Identification of SPP1+ macrophages as an immune suppressor in hepatocellular carcinoma using single-cell and bulk transcriptomics

作者：Han Jin, Woonghee Kim, Meng Yuan, Xiangyu Li, Hong Yang, Mengzhen Li, Mengnan Shi, Hasan Türkez, Mathias Uhlén, Cheng Zhang, Adil Mardinoğlu · 发表于：Frontiers in Immunology · 年份：2024 · DOI：10.3389/fimmu.2024.1446453 · 被引用次数：10 · 研究领域：Single-cell and spatial transcriptomics、Immune cells in cancer、Ferroptosis and cancer prognosis

Introduction Macrophages and T cells play crucial roles in liver physiology, but their functional diversity in hepatocellular carcinoma (HCC) remains largely unknown. Methods Two bulk RNA-sequencing (RNA-seq) cohorts for HCC were analyzed using gene co-expression network analysis. Key gene modules and networks were mapped to single-cell RNA-sequencing (scRNA-seq) data of HCC. Cell type fraction of bulk RNA-seq data was estimated by deconvolution approach using single-cell RNA-sequencing data as a reference. Survival analysis was carried out to estimate the prognosis of different immune cell types in bulk RNA-seq cohorts. Cell-cell interaction analysis was performed to identify potential links between immune cell types in HCC. Results In this study, we analyzed RNA-seq data from two large-scale HCC cohorts, revealing a major and consensus gene co-expression cluster with significant implications for immunosuppression. Notably, these genes exhibited higher enrichment in liver macrophages than T cells, as confirmed by scRNA-seq data from HCC patients. Integrative analysis of bulk and single-cell RNA-seq data pinpointed SPP1 + macrophages as an unfavorable cell type, while VCAN + macrophages, C1QA + macrophages, and CD8 + T cells were associated with a more favorable prognosis for HCC patients. Subsequent scRNA-seq investigations and in vitro experiments elucidated that SPP1, predominantly secreted by SPP1 + macrophages, inhibits CD8 + T cell proliferation. Finally, targeting SPP1...