The liver maintains immunological tolerance despite constant exposure to microbial and food-derived antigens within hepatic sinusoids. Liver sinusoidal endothelial cells (LSECs), with their unique fenestrated morphology, act as antigen presenting cells (APCs) and facilitate direct interaction between circulating T cells and other hepatic APCs, such as Kupffer cells and hepatocytes. This highlights the critical role of LSECs in antigen surveillance and tolerance.

In this study, using mouse models with endothelial-specific Runx3 deletion, we demonstrate that Runx3 in LSECs plays a crucial role in regulating hepatic immune homeostasis. Single-cell RNA sequencing analysis revealed that distinct CD8⁺ T cell populations were upregulated in these mouse livers: Cx3cr1⁺ cells under steady-state conditions, resembling effector memory T cells and Cxcr6⁺ cells during TAA-induced liver injury, resembling liver-resident T cells.

Mechanistically, Runx3-deleted LSECs exhibited enhanced IRF transcriptional activity and antigen presenting capacity. In vitro studies confirmed that Runx3 deletion activated the STAT1/IRF1 pathway, leading to enhanced CD8⁺ T cell priming. This effect was attenuated by JAK/STAT inhibition, indicating that Runx3 deficiency promotes CD8⁺ T cell differentiation into Cx3cr1⁺ effectors through STAT1/IRF1-dependent mechanisms. Furthermore, upon TGF-β exposure, T cells primed by Runx3-deficient LSECs acquired tissue residency with increased Cxcr6 expression, potentiating their pathogenicity and accelerating liver fibrosis.

Our findings reveal that endothelial Runx3 maintains the tolerogenic function of LSECs by restraining antigen presentation and subsequent CD8⁺ T cell activation. This work identifies a critical mechanism for preserving hepatic immune tolerance and provides insights for therapeutic interventions targeting T cell priming in liver diseases.