Transplant immunosuppressant therapies induce unique functional changes in and re-shape gut immune homeostasis

Current immunosuppressants effectively suppress adaptive and innate immune responses, but their broad, antigen-non-specific effects often result in significant complications. Here we investigated understudied immunosuppressant effects of four major immunosuppressant classes including tacrolimus, prednisone, mycophenolate mofetil (MMF), and Fingolimod (FTY), on the gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking. Despite their distinct mechanisms of action, all drugs induced progressive alterations from moderate early changes to substantial alterations in the gut microbiome composition and metabolic pathways with prolonged treatment, converging to a shared dysbiotic state. This was accompanied by significant metabolic alterations and distinct phases of intestinal transcriptional responses. Time-dependent changes in lymph node (LN) reorganization and cellular composition were also observed, showing compartmentalized immune regulation in mesenteric and peripheral lymphoid tissues. Together, these findings highlight the underappreciated complexity and temporal dynamics of immunosuppressant effect, linking drug-induced changes in gut microbiome and compartmentalized immune regulation in lymphoid tissues. Notably, MMF and FTY demonstrated most robust immunomodulatory properties, and were able to suppress alloantigen-induced inflammation through mediating regulatory T cells and LN remodeling. Understanding these relationships provides new opportunities for refining immunosuppressive strategies to mitigate treatment-related complications in transplant patients, ultimately improving long-term organ transplant outcomes.