Biology subjects

Higgins, P.

Publications and source records attributed to Higgins, P..

4 recordsLinked to original sources

bioRxiv2025

Miniature bioreactor arrays for modeling functional and structural dysbiosis in inflammatory bowel disease

Alterations in the gut microbiota, known as gut dysbiosis, are associated with inflammatory bowel disease (IBD). There is a need for model systems that can recapitulate the IBD gut microbiome to better understand the mechanistic impact of differences in microbiota composition and its functional consequences in a controlled laboratory setting. To this end, we introduced fecal samples from patients with Crohns disease (CD) and ulcerative colitis (UC), as well as from healthy control subjects, to miniature bioreactor arrays (MBRAs) and analyzed the microbial communities over time. We then performed two functional assessments. First, we evaluated the colitogenic potential of the CD microbiotas in genetically susceptible germ-free IL-10-deficient mice and found that colitogenic capacity was preserved in a bioreactor-cultivated CD microbiota. Second, we tested impaired colonization resistance against Clostridioides difficile in UC microbiotas using the MBRA system and found that UC microbiotas were innately susceptible to C. difficile colonization while healthy microbiotas were resistant, consistent with what is seen clinically. Overall, our results demonstrate that IBD microbiotas perform comparably to healthy donor microbiotas in the MBRA system, successfully recapitulating microbial structure while preserving IBD-specific functional characteristics. These findings establish a foundation for further mechanistic research into the IBD microbiota using MBRAs.

microbiology↗

bioRxiv2025

Immune phenotype-guided identification of disease-associated pathobionts in Crohn's disease

Aberrant immune activation within the gut mucosa and gut dysbiosis have been implicated in the pathogenesis of Crohns disease (CD). However, the specific immune responses triggered by dysbiotic microbiota, as well as the bacteria responsible for this activation, remain incompletely understood. Here, using the human microbiota-associated (HMA) mouse system, we demonstrated that colonization with dysbiotic gut microbiota from CD patients specifically induces the accumulation of mononuclear phagocytes, which may drive an interleukin-1 (IL-1)-driven inflammatory signature. Moreover, we identified pathobiont strains with a potent IL-1{beta}-inducing capacity, termed IL-1{beta}-inducing pathobionts (IBIP). Isolated IBIP strains exhibit genetic and functional similarities to adherent-invasive Escherichia coli but harbor unique virulence-associated genes. Colonization with the IBIP E. coli strain exacerbated experimental colitis in an IL-1 signal-dependent manner. Notably, the colonization of IBIP E. coli can be detected by measuring the levels of specific immunoglobulin A (IgA) in their stool samples. Moreover, the level of IBIP-reactive IgA in stool may serve as a predictive biomarker for treatment response to anti-TNF therapies in treatment-naive pediatric CD patients. Altogether, IBIP colonization could help identify CD patients with inflammatory dysbiosis who are likely to be refractory to anti-TNF therapies.

immunology↗

bioRxiv2025

A gut-selective Axl Inhibitor Attenuates Intestinal Fibrosis in myofibroblast cell models and the Mouse S. Typhimurium Model in vivo

BackgroundIntestinal fibrosis leads to intestinal failure in Crohns disease (CD), but we have no effective antifibrotic medical therapies. Axl inhibitors have been studied in the treatment of fibrosis in liver and lung, but not in intestine. The objective of this study was to test whether CCG264341, a novel gut selective Axl inhibitor, can treat intestinal fibrosis in both in vitro and in vivo IBD fibrosis models. MethodsCCD-18Co human intestinal myofibroblasts were co-treated with 100 ng/mL Fas ligand (FASL) and a dose range of CCG264341 for 5 hours, or treated with TGF{beta} for 48 hours, followed by protein isolation and western blot analysis. Tissue PK experiments in mice were performed to select the CCG264341 dose for the in vivo model. For the in vivo model, intestinal fibrosis was induced in CBA/J mice by S. typhimurium infection, Mice were treated with CCG264341 daily during days 4-21 after S. typhimurium infection, followed by sac on day 22. Cecum and proximal colon (affected tissue) was analyzed by gross pathology, histological fibrosis scoring, qRT-PCR, western blot, and immunofluorescence staining. ResultsCCG264341 at doses of 0.1/0.3/1.0 {micro}M sensitizes CCD-18Co myofibroblasts to FasL-mediated apoptosis over FasL alone, and this effect was dose dependent, per cleaved Parp protein quantitation. With TGF{beta} treatment, Axl protein expression was increased, along with Col1a1, MYLK, SMA and FN1 protein upregulation. CCG264341 could reduce AXL protein and downstream signal p-Akt expression with dose dependence, along with reduced Col1a1, MYLK, SMA and FN1 protein expression after treatment with CCG264341 treatment. The highest CCG264341 concentrations were detected in the terminal ileum after 5 hours oral feeding in PK experiments, and much lower compound concentrations could still be detected in other organs. A dose of 25mg/kg daily was selected for the mouse intestinal fibrosis treatment model. In the murine S. typhimurium model, AXL protein and downstream signals p-Akt, p-Erk and P-Stat3 expression were all increased in colon and cecum, with the expression of the fibrosis related proteins upregulated. CCG264341 treatment significantly inhibited AXL expression, with downstream signals and fibrosis related protein downregulation. By blinded histopathology with H&E and trichrome staining, as well as immunofluorescence for fibrosis related proteins, colon fibrosis scores significantly decreased. ConclusionsCCG264341is a partially gut selective Axl inhibitor. This compound could play a therapeutic role in IBD fibrosis models. Further work to improve gut selectivity and anti-fibrotic efficacy are needed, but this is a promising pathway for future therapeutic intervention in Crohns disease.

immunology↗

bioRxiv2024

Genome Analyses of A Worldwide Multisource Collection of Klebsiella variicola Reveal Adaptation Relevant for Human Infection

AO_SCPLOWBSTRACTC_SCPLOWKlebsiella variicola (K.var), part of the Klebsiella pneumoniae (K.pne) species complex, is an emerging human pathogen originally associated with plants. Phylogenomic analyses of a global dataset of isolates categorised as human, animal, plant, or environmental strains suggest that K.var are broadly disseminated regardless of hosts or habitats and exhibit genomic variability that is relevant for occupying and transmitting within and across multiple sources. Ancestral state analyses confirm that K.var are originally derived from non-human sources. Genome-wide association analyses of human versus non-human isolates of K.var indicate isolates from human origins are linked to the loss of cold-shock response genes such as lpxP and cspB. Importantly, human K.var isolates also showed enriched antimicrobial resistance gene content and diversity acquired through mobile genetic elements, horizontal gene transfer and mutations within the chromosomal loci which underscore the impact of antimicrobial exposure and proximity to antibiotic resistant K.pne in nosocomial environments. Capsular profiles of K.var suggest high levels of variability in gene composition and indicate that gene functionality for wcaJ in capsule formation differs between K.var and K.pne. Although capsular specialisation was not observed in a host/habitat or lineage-dependent manner, human isolates harbour, on average, a higher siderophore gene content in addition to mrkD mutations which impact on fimbriae and biofilm formation. There is limited evidence of any specific K.var lineages exhibiting convergence of both virulence and antimicrobial resistance genotypes which suggest that these attributes are evolving independently in clinical strains. Our work highlights that gene attrition and acquisition provide a basis for adaptation of K.var as human pathogens. The broad distribution and evolution of K.var highlight the need for improved diagnostic precision and surveillance under a One Health framework.

microbiology↗