Background: Elucidating the immune landscape of liver transplantation (LT), particularly the role of tissue-resident memory T cells (TRMs), remains a pressing challenge in transplant immunology.
Methods: We conducted a multi-omics investigation of liver allografts from both human (n = 17) and murine (n = 16) cohorts, integrating single-cell RNA sequencing, bulk RNA sequencing, and complementary immunological analyses.
Results: Cross-species profiling of 235,116 cells revealed a rejection-associated expansion of CD8⁺ TRMs in liver grafts undergoing immune-mediated injury. These cells exhibited a distinct molecular signature, with upregulated expression of residency markers (CD69, CXCR6, CD49A, CD103), inhibitory receptors (PD-1, CTLA-4, TIGIT), cytotoxic mediators (GZMB, IFNG), and proliferative indicators (PCNA, TOP2A). Transcriptional activation of EOMES and RUNX3 further characterized their effector state. Cell–cell communication analyses and functional validation assays demonstrated robust interactions between CD8⁺ TRMs and Kupffer cells, particularly during rejection episodes.

Conclusion: Our findings identify CD8+ TRMs as central orchestrators of liver allograft rejection and highlight their potential as prognostic biomarkers and therapeutic targets for promoting transplant tolerance.