Abstract 6476: Multimodal single cell analysis of cholangiocarcinoma subtypes reveals distinct immune microenvironments
Authors: Hannah E. Stumpf, Jingchun Yang, Haidong Dong, Rory L. Smoot, Sumera I. Ilyas
Journal: Cancer Research (2025)

Abstract Cholangiocarcinoma (CCA), an aggressive cancer of the bile ducts, is classified into intrahepatic (iCCA), perihilar (pCCA), and distal (dCCA) anatomic subtypes. Each subtype has a distinct epidemiology and pathogenesis. The tumor immune microenvironment (TIME) of each subtype is poorly understood. CCAs are poorly immunogenic tumors and systemic therapy has had subpar efficacy in CCA subtypes. Thus, we hypothesized that each anatomic subtype has a distinct TIME. To address this hypothesis, we completed single cell sequencing of tumor, liver, and bile duct from patients with either iCCA or pCCA/dCCA. 182,054 cells from paired liver (n=16), tumor (n=16) (9 iCCA, 7 pCCA/dCCA), and normal bile duct (n=9) samples were obtained from treatment-naïve patients undergoing resection from June 2020 to August 2023. The tissues were homogenized and flow sorted for immune (CD45+) populations immediately following resection. The cells then underwent single cell RNA sequencing (scRNA-seq) and cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) with antibodies for 157 proteins. Multiple immunocompetent, syngeneic/orthotopic murine models of iCCA with distinct genetic drivers were used to assess immunotherapeutics (PMID: 38458319). Immune cells of interest were isolated by flow sorting and functionally validated via suppression assays and multiparameter flow cytometry. Additionally, a novel pCCA murine model was established by injection of an Pik3caH1047R/p27Kip1-derived extrahepatic biliary cancer cell line into the porta/hilar tissue plane. Compared to non-involved liver, the bile duct immune microenvironment composition closely resembled that of the tumor. Multimodal analysis demonstrated both human and murine iCCA tumors have a significant upregulation of regulatory T cells (Treg) expressing T cell immunoreceptor with Ig and ITIM domain (TIGIT) compared to controls. Suppression assay with intratumoral TIGIT+ Treg from mouse compared with TIGIT- Treg indicate TIGIT+ Treg are more potent in inhibiting proliferation of CD8+ T cells. Moreover, TIGIT blockade using a monoclonal antibody resulted in a significant reduction in tumor burden in multiple iCCA murine models, including SB1, a model resistant to anti-PD-(L)1 monotherapy. Meanwhile, human pCCA tumors had a significant increase in IgA+ plasma cells compared to iCCA tumors. An innovative genetically and anatomically relevant pCCA murine model was developed to interrogate this unique plasma cell population. In summary, these data suggest that iCCA and pCCA have distinct immune microenvironments which likely impacts the differences in response to ICB between the subtypes observed in phase III clinical trials. Additionally, the uninvolved, tumor-adjacent bile duct immune microenvironment resembles that of the tumor, suggesting a pre-malignant niche that facilitates tumor development. Citation Format: Hannah E. Stumpf, Jingchun Yang, Haidong Dong, Rory L. Smoot, Sumera I. Ilyas. Multimodal single cell analysis of cholangiocarcinoma subtypes reveals distinct immune microenvironments [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 6476.