Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma

Miao Su; Kuang-Yuan Qiao; Xiao-Li Xie; Xin-Ying Zhu; Fu-Lai Gao; Chang-Juan Li; Dong-Qiang Zhao

doi:10.3389/fgene.2020.615680

Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma

Front Genet. 2021 Feb 4:11:615680. doi: 10.3389/fgene.2020.615680. eCollection 2020.

Authors

Miao Su^{1

2}, Kuang-Yuan Qiao³, Xiao-Li Xie¹, Xin-Ying Zhu^{1

4}, Fu-Lai Gao¹, Chang-Juan Li¹, Dong-Qiang Zhao¹

Affiliations

¹ Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
² Department of Gastroenterology, Hengshui People's Hospital, Hengshui, China.
³ Basic Medical College, Hebei Medical University, Shijiazhuang, China.
⁴ Department of Gastroenterology, The Third Hospital of Hebei Medical University, Shijiazhuang, China.

Abstract

Analysis of single-cell RNA sequencing (scRNA-seq) data of immune cells from the tumor microenvironment (TME) may identify tumor progression biomarkers. This study was designed to investigate the prognostic value of differentially expressed genes (DEGs) in intrahepatic cholangiocarcinoma (ICC) using scRNA-seq. We downloaded the scRNA-seq data of 33,991 cell samples, including 17,090 ICC cell samples and 16,901 ICC adjacent tissue cell samples regarded as normal cells. scRNA-seq data were processed and classified into 20 clusters. The immune cell clusters were extracted and processed again in the same way, and each type of immune cells was divided into several subclusters. In total, 337 marker genes of macrophages and 427 marker genes of B cells were identified by comparing ICC subclusters with normal subclusters. Finally, 659 DEGs were obtained by merging B cell and macrophage marker genes. ICC sample clinical information and gene expression data were downloaded. A nine-prognosis-related-gene (PRG) signature was established by analyzing the correlation between DEGs and overall survival in ICC. The robustness and validity of the signature were verified. Functional enrichment analysis revealed that the nine PRGs were mainly involved in tumor immune mechanisms. In conclusion, we established a PRG signature based on scRNA-seq data from immune cells of patients with ICC. This PRG signature not only reflects the TME immune status but also provides new biomarkers for ICC prognosis.

Keywords: differentially expressed genes; immune cells; intrahepatic cholangiocarcinoma; progression; single-cell RNA sequencing.