Biology subjects

Begun, J.

Publications and source records attributed to Begun, J..

11 recordsLinked to original sources

bioRxiv2026

The microbiome determines the phenotype in CTLA-4 insufficient mice and men

CTLA-4 (haplo)insufficiency displays incomplete penetrance and phenotypic heterogeneity, indicating the involvement of additional disease modifiers beyond the genetic defect. Microbiome analyses reveal a positive association between disease severity and intestinal dysbiosis, highlighting the microbiome as a critical contributor. To investigate this relationship mechanistically, we generated Ctla4/- wildlings harboring a natural microbiota. Unlike specific pathogen free (SPF) counterparts, which remain healthy, Ctla4/- wildlings spontaneously develop disease phenotypes resembling human CTLA-4 haploinsufficiency. Disease onset is followed by reduced microbial diversity and expansion of pathobionts. Integrative immunophenotyping shows that the natural microbiota synergizes with Ctla4 haploinsufficiency to reshape innate and adaptive immune compartments, generating a sustained pro-inflammatory milieu and reduced CTLA-4 expression in the cecum. Furthermore, microbiota-derived metabolites promote inflammatory cytokine production in both murine and human primary T cells via NF-{kappa}B activation. Collectively, Ctla4/- wildlings constitute an effective model for dissecting microbiome-immune crosstalk in CTLA-4 (haplo)insufficiency and for exploring therapeutic strategies.

immunology↗

bioRxiv2026

Microbial Immunomodulatory Function is Altered in Inflammatory Bowel Disease Independent of Microbial Composition

Inflammatory bowel diseases (IBD) are chronic and relapsing immune-mediated conditions in which the NF-{kappa}B and STAT3 signalling pathways play central roles in pathogenesis. While gut microbiome dysbiosis is well described in IBD, its functional consequences, particularly microbial immunomodulatory function (MIF) remain poorly defined. Here, we integrated functional assays with metagenomic profiling to characterise microbiome-driven immune modulation in IBD. Faecal water from non-IBD controls and IBD patients was assessed using NF-{kappa}B and STAT3 reporter systems, alongside high-throughput screening of 2,820 bacterial isolates (94 per subject). Despite minimal differences in overall microbial composition, faecal water from patients with ulcerative colitis (UC) and Crohns disease (CD) significantly increased NF-{kappa}B activity under both basal and TNF-stimulated conditions. Non-IBD controls harboured a higher proportion of suppressive bacterial isolates (21.52%) compared to UC (5.64%) and CD (2.45%), whereas activating isolates were enriched in IBD (UC: 34.47%; CD: 39.36% vs. non-IBD: 5.35%). Similar trends were observed for IL-23-mediated STAT3 activation. Integration of metagenomic and pathway-level analyses identified 24 KEGG pathways associated with inflammatory signalling and faecal lipocalin-2, as well as amino acid, carbohydrate, lipid, cofactor, and nucleotide metabolism. These findings demonstrate that the IBD microbiome is functionally reprogrammed toward pro-inflammatory activity, independent of compositional changes. Defining patient-specific MIF profiles may provide a framework for precision microbiome-based therapeutic strategies in IBD.

microbiology↗

bioRxiv2026

Bioactive produced by Enterococcus Faecalis targets IL-23 signalling and protects against colitis and joint disease

The IL-23/Th17 axis is a central driver of intestinal and spondyloarthritic inflammation, yet upstream regulatory mechanisms linking microbial signals to IL-23 production remain incompletely defined. NF-{kappa}B signalling, particularly via the c-Rel subunit, is a critical transcriptional regulator of IL23A (p19), positioning c-Rel as a nodal checkpoint in mucosal inflammation. Here, we demonstrate that cell-free supernatant derived from Enterococcus faecalis AHG0090 (AHG0090-CS) suppresses c-Rel-dependent IL-23 signalling and attenuates inflammatory pathology across murine models of gut and joint disease. In the ZAP-70 mutant SKG model of spondyloarthritis and ileitis, AHG0090-CS significantly reduced weight loss, joint scores, and histological gut inflammation following curdlan challenge. In the Winnie model of spontaneous colitis, treatment similarly diminished inflammatory cytokine production. Mechanistically, AHG0090-CS reduced IL-23p19 mRNA and protein expression in intestinal tissue and lamina propria myeloid cells, accompanied by decreased nuclear c-Rel intensity. Suppression extended to downstream IL-23-associated cytokines including IL-17A, GM- CSF, MCP-1 and IL-6. In human peripheral blood mononuclear cells and macrophages, AHG0090-CS attenuated LPS-induced IL-23 and pro-inflammatory cytokine production, supporting translational relevance. Collectively, these findings identify microbial modulation of c-Rel-dependent IL-23 signalling as a tractable mechanism to restrain gut-joint inflammation and highlight targeting upstream NF-{kappa}B pathways as a therapeutic strategy in IL-23-driven immune-mediated disease.

microbiology↗

bioRxiv2026

Endotoxemia and TLR4 via tissue resident macrophages triggers anemia in mouse model of colitis

Anemia is one of the most debilitating and frequent complication of inflammatory bowel diseases (IBD) and is often treated with iron supplementation, which has limited efficacy and causes additional co-morbidities. Damaged intestinal barrier function is a hallmark of IBD and causes the translocation of endotoxins from gut bacteria into the bloodstream. A previous study in mice reported that endotoxins suppress erythropoiesis by reprogramming erythroblastic island macrophages (EBI M{varphi}). Here, we show that IBD patients and mice with acute colitis developed endotoxemia associated with anemia. Endotoxemia in IBD patients was negatively correlated with blood erythrocyte counts. In line with this, mice with acute colitis caused by drinking water containing dextrin sodium sulphate (DSS) had endotoxemia together with anemia characterized by reduced red blood cell counts, hemoglobin content and hematocrit, and reduced medullary erythropoiesis which was in part compensated by increased extramedullary erythropoiesis. As the endotoxin receptor TLR4 is expressed by CD169+ gut-resident macrophages as well as erythroid island macrophages in the bone marrow, we tested the hypothesis that TLR4 expressed by these CD169+ macrophages mediate both inflammatory colitis and anemia. Indeed, mice with a conditional deletion of the Tlr4 gene specifically in CD169+ tissue-resident macrophages were protected from DSS-induced anemia, inflammation and colitis. In addition, treatment with the TLR4 inhibitor C34 abated inflammation and anemia in DSS mice. These results suggest that endotoxins leaking from the inflamed gut may play a crucial role in IBD and associated anemia via CD169+ tissue-resident macrophages and that drugs targeting TLR4 may protect against IBD-associated anemia.

immunology↗

bioRxiv2024

A rational approach for the targeted discovery and characterisation of microbiome-derived therapeutics

The human gut microbiome is intrinsically involved in health and disease, representing a wealth of untapped therapeutic potential. Here, we demonstrate the utility and potential of a metagenome guided, large cohort-based approach for the rational selection of live biotherapeutics from the human gut. We applied this approach to Inflammatory Bowel Disease (IBD), identifying several lead candidates that were significantly depleted in individuals with IBD compared to healthy controls. Their therapeutic potential was assessed in preclinical models of IBD where they improved markers of disease pathology by reducing inflammation and promoting mucosal healing and wound repair. All leads had excellent safety profiles in silico and in vitro, and several additionally presented favourable manufacturing properties, supporting their progression into clinical trials. We believe that this rational approach will be generalisable to any disease state with underlying microbiome aetiology and will expedite the development of novel microbiome-derived therapeutics to improve human health.

microbiology↗

bioRxiv2024

A truncation mutant of adenomatous polyposis coli (APC) impairs apical cell extrusion through elevated epithelial tissue tension

Tissue tension encompasses the mechanical forces exerted on solid tissues within animal bodies, originating from various sources such as cellular contractility, interactions with neighbouring cells and the extracellular matrix. Emerging evidence indicates that an imbalance in tissue tension can influence structural organisation, homeostasis and potentially contribute to disease. For instance, heightened tissue tension can impede apical cell extrusion, leading to the retention of apoptotic or transformed cells. In this study, we investigate the potential role of adenomatous polyposis coli (APC) in modulating tissue tension. Our findings reveal that expression of an APC truncation mutant elevates epithelial tension via the RhoA/ROCK pathway. This elevation induces morphological alterations and hampers apoptotic cell extrusion in cultured epithelial cells and organoids, both of which could be mitigated by pharmacologically restoring the tissue tension. This raises the possibility that APC mutations may exert pathogenetic effects by altering tissue mechanics.

cell biology↗

bioRxiv2023

Pre-existing tissue mechanical hypertension at adherens junctions disrupts apoptotic extrusion in epithelia

Apical extrusion is a tissue-intrinsic process that allows epithelia to eliminate unfit or surplus cells. This is exemplified by the early extrusion of apoptotic cells, which is critical to maintain the epithelial barrier and prevent inflammation. Apoptotic extrusion is an active mechanical process, which involves mechanotransduction between apoptotic cells and their neighbours, as well as local changes in tissue mechanics. Here we report that the pre-existing mechanical tension at adherens junctions conditions the efficacy of apoptotic extrusion. Specifically, increasing baseline mechanical tension by overexpression of a phosphomimetic Myosin II regulatory light chain (MRLC) compromises apoptotic extrusion. This occurs when tension is increased in either the apoptotic cell or its surrounding epithelium. Further, we find that the pro-inflammatory cytokine, TNF, stimulates Myosin II and increases baseline AJ tension to disrupt apical extrusion, causing apoptotic cells to be retained in monolayers. Importantly, reversal of mechanical tension with an inhibitory MRLC mutant or tropomyosin inhibitors is sufficient to restore apoptotic extrusion in TNF-treated monolayers. Together, these findings demonstrate that baseline levels of tissue tension are important determinants of apoptotic extrusion, which can potentially be co-opted by pathogenetic factors to disrupt the homeostatic response of epithelia to apoptosis.

cell biology↗

bioRxiv2021

An extremes of phenotype approach confirms significant genetic heterogeneity in patients with ulcerative colitis.

Ulcerative colitis (UC) is a major form of inflammatory bowel disease with increasing global incidence. There is significant phenotypic heterogeneity defined by a range of clinical variables including age of onset and disease extent. Clinical outcomes range from long-term remission on minimal therapy to surgical resection. Close to 70% of UC risk can be attributed to genetics and understanding the genetic mechanisms contributing to this risk and disease heterogeneity is vital for understanding disease pathogenesis and improving patient outcomes through targeted screening and therapies. This study aims to characterise the genetic heterogeneity of UC by identifying genomic risk variants specific to mild and/or severe forms of UC, exploring variations in the effect size of known risk variants and assessing the clinical value of a genetic risk score (GRS). We conducted genome-wide association (GWA) analyses in 287 patients with mild UC, 311 patients with severe UC and 583 age- and gender-matched controls. Odds ratios (OR) for mild vs control, severe vs control and combined mild and severe UC vs control were calculated. Using the combined UC data, two independent loci in the HLA region reached genome-wide significance. An additional genome-wide significant signal on chromosome 1 was identified in severe cases only. OR for known risk loci varied between mild and severe patients and were similar to previously published results. Effect estimates from the most recent UC GWA meta-analysis were used to calculate a GRS for each individual. A higher mean GRS was observed in both mild and severe UC cases compared to controls however, there was no difference between the mean GRS for mild and severe UC. Heterogeneity in effect sizes of UC associated variants between mild and severe disease burden suggests the presence of genetically distinct signatures. While large consortium data are needed to identify genome-wide significant variants, additional risk loci may be identified by targeted recruitment of individuals with a history of severe disease. Author SummaryUlcerative colitis (UC) is a chronic and often debilitating form of inflammatory bowel disease affecting approximately 0.3% of the population in industrialized economies. The disease displays significant clinical heterogeneity including age at presentation, disease severity, and the propensity to develop disease-related complications. Several previous studies have demonstrated the heritability of UC, identifying over 30 loci specific to the disease. The majority of these loci have small to modest effect sizes other than those within the Human Leucocyte Antigen (HLA) region on chromosome 6. Using stringent clinical criteria for defining mild and severe forms of UC in an extremes of phenotype approach, we undertook a genome wide association study in a dataset of 1222 participants to investigate genetic heterogeneity in this disease. We demonstrated substantial differences in genetic associations in severe UC as compared to mild UC. While over 2,000 SNPs achieved genome-wide significance in the severe UC analysis, none reached significance for mild UC. These results were reflected in significant differences in odds ratios. We identified Complement Factor B (CFB) as a potential susceptibility gene for severe UC in the Caucasian population with additional tissue gene expression demonstrating a positive correlation with disease severity.

genetics↗

bioRxiv2021

Expression of CD49f defines subsets of human regulatory T cells with divergent transcriptional landscape and function that correlate with ulcerative colitis disease activity

ObjectiveAdoptive regulatory T cell (Treg) therapy is being trialled for treatment of different autoimmune disorders, including inflammatory bowel diseases (IBD). In-depth understanding of the biological variability of Treg in the human blood may be required to improve IBD immune monitoring and treatment strategies. MethodsThrough a combination of quantitative proteomic, multiparametric flow cytometry, RNA-sequencing data analysis and functional assays on Treg enriched from the blood of ulcerative colitis (UC) patients and healthy controls, we investigated the association between CD49f expression, Treg phenotype and function, and UC disease activity. ResultsHigh-dimensional analysis and filtering defined two distinct subsets of human Treg based on the presence or absence of CD49f with divergent transcriptional landscape and functional activities. CD49f negative Treg are enriched for functional Treg markers and present significantly increased suppressive capacity. In contrast, CD49f high Treg display a pro-inflammatory Th17-like phenotype and accumulate in the blood of UC patients. Dysregulation on CD49f Treg subsets in UC patients correlate with disease activity. ConclusionOverall our findings uncover the importance of CD49f expression on Treg in physiological immunity and in pathological autoimmunity.

immunology↗

bioRxiv2019

Secreted microbial metabolites modulate gut immunity and inflammatory tone

Evidence is emerging that microbiome-immune system crosstalk regulates the tenor of host intestinal immunity and predisposition to inflammatory bowel disease (IBD). We identified five NF-{kappa}B suppressive strains affiliated with Clostridium clusters IV, XIVa and XV that independently suppressed secretion of the chemokine IL-8 by peripheral blood mononuclear cells and gut epithelial organoids from healthy human subjects, as well as patients with the predominant IBD subtypes, Crohns disease and ulcerative colitis. The NF-{kappa}B suppressive Clostridium bolteae AHG0001, but not C. bolteae BAA-613, suppressed cytokine-driven inflammatory responses and endoplasmic reticulum stress in gut epithelial organoids derived from Winnie mice that develop spontaneous colitis. This predicted in vivo responses thereby validating a precision medicine approach to treat Winnie colitis and suggesting the microbiome may function as an extrinsic regulator of host immunity. Finally, we identified a novel molecule associated with NF-{kappa}B suppression indicating gut bacteria could be harnessed to develop new therapeutics.

microbiology↗

bioRxiv2018

Enterococcus faecalis AHG0090 is a genetically tractable bacterium and produces a secreted peptidic bioactive that suppresses NF-kB activation in human gut epithelial cells

Enterococcus faecalis is an early coloniser of the human infant gut and contributes to the development of intestinal immunity. To better understand the functional capacity of E. faecalis we constructed a broad host range RP4 mobilisable vector, pEHR513112, that confers chloramphenicol resistance and used a metaparental mating approach to isolate E. faecalis AHG0090 from a faecal sample collected from a healthy human infant. We demonstrated that E. faecalis AHG0090 is genetically tractable and could be manipulated using traditional molecular microbiology approaches. E. faecalis AHG0090 was comparable to the gold-standard anti-inflammatory bacterium Faecalibacterium prausnitzii A2-165 in its ability to suppress cytokine mediated NF-[Kcy]B activation in human gut derived LS174T goblet cell-like and Caco-2 enterocyte-like cell lines. E. faecalis AHG0090 and F. prausnitzii A2-165 produced secreted low molecular weight NF-[Kcy]B suppressive peptidic bioactives. Both bioactives were sensitive to heat and proteinase K treatments although the E. faecalis AHG0090 bioactive was more resilient to both forms of treatment. As expected, E. faecalis AHG0090 suppressed IL-1{beta} induced NF-[Kcy]B-p65 subunit nuclear translocation and expression of the NF-[Kcy]B regulated genes IL-6, IL-8 and CXCL-10. Finally, we determined that E. faecalis AHG0090 is distantly related to other commensal strains and likely encodes niche factors that support effective colonisation of the infant gut.

microbiology↗