Abstract 5812: Single-cell dissection of checkpoint inhibitor hepatitis reveals insights into immune tolerance in the human liver
Authors: Molly Fisher Thomas, Thomas Chan, Neal Smith, Marc Sherman, Swetha Ramesh, Alice Tirard, John McGuire, Mazen Nasrallah, Kasidet Manakongtreecheep, Jessica Tantivit, Leyre Zubiri, Dejan Juric, Ryan Sullivan, Nir Hacohen, Genevieve Boland, Georg Lauer, Kerry Reynolds, Alexandra-Chloé Villani
Journal: Cancer Research (2025)

Abstract Background: Immune checkpoint inhibitors (ICIs) to treat cancer have revolutionized immuno-oncology. However, therapy is limited by frequent immune-related adverse events, including immune-mediated liver injury from checkpoint inhibitors (ILICI), which occurs in ∼1-17% of patients on anti-PD-1 and/or CTLA-4 therapy. While ILICI is often mild, it can cause severe hepatic dysfunction, delay cancer therapy, and require immunosuppressive treatments that may compromise anti-tumor immune responses. ILICI shares clinical and histologic features with autoimmune hepatitis (AIH). Therefore, the study of ILICI and AIH is important for understanding how immune tolerance is lost across a spectrum of inflammatory liver diseases. Methods: To characterize the cellular and molecular underpinnings of ILICI, we used single-cell and single-nuclei RNA sequencing with paired antigen receptor sequencing to characterize ∼300, 000 cells from paired liver and blood specimens from 23 patients (9 ILICI, 4 AIH, 3 controls on ICB, 7 controls not on ICB) and ∼150, 000 peripheral blood cells from an additional 28 control patients on ICB. ILICI was defined by a hepatocellular or cholestatic rise in liver function tests and centrilobular or panlobular inflammatory liver injury. Controls had drug-induced liver injury, hepatic steatosis, or venous outflow obstruction. Results: Both AIH and ILICI patients showed marked expansion of clonally-related liver CXCR6Hi GZMKHi tissue-resident memory CD8 T cells expressing IFNG and GZMB and multiple CD4 T cell populations including cytotoxic GZMAHi effectors, CXCL13Hi effectors, and T regulatory cells. Compared to patients with AIH, those with ILICI showed a marked expansion of intravascular CX3CR1Hi CD8 T cells and a relative depletion of tissue dendritic cells while only patients with AIH had expanded plasma B cells. Analysis of matched blood samples from the same patient cohort revealed how cellular and transcriptional signatures in the liver were mirrored in circulating immune cells. Further analysis revealed that patients with ILICI and AIH had a marked interferon stimulated gene signature in a subset of hepatocytes, increased cholangiocyte progenitors, and increased periportal liver endothelial cells, which suggests significant liver parenchymal remodeling. Lastly, we identified a CXCL10-expressing cholangiocyte population that was expanded in both AIH and ILICI and was most pronounced in an individual with checkpoint inhibitor-associated cholangitis. Conclusions: In defining the cellular and transcriptional programs that are altered in ILICI and AIH, we have identified novel immune perturbations implicating PD-1 and CTLA-4 in liver immune tolerance. These discoveries offer promising avenues for the development of targeted diagnostics and therapeutics in the management of liver-related toxicities associated with immunotherapy. Citation Format: Molly Fisher Thomas, Thomas Chan, Neal Smith, Marc Sherman, Swetha Ramesh, Alice Tirard, John McGuire, Mazen Nasrallah, Kasidet Manakongtreecheep, Jessica Tantivit, Leyre Zubiri, Dejan Juric, Ryan Sullivan, Nir Hacohen, Genevieve Boland, Georg Lauer, Kerry Reynolds, Alexandra-Chloé Villani. Single-cell dissection of checkpoint inhibitor hepatitis reveals insights into immune tolerance in the human liver [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5812.