Dissecting Intra-Tumoral Changes Following Immune Checkpoint Blockades in Intrahepatic Cholangiocarcinoma via Single-Cell Analysis

PurposeTo dissect the tumor ecosystem following immune checkpoint blockades (ICBs) in intrahepatic cholangiocarcinoma (ICC) at a single-cell level. MethodsSingle-cell RNA sequencing (scRNA-seq) data of 10 ICC patients for the ICB clinical trial were extracted from GSE125449 and systematically reanalyzed. Bulk RNA-seq data of 255 ICC patients were analyzed. Infiltration levels of SPP1(+)CD68(+) tumor-associated macrophages (TAMs) were examined by dual immunofluorescence (IF) staining in 264 resected ICC samples. The correlation between SPP1(+) TAMs and clinicopathological features as well as their prognostic significance was evaluated. ResultsAmong the 10 patients, five received biopsy at baseline, and others were biopsied at different timings following ICBs. Single-cell transcriptomes for 5,931 cells were obtained. A tighter cellular communication network was observed in ICB-treated ICC. We found a newly emerging VEGF signaling mediated by PGF-VEGFR1 between cancer-associated fibroblasts (CAFs) and endothelial cells in ICC following ICBs. SPP1 expression was dramatically upregulated, and SPP1(+) TAM gene signatures were enriched in TAMs receiving ICB therapy. We also identified SPP1(+) TAMs as an independent adverse prognostic indicator for survival in ICC. ConclusionOur analyses provide an overview of the altered tumor ecosystem in ICC treated with ICBs and highlight the potential role of targeting CAFs and SPP1(+)TAMs in developing a more rational checkpoint blockade-based therapy for ICC.

Automated summary

This study dissected the tumor ecosystem in intrahepatic cholangiocarcinoma (ICC) treated with immune checkpoint blockades (ICBs) using single-cell RNA sequencing data and immunofluorescence staining. The results revealed a tighter cellular communication network and the involvement of VEGF signaling mediated by PGF-VEGFR1 in ICC following ICBs. SPP1(+) tumor-associated macrophages (TAMs) were identified as an adverse prognostic indicator for ICC patients.