EBV-reactive KIR⁺ CX3CR1⁺ CD8⁺ T cells mediate liver transplantation tolerance

Immune tolerance after transplantation reduces immunosuppression-related complications and improves overall survival. The unique tolerogenic microenvironment of the liver enables a proportion of liver transplantation (LT) recipients to develop tolerance with intact liver function. However, the underlying immunological mechanisms remain unclear.

We integrated single-cell transcriptome/TCR profiling, flow cytometry, in vitro killing assays, HLA-E peptidome analysis in a retrospective cohort of 347 LT recipients, murine LT models, and a prospective immunosuppressant withdrawal trial involving 20 pediatric LT recipients, with a median follow-up of 26 months.

We demonstrated that Epstein-Barr virus (EBV)-derived peptides can be presented by HLA-E on alloreactive CD4⁺ T cells to prime KIR⁺ CX3CR1⁺ CD8⁺ T cells, thereby promoting immune tolerance after LT. As a subset of CD8⁺ T_EMRA cells, KIR⁺ CX3CR1⁺ CD8⁺ T cells utilize perforin and granzyme B to suppress alloreactive CD4⁺ T cells after LT. In vitro analysis revealed that the EBV-derived peptide SQAPLPCVL could stabilize HLA-E expression on alloreactive CD4⁺ T cells and mediate their recognition and elimination by KIR⁺ CX3CR1⁺ CD8⁺ T cells through a TCR-dependent mechanism. Furthermore, BATF was indispensable for the induction of KIR⁺ CX3CR1⁺ CD8⁺ T cells. In the prospective immunosuppressant withdrawal clinical trial, the peripheral ratios of CD8⁺ T_EMRA and KIR⁺ CX3CR1⁺ CD8⁺ T cells were suggested to be potentially useful for identifying tolerant recipients.

Our study demonstrated a new immune tolerance mechanism mediated by KIR⁺ CX3CR1⁺ CD8⁺ T cells and established a connection between viral infection and tolerance formation, providing new insights into strategies for inducing tolerance after transplantation.

This study uncovers a mechanism by which Epstein Barr virus-derived peptides mark alloreactive CD4⁺ T cells for specific elimination by KIR⁺ CX3CR1⁺ CD8⁺ T cells, providing a functional explanation for the association between viral infection and transplant tolerance. Our findings also suggest that peripheral frequencies of CD8⁺ T_EMRA cells may serve as candidate biomarkers to help identify tolerant recipients during immunosuppression weaning, although their clinical utility remains to be validated in larger cohorts. Beyond their biomarker potential, the BATF-dependent differentiation of KIR⁺ CX3CR1⁺ CD8⁺ T cells paves the way for cellular strategies to induce tolerance after liver transplantation.