Evaluation of causal relationships between genetic liability to inflammatory bowel disease and autism spectrum disorder by Mendelian randomization analysis

BACKGROUND

Emerging observational studies have indicated the association between autism spectrum disorder (ASD) and IBD, including Crohn's disease (CD) and ulcerative colitis (UC), whereas the causality remains unknown.

METHODS

Summary-level data from large-scale genome-wide association (GWAS) studies of IBD and ASD were retrieved. Mendelian randomisation analyses were performed with a series of sensitivity tests.

RESULTS

Genetic predisposition to ASD was not associated with the risk of IBD (odds ratio [OR] = 0.99, 95% confidence interval [CI = 0.91-1.06, p = 0.70; OR [95% CI]: 1.03 [0.93-1.13], p = 0.58 for CD; OR [95% CI]: 0.96 [0.87-1.05], p = 0.37 for UC) in the IIBDGC dataset. In the FinnGen dataset, their causal effects were unfounded (OR [95% CI]: 1.04 [0.94-1.15], p = 0.49 for IBD; OR [95% CI]: 1.08 [0.89-1.31], p = 0.42 for CD; OR [95% CI]: 1.00 [0.88-1.13], p = 0.95 for UC). In the meta-analysis of two datasets, the OR was 1.01 (95% CI 0.96-1.07, p = 0.45). For the risk of ASD under genetic liability to IBD, the OR from meta-analysis was 1.03 (95% CI 1.01-1.05, p = 0.01).

CONCLUSION

Our findings indicate genetic predisposition to ASD might not increase the risk of IBD, whereas genetic liability to IBD is associated with an increased risk of ASD. Further investigations using more powerful datasets are warranted.

Human colitis-associated colorectal carcinoma progression is accompanied by dysbiosis with enriched pathobionts

Dysbiosis and pathobionts contribute to inflammation and the risk of colitis-associated carcinoma (CAC) in animal models, but their roles in humans with this uncommon disease are unknown. We identified microbiome differences in human CAC compared with longstanding inflammatory bowel disease (IBD) and sporadic colorectal carcinoma (CRC). Twenty-four CAC resections were matched with CRC and IBD controls. Methods included histopathology, 16S rDNA metagenomics, and pathobiont-specific qPCR. Beta diversity differed by diagnosis (PERMANOVA p = 0.007). The distinguishing taxa included Akkermansia enriched in CRC, and Bacteroides spp. enriched in IBD. The non-neoplastic mucosae presented distinct beta diversity (p = 0.005), but the CAC/CRC tumor microbiomes were similar (p = 0.7). Within metastases and margins, Enterobacteriaceae were enriched in CAC, and Bacteroidales in CRC. Pathobiont-specific qPCR confirmed a greater frequency of pks+ E. coli and enterotoxigenic Bacteroides fragilis in CAC than IBD. High alpha diversity was associated with active inflammation, advanced cancer stage, and shorter overall survival (log-rank p = 0.008). Mucosal microbiomes distinguish CAC from longstanding IBD, implicating pathobionts as markers for disease progression. Integrating our findings with prior animal model research, pathobionts promote carcinogenesis in IBD patients through genotoxicity and host cell signaling.

Inpatient Nutritional Considerations in Inflammatory Bowel Disease

PURPOSE OF REVIEW

This review aims to explain the causes, diagnosis, and treatment of malnutrition in hospitalized patients with inflammatory bowel disease (IBD), focusing on both adults and children.

RECENT FINDINGS

Malnutrition is common among IBD patients, affecting up to 85% of individuals, and is linked to higher rates of illness, death, and longer hospital stays. Recent studies highlight the importance of early detection using tools like the Subjective Global Assessment (SGA) and handgrip strength tests. Nutritional interventions-such as exclusive enteral nutrition (EEN) and parenteral nutrition (PN)-have proven effective in inducing remission and improving patient outcomes, especially in pediatric Crohn's disease. New evidence suggests that optimizing nutrition before and after surgery, as well as using immunonutrition, may reduce postoperative complications. Early identification and management of malnutrition in hospitalized IBD patients may be important for improving clinical outcomes. Using appropriate nutritional screening tools and creating personalized nutrition plans can help with recovery, decrease hospital stays, and improve quality of life. Further research is needed to develop standard protocols for nutritional assessment and treatment in this patient population.

Adenosine-generating CD39+ plasmablasts predispose to successful infliximab therapy in pediatric IBD

B cells display several immunoregulatory mechanisms including the production of interleukin-10. Ectonucleotidases like CD39 and CD73 influence immune homeostasis by metabolizing eATP and generating immunosuppressive adenosine. The major objective was to examine the expression of those immunoregulatory molecules on B-cell subsets, and, more specifically, to determine their association with an infliximab (IFX) treatment in a pediatric inflammatory bowel disease (IBD) cohort. 42 IBD patients were assessed for IFX response after 12 mo of therapy and compared against 14 healthy controls (HC). Although IL10-producing plasmablasts were decreased in IFX nonresponders (NRS), we detected an up-regulation of CD39 on plasmablasts and increased fractions of CD39/CD73-co-expressing naïve and memory B cells in responding patients (RS). In addition, B cells of responders proved to have superior ATP degradation capacities and adenosine production before therapy initiation compared with NRS and HC. Moreover, IFX nonresponders had a marked deficiency of α4β7hi plasmablasts, whereas both cohorts had fewer CCR9-expressing plasmablasts. Consequently, CD39+ plasmablasts were decreased in biopsies of inflamed mucosal tissues, especially in IFX nonresponders. Our results highlight the regulatory potential of CD39/CD73-expressing B cells in pediatric IBD and suggest CD39+ plasmablasts as a potential determinant of a successful immunosuppressive therapy with IFX.

Pediatric autoimmune diseases in the light of COVID-19 pandemic, A retrospective observational big data study

Background

The COVID-19 pandemic has raised concerns about potential links between SARS-CoV-2 infection and autoimmune diseases. This study investigated changes in the incidence rate (IR) of autoimmune diseases among children following the pandemic's onset.

Methods

A retrospective cross-sectional study analyzed data from Clalit Health Services, Israel's largest healthcare provider, examining the IR of different autoimmune diseases in children aged 0-18. The study compared pre-pandemic (2019) with pandemic/post-pandemic periods (2020-2023), encompassing a cohort of over 1.5 million children.

Results

Significant IR increases were observed across multiple autoimmune diseases. Rheumatic diseases (Juvenile Idiopathic Arthritis, Systemic Lupus Erythematosus, Henoch Schoenlein Purpura (HSP)) showed consistent increases, with HSP demonstrating the most pronounced trend. Endocrine disorders exhibited diverse patterns, with autoimmune thyroid diseases and Type 1 diabetes showing overall increases, while diabetic ketoacidosis exhibited an initial spike followed by a decline. Gastrointestinal diseases displayed heterogeneous patterns; Celiac disease and Ulcerative colitis showed general increases, Crohn's disease showed a downward trend, and autoimmune hepatitis exhibited an initial significant decrease followed by a significant increase. Dermatological conditions, including Psoriasis and Vitiligo, demonstrated consistent elevations throughout 2020-2023. Immune Thrombocytopenia Purpura showed initial decreases followed by significant increases in 2022-2023.

Conclusions

This comprehensive analysis reveals significant changes in pediatric autoimmune disease incidence following the COVID-19 pandemic, suggesting potential associations between SARS-CoV-2 infection and autoimmune dysregulation. The diverse patterns observed across different conditions highlight the complex interplay between viral infection and autoimmunity, emphasizing the need for continued surveillance and investigation of long-term immunological consequences of COVID-19 in pediatric populations.

Cross-tissue transcriptome-wide association study reveals novel psoriasis susceptibility genes

Background

Psoriasis is a chronic, immune-mediated inflammatory skin disorder with a strong genetic component. Although numerous GWAS have identified risk loci, many associated variants lie in non-coding regions, complicating functional interpretation.

Objective

This study aimed to identify novel psoriasis susceptibility genes by integrating large-scale GWAS and eQTL data using a cross-tissue TWAS approach.

Methods

We integrated psoriasis GWAS summary statistics from the FinnGen database with GTEx V8 eQTL data. A cross-tissue TWAS was performed using UTMOST, followed by validation with single-tissue TWAS via FUSION. Conditional and joint analyses were conducted to delineate independent genetic signals, and gene-based analysis was performed using MAGMA. Causal relationships were evaluated using Mendelian randomization (MR) and Bayesian colocalization analyses. Key SNPs were functionally characterized using CADD, GERP++, and RegulomeDB for pathogenicity prediction and regulatory potential assessment. Finally, functional network analysis was conducted using GeneMANIA.

Results

The cross-tissue TWAS identified 259 genes significantly associated with psoriasis (p < 0.05), with 12 remaining significant after FDR correction. Single-tissue TWAS validation revealed 655 significant genes, with an overlap of three protein-coding candidates: POLI, NFKB1, and ZFYVE28. Cross-validation with MAGMA refined the candidate set to NFKB1 and ZFYVE28. MR and colocalization analyses supported a causal relationship for NFKB1 in Skeletal Muscle, Transverse Colon, and Cultured Fibroblasts, and for ZFYVE28 in Subcutaneous Adipose Tissue and Esophageal Mucosa tissues. Functional annotation identified key SNPs including rs4235405, rs3774960, and rs1598856 for NFKB1, and rs1203786 for ZFYVE28, with varying degrees of pathogenicity and regulatory potential. GeneMANIA network analysis further implicated NFKB1 in NF-κB signaling and ZFYVE28 in vesicle-mediated transport.

Conclusion

Our integrative multi-omics approach identifies NFKB1 and ZFYVE28 as novel psoriasis susceptibility genes, providing potential biomarkers and therapeutic targets for this complex disease.

'We need to make "shit" sexy' a qualitative study exploring treatment adherence in adolescents with inflammatory bowel disease

Background: Adolescents with inflammatory bowel disease (IBD) are faced with the complexities of acquiring self-management behaviours at a time when they are also navigating developmental challenges associated with adolescence. To date, limited treatment adherence interventions exist to support adolescents with IBD. Aim: To explore the experience and support needs of adolescents with IBD to facilitate optimum treatment adherence. Method: Thirty-three semi-structured interviews were conducted with adolescents with IBD (n = 12), parents of adolescents with IBD (n = 13) and healthcare professionals who support adolescents with IBD (n = 8). Adolescents and parents completed a creative task to prioritise adherence barriers and adherence intervention strategies. Results: The analysis generated three key themes: (1) striving for normality, (2) taking responsibility for IBD management and (3) seeking supportive environments. Living with IBD was often perceived as living a limited life, as adolescents had to manage their symptoms, which resulted in feelings of difference and stigmatisation. To manage their IBD, adolescents were required to develop treatment routines and communicate their health needs. Parents wanted to protect their child from the burden of living with IBD. Synthesis of findings with a creative mapping task generated seven priorities for intervention. Discussion: Adolescents discussed the complexity behind their adherence behaviours and the formation of treatment perceptions. The adherence barriers identified within this research can be utilised to develop a treatment adherence intervention that is effective for adolescents with IBD.

RNF186 gene variant and zonulin levels in inflammatory bowel disease: A pilot study

BACKGROUND AND STUDY AIM

Inflammatory bowel disease (IBD) is a chronic inflammatory disorder of the gastrointestinal tract characterized by inflammation and ulceration of the intestinal mucosa, represented by Crohn's disease (CD) and ulcerative colitis (UC). The aim of this study is to investigate the relationship between the Ring Finger Protein 186 (RNF186) rs3806308 variant and IBD, as well as to determine whether zonulin levels are associated with IBD.

PATIENTS AND METHODS

Ninety-nine patients with inflammatory bowel disease were included in the study. The real-time PCR method was used to detect RNF186 gene polymorphism. Also serum zonulin levels were determined by using Enzyme Linked Immunosorbent Assay (ELISA) technique.

RESULTS

No difference was found between the groups in terms of RNF186 genotype and allele distributions (p > 0.05). CC genotype was associated with high levels of C-reactive protein (CRP) in total patients and CD compared to CT (p < 0.05).

CONCLUSION

The present study is the first study conducted in our country in terms of examining RNF 186 gene polymorphism and serum zonulin levels.

NDP52 and its emerging role in pathogenesis

Autophagy is a pro-survival process that regulates the degradation and renewal of cellular components, making it a crucial mechanism for cellular homeostasis. There are selective forms of autophagy that are specific to a number of substrates, such as pathogens (bacteria or viruses), protein aggregates or excess/damaged organelles. These processes involve as key players autophagy receptors, that link the cargo to be degraded to the autophagic machinery. Among them, NDP52 (also known as CALCOCO2) has been described to act as a "bridge" between the autophagy machinery and (1) damaged mitochondria in the mitophagy process; (2) pathogens during xenophagy or (3) proteins in the process of aggrephagy. The aim of this review is to summarize the major functions of NDP52, and to highlight the existence of two human NDP52 variants that have been described as risk or protective factors for Crohn's disease or Multiple Sclerosis and Alzheimer's disease patients, respectively. As these three diseases share common pathological features that lead to inflammation, such as mitochondria or gut microbiota dysfunctions, but also pathogenic infections, it seems clear that NDP52 could be a key player at the crossroad by acting indirectly on inflammation, and therefore a potential target for clinical applications and benefits.

Gut microbiota modulate intestinal inflammation by endoplasmic reticulum stress-autophagy-cell death signaling axis

The intestinal tract, a complex organ responsible for nutrient absorption and digestion, relies heavily on a balanced gut microbiome to maintain its integrity. Disruptions to this delicate microbial ecosystem can lead to intestinal inflammation, a hallmark of inflammatory bowel disease (IBD). While the role of the gut microbiome in IBD is increasingly recognized, the underlying mechanisms, particularly those involving endoplasmic reticulum (ER) stress, autophagy, and cell death, remain incompletely understood. ER stress, a cellular response to various stressors, can trigger inflammation and cell death. Autophagy, a cellular degradation process, can either alleviate or exacerbate ER stress-induced inflammation, depending on the specific context. The gut microbiome can influence both ER stress and autophagy pathways, further complicating the interplay between these processes. This review delves into the intricate relationship between ER stress, autophagy, and the gut microbiome in the context of intestinal inflammation. By exploring the molecular mechanisms underlying these interactions, we aim to provide a comprehensive theoretical framework for developing novel therapeutic strategies for IBD. A deeper understanding of the ER stress-autophagy axis, the gut microbial-ER stress axis, and the gut microbial-autophagy axis may pave the way for targeted interventions to restore intestinal health and mitigate the impact of IBD.

Pediatric Vaccine-Induced Antibody Thresholds: Rethinking Pre-Immunosuppression Serologic Testing and Revaccination Implications

BACKGROUND

Immune response to vaccination is assessed when adequate vaccine protection is in question or immunosuppression is imminent through measurement of antibody levels, which wane as time from vaccination increases. The serologic cutoff value for adequate response is based on thresholds derived from studies in adults, and age-appropriate thresholds for children have not been established. We sought to investigate age-specific differences in antibody levels in healthy children to guide determination of vaccine immunity status when clinically indicated.

METHODS

This cross-sectional study assessed clinical serology for measles, mumps, rubella (MMR), varicella, and hepatitis B (HepB) in an age-stratified cohort of 471 healthy children who were up to date for vaccination (1 to 18 years). Remnant specimens with sufficient volume were collected from July 23, 2019, to November 17, 2020, as convenience samples and chart reviewed for inclusion.

RESULTS

While children of all ages had detectable titers to MMR, median titers for HepB and varicella waned by ages 11 to 12 and 9 to 10 years, respectively. Children had titers above adult thresholds for MMR at all measured timepoints, retrospectively resulting in 24.6% (95% CI, 21.6%-27.8%) of children having an inappropriate MMR classification when adult instead of pediatric thresholds were used. Current use of HepB and varicella serology may be inappropriate due to the rapid waning of titers. The adequacy of an individual's response to one vaccine component did not infer adequate responses to other components.

CONCLUSIONS

Application of age-appropriate reference intervals for vaccine serologic tests will provide a foundation for improved treatment recommendations and standards of care.

Impact of Amerindian ancestry on clinical outcomes in Crohn's disease and ulcerative colitis in a Latino population

Research in Inflammatory Bowel Disease (IBD) assessing the genetic structure and its association with IBD phenotypes is needed, especially in IBD-underrepresented populations such as the South American IBD population. Aim. We examine the correlation between Amerindian ancestry and IBD phenotypes within a South American cohort and investigate the association between previously identified IBD risk variants and phenotypes. We assessed the ancestral structure (IBD = 291, Controls = 51) to examine the association between Amerindian ancestry (AMR) and IBD variables. Additionally, we analyzed the influence of known IBD genetic risk factors on disease outcomes. We used Chi-square and Fisher's tests to analyze the relationship between phenotypes and ancestry proportions, calculating odds ratios (OR) and confidence intervals (CI). Logistic regression examined genetic variants associations with IBD outcomes, and classification models for predicting prolonged remission were developed using decision tree and random forest techniques. The median distribution of global ancestry was 58% European, 39% Amerindian, and 3% African. There were no significant differences in IBD risk based on ancestry proportion between cases and controls. In Ulcerative colitis (UC), patients with a high Amerindian Ancestry Proportion (HAAP) were significantly linked to increased chances of resective surgery (OR = 4.27, CI = 1.41-12.94, p = 0.01), pouch formation (OR = 7.47, CI = 1.86-30.1, p = 0.003), and IBD reactivation during COVID-19 infection (OR = 5.16, CI = 1.61-6.53, p = 0.005). Whereas, in the Crohn's Disease (CD) group, the median Amerindian ancestry proportion was lower in the group with perianal disease (33.5% versus 39.5%, P value = 0.03). CD patients with High Amerindian Ancestry proportion had lower risk for surgery (OR = 0.17, CI = 0.03-0.83, P value = 0.02). Our study highlights the impact of Amerindian ancestry on IBD phenotypes, suggesting a role for genetic and ancestral factors in disease phenotype. Further investigation is needed to unravel the underlying mechanisms driving these associations.

AGR2-mediated cell-cell communication controls the antiviral immune response by promoting the thiol oxidation of TRAF3

Protein disulfide isomerases (PDIs) are essential catalysts for the formation and isomerization of disulfide bonds in diverse substrate proteins and exert multiple functions under pathophysiological conditions. Here, we show that anterior gradient 2 (AGR2), a member of PDIs, acts as a negative regulator in antiviral immunity. RNA virus infection stimulated the expression and secretion of AGR2 in epithelial cells. While AGR2 is absent in immune cells, both intracellular AGR2 and extracellular AGR2 compromised type I interferon (IFN-I) production in vitro and in vivo. The inhibitory effect of secreted AGR2 on the immune response resulted from its crosstalk with immune cells, such as macrophages, by which eAGR2 was internalized via endocytosis depending on its adhesion motif. We further identified AGR2 as a novel binding protein of TRAF3, which forms a disulfide bond between Cys81 of AGR2 and Cys296 on TRAF3. This interaction led to the inhibition of TRAF3 K63-linked ubiquitination and TRAF3-TBK1 complex formation, ultimately impairing TRAF3's ability to induce IFN-I production. The TRAF3 Cys296 mutation diminishes oxidative modification by AGR2 but enhances self-association of TRAF3 and IFN-I production. Our study demonstrated a cysteine-dependent oxidative modification of TRAF3 by AGR2 that suppresses TRAF3 activity and maintains innate immune homeostasis.

Uncovering shared genetic features between inflammatory bowel disease and systemic lupus erythematosus

Inflammatory bowel disease (IBD) is an autoimmune disease (AD) characterized by chronic, relapsing intestinal inflammation. Systemic lupus erythematosus (SLE) is a complex autoimmune disease with multisystem involvement and overactivation of both innate and adaptive immunity. The extra intestinal manifestations (EIMs) that commonly occur in IBD include many of the organ sites that are affected by SLE. ADs are often comorbid with one another and may have shared underlying genetic features and architectures contributing to their pathogenesis and disease course. We performed both epidemiological and post-genome wide association study (GWAS) analyses to investigate the shared genetic features between IBD and systemic lupus erythematosus (SLE). Specifically, we performed epidemiological association analysis in the All of Us Research Program (AoURP) and genome-wide/local genetic correlation analysis and cell-type specific SNP heritability enrichment analysis using previously published summary level data. A significant epidemiologic association exists between IBD and SLE with an adjusted odds ratio (aOR) of 2.94 (95% CI: 2.45-3.53; P < 0.001) in a multivariable model accounting for confounders in the AoURP data. Genome-wide genetic correlation analysis in previously published summary level data demonstrated a significant genetic correlation between IBD, CD, and UC with SLE, and local genetic correlation analysis demonstrated several positive and significant correlations in local genomic regions harboring disease variants in genes common to both SLE and IBD etiology, including variants in ELF1, CD226, JAZF1, WDFY4, and JAK2. Cell-type SNP heritability enrichment analysis identified both overlapping and distinct functional categories contributing to SNP heritability across IBD phenotypes. Notably, IBD-related phenotypes demonstrated significant enrichment in T-lymphocyte functional groups while SLE signal appeared in distinct categories, such as B-lymphocytes (along with CD). Gene-level collapsing analysis of rare variants in the United Kingdom BioBank (UKBB) identified overlapping nominally-significant genes between SLE and IBD, CD, and UC. By leveraging several post-GWAS methods, the present study identifies shared genetic features between IBD and SLE, highlighting similarities and differences in the genetic features that contribute to the pathogenesis of each disease.

Global prevalence of biologic drugs use in inflammatory bowel diseases: a systematic review and meta-analysis

OBJECTIVES

Biologics are increasingly essential in managing inflammatory bowel diseases (IBDs) worldwide, as they can modify disease progression and improve patients' quality of life. This study aimed to analyze the global prevalence of and geographic variations in the use of biological drugs for IBD.

MATERIALS AND METHODS

Articles published up to 21 July 2024, were identified from the PubMed/MEDLINE, Web of Science, Scopus, Embase, IBECS, WPRIM, BRISA/RedETSA and LILACS databases. Population-based studies (cohort, case-control and cross-sectional) and studies using administrative databases with data on the prevalence of biological medicine use in patients with IBD were included. Two reviewers independently screened the studies, extracted data, and assessed methodological quality. Estimates were pooled using a random-effects meta-analysis, whereas heterogeneity was evaluated using Cochran's Q test and I2.

RESULTS

Of the 8239 titles, 68 (n = 3,482,385 patients) were included. An increase in the number of studies on the subject has been reported since 2017, and these studies have been mostly concentrated in high-income countries. A 15.06% (95% CI 11.84-18.28%) prevalence of biologic use in IBD worldwide was reported, predominantly concentrated in the use of anti-TNF agents 15.01% (95% CI 10.35-19.67%). Furthermore, patients with Crohn's disease (CD) had a greater prevalence of biologic use (21.41%; 95% CI 16.31-26.50%) than ulcerative colitis (UC) patients (9.70%; 95% CI 6.20-13.18%).

CONCLUSIONS

Further studies using population-based and administrative data and stratifying their analyses by disease type are required to confirm our findings. Future studies should be conducted in Latin America, Asia and Africa.

Crohn's Colitis Care, a Disease-Specific Electronic Medical Record, Enhances Data Capture in Pediatric Inflammatory Bowel Disease Care

Background and Aim

Crohn's Colitis Care, a structured, disease-specific electronic medical record, is proven to promote more complete data capture in adult Inflammatory Bowel Disease care. This study aimed to determine whether similar effectiveness was seen in pediatrics.

Methods

Matched patient records from a hospital's standard electronic medical record (pre-Crohn's Colitis Care) and those in Crohn's Colitis Care were retrospectively reviewed (12 months each). The presence of disease-specific data items per platform were compared (21 core, 5 age-specific). Data are presented as percentage recorded (recorded items/total eligible for age). Descriptive and statistical analytics were used.

Results

Paired records were reviewed for 114 children, of whom 78 (68%) had Crohn's disease and 69 (61%) were male. Median age at diagnosis was 13.5 years (IQR12.0-15.5), with mean disease duration 3.6 years (±2.4). Crohn's Colitis Care was more likely to capture 9 items: general wellbeing, stool urgency and frequency, disease duration, comorbidities, pubertal stage, sexual activity, alcohol and drug usage (each p < 0.05). The standard platform was more likely to capture 4 items: liquid stools, phenotype, disease indices, and vaccinations (each p < 0.05). Crohn's Colitis Care achieved more eligible data items recorded per patient (75.3% ±11.5 vs. 67.7% ± 8.9; p < 0.001). Item completion rate in both platforms inversely correlated with patient age (p < 0.05).

Conclusions

Consistent with findings in adult care, Crohn's Colitis Care achieved more complete disease-data capture in pediatrics compared to a standard platform. Given that not all items were better recorded in the structured platform, work to understand and address barriers is needed to optimize complete data capture for care and research.

Dietary essential oil components: A systematic review of preclinical studies on the management of gastrointestinal diseases

BACKGROUND

The gut is responsible for the digestion and absorption of nutrients, immune regulation, and barrier function. However, factors like poor diet, stress, and infection, can disrupt the balance of the gut microbiota and lead to intestinal inflammation and dysfunction.

PURPOSE

This systematic review aims to evaluate the effects of dietary plants-derived essential oil components on gut health and intestinal functions in animal models.

METHODS

The literature was gathered from the Scopus, Web of Science, PubMed, and Embase databases by using related search terms, such as "dietary plants", "dietary sources", "essential oils", "gut health", "intestine", "anti-inflammatory", "antioxidant", and "gut microbiota".

RESULTS

The results indicate that plant-derived dietary essential oil components, such as butyrolactone-I, carvacrol, cinnamaldehyde, citral, D-limonene, eugenol, farnesol, geraniol, indole, nerolidol, oleic acid, thymol, trans-anethole, vanillin, α-bisabolol, α-linolenic acid, α-pinene, α-terpineol, β-carotene, β-caryophyllene, and β-myrcene have been found to regulate gut health by influencing vital signalling pathways associated with inflammation. Dietary essential oil components modulate the expression of tumor necrosis factor alpha, interleukin 1 beta (IL-1β), interleukin (IL)-6, IL-10, inducible nitric oxide synthase, cyclooxygenase-2, toll-like receptor-4, matrix metalloproteinase, and interferon gamma in mitigating gut inflammation. The primary signalling molecules controlled by these molecules were AMP-activated protein kinase (AMPK), protein kinase B, extracellular signal-regulated kinase, c-Jun N-terminal kinase, mitogen-activated protein kinase, myeloid differentiation primary response 88, nuclear factor erythroid-2-related factor-2, and phosphoinositide 3-kinase (PI3K). Moreover, these phytochemicals have been shown to improve glucose homeostasis by regulating glucose transporter 4, glucagon-like peptide-1, peroxisome proliferator-activated receptor gamma, nuclear factor kappa B, AMPK, PI3K, and uncoupling protein-1. They can also reduce thiobarbituric acid reactive substance, malondialdehyde, and oxidative stress and enhance superoxide dismutase, catalase, and glutathione peroxidase levels.

CONCLUSION

In conclusion, dietary plants-derived essential oil components have the potential to mitigate inflammation and oxidative stress in the gut. However, additional clinical investigations are necessary to confirm their complete potential in improving human gut health functions.

Gut Microbiome Signature in Predisease Phase of Inflammatory Bowel Disease: Prediction to Pathogenesis to Prevention

Advances in understanding the pathogenesis of inflammatory bowel disease (IBD) point toward a key role of the gut microbiome. We review the data describing the changes in the gut microbiome from IBD case-control studies and compare these findings with emerging data from studies of the preclinical phase of IBD. What is apparent is that assessing changes in the composition and function of the gut microbiome during the preclinical phase helps address confounding factors, such as disease activity and drug therapy, which can directly influence the gut microbiome. Understanding these changes in the predisease phase provides a means of predicting IBD in high-risk populations and offers insights into possible mechanisms involved in disease pathogenesis. Finally, we discuss strategies to use this information to design interventions aimed at modulating the microbiome as a means of preventing or delaying the onset of IBD.

Mycoplasma hyopneumoniae nuclease Mhp597 negatively regulates TBK1-IRF3-IFN-I pathway by targeting vimentin to facilitate infection

Infection with Mycoplasma hyopneumoniae (M. hyopneumoniae) leads to chronic infectious pneumonia in pigs, resulting in significant distress and economic losses in the global pig industry. The pathogen secretes various proteins, including toxins, adhesins, and virulence-related enzymes, which facilitate adhesion, invasion, and immune evasion processes between bacteria and the host. However, the effector proteins of M. hyopneumoniae are predominantly uncharacterized. In this study, we demonstrate that the nuclease Mhp597 functions as a potential effector protein of M. hyopneumoniae, and we elucidate its mechanism of action in facilitating immune evasion. Our findings indicate that Mhp597 exhibits high expression efficiency in host cells and significantly inhibits IFN-α and IFN-β protein expression. Using yeast two-hybrid and co-immunoprecipitation experiments, we established that Mhp597 interacts with porcine alveolar macrophage vimentin (Vim) via specific amino acid residues (Arg 232, Lys 256, Phe 263, and Lys 317). Further analysis revealed that Mhp597 inhibited the phosphorylation of TBK1 and IRF3 via Vim, thereby suppressing type I interferon (IFN-I) production and promoting the proliferation of M. hyopneumoniae within host cells. In conclusion, this study provides the first detailed account of the molecular mechanism by which Mhp597 negatively regulates the TBK1-IRF3-IFN-I signaling pathway through Vim, thus facilitating immune evasion and proliferation of M. hyopneumoniae within host cells. These findings enhance our understanding of the pathogenic mechanisms of M. hyopneumoniae and suggest potential molecular targets for the development of novel therapeutic strategies.

Global evolution of inflammatory bowel disease across epidemiologic stages

During the twentieth century, inflammatory bowel disease (IBD) was considered a disease of early industrialized regions in North America, Europe and Oceania1. At the turn of the twenty-first century, IBD incidence increased in newly industrialized and emerging regions in Africa, Asia and Latin America, while the prevalence in early industrialized regions continued to grow steadily2-4. Changes in the incidence and prevalence denote the evolution of IBD across four epidemiologic stages: stage 1 (emergence), characterized by low incidence and prevalence; stage 2 (acceleration in incidence), marked by rapidly rising incidence and low prevalence; and stage 3 (compounding prevalence), where the incidence decelerates, plateaus or declines while the prevalence steadily increases. A fourth stage (prevalence equilibrium) has been proposed in which the prevalence slope plateaus due to demographic shifts in an ageing IBD population, but it has not yet been evidenced. To date, these stages have remained theoretical, lacking specific numerical indicators to define transition points. Here, using real-world data from 522 population-based studies encompassing 82 global regions and spanning more than a century (1920-2024), we show spatiotemporal transitions across stages 1-3 and model stage 4 progression. Understanding the evolution of IBD across epidemiologic stages enables healthcare systems to better anticipate the future worldwide burden of IBD.

A Mendelian randomization study on the causal association of circulating cytokines with diabetic nephropathy

BACKGROUND

Circulating cytokines were reported to be related to diabetic nephropathy (DN) in observational studies. However, the causal relationship between them remains unknown. This study aimed to investigate the causal relationship between DN and circulating cytokines with genetic data in the frame of Mendelian Randomization (MR).

METHODS

We performed a two-sample MR analysis to investigate the causal relationship in individuals of European ancestry, utilizing publicly available genome-wide association study (GWAS) statistics. We selected eligible instrumental SNPs that were significantly related to the circulating cytokines. Multiple MR analysis approaches were employed, including inverse variance weighted (IVW), Weighted Median, MR-Egger, Weighted Mode, Simple Mode, and MR pleiotropy residual sum and outlier (MR-PRESSO) methods.

RESULTS

We found evidence supporting the causal role of genetically predicted circulating levels in the increased risk of DN. Specifically, we observed associations for interferon-gamma [OR = 1.352, 95% CI: 1.089-1.678, P = 0.006], stem cell factor [OR = 1.252, 95% CI: 1.028-1.525, P = 0.025], and stromal-cell-derived factor 1 alpha [OR = 1.326, 95% CI: 1.017-1.727, P = 0.037]. Additionally, MR analysis revealed a negative causal association between macrophage inflammatory protein 1b and DN [OR = 0.921, 95% CI: 0.858-0.988, P = 0.022]. The results obtained from MR-Egger, Weighted Median, Weighted Mode, and Simple Mode methods were consistent with the Inverse Variance Weighted (IVW) estimates. Sensitivity analyses showed no evidence of horizontal pleiotropy, suggesting that the causal estimates were not biased.

CONCLUSIONS

Our findings offer promising leads for developing novel therapeutic targets for DN. By identifying the role of inflammatory cytokines in this debilitating condition through a genetic epidemiological approach, our study made contributions to a better understanding of the underlying disease mechanisms.

Healthcare transition and inflammatory bowel disease: the challenges experienced by young adults after transfer from paediatric to adult health services

In recent years, there has been a steady increase in research on healthcare transition for patients with Inflammatory Bowel Disease (IBD). However, the focus has been mainly on preparing young people for the transfer to adult health services. Consequently, there is limited information on the post-transfer challenges and perspectives of these young patients, as they also transition into young adulthood. A qualitative study was conducted using in-depth semi-structured interviews to explore the post-transfer experiences of 12 young adults (18-25 years old) with paediatric-onset IBD. The interviews were audiotaped, transcribed and analysed using thematic analysis. Four over-arching themes were generated, describing the numerous and diverse post-transfer challenges experienced by participants: Living with IBD, Psychosocial Adversity, Maintaining Wellbeing, and Adjusting to Adult Health Services. The symptom impact was discussed extensively, especially in relation to fatigue. Numerous non-IBD psychosocial stresses were reported, whilst illness-related stressors were mentioned to a lesser extent. Participants demonstrated a pragmatic acceptance of the necessity for medication, however barriers to adherence persisted. The limited use of strategies to manage stress and negative emotions was highlighted, as was the continued reliance on parental support. The move to adult health services was initially confronting, however, participants eventually adjusted. Healthcare transition interventions which extend beyond the current preparatory paediatric focus are required, to provide ongoing age-appropriate, post-transfer support for young people, as they encounter the challenges of young adulthood, whilst living with IBD.

Insights into Modeling Inflammatory Bowel Disease from Stem Cell Derived Intestinal Organoids

Inflammatory bowel disease (IBD), encompassing Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial, immune-mediated condition marked by chronic gastrointestinal inflammation. This condition significantly impairs patients' quality of life and represents a major public health challenge globally. Pathogenesis of IBD arises from complex interplay among genetic predisposition, environmental factors, immune dysregulation, and microbial dysbiosis. Although significant strides have been made in unraveling these mechanisms, existing therapeutic options remain inadequate in addressing the full spectrum of clinical needs, underscoring the urgent demand for innovative strategies. Regenerative medicine has emerged as a promising frontier, offering novel tools for therapeutic development. We briefly consolidated current knowledge on IBD pathogenesis and treatments, emphasized the pivotal potential of human intestinal organoids (including adult stem cell-derived organoids and pluripotent stem cell- derived organoids) as a robust platform for mechanistic studies and treatment exploration. Leveraging this technology, we aim to advance personalized and next-generation therapies for IBD.

Characteristic immune cell interactions in livers of children with acute hepatitis revealed by spatial single-cell analysis identify a possible postacute sequel of COVID-19

BACKGROUND

A rise in paediatric cases of acute hepatitis of unknown origin (AHUO) was observed in 2022, some requiring liver transplantation. A link to adeno-associated virus 2 infection and CD4+T-cell mediated disease was reported in cohorts in the UK and USA but does not explain all cases.

OBJECTIVE

To determine the intrahepatic immune cell interactions in the inflamed liver and a possible contribution of SARS-CoV-2 infection.

DESIGN

Patients with acute non-A non-E hepatitis (10/12 AHUO, 2/12 subacute) during February 2022-December 2022 undergoing liver biopsy were recruited in a European patient cohort. Hepatological, virological, histopathological and highly multiplexed spatial and single-cell analyses of liver biopsies were performed.

RESULTS

Patients were negative for adenoviral and SARS-CoV-2 PCR. Three patients had a positive adenoviral serology and 10/12 patients had a history or serological evidence of SARS-CoV-2 infection. Imaging mass cytometry identified significant intrahepatic immune infiltration with an enrichment of CD8+T-cells. The highest CD8 infiltration and concomitant peripheral immune activation were observed in patients with the most severe hepatitis. CD8+T-cell infiltration was connected to histomorphological interface hepatitis and bridging necrosis. Cellular neighbourhood analysis indicated disease-associated microanatomic interactions between CX3CR1+ endothelial and myeloid cell populations, interacting with effector CD8+T-cells suggesting a pathogenic cellular triad. Of note, we detected intrahepatic SARS-CoV-2 antigens in ACE2-expressing cells in the areas with significant pathology in 11/12 samples using several different detection methods. 10/12 patients were treated with corticosteroid therapy and no liver transplantation was required.

CONCLUSIONS

We identified a possible manifestation of an immune-mediated postacute sequel to COVID-19 associated with a characteristic immune infiltrate in children with AHUO. COVID-19 testing should be considered in paediatric AHUO.

Adalimumab Biosimilars Demonstrate Long-Term Durability and Cost-Effectiveness in Paediatric Inflammatory Bowel Disease: A Real-World Two-Centre European Cohort Study

Purpose

Adalimumab biosimilars are increasingly used in paediatric Inflammatory Bowel Disease (PIBD), but data remain limited. This study assessed their durability, efficacy, safety and cost implications in PIBD.

Patients and Methods

Consecutive PIBD patients who started adalimumab biosimilars between October 2018 and December 2023 at two centres in Scotland and Italy, with at least 6 months follow-up, were included. Demographic, disease, treatment, and adverse event data were collected. Disease activity was assessed at baseline, 6, 12, 24, 36 months, and at last follow-up. Durability was evaluated using Kaplan-Meier analysis.

Results

In total 130 patients (81 males; median age 12.3 years) were included (115 Crohn's Disease, 7 Ulcerative Colitis, 8 IBD unclassified). The biosimilars were ABP 501 (85%), GP2017 (14%), SB5 (1%); 41 (32%) patients switched from originator. After a median follow-up of 26 months, 87/130 (67%) patients remained on biosimilars, while 43 discontinued at a median of 14 months. Durability probabilities were 93%, 86%, 75%, 62%, and 57% at 6, 12, 24, 36, and 54 months, respectively. Patients previously exposed to ADA originator had a lower risk of biosimilar failure (hazard ratio, adjusted for age at diagnosis: 0.51 [95% confidence interval: 0.26-0.99], p=0.047). Trough levels ≥11.6 μg/mL at 6 months were associated with greater durability (AUC=0.68, p=0.007). Adverse events occurred in 46/130 patients, mainly psoriasis and injection site reactions (13% each), with one lymphoma. Estimated cost savings were 5,030€ per patient/year.

Conclusion

This real-life study demonstrated high durability and remission rates for adalimumab biosimilars in PIBD, confirming their clinical, cost-effectiveness and safety profile in children.

Integrated multimodel analysis of intestinal inflammation exposes key molecular features of preclinical and clinical IBD

BACKGROUND

IBD is a chronic inflammatory condition driven by complex genetic and immune interactions, yet preclinical models often fail to fully recapitulate all aspects of the human disease. A systematic comparison of commonly used IBD models is essential to identify conserved molecular mechanisms and improve translational relevance.

OBJECTIVE

We performed a multimodel transcriptomic analysis of 13 widely used IBD mouse models to uncover coregulatory gene networks conserved between preclinical colitis/ileitis and human IBD and to define model-specific and conserved cellular, subcellular and molecular signatures.

DESIGN

We employed comparative transcriptomic analyses with curated and a priori statistical correlative methods between mouse models versus IBD patient datasets at both bulk and single-cell levels.

RESULTS

We identify IBD-related pathways, ontologies and cellular compositions that are translatable between mouse models and patient cohorts. We further describe a conserved core inflammatory signature of IBD-associated genes governing T-cell homing, innate immunity and epithelial barrier that translates into the new mouse gut Molecular Inflammation Score (mMIS). Moreover, specific mouse IBD models have distinct signatures for B-cell, T-cell and enteric neurons. We discover that transcriptomic relatedness of models is a function of the mode of induction, not the canonical immunotype (Th1/Th2/Th17). Moreover, the model compendium database is made available as a web explorer (http://trr241.hosting.rrze.uni-erlangen.de/SEPIA/).

CONCLUSION

This integrated multimodel approach provides a framework for systematically assessing the molecular landscape of intestinal inflammation. Our findings reveal conserved inflammatory circuits, refine model selection, offering a valuable resource for the IBD research community.

Deciphering distinct genetic risk factors for FTLD-TDP pathological subtypes via whole-genome sequencing

Frontotemporal lobar degeneration with neuronal inclusions of the TAR DNA-binding protein 43 (FTLD-TDP) is a fatal neurodegenerative disorder with only a limited number of risk loci identified. We report our comprehensive genome-wide association study as part of the International FTLD-TDP Whole-Genome Sequencing Consortium, including 985 patients and 3,153 controls compiled from 26 institutions/brain banks in North America, Europe and Australia, and meta-analysis with the Dementia-seq cohort. We confirm UNC13A as the strongest overall FTLD-TDP risk factor and identify TNIP1 as a novel FTLD-TDP risk factor. In subgroup analyzes, we further identify genome-wide significant loci specific to each of the three main FTLD-TDP pathological subtypes (A, B and C), as well as enrichment of risk loci in distinct tissues, brain regions, and neuronal subtypes, suggesting distinct disease aetiologies in each of the subtypes. Rare variant analysis confirmed TBK1 and identified C3AR1, SMG8, VIPR1, RBPJL, L3MBTL1 and ANO9, as novel subtype-specific FTLD-TDP risk genes, further highlighting the role of innate and adaptive immunity and notch signaling pathway in FTLD-TDP, with potential diagnostic and novel therapeutic implications.

Genome-wide association study reveals a novel tuberculosis susceptibility locus in multiple East Asian and European populations

Background

Tuberculosis (TB) continues to be a leading cause of morbidity and mortality worldwide. Past genome-wide association studies (GWAS) have explored TB susceptibility across various ethnic groups, yet a significant portion of TB heritability remains unexplained.

Methods

We conducted GWAS in the Singapore Chinese and Vietnamese, followed by a comprehensive meta-analysis incorporating 4 independent East Asian datasets, resulting in a total of 11,841 cases and 197,373 population controls.

Findings

We identified a novel susceptibility locus for pulmonary TB (PTB) at 22q12.2 in East Asians [rs6006426, OR (95%Cl) =1.097(1.066, 1.130), P meta =3.31×10 -10 ]. The association was further validated in Europeans [OR (95%Cl) =1.101(1.002, 1.211), P =0.046] and was strengthened in the combined meta-anlaysis including 12,736 PTB cases and 673,864 controls [OR (95%Cl) =1.098(1.068, 1.129), P meta =4.33×10 -11 ]. rs6006426 affected SF3A1 expression in various immune cells ( P from 0.003 to 6.17×10 -18 ) and OSM expression in monocytes post lipopolysaccharide stimulation ( P =5.57×10 -4 ). CRISPR-Cas9 edited zebrafish embryos with osm depletion resulted in decreased burden of Mycobacterium marinum ( M.marinum ) in infected embryos ( P =0.047).

Interpretation

Our findings offer novel insights into the genetic factors underlying TB and reveals new avenues for understanding its etiology.

The phenotypic and genetic association between endometriosis and immunological diseases

STUDY QUESTION

Is there an increased risk of immunological diseases among endometriosis patients, and does a shared genetic basis contribute to this risk?

SUMMARY ANSWER

Endometriosis patients show a significantly increased risk of autoimmune, autoinflammatory, and mixed-pattern diseases, including rheumatoid arthritis, multiple sclerosis, coeliac disease, osteoarthritis, and psoriasis, with genetic correlations between endometriosis and osteoarthritis, rheumatoid arthritis, and multiple sclerosis, and a potential causal link to rheumatoid arthritis.

WHAT IS KNOWN ALREADY

The epidemiological evidence for an increased risk of immunological diseases among women with endometriosis is limited in scope and has varied in robustness due to the opportunity for biases. The presence of a biological basis for increased comorbidity across immunological conditions has not been investigated. Here we investigate the phenotypic and genetic association between endometriosis and 31 immune conditions in the UK Biobank.

STUDY DESIGN, SIZE, DURATION

Phenotypic analyses between endometriosis and immune conditions (17 classical autoimmune, 10 autoinflammatory, and 4 mixed-pattern diseases) were conducted using two approaches (8223 endometriosis, 64 620 immunological disease cases): (i) retrospective cohort study design to incorporate temporality between diagnoses and (ii) cross-sectional analysis for simple association. Genome-wide association studies (GWAS) and meta-analyses for those immune conditions that showed phenotypic association with endometriosis (1493-77 052 cases) were conducted.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Comprehensive phenotypic association analyses were conducted in females in the UK Biobank. GWAS for immunological conditions were conducted in females-only and sex-combined study populations in UK Biobank and meta-analysed with existing largest available GWAS results. Genetic correlation and Mendelian randomization (MR) analyses were conducted to investigate potential causal relationships. Those immune conditions with significant genetic correlation with endometriosis were included in multi-trait analysis of GWAS to boost discovery of novel and shared genetic variants. These shared variants were functionally annotated to identify affected genes utilizing expression quantitative trait loci (eQTL) data from GTEx and eQTLGen databases. Biological pathway enrichment analysis was conducted to identify shared underlying biological pathways.

MAIN RESULTS AND THE ROLE OF CHANCE

In both retrospective cohort and cross-sectional analyses, endometriosis patients were at significantly increased (30-80%) risk of classical autoimmune (rheumatoid arthritis, multiple sclerosis, coeliac disease), autoinflammatory (osteoarthritis), and mixed-pattern (psoriasis) diseases. Osteoarthritis (genetic correlation (rg) = 0.28, P = 3.25 × 10-15), rheumatoid arthritis (rg = 0.27, P = 1.5 × 10-5) and multiple sclerosis (rg = 0.09, P = 4.00 × 10-3) were significantly genetically correlated with endometriosis. MR analysis suggested a causal association between endometriosis and rheumatoid arthritis (OR = 1.16, 95% CI = 1.02-1.33). eQTL analyses highlighted genes affected by shared risk variants, enriched for seven pathways across all four conditions, with three genetic loci shared between endometriosis and osteoarthritis (BMPR2/2q33.1, BSN/3p21.31, MLLT10/10p12.31) and one with rheumatoid arthritis (XKR6/8p23.1).

LIMITATIONS, REASONS FOR CAUTION

We conducted the first female-specific GWAS analyses for immune conditions. Given the novelty of these analyses, the sample sizes from which results were derived were limited compared to sex-combined GWAS meta-analyses, which limited the power to use female-specific summary statistics to uncover the shared genetic basis with endometriosis in follow-up analyses. Secondly, the 39 genome-wide significant endometriosis-associated variants used as instrumental variables in the MR analysis explained approximately 5% of disease variation, which may account for the nominal or non-significant MR results.

WIDER IMPLICATIONS OF THE FINDINGS

Endometriosis patients have a moderately increased risk for osteoarthritis, rheumatoid arthritis, and to a lesser extent, multiple sclerosis, due to underlying shared biological mechanisms. Clinical implications primarily involve the need for increased awareness and vigilance. The shared genetic basis opens up opportunities for developing new treatments or repurposing therapies across these conditions.

STUDY FUNDING/COMPETING INTEREST(S)

We thank all the UK Biobank and 23andMe participants. Part of this research was conducted using the UK Biobank Resource under Application Number 9637. N.R. was supported by a grant from the Wellbeing of Women UK (RG2031) and the EU Horizon 2020 funded project FEMaLe (101017562). A.P.M. was supported in part by Versus Arthritis (grant 21754). H.F. was supported by the National Natural Science Foundation of China (grant 32170663). N.R., S.A.M., and K.T.Z. were supported in part by a grant from CDMRP DoD PRMRP (W81XWH-20-PRMRP-IIRA). K.T.Z. and C.M.B. reported grants in 3 years prior, outside the submitted work, from Bayer AG, AbbVie Inc., Volition Rx, MDNA Life Sciences, PrecisionLife Ltd., and Roche Diagnostics Inc. S.A.M. reports grants in the 3 years prior, outside this submitted work, from AbbVie Inc. N.R. is a consultant for Endogene.bio, outside this submitted work. The other authors have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER

N/A.

Characterizing selection on complex traits through conditional frequency spectra

Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). The power to detect a trait-associated variant in GWAS is a function of its frequency and effect size - but for traits under selection, the effect size of a variant determines the strength of selection against it, constraining its frequency. Recognizing the biases inherent to GWAS ascertainment, we propose studying the joint distribution of allele frequencies across populations, conditional on the frequencies in the GWAS cohort. Before considering these conditional frequency spectra, we first characterized the impact of selection and non-equilibrium demography on allele frequency dynamics forwards and backwards in time. We then used these results to understand conditional frequency spectra under realistic human demography. Finally, we investigated empirical conditional frequency spectra for GWAS variants associated with 106 complex traits, finding compelling evidence for either stabilizing or purifying selection. Our results provide insights into polygenic score portability and other properties of variants ascertained with GWAS, highlighting the utility of conditional frequency spectra.

Disease-specific B cell clones are shared between patients with Crohn's disease

B cells have important functions in gut homeostasis, and dysregulated B cell populations are frequently observed in patients with inflammatory bowel diseases, including both ulcerative colitis (UC) and Crohn's disease (CD). How these B cell perturbations contribute to disease remains largely unknown. Here, we perform deep sequencing of the B cell receptor (BCR) repertoire in four cohorts of patients with CD, together with healthy controls and patients with UC. We identify BCR clones that are shared between patients with CD but not found in healthy individuals nor in patients with UC, indicating CD-associated B cell immune responses. Shared clones are present in the inflamed gut mucosa, draining intestinal lymph nodes and blood, suggesting the presence of common CD-associated antigens that drive B cell responses in CD patients.

Peptide-specific natural killer cell receptors

Class I and II human leukocyte antigens (HLA-I and HLA-II) present peptide antigens for immunosurveillance by T cells. HLA molecules also form ligands for a plethora of innate, germline-encoded receptors. Many of these receptors engage HLA molecules in a peptide sequence independent manner, with binding sites outside the peptide binding groove. However, some receptors, typically expressed on natural killer (NK) cells, engage the HLA presented peptide directly. Remarkably, some of these receptors display exquisite specificity for peptide sequences, with the capacity to detect sequences conserved in pathogens. Here, we review evidence for peptide-specific NK cell receptors (PSNKRs) and discuss their potential roles in immunity.

SURFBAT: a surrogate family based association test building on large imputation reference panels

Genotype-phenotype association tests are typically adjusted for population stratification using principal components that are estimated genome-wide. This lacks resolution when analyzing populations with fine structure and/or individuals with fine levels of admixture. This can affect power and precision, and is a particularly relevant consideration when control individuals are recruited using geographic selection criteria. Such is the case in France where we have recently created reference panels of individuals anchored to different geographic regions. To make correct comparisons against case groups, who would likely be gathered from large urban areas, new methods are needed. We present SURFBAT (a surrogate family based association test), which performs an approximation of the transmission-disequilibrium test. Our method hinges on the application of genotype imputation algorithms to match similar haplotypes between the case and control groups. This permits us to approximate local ancestry informed posterior probabilities of un-transmitted parental alleles of each case individual. This is achieved by assuming haplotypes from the imputation panel are well-matched for ancestry with the case individuals. When the first haplotype of an individual from the imputation panel matches that of a case individual, it is assumed that the second haplotype of the same reference individual can be used as a locally ancestry matched control haplotype and to approximately impute un-transmitted parental alleles. SURFBAT provides an association test that is inherently robust to fine-scale population stratification and opens up the possibility of efficiently using large imputation reference panels as control groups for association testing. In contrast to other methods for association testing that incorporate local-ancestry inference, SURFBAT does not require a set of ancestry groups to be defined, nor for local ancestry to be explicitly estimated. We demonstrate the interest of our tool on simulated datasets, as well as on a real-data example for a group of case individuals affected by Brugada syndrome.

1000-plex antibody array proteomic screen uncovers PGRPS, Haptoglobin, Serpin A4 and Fibrinogen as potential stool biomarkers of pediatric inflammatory bowel disease

Easy to obtain and in close proximity to the affected areas, fecal samples offer significant potential for the advancement of non-invasive diagnostic methods for inflammatory bowel disease (IBD). A cross-sectional antibody array-based proteomic screen of 1000 fecal protein biomarkers was conducted using stool from treatment naïve control, Crohn's disease (CD), and ulcerative colitis (UC) subjects (control = 24, CD = 39, UC = 10). 71 proteins were significantly elevated in IBD stool (p < 0.05; FC > 2), pointing to cytokine signaling, inflammatory response and extra-cellular matrix functional pathways. Several proteins outperformed fecal calprotectin in distinguishing IBD from control stool, including Haptoglobin, IL-1 R9, GDF-15, PGRPS, Serpin A4, INSRR, SSEA-1, Fibrinogen, IGFBP-1, and TGF-β RI/ALK-5. Upon ELISA validation, PGRPS (AUC = 0.96), Haptoglobin (AUC = 0.91), Serpin A4 (AUC = 0.73), emerged as the most discriminatory biomarkers. Taken together with previous cross-sectional and longitudinal studies, the present findings authenticate stool PGRPS, Haptoglobin, Serpin A4 and fibrinogen as potential stool biomarkers of UC and CD, worthy of further prospective studies to identify more reliable and accurate non-invasive biomarkers for IBD.

Safety and Diagnostic Utility of Brain Biopsy and Metagenomics in Decision-Making for Patients with Inborn Errors of Immunity (IEI) and Unexplained Neurological Manifestations

Unexplained neurological symptoms can pose a diagnostic challenge in patients with inborn errors of immunity (IEI) where the aetiology can be varied, and diverse pathologies may require contrasting treatments. Brain biopsy, the process of sampling brain tissue directly, has historically provided histological and microbiological information and can now be exploited for deep metagenomic next generation analysis (mNGS). We conducted a retrospective analysis of clinical and diagnostic data on paediatric patients with IEI who had a brain biopsy between 2010 and 2022 at a UK tertiary centre where 14 patients fulfilled our search criteria. We report on clinical characteristics, adverse events and the additional impact of mNGS of brain biopsies, where these were conducted. We found that brain biopsy enabled diagnostics with manageable complications in most cases, either by tissue or metagenomics analysis (n = 11/14, 79%). We found that mNGS analysis improved the diagnostic yield of brain biopsy in 29% of IEI cases (n = 4/14). Brain biopsy enabled a change in management in 71% of cases (n = 10/14). This series provides compelling evidence for the safe and purposeful use of brain biopsy in children with IEI.

Ferroptosis in immune chaos: Unraveling its impact on disease and therapeutic potential

Since its introduction in 2012, ferroptosis has garnered significant attention from researchers over the past decade. Unlike autophagy and apoptosis, ferroptosis is an atypical iron-dependent programmed cell death that falls under necrosis. It is regulated by various cellular metabolic and signaling processes, which encompass amino acid, lipid, iron, and mitochondrial metabolism. The initiation of ferroptosis occurs through iron-dependent phospholipid peroxidation. Notably, ferroptosis exhibits a dual effect and is associated with various diseases. A significant challenge lies in managing autoimmune disorders with unknown origins that stem from the reactivation of the immune system. Two contributing factors to autoimmunity are the aberrant stimulation of cell death and the inadequate clearance of dead cells, which can expose or release intracellular components that activate the immune response. Ferroptosis is distinct from other forms of cell death, such as apoptosis, necroptosis, autophagy, and pyroptosis, due to its unique morphological, biochemical, and genetic characteristics and specific relationship with cellular iron levels. Recent studies indicate that immune cells can both induce and undergo ferroptosis. To better understand how ferroptosis influences immune responses and its imbalance in disease, a molecular understanding of the relationship between ferroptosis and immunity is essential. Consequently, further research is needed to develop immunotherapeutics that target ferroptosis. This review primarily focuses on the role of ferroptosis in immune-related disorders.

Structural Variations in Ulcerative Colitis-associated Escherichia coli Reduce Fructose Utilization and Aggravate Inflammation Under High-Fructose Diet

BACKGROUND AND AIMS

Structural variations (SVs) have significant effects on microbial phenotypes. The underlying mechanism of functional changes caused by gut microbial SVs in the development of ulcerative colitis (UC) need further investigation.

METHODS

We performed long-read (Oxford Nanopore Technology-based) and short-read (Illumina-based) metagenomic sequencing on stool samples from 93 patients with UC and 100 healthy controls (HCs) and analyzed microbial SVs. A total of 648 Escherichia coli strains from fecal samples of patients with UC (UC-strains) and HCs (HC-strains) were isolated. SV-associated scrK gene deletion was verified via whole-genome sequencing or targeted polymerase chain reaction. Then, representative UC-strains, HC-strains, and scrK-knockout E coli were used for the in vitro and in vivo experiments to investigate the effects of specific SVs in E coli on fructose utilization ability and colitis.

RESULTS

E coli in UC with the highest fold change had SV-affected functional differences on fructose metabolism to that of HCs. The fructose utilization gene deletion was common in UC-strains, ostensibly reducing fructose utilization in vitro and leading to fructose-dependent aggravation of colitis in murine models. UC-strains and HC-strains induced comparable colitis under low fructose. However, high fructose exacerbated colitis severity exclusively in UC-strain-colonized mice, with elevated intestinal fructose residues, significant microbiome/metabolome changes, increased inflammation, and gut barrier disruption. These changes were mechanistically dependent on the deletion of the fructose utilization gene scrK.

CONCLUSIONS

SV-caused difference in fructose utilization and proinflammatory properties in E coli from patients with UC influence the development of UC, emphasizing the importance of fine-scale metagenomic studies in disease.

The Role of ETS2 in Macrophage Inflammation

Autoimmune and inflammatory diseases are rising globally yet widely effective therapies remain elusive. Most treatments have limited efficacy, significant potential side effects, or eventually lose response, underscoring the urgent need for new therapeutic approaches. We recently discovered that ETS2, a transcription factor, functions as a master regulator of macrophage-driven inflammation-and is causally linked to the pathogenesis of multiple inflammatory diseases via human genetics. The pleotropic inflammatory effects of ETS2 included upregulation of many cytokines that are individually targeted by current disease therapies, including TNFα, IL-23, IL1β, and TNF-like ligand 1A signaling. With the move toward combination treatment-to maximize efficacy-targeting ETS2 presents a unique opportunity to potentially induce a broad therapeutic effect. However, there will be multiple challenges to overcome since direct ETS2 inhibition is unlikely to be feasible. Here, we discuss these challenges and other unanswered questions about the central role that ETS2 plays in macrophage inflammation.

Unveiling the influence of lipidomes on inflammatory bowel disease: a bidirectional mendelian randomization study

BACKGROUND

Plasma lipid homeostasis is pivotal in maintaining intestinal health. Inflammatory bowel disease (IBD), encompassing ulcerative colitis (UC) and Crohn's disease (CD) as distinct subtypes, manifests unique metabolic signatures. However, the specific roles of lipids in the pathogenesis and therapeutic targeting of IBD remain inadequately explored. This study aims to delineate the genetic influences of plasma lipids on IBD risk.

METHODS

We obtained genome-wide association study (GWAS) summary statistics of lipidomes and IBD (including UC and CD) from published studies to perform two-sample Mendelian randomization (MR) analyses. Outliers were removed using radial MR, followed by the application of the inverse-variance weighted (IVW) method to assess causal relationships. Sensitivity analyses were also conducted to validate the robustness of the primary results of the MR analyses. Additionally, reverse MR analyses were performed to evaluate the potential for reverse causality.

RESULTS

The MR analysis identified fourteen lipid species significantly associated with IBD, four with UC, and ten with CD. Phosphatidylcholine (PC; P < 0 .05) and lysophosphatidylcholine (OR = 0.83, P < 0.001) were instrumental in UC, while in CD, alongside these, cholesterol ester (OR = 0.86, P < 0.001), diacylglycerol (OR = 1.21, P = 0.004), and lysophosphatidylethanolamine (OR = 1.30, P < 0.001) also demonstrated causal links. Reverse MR analysis revealed no significant associations between IBDs and 179 lipid species.

CONCLUSION

This bidirectional MR study has uncovered genetic evidence of a causal relationship between lipidome and IBD, identifying potential therapeutic targets for IBD treatment. The findings suggest that elevated partial phosphatidylcholine, lysophosphatidylcholine, and cholesterol ester levels could reduce the risk of IBD, indicating a potential protective role for these lipid molecules. This study also underscores the critical role of lipidome variability in advancing our understanding of IBD's pathogenic processes and in developing targeted therapies.

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.