Transplant immunosuppressant therapies induce unique functional changes in lymph node 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 conducted a systematic investigation of drug effects on gut microbiome, metabolic pathways, lymphoid architecture and lymphocyte trafficking of four major immunosuppressants classes including tacrolimus, prednisone, mycophenolate mofetil (MMF), and Fingolimod (FTY). We show that immunosuppressants induced progressive alterations in the gut microbiome and metabolic pathways, where initial drug-specific effects converged by day 30 into a common dysbiotic state enriched in Muribaculaceae. Gut transcriptome analyses revealed minimal overlap in differentially expressed genes between early and late time points, indicating transient early effects and marked late-stage changes induced by these drugs. These microbiome and metabolic shifts were accompanied by time-dependent changes in lymph node (LN) organization and cellular composition, transitioning between pro-tolerogenic and pro-inflammatory states. Under alloantigen-stimulated conditions, MMF and FTY suppressed inflammation through dual regulation of regulatory T cells and LN remodeling, mediated through LN stromal cell-derived laminins. Together, our findings highlight previously underappreciated temporal dynamics in immunosuppressant mechanisms, linking immune tissue organization, gut microbiome and intestinal responses to long-term immunosuppression and metabolic complications in transplant patients.