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The Markham Lab

Investigating how changes in the gut microbiome affect colorectal cancer and gastrointestinal infections

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     Our lab focuses on understanding how changes in the gastrointestinal microbiome affect colon health and disease. One area of specific interest is C. difficile infection and bacterial toxin pathogenesis. Our preliminary data show C. difficile toxin B (TcdB) transactivates receptor tyrosine kinases (RTK) in host colon tissue. These receptors are key mediators of colonic stem cell behavior. Our data also suggest these receptors facilitate TcdB-induced cell death. The effect of TcdB on RTK signaling has not been studied in vivo, and their impact on C. difficile infection and pathogenesis is not known. We hypothesize TcdB induces RTK signaling as an important component of pathogenesis in C. difficile infection. Moving forward, we expect the results will determine: (1) the ability of TcdB toxins to alter RTK pathways in vivo; (2) the impact and mechanism of RTK inhibition on TcdB-mediated cell death; (3) the specific cell subtypes affected during TcdB-mediated injury. The overarching goal is to reveal targets for therapeutic or preventive strategies that interdict C. difficile pathogenesis.


     A second project has gained momentum and originated as part of the Vanderbilt Colon Molecular Atlas Project (ColonMAP). This program aims to generate an interactive spatiotemporal map of pre-cancerous lesions in the colon at single-cell resolution using an integrated multi-omics approach. Independently, our focus is to understand how the disrupted spatial organization of the gut microbiota known as invasive biofilm formation may accelerate colorectal cancer (CRC). To investigate the critical bacterial species and host cell alterations involved in biofilm-associated CRC development, we colonized germ-free mice with mucosal bacterial slurries (pro-tumorigenic versus non-tumorigenic) derived from biofilm-positive human CRCs. Our single-cell RNA sequencing (scRNA-seq) analysis of host colonic tissue revealed increased tumor-associated neutrophils with the tumorigenic slurry and increased regulatory macrophages in the non-tumorigenic slurry. The pro-tumorigenic slurry induced consistent upregulation of MHC class II and reactive oxygen species-generating genes indicative of a mounting innate and adaptive immune response across colonocytes, goblet cells and stem cells. Ongoing experiments are aimed at using spatial transcriptomics and multiplex immunofluorescence to understand how these cell type-specific transcriptional changes are geographically related to bacterial biofilms.

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