Biology subjects

Cham, C.

Publications and source records attributed to Cham, C..

7 recordsLinked to original sources

bioRxiv2025

Epithelia mediate inflammation with myeloid cells in Crohn's disease patients under treatment

Many Crohn's disease patients fail to respond to biologic therapies targeting canonical immune pathways, and the mechanisms underlying treatment non-response remain poorly understood. Integrating single-cell and spatial transcriptomics, we generated a comprehensive mucosal atlas of 380,000 cells spanning the terminal ileum and ascending colon of healthy donors and Crohn's disease patients receiving biologics. We revealed site-specific programs centered on TNF-expressing macrophages embedded within epithelial-stromal networks: follicle-associated enterocytes dictated immune activation in the ileum, while FAP-expressing stromal cells served this role in the colon. Co-expression network analysis further identified lineage-specific programs associating non-response, including a novel epithelial marker BPIFB1 independent of known genetic risk loci. Co-expression marker Z-scores significantly differed between responders and non-responders in published datasets. Together, these findings define a non-responder-specific epithelial-stromal-immune ecosystem that sustains chronic inflammation, providing a framework for stratifying treatment resistance and informing therapeutic strategies in Crohn's disease and other barrier organ disorders.

immunology↗

bioRxiv2024

Diet outperforms microbial transplant to drive microbiome recovery post-antibiotics

High-fat, low-fiber Western-style diets (WD) induce microbiome dysbiosis characterized by reduced taxonomic diversity and metabolic breadth1,2, which in turn increases risk for a wide array of metabolic3-5, immune6 and systemic pathologies. Recent work has established that WD can impair microbiome resilience to acute perturbations like antibiotic treatment7,8, although we know little about the mechanism of impairment and the specific host consequences of prolonged post-antibiotic dysbiosis. Here, we characterize the trajectory by which the gut microbiome recovers its taxonomic and functional profile after antibiotic treatment in mice on regular chow (RC) and WD, and find that only mice on RC undergo a rapid successional process of recovery. Metabolic modeling indicates that RC diet promotes the development of syntrophic cross- feeding interactions, while on WD, a dominant taxon monopolizes readily available resources without releasing syntrophic byproducts. Intervention experiments reveal that an appropriate dietary resource environment is both necessary and sufficient for rapid and robust microbiome recovery, whereas microbial transplant is neither. Furthermore, prolonged post-antibiotic dysbiosis in mice on WD renders them susceptible to infection by the intestinal pathogen Salmonella enterica serovar Typhimurium. Our data challenge widespread enthusiasm for fecal microbiota transplant (FMT) as a strategy to address dysbiosis and demonstrate that specific dietary interventions are, at minimum, an essential prerequisite for effective FMT, and may afford a safer, more natural, and less invasive alternative to FMT.

microbiology↗

bioRxiv2023

HMGB1 acts as an agent of host defense at the gut mucosal barrier

Mucosal barriers provide the first line of defense between internal body surfaces and microbial threats from the outside world.1 In the colon, the barrier consists of two layers of mucus and a single layer of tightly interconnected epithelial cells supported by connective tissue and immune cells.2 Microbes colonize the loose, outer layer of colonic mucus, but are essentially excluded from the tight, epithelial-associated layer by host defenses.3 The amount and composition of the mucus is calibrated based on microbial signals and loss of even a single component of this mixture can destabilize microbial biogeography and increase the risk of disease.4-7 However, the specific components of mucus, their molecular microbial targets, and how they work to contain the gut microbiota are still largely unknown. Here we show that high mobility group box 1 (HMGB1), the prototypical damage-associated molecular pattern molecule (DAMP), acts as an agent of host mucosal defense in the colon. HMGB1 in colonic mucus targets an evolutionarily conserved amino acid sequence found in bacterial adhesins, including the well-characterized Enterobacteriaceae adhesin FimH. HMGB1 aggregates bacteria and blocks adhesin-carbohydrate interactions, inhibiting invasion through colonic mucus and adhesion to host cells. Exposure to HMGB1 also suppresses bacterial expression of FimH. In ulcerative colitis, HMGB1 mucosal defense is compromised, leading to tissue-adherent bacteria expressing FimH. Our results demonstrate a new, physiologic role for extracellular HMGB1 that refines its functions as a DAMP to include direct, virulence limiting effects on bacteria. The amino acid sequence targeted by HMGB1 appears to be broadly utilized by bacterial adhesins, critical for virulence, and differentially expressed by bacteria in commensal versus pathogenic states. These characteristics suggest that this amino acid sequence is a novel microbial virulence determinant and could be used to develop new approaches to diagnosis and treatment of bacterial disease that precisely identify and target virulent microbes.

microbiology↗

bioRxiv2021

Discriminative and affective touch converge: Somatosensory cortex represents A-beta input in a CT-like manner

Current theory divides the human mechanical sense into discriminative and affective systems. A discriminative system supports tactile exploration and manipulation via fast A{beta} signaling, whereas an affective system supports the pleasure of friendly interpersonal touch via slow CT signaling. To probe this system segregation, we recorded the electroencephalogram from participants being stroked and reporting stroke pleasantness. We observed a somatosensory negativity that was maximal for CT optimal as compared with sub-optimal velocities, that predicted subjective pleasantness, and showed only for stroking of hairy skin known to be CT innervated. Importantly, the latency of this negativity preceded C fiber input to the brain by several hundred milliseconds and is best explained by interactions between CT and A{beta} processes in the spinal cord. Our data challenge the divide between discriminative and affective touch implying instead that both fast A{beta} and slow CT signaling play an important role in tactile pleasure.

neuroscience↗

bioRxiv2020

High fat diet disrupts diurnal interactions between REG3g and small intestinal gut microbes resulting in metabolic dysfunction

Gut microbial diurnal oscillations are important diet-dependent drivers of host circadian rhythms and metabolism that ensure optimal energy balance. Yet, the interplay between diet, microbes, and host factors that sustain intestinal oscillations is complex and poorly understood. Here, we report the host C-type lectin antimicrobial peptide Reg3{gamma} works with key ileal microbes to orchestrate these interactions in a bi-directional manner, independent from the intestinal core circadian clock. High fat diet diminishes physiologically relevant microbial oscillators essential for host metabolic homeostasis, resulting in arrhythmic host Reg3{gamma} expression and increased abundance and oscillation of Reg3{gamma}-independent gut microbes. This illustrates a transkingdom co-evolved biological rhythm involving reciprocating, sensor-effector signals between key host and microbial components that ultimately drive metabolism, but are also heavily influenced by diet. Restoring the gut microbiotas capacity to sense and transduce dietary signals mediated by specific host factors such as Reg3{gamma} could be harnessed to improve metabolic dysfunction.

microbiology↗

bioRxiv2020

Early-life microbial intervention reduces colitis risk promoted by antibiotic-induced gut dysbiosis

Perturbations in the early life gut microbiome are associated with increased risk to complex immune disorder like inflammatory bowel diseases. We previously showed maternal antibiotic-induced gut dysbiosis vertically passed to offspring increases experimental colitis risk in IL-10 gene deficient (IL-10-/-) mice. While this could arise from emergence of pathobionts or loss/lack of essential microbes needed for appropriate immunological education, our findings suggest the latter. A dominant Bacteroides strain absent following antibiotic-induced perturbation was cultivated from murine fecal samples. Addition of this strain into mice with antibiotic-induced dysbiosis significantly promoted immune tolerance and reduced incidence of colitis in IL-10-/- mice, but only if engrafted early in life, and not during adulthood. Thus, key members of the gut microbiome are essential for development of immune tolerance to commensal microbes in early life and their addition in presence of gut dysbiosis during this period can reduce colitis risk in genetically prone hosts. HighlightsO_LISpecific gut microbes promote early life immune tolerance to key commensal microbes C_LIO_LILoss of early life keystone microbes increases colitis risk in genetically prone hosts C_LIO_LIEmergence of absent commensal microbes late in life worsened colitis outcome C_LIO_LIEarly life exposure to a missing keystone Bacteroides strain reduced colitis risk C_LI

microbiology↗

bioRxiv2019

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

Traditional cultivation approaches in microbiology are labor-intensive, low-throughput, and often yield biased sampling of taxa due to ecological and evolutionary factors. New strategies are needed to enable ample representation of rare taxa and slow-growers that are outcompeted by fast-growing organisms. We developed a microfluidic platform that anaerobically isolates and cultivates microbial cells in millions of picoliter droplets and automatically sorts droplets based on colony density. We applied our strategy to mouse and human gut microbiomes and used 16S ribosomal RNA gene amplicons to characterize taxonomic composition of cells grown using different media. We found up to 4-fold increase in richness and larger representation of rare taxa among cells grown in droplets compared to conventional culture plates. Automated sorting of droplets for slow-growing colonies further enhanced the relative abundance of rare populations. Our method improves the cultivation and analysis of diverse microbiomes to gain deeper insights into microbial functioning and lifestyles.

microbiology↗