Intestinal microbiome restoration in allogeneic stem cell transplantation

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PROJECT SUMMARY Allogeneic hematopoietic cell transplantation (allo-HCT) is often associated with a clinical complication known as graft-versus-host disease (GVHD), a major driver of mortality after allo-HCT. Current approaches to the prophylaxis of GVHD are primarily immunosuppressive therapies that can dampen the intended activity of the transplanted immune cells against the tumor and cause delayed immune reconstitution. Gastrointestinal (GI) microbiota, the highest microbial colonization in the body, has long been understood to contribute to the pathophysiology of GVHD. Indeed, patients undergoing allo-HCT are subject to dramatic immunological and microbiota perturbations, developing pre-HCT and continuing during transplant; GI microbiome diversity before and after transplant are independently associated with clinical outcome. When GVHD occurs, the GI tract is frequently involved, and patients often succumb to GVHD. New approaches to prevent GVHD and other transplant-related complications are urgently needed. We hypothesize that restoring the health of the intestinal microbial community early post-HCT is feasible and associated with improved transplant outcomes and immune reconstitution. In 2 studies of fecal microbiota transplantation (FMT) in allo-HCT, our group reported that an FMT intervention is a safe way to restore microbiota diversity. However, FMT has batch-to-batch variability depending on specific donors and carries the risks of transmission of infectious organisms or antibiotic-resistance genes. Here, we propose an entirely novel approach: a rationally designed oral-ecobiotic capsule that delivers a defined composition of pure bacterial strains. An oral, defined blend of strains offers advantages of predictable and reproducible pharmacology and would be immediately scalable to future studies. On this multi-PI proposal, we will capitalize on samples from an ongoing, investigator-initiated multicenter placebo-controlled phase 1b trial, led by PI Doris Ponce, which is first-in-human evaluating a clonally-derived multi-strain bacterial consortia for the prevention and restoration of the GI microbiome (NCT04995653). Our group has shown in a large multicenter study that early intestinal microbiome dysbiosis occurred universally among centers and had an association with transplant outcomes. In addition, innovative preclinical models of microbiome dysbiosis serve as the basis for the translational study and proposed microbiome analyses. Project objectives: Along with PI Marcel van den Brink, to evaluate the effects of intestinal microbiota restoration in allo-HCT recipients. We will pursue 2 specific aims that will evaluate the effects of microbiome restoration in the GI microbiome, allo-HCT outcomes, and immune reconstitution. Expected outcome: Results will provide new mechanistic insights into interactions between the intestinal microbiome and host immunity. Impact: Findings will inform future research not only for the reduction of transplant-related complications including GVHD, but also for other conditions in which GI injury occurs such as chemotherapy and/or radiation-induced toxicity and non-malignant inflammatory GI conditions. The proposed project outlines an entirely novel framework for targeting the GI microbiome in HCT.