed with IBD, 48 (40.68%) had CD, 57 (48.31%) had UC, and 13 (11.01%) had IBD-U. Between 2011 and 2016, 48 new IBD patients were diagnosed, with a further 70 new cases added between 2017 and 2022, representing a significant increase over the period (P = 0.033). Also, a significant increase was seen for UC, i.e. rising from 19 new cases between 2011 and 2016, to 38 between 2017 and 2022 (P = 0.015). The increase in CD was not significant.

Conclusion

The incidence of pediatric IBD in the central-northern district of Poland is lower than other countries, it nonetheless appears to be increasing, particularly in children with UC. The number of IBD diagnoses in children has increased by nearly 50% over the last 6 years.

The Pathogenesis of Inflammatory Bowel Diseases

Inflammatory bowel diseases (IBDs) are relapsing, remitting inflammatory diseases of the intestinal tract. Familial aggregation and genome-wide association studies revealed susceptibility variants that point toward a combination of innate immune and adaptive immune dysregulation that in concert with environmental factors, such as our microbiome, can initiate and perpetuate inflammation. Innate immune perturbations include functional abnormalities in the intestinal barrier, endoplasmic reticulum stress, and abnormal recognition of microbes. Adaptive immune changes include dysregulation of cytokines, regulatory T cells, and leukocyte migration. IBD is linked with an abnormal wound-healing response leading to fibrosis. This article summarizes key pathogenic mechanisms in the pathogenesis of IBDs.

Investigation of an outbreak of novel hepatitis of unknown aetiology in children and adolescents, Ireland, 2021 to 2023

An outbreak of severe acute hepatitis of unknown aetiology in children (HUAC) was reported by the United Kingdom (UK) in spring 2022. Within days, a corresponding increase was identified in Ireland. A multi-agency incident management team (IMT), led by the Health Protection Surveillance Centre (HPSC), established a national case definition, trawling questionnaire, testing protocol and communications plan. Between 1 October 2021 and 12 May 2023, 44 probable and three possible cases of HUAC were identified in Ireland with a median age of 3 years. Adeno-associated virus 2 (AAV2), detected in 18 of 31 probable cases, and SARS-CoV-2 antibodies in 22 of 37 of probable cases were the most common infectious agents, followed by human herpes virus 7 (18/33) and adenovirus (20/44). Immunological findings included the human leukocyte antigen (HLA) class II HLA-DRB1*04:01 allele in 17 of 32 cases. Autoantibodies were found in 15 of 40 patients. Our findings corroborate those of the UK, which suggested a link between HUAC and AAV2 and another virus, in children predisposed due to presence of a particular HLA class II type. Close collaboration with the UK, the European Centre for Disease Prevention and Control (ECDC) and World Health Organization (WHO) was invaluable in the investigation.

Evaluating the impact of modeling choices on the performance of integrated genetic and clinical models

PURPOSE

The value of genetic information for improving the performance of clinical risk prediction models has yielded variable conclusions. Many methodological decisions have the potential to contribute to differential results. We performed multiple modeling experiments integrating clinical and demographic data from electronic health records with genetic data to understand which decisions may affect performance.

METHODS

Clinical data in the form of structured diagnostic codes, medications, procedural codes, and demographics were extracted from 2 large independent health systems, and polygenic risk scores (PRS) were generated across all patients of European ancestry with genetic data in the corresponding biobanks. Crohn's disease was studied based on its substantial genetic component, established electronic health records-based definition, and sufficient prevalence for training and testing. We investigated the impact of choices regarding the PRS integration method, training sample, model complexity, and performance metrics.

RESULTS

Overall, our results showed that including PRS resulted in higher performance, but this gain was only robust in situations with limited clinical information. We found consistent performance increases from more compute-intensive models, such as random forest, but the impact of other decisions varied by site.

CONCLUSION

This work highlights the importance of considering methodological decision points in interpreting the impact of PRS on prediction performance in clinical models.

The identification of blood-derived response eQTLs reveals complex effects of regulatory variants on inflammatory and infectious disease risk

Hundreds of risk loci for immune mediated inflammatory and infectious diseases have been identified by genome-wide association studies (GWAS). Yet, what causal variants and genes in risk loci underpin the observed associations remains poorly understood for most. The identification of colocalized cis-expression Quantitative Trait Loci (cis-eQTLs) is a promising way to identify candidate causative genes. The catalogue of cis-eQTLs of the immune system is likely incomplete as many cis-eQTLs may be context-specific. We built a large cohort of 406 healthy individuals and expanded the immune cis-regulome through their whole blood transcriptome obtained after stimulation with specific toll-like receptor (TLR) agonists and T-cell receptor (TCR) antagonist. We report three mechanisms that may explain why an eQTL could only be revealed after immune stimulation. More than half of the cis-eQTLs detected in this study would have been overlooked without specific immune stimulations. We then mined this new catalogue of response (r)eQTLs, with public GWAS summary statistics of three diseases through a colocalization approach: inflammatory bowel diseases, rheumatoid arthritis and COVID-19 disease. We identified reQTL-specific colocalizations for risk loci for which no matching eQTL were reported before, revealing interesting new candidate causal genes.

Tracing the Evolution of Human Immunity Through Ancient DNA

Infections have imposed strong selection pressures throughout human evolution, making the study of natural selection's effects on immunity genes highly complementary to disease-focused research. This review discusses how ancient DNA studies, which have revolutionized evolutionary genetics, increase our understanding of the evolution of human immunity. These studies have shown that interbreeding between modern humans and Neanderthals or Denisovans has influenced present-day immune responses, particularly to viruses. Additionally, ancient genomics enables the tracking of how human immunity has evolved across cultural transitions, highlighting strong selection since the Bronze Age in Europe (<4,500 years) and potential genetic adaptations to epidemics raging during the Middle Ages and the European colonization of the Americas. Furthermore, ancient genomic studies suggest that the genetic risk for noninfectious immune disorders has gradually increased over millennia because alleles associated with increased risk for autoimmunity and inflammation once conferred resistance to infections. The challenge now is to extend these findings to diverse, non-European populations and to provide a more global understanding of the evolution of human immunity.

Machine learning analysis of FOSL2 and RHoBTB1 as central immunological regulators in knee osteoarthritis synovium

BackgroundKnee osteoarthritis is a debilitating disease with a complex pathogenesis. Synovitis, which refers to inflammation of the synovial membrane surrounding the joint, is believed to play an important role in the development and progression of knee osteoarthritis. To better understand the molecular mechanisms underlying knee osteoarthritis, we conducted a comprehensive analysis of gene expression in knee osteoarthritis synovium using machine learning.MethodsDifferentially expressed genes between knee osteoarthritis and control synovial tissues were analyzed using the GSE55235 dataset. We employed several machine learning algorithms, including least absolute shrinkage and selection operator and support vector machine-recursive feature elimination, to screen for key genes. Then, we validated the key genes using an external dataset (GSE51588) and an in vitro knee osteoarthritis animal model. CIBERSORT was used to compare immune cell infiltration levels between knee osteoarthritis and control synovial tissues and determine their relationship with the key genes. Finally, we performed a Connectivity Map analysis to screen for potential small-molecule compounds. Moreover, we conducted single-cell RNA sequencing analysis using knee joint tissues to annotate different subtypes of cells.ResultsA total of 930 differentially expressed genes were identified. Least absolute shrinkage and selection operator regression and support vector machine-recursive feature elimination identified FOSL2 and RHoBTB1 as key genes. The expression levels of both genes were further validated in the GSE51588 dataset as well as verified through an in vitro experiment involving a knee osteoarthritis mouse model. Multiple significant correlation pairs were found between the immune cell infiltration levels. We unveiled the genetic basis of knee osteoarthritis using genome-wide association study and specific signaling pathways through gene set enrichment analysis. The GeneCards database was used to obtain 3032 pathogenic genes associated with knee osteoarthritis, and we found that RHoBTB1 expression was significantly negatively correlated and FOSL2 expression was significantly positively correlated with interleukin-1β expression. We predicted several small-molecule compounds based on Connectivity Map analysis. Finally, single-cell RNA sequencing analysis revealed the expression levels of the two key genes in chondrocytes and tissue stem cells.ConclusionFOSL2 and RHoBTB1 may play key roles in the pathogenesis of knee osteoarthritis, exhibiting correlations with immune cell infiltration levels. These findings indicate that these genes have potential as therapeutic targets. However, further research and validation are necessary to confirm their exact roles and therapeutic potential in knee osteoarthritis.

Effect of Bacteroides on Crohn's disease

Crohn's disease (CD), also known as cicatrizing enteritis, is an inflammatory bowel disease that occurs in the distal ileum and right colon of unknown cause and is also called inflammatory bowel disease (IBD) with ulcerative colitis (UC). In recent years, intestinal biota have been confirmed to play a significant role in various gastrointestinal diseases. Studies have found that intestinal microbiota disorders are closely associated with the onset and progression of Crohn's disease. Bacteroidetes, the second largest microbiota in the intestine, are crucial for equilibrium in the microbiota and intestinal environment. Certain Bacteroides can induce the development of Crohn's disease and aggravate intestinal inflammation directly or through their metabolites. Conversely, certain Bacteroides can reduce intestinal inflammation and symptoms of Crohn's disease. This article reviews the effect of several intestinal Bacteroides in the onset and progression of Crohn's disease and their impact on its treatment.

Maintenance-phase serum anti-TNF levels are not associated with mucosal healing in pediatric Crohn's disease

OBJECTIVES

Mucosal healing (MH) is a key therapeutic target in Crohn's disease (CD) and is associated with improved outcomes. While adult studies indicate a positive correlation between serum anti-tumor necrosis factor (TNF) levels and MH, data in pediatric patients is limited. We aimed to define the association of serum anti-TNF levels with MH in pediatric patients with CD during maintenance therapy.

METHODS

Retrospective data (2014-2023) was collected from pediatric CD patients treated with infliximab or adalimumab who performed an ileocolonoscopy at least 26 weeks after initiating therapy. Serum anti-TNF levels around endoscopic time were compared with endoscopic findings. MH was defined as complete absence of inflammatory or ulcerative lesions across all segments of the gastrointestinal tract. Univariable and multivariable logistic regression analysis was conducted to identify factors associated with MH.

RESULTS

Data were obtained from 107 patients (41 infliximab and 66 adalimumab), with a median age at diagnosis of 12.6 (9.9-14.0) years. Median time until ileocolonoscopy following anti-TNF initiation was 89.0 (56.3-152.3) weeks. MH was identified in 31 (29.0%) patients. Anti-TNF serum levels were comparable in the MH and non-MH groups (9.5 [4.9-13.9] vs. 9.3 [6.4-15.7] µg/mL; p = 0.73), without differences in patients treated with infliximab or adalimumab. In multivariable analysis, diagnosis weight Z-score (odds ratio [OR] = 2.860, 95% confidence interval [CI] = 1.005-8.138; p = 0.049), along with C-reactive protein (OR = 0.037, 95% CI = 0.002-0.687; p = 0.027) and fecal calprotectin (OR = 0.995, 95% CI = 0.990-1.000; p = 0.037) at time of ileocolonoscopy were significantly associated with MH.

CONCLUSIONS

In our cohort, anti-TNF levels during maintenance were not associated with MH in pediatric CD.

British Society of Gastroenterology guidelines for diagnosis and management of autoimmune hepatitis

Autoimmune hepatitis (AIH) is a chronic inflammatory liver disease which, if untreated, often leads to cirrhosis, liver failure and death. The last British Society of Gastroenterology (BSG) guideline for the management of AIH was published in 2011. Since then, our understanding of AIH has advanced in many areas. This update to the previous guideline was commissioned by the BSG and developed by a multidisciplinary group. The aim of this guideline is to review and summarise the current evidence, in order to inform and guide diagnosis and management of patients with AIH and its variant syndromes. The main focus is on AIH in adults, but the guidelines should also be relevant to older children and adolescents.