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Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions
In vitro differentiation or expansion of stem and progenitor cells under chemical stimulation or genetic manipulation is used for understanding the molecular mechanisms of cell differentiation and self-renewal. However, concerns around the cell identity of in vitro–cultured cells exist. Bioinformati...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2021
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267371/ https://www.ncbi.nlm.nih.gov/pubmed/34249906 http://dx.doi.org/10.3389/fcell.2021.644261 |
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author | He, Xuelin Liu, Li Chen, Baode Wu, Chao |
author_facet | He, Xuelin Liu, Li Chen, Baode Wu, Chao |
author_sort | He, Xuelin |
collection | PubMed |
description | In vitro differentiation or expansion of stem and progenitor cells under chemical stimulation or genetic manipulation is used for understanding the molecular mechanisms of cell differentiation and self-renewal. However, concerns around the cell identity of in vitro–cultured cells exist. Bioinformatics methods, which rely heavily on signatures of cell types, have been developed to estimate cell types in bulk samples. The Tabula Muris Senis project provides an important basis for the comprehensive identification of signatures for different cell types. Here, we identified 46 cell type–specific (CTS) gene clusters for 83 mouse cell types. We conducted Gene Ontology term enrichment analysis on the gene clusters and revealed the specific functions of the relevant cell types. Next, we proposed a simple method, named CTSFinder, to identify different cell types between bulk RNA-Seq samples using the 46 CTS gene clusters. We applied CTSFinder on bulk RNA-Seq data from 17 organs and from developing mouse liver over different stages. We successfully identified the specific cell types between organs and captured the dynamics of different cell types during liver development. We applied CTSFinder with bulk RNA-Seq data from a growth factor–induced neural progenitor cell culture system and identified the dynamics of brain immune cells and nonimmune cells during the long-time cell culture. We also applied CTSFinder with bulk RNA-Seq data from reprogramming induced pluripotent stem cells and identified the stage when those cells were massively induced. Finally, we applied CTSFinder with bulk RNA-Seq data from in vivo and in vitro developing mouse retina and captured the dynamics of different cell types in the two development systems. The CTS gene clusters and CTSFinder method could thus serve as promising toolkits for assessing the cell identity of in vitro culture systems. |
format | Online Article Text |
id | pubmed-8267371 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-82673712021-07-10 Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions He, Xuelin Liu, Li Chen, Baode Wu, Chao Front Cell Dev Biol Cell and Developmental Biology In vitro differentiation or expansion of stem and progenitor cells under chemical stimulation or genetic manipulation is used for understanding the molecular mechanisms of cell differentiation and self-renewal. However, concerns around the cell identity of in vitro–cultured cells exist. Bioinformatics methods, which rely heavily on signatures of cell types, have been developed to estimate cell types in bulk samples. The Tabula Muris Senis project provides an important basis for the comprehensive identification of signatures for different cell types. Here, we identified 46 cell type–specific (CTS) gene clusters for 83 mouse cell types. We conducted Gene Ontology term enrichment analysis on the gene clusters and revealed the specific functions of the relevant cell types. Next, we proposed a simple method, named CTSFinder, to identify different cell types between bulk RNA-Seq samples using the 46 CTS gene clusters. We applied CTSFinder on bulk RNA-Seq data from 17 organs and from developing mouse liver over different stages. We successfully identified the specific cell types between organs and captured the dynamics of different cell types during liver development. We applied CTSFinder with bulk RNA-Seq data from a growth factor–induced neural progenitor cell culture system and identified the dynamics of brain immune cells and nonimmune cells during the long-time cell culture. We also applied CTSFinder with bulk RNA-Seq data from reprogramming induced pluripotent stem cells and identified the stage when those cells were massively induced. Finally, we applied CTSFinder with bulk RNA-Seq data from in vivo and in vitro developing mouse retina and captured the dynamics of different cell types in the two development systems. The CTS gene clusters and CTSFinder method could thus serve as promising toolkits for assessing the cell identity of in vitro culture systems. Frontiers Media S.A. 2021-06-25 /pmc/articles/PMC8267371/ /pubmed/34249906 http://dx.doi.org/10.3389/fcell.2021.644261 Text en Copyright © 2021 He, Liu, Chen and Wu. https://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 | Cell and Developmental Biology He, Xuelin Liu, Li Chen, Baode Wu, Chao Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title | Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title_full | Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title_fullStr | Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title_full_unstemmed | Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title_short | Using Cell Type–Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions |
title_sort | using cell type–specific genes to identify cell-type transitions between different in vitro culture conditions |
topic | Cell and Developmental Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8267371/ https://www.ncbi.nlm.nih.gov/pubmed/34249906 http://dx.doi.org/10.3389/fcell.2021.644261 |
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