NUDT1 promotes the accumulation and longevity of CD103+ TRM cells in primary biliary cholangitis

Abstract

Background & aims: Pyruvate dehydrogenase (PDC)-E2 specific CD8⁺ T cells play a leading role in biliary destruction in PBC. However, there are limited data on the characterization of these autoantigen-specific CD8⁺ T cells, particularly in the liver. Herein, we aimed to identify pathogenic intrahepatic CD8⁺ T-cell subpopulations and investigate their immunobiology in PBC.

Methods: Phenotypic and functional analysis of intrahepatic T-cell subsets were performed by flow cytometry. CD103⁺ T_RM cell frequency was evaluated by histological staining. The transcriptome and metabolome were analyzed by RNA-seq and liquid chromatography-mass spectrometry, respectively. Cytotoxicity of T_RM cells against cholangiocytes was assayed in a 3D organoid co-culture system. Moreover, the longevity (long-term survival) of T_RM cells in vivo was studied by 2-octynoic acid-BSA (2OA-BSA) immunization, Nudt1 conditional knock-out and adoptive co-transfer in a murine model.

Results: Intrahepatic CD103⁺ T_RM (CD69⁺CD103⁺CD8⁺) cells were significantly expanded, hyperactivated, and potentially specifically reactive to PDC-E2 in patients with PBC. CD103⁺ T_RM cell frequencies correlated with clinical and histological indices of PBC and predicted poor ursodeoxycholic acid response. NUDT1 blockade suppressed the cytotoxic effector functions of CD103⁺ T_RM cells upon PDC-E2 re-stimulation. NUDT1 overexpression in CD8⁺ T cells promoted tissue-residence programming in vitro; inhibition or knockdown of NUDT1 had the opposite effect. Pharmacological blockade or genetic deletion of NUDT1 eliminated CD103⁺ T_RM cells and alleviated cholangitis in mice immunized with 2OA-BSA. Significantly, NUDT1-dependent DNA damage resistance potentiates CD8⁺ T-cell tissue-residency via the PARP1-TGFβR axis in vitro. Consistently, PARP1 inhibition restored NUDT1-deficient CD103⁺ T_RM cell durable survival and TGFβ-Smad signaling.

Conclusions: CD103⁺ T_RM cells are the dominant population of PDC-E2-specific CD8⁺ T lymphocytes in the livers of patients with PBC. The role of NUDT1 in promoting pathogenic CD103⁺ T_RM cell accumulation and longevity represents a novel therapeutic target in PBC.

Lay summary: Primary biliary cholangitis (PBC) is a rare inflammatory condition of the bile ducts. It can be treated with ursodeoxycholic acid, but a large percentage of patients respond poorly to this treatment. Liver-infiltrating memory CD8⁺ T cells recognizing the PDC-E2 immunodominant epitope are critical in the pathogenesis of PBC. We identifed the key pathogenic CD8⁺ T cell subset, and worked out the mechanisms of its hyperactivation and longevity, which could be exploited therapeutically.

Keywords: DNA damage response; NUDT1; PDC-E2; Primary biliary cholangitis; Tissue-resident memory T cells.