Transcriptomic profiling of autoimmune hepatitis identifies TRAT1 as an in vitro negative regulator of NK cell effector functions

Background T cell receptor-associated transmembrane adaptor 1 (TRAT1) is a well-characterized regulator of T-cell signaling, yet its functional roles in innate lymphocytes remain largely undefined. This study aimed to identify autoimmune hepatitis (AIH)-associated immune targets and perform an exploratory functional characterization of TRAT1 in NK-cell models. Methods We performed transcriptomic analysis on liver tissues from AIH patients and disease controls to prioritize candidate genes. Public datasets and a Concanavalin A (ConA)-induced acute immune-mediated hepatitis murine model were used for contextualization and experimental support for Trat1 expression and immune cell dynamics. The functional role of TRAT1 in NK cells was assessed using NK92-MI cells and primary human NK cells with siRNA-mediated TRAT1 knockdown (KD). TRAT1 expression kinetics and cytotoxicity were examined in both systems, whereas proliferation, effector molecule production, surface receptor expression, calcium flux, and mitogen-activated protein kinase (MAPK) signaling were further analyzed in NK92-MI cells. Results TRAT1 was prioritized as an AIH-enriched immune-related candidate gene in this discovery cohort. In the ConA-induced acute immune-mediated hepatitis model, Trat1 expression was selectively elevated in sorted hepatic NK-cell-enriched populations. In vitro , TRAT1 mRNA expression transiently increased in both NK92-MI and primary human NK cells upon activation; its knockdown subsequently enhanced their cytotoxicity against target cells. In NK92-MI cells, TRAT1 deficiency led to enhanced proliferation and elevated production of Interferon-gamma (IFN-γ), Tumor necrosis factor-alpha (TNF-α), Granzyme B (GZMB), and perforin. TRAT1 deficiency also selectively upregulated activating receptors NCR1 (NKp46) and NCR2 (NKp44) while downregulating NKG2D. Mechanistically, TRAT1 KD was associated with increased Ca² + influx, phospholipase C gamma 2 (PLCγ2) phosphorylation, and the phosphorylation of ERK1/2 and p38. Conclusion Through an exploratory transcriptomic discovery approach, this study suggests that TRAT1 acts as an in vitro candidate negative modulator of NK-cell effector functions, potentially involving calcium and MAPK signaling in NK92-MI cells. These data support TRAT1 as a candidate mechanistic lead for future validation in larger clinical cohorts and lineage-specific in vivo models.