Biology subjects

Kumamoto, C. A.

Publications and source records attributed to Kumamoto, C. A..

7 recordsLinked to original sources

bioRxiv2026

Colonic epithelial regeneration shapes susceptibility to Clostridioides difficile infection

Clostridioides difficile infection (CDI) susceptibility and severity are strongly associated with preexisting colonic inflammation. However, chronic inflammatory conditions such as cystic fibrosis rarely progress to symptomatic CDI despite high rates of C. difficile colonization, suggesting that inflammation alone is insufficient to explain disease vulnerability. Notably, populations relatively protected from symptomatic CDI exhibit impaired regenerative capacity within the colon epithelium. Here, we used single cell RNA sequencing of human colonoid monolayers to map markers of CDI susceptibility and severity to cell populations associated with inflammation and epithelial repair. We identified an inducible microfold-like (M-like) population that is largely absent from the healthy colon but emerges during inflammation and regeneration. These cells were enriched for markers of severe CDI, C. difficile toxin interaction genes, and elevated CCL20 and CFTR expression. Spatial imaging localized CCL20-producing cells to wound-like gaps in mock and CDI-treated colonoids, identifying a repair-associated niche active independent of infection. Following exposure to C. difficile, wound-healing transcription within the M-like lineage declined while tuft-like populations expanded and upregulated genes associated with immune cell recruitment. These findings demonstrate that epithelial regeneration shapes host CDI vulnerability. IMPORTANCEClostridioides difficile infection can lead to severe illness and death in vulnerable populations despite available treatments. Clinical signs of inflammation during active Clostridioides difficile infection are strongly associated with disease outcome, yet these responses primarily reflect tissue damage already underway, limiting opportunities to prevent progression. In contrast, conditions linked to severe disease, including inflammatory bowel disease and antibiotic exposure, are associated with colonic inflammation before infection or at the time of diagnosis, highlighting an opportunity for earlier identification of high-risk individuals. Using human colonoid single cell transcriptomics and spatial imaging, we identified a microfold-like cell population enriched for inflammatory mediators and Clostridioides difficile toxin interaction genes linked to severe disease. This population was active even in the absence of infection, suggesting that repair-associated populations within the inflamed colon may help identify susceptibility to severe CDI before clinical progression occurs.

microbiology↗

bioRxiv2026

Clostridioides difficile stimulates CCL20 expression in human colonoid monolayers in a transwell-based co-culture system that supports its anaerobic growth

The pathogenic bacterium Clostridioides difficile is a major cause of antibiotic-associated diarrheal disease. Treatment of the disease is challenging because antibiotics used for treatment may also perpetuate the conditions that contributed to initial susceptibility. Elucidating the mechanisms of C. difficile/intestinal epithelium interaction is needed to facilitate the development of new therapeutic options. The studies described in this communication demonstrate the development of a tissue culture system that supported the growth of C. difficile in co-culture with a model of the human intestinal epithelium produced from colonoids, organoids derived from human colonic biopsies. Epithelial cell responses to C. difficile included upregulation of CCL20, encoding a chemokine that was previously shown to be upregulated in response to C. difficile challenge. Additionally, bacteria associated with the monolayer in a non-toxin dependent manner. This system will support future investigation of epithelium/C. difficile interactions during CDI and identification of mechanisms that drive pathogenesis by C. difficile in the human intestine.

microbiology↗

bioRxiv2025

Candida albicans Colonization Modulates Murine Ethanol Consumption and Behavioral Responses Through Elevation of Serum Prostaglandin E2 and Impact on the Striatal Dopamine System

Candida albicans is a commensal yeast that is a common component of the gastrointestinal (GI) microbiome of humans. C. albicans has been shown to bloom in the GI tract of individuals with alcohol use disorder (AUD) and can promote and increase the severity of alcoholic liver disease (ALD). However, the effects of C. albicans blooms on the host in the context of AUD or AUD-related phenotypes, such as ethanol preference, have been unstudied. In this work, we report a reduction in ethanol consumption and preference in mice colonized with C. albicans. C. albicans-colonized mice exhibited elevated levels of serum PGE2 and reduced ethanol preference was reversed by injection with antagonists of PGE2 receptors. Further, injection of mice with a PGE2 derivative decreased their ethanol preference. These results show that PGE2 acting on its receptors EP1 and EP2 drives reduced ethanol preference in C. albicans-colonized mice. We also showed altered transcription of dopamine receptors in the dorsal striatum of C. albicans-colonized mice and more rapid acquisition of ethanol conditioned taste aversion, suggesting alterations to reinforcement or aversion learning. Finally, C. albicans-colonized mice were more susceptible to ethanol-induced motor coordination impairment showing significant alterations to the behavioral effects of ethanol. This study identifies a member of the fungal microbiome that alters ethanol preference and demonstrates a role for PGE2 signaling in these phenotypes. ImportanceCandida albicans is a commensal yeast that is found in the gut of most individuals. C. albicans has been shown to contribute to alcoholic liver disease. Outside of this, the impact of intestinal fungi on alcohol-use disorder (AUD) had been unstudied. As AUD is a complex disorder characterized by high relapse rates, and there are only 3 FDA-approved therapies for the maintenance of abstinence, it is important to study novel AUD contributors to find new therapeutic targets. Here we show that an intestinal fungus, C. albicans, can alter mammalian ethanol consumption through an immune modulator, prostaglandin E2. The results highlight novel contributors to AUD-related phenotypes and further implicate the gut-brain axis in AUD. Future studies could lead to new therapeutic avenues for the treatment of AUD.

microbiology↗

bioRxiv2023

Selection of Ethanol Tolerant Strains of Candida albicans by Repeated Ethanol Exposure Results in Strains with Reduced Susceptibility to Fluconazole

Candida albicans is a commensal yeast that has important impacts on host metabolism and immune function, and can establish life-threatening infections in immunocompromised individuals. Previously, C. albicans colonization has been shown to contribute to the progression and severity of alcoholic liver disease. However, relatively little is known about how C. albicans responds to changing environmental conditions in the GI tract of individuals with alcohol use disorder, namely repeated exposure to ethanol. In this study, we repeatedly exposed C. albicans to high concentrations (10% vol/vol) of ethanol--a concentration that can be observed in the upper GI tract of humans following consumption of alcohol. Following this repeated exposure protocol, ethanol small colony (Esc) variants of C. albicans isolated from these populations exhibited increased ethanol tolerance, altered transcriptional responses to ethanol, and cross-resistance/tolerance to the frontline antifungal fluconazole. These Esc strains exhibited chromosomal copy number variations and carried polymorphisms in genes previously associated with the acquisition of fluconazole resistance during human infection. This study identifies a selective pressure that can result in evolution of fluconazole tolerance and resistance without previous exposure to the drug.

microbiology↗

bioRxiv2021

An Intersection between Iron Availability and Candida albicans Invasive Filamentation

Candida albicans filamentation, the ability to convert from oval yeast cells to elongated hyphal cells, is a key factor in its pathogenesis. Previous work has shown that the integral membrane protein Dfi1 is required for filamentation in cells grown in contact with a semi-solid surface. Investigations into the downstream targets of the Dfi1 pathway revealed potential links to two transcription factors - Sef1 and Czf1. Sef1 regulates iron uptake and iron utilization genes in low iron conditions, leading us to hypothesize that there exists a link between iron availability and contact-dependent invasive filamentation. Here, we showed that Sef1 was not required for contact dependent filamentation, but it was required for WT expression levels of a number of genes during growth in contact conditions. Czf1 is required for contact-dependent filamentation and for WT levels of expression of several genes. Constitutive expression and activation of either Sef1 or Czf1 individually in a dfi1 null strain resulted in a complete rescue of the dfi1 null filamentation defect. Because Sef1 is normally activated in low-iron environments, we embedded WT and dfi1 null cells in iron-free agar medium supplemented with various concentrations of Ferrous Ammonium Sulfate (FAS). dfi1 null cells embedded in media with a low concentration of iron (20uM FAS) showed increased filamentation in comparison to mutant cells embedded in higher concentrations of iron (50-500uM). WT cells produced filamentous colonies in all concentrations. Together, this data indicates that Dfi1, Czf1, Sef1, and environmental iron regulate C. albicans contact-dependent filamentation. ImportanceCandida albicans is an opportunistic pathogen responsible for a larger proportion of candidiasis and candidemia cases than any other Candida species (CDC). The ability of C. albicans cells to invade and cause disease is linked to their ability to filament and form hyphae. Despite this, there are gaps in our knowledge of the environmental cues and intracellular signaling that triggers the switch from commensal organism to filamentous pathogen. Here we identified a link between contact-dependent filamentation and iron availability. Over the course of tissue invasion, C. albicans cells encounter a number of different iron microenvironments, from the iron-rich gut to iron-poor tissues. Increased expression of Sef1-depndent iron uptake genes as a result of contact-dependent signaling will promote the adaptation of C. albicans cells to a low iron availability environment.

microbiology↗

bioRxiv2019

A novel genetic circuitry governing hypoxic metabolic flexibility, commensalism and virulence in the fungal pathogen Candida albicans

Inside the human host, the pathogenic yeast Candida albicans colonizes predominantly oxygen-poor niches such as the gastrointestinal and vaginal tracts, but also oxygen-rich environments such as cutaneous epithelial cells and oral mucosa. This suppleness requires an effective mechanism to reprogram reversibly the primary metabolism in response to oxygen variation. Here, we have uncovered that Snf5, a subunit of SWI/SNF chromatin remodeling complex, is a major transcriptional regulator that links oxygen status to the metabolic capacity of C. albicans. Snf5 and other subunits of SWI/SNF complex were required to activate genes of alternative carbon utilization and other carbohydrates related process specifically under hypoxia. snf5 mutant exhibited an altered metabolome reflecting that SWI/SNF plays an essential role in maintaining metabolic homeostasis and carbon flux in C. albicans under hypoxia. Snf5 was necessary to activate the transcriptional program linked to both commensal and invasive growth. Accordingly, snf5 was unable to maintain its growth in the stomach, the cecum and the colon of mice. snf5 was also avirulent as it was unable to invade Galleria larvae or to cause damage to human enterocytes and murine macrophages. Among candidates of signaling pathways in which Snf5 might operate, phenotypic analysis revealed that mutants of Ras1-cAMP-PKA pathway, as well as mutants of Yak1 and Yck2 kinases exhibited a similar carbon flexibility phenotype as did snf5 under hypoxia. Genetic interaction analysis indicated that the adenylate cyclase Cyr1, a key component of the Ras1-cAMP pathway, but not Ras1, interacted genetically with Snf5. Our study yielded unprecedented insight into the oxygen-sensitive regulatory circuit that control metabolic flexibility, stress, commensalism and virulence in C. albicans.\n\nAuthor SummaryA critical aspect of eukaryotic cell fitness is the ability to sense and adapt to variations in oxygen concentrations in their local environment. Hypoxia leads to a substantial remodeling of cell metabolism and energy homeostasis, and thus, organisms must develop an effective regulatory mechanism to cope with oxygen depletion. Candida albicans is an opportunistic yeast that is the most prevalent human fungal pathogens. This yeast colonizes diverse niches inside the human host with contrasting carbon sources and oxygen concentrations. While hypoxia is the predominant conditions that C. albicans encounters inside most of the niches, the impact of this condition on metabolic flexibility, a major determinant of fungal virulence, was completely neglected. Here, we uncovered that the chromatin remodelling complex SWI/SNF is master regulatory circuit that links oxygen status to a broad spectrum of carbon utilization routes. Snf5 was essential for the maintenance of C. albicans as a commensal and also for the expression of its virulence. The oxygen-sensitive regulators identified in this work provide a framework to comprehensively understand the virulence of human fungal pathogens and represent a therapeutic value to fight fungal infections.

microbiology↗

bioRxiv2018

A synthetic system that combats fungal infections

Due to a limited set of antifungals available and problems in early diagnosis invasive fungal infections caused by Candida species are among the most common hospital-acquired infections with staggering mortality rates. Here, we describe an engineered system able to sense and respond to the fungal pathogen Candida albicans, the most common cause of candidemia. In doing so, we identified hydroxyphenylacetic acid (HPA) as a novel molecule secreted by C. albicans. Furthermore, we engineered E. coli to be able to sense HPA produced by C. albicans. Finally, we constructed a sense-and-respond system by coupling the C. albicans sensor to the production of an inhibitor of hypha formation thereby reducing filamentation, virulence factor expression and fungal-induced epithelial damage. This system could be used as a basis for the development of novel prophylactic approaches to prevent fungal infections.

synthetic biology↗