Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma
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...
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Frontiers Media S.A.
2021-02-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2020.615680/full |
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| author | Miao Su Miao Su Kuang-Yuan Qiao Xiao-Li Xie Xin-Ying Zhu Xin-Ying Zhu Fu-Lai Gao Chang-Juan Li Dong-Qiang Zhao |
| author_facet | Miao Su Miao Su Kuang-Yuan Qiao Xiao-Li Xie Xin-Ying Zhu Xin-Ying Zhu Fu-Lai Gao Chang-Juan Li Dong-Qiang Zhao |
| author_sort | Miao Su |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-24T04:49:33Z |
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| id | doaj.art-315b887a7da64f63b05f7db9a1de2567 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-24T04:49:33Z |
| publishDate | 2021-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-315b887a7da64f63b05f7db9a1de25672022-12-21T17:14:35ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-02-011110.3389/fgene.2020.615680615680Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic CholangiocarcinomaMiao Su0Miao Su1Kuang-Yuan Qiao2Xiao-Li Xie3Xin-Ying Zhu4Xin-Ying Zhu5Fu-Lai Gao6Chang-Juan Li7Dong-Qiang Zhao8Department of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, Hengshui People's Hospital, Hengshui, ChinaBasic Medical College, Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Third Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaDepartment of Gastroenterology, The Second Hospital of Hebei Medical University, Shijiazhuang, ChinaAnalysis 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.https://www.frontiersin.org/articles/10.3389/fgene.2020.615680/fullintrahepatic cholangiocarcinomasingle-cell RNA sequencingimmune cellsdifferentially expressed genesprogression |
| spellingShingle | Miao Su Miao Su Kuang-Yuan Qiao Xiao-Li Xie Xin-Ying Zhu Xin-Ying Zhu Fu-Lai Gao Chang-Juan Li Dong-Qiang Zhao Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma Frontiers in Genetics intrahepatic cholangiocarcinoma single-cell RNA sequencing immune cells differentially expressed genes progression |
| title | Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma |
| title_full | Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma |
| title_fullStr | Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma |
| title_full_unstemmed | Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma |
| title_short | Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma |
| title_sort | development of a prognostic signature based on single cell rna sequencing data of immune cells in intrahepatic cholangiocarcinoma |
| topic | intrahepatic cholangiocarcinoma single-cell RNA sequencing immune cells differentially expressed genes progression |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2020.615680/full |
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