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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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Autores principales: Su, Miao, Qiao, Kuang-Yuan, Xie, Xiao-Li, Zhu, Xin-Ying, Gao, Fu-Lai, Li, Chang-Juan, Zhao, Dong-Qiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890365/
https://www.ncbi.nlm.nih.gov/pubmed/33613623
http://dx.doi.org/10.3389/fgene.2020.615680
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author Su, Miao
Qiao, Kuang-Yuan
Xie, Xiao-Li
Zhu, Xin-Ying
Gao, Fu-Lai
Li, Chang-Juan
Zhao, Dong-Qiang
author_facet Su, Miao
Qiao, Kuang-Yuan
Xie, Xiao-Li
Zhu, Xin-Ying
Gao, Fu-Lai
Li, Chang-Juan
Zhao, Dong-Qiang
author_sort Su, Miao
collection PubMed
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.
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spelling pubmed-78903652021-02-19 Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma Su, Miao Qiao, Kuang-Yuan Xie, Xiao-Li Zhu, Xin-Ying Gao, Fu-Lai Li, Chang-Juan Zhao, Dong-Qiang Front Genet Genetics 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. Frontiers Media S.A. 2021-02-04 /pmc/articles/PMC7890365/ /pubmed/33613623 http://dx.doi.org/10.3389/fgene.2020.615680 Text en Copyright © 2021 Su, Qiao, Xie, Zhu, Gao, Li and Zhao. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Su, Miao
Qiao, Kuang-Yuan
Xie, Xiao-Li
Zhu, Xin-Ying
Gao, Fu-Lai
Li, Chang-Juan
Zhao, Dong-Qiang
Development of a Prognostic Signature Based on Single-Cell RNA Sequencing Data of Immune Cells in Intrahepatic Cholangiocarcinoma
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 Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7890365/
https://www.ncbi.nlm.nih.gov/pubmed/33613623
http://dx.doi.org/10.3389/fgene.2020.615680
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