A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.

Induced pluripotent stem cells (iPSCs) derived from somatic cells (SCs) and embryonic stem cells (ESCs) provide promising resources for regenerative medicine and medical research, leading to a daily identification of new cell lines. However, an efficient system to discriminate the different types of...

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Autores principales:	Anyou Wang, Ying Du, Qianchuan He, Chunxiao Zhou
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2013
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7862593a54be44579970263d08203210
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spelling	oai:doaj.org-article:7862593a54be44579970263d082032102021-11-18T07:57:42ZA quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.1932-620310.1371/journal.pone.0056095https://doaj.org/article/7862593a54be44579970263d082032102013-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23418520/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Induced pluripotent stem cells (iPSCs) derived from somatic cells (SCs) and embryonic stem cells (ESCs) provide promising resources for regenerative medicine and medical research, leading to a daily identification of new cell lines. However, an efficient system to discriminate the different types of cell lines is lacking. Here, we develop a quantitative system to discriminate the three cell types, iPSCs, ESCs, and SCs. The system consists of DNA-methylation biomarkers and mathematical models, including an artificial neural network and support vector machines. All biomarkers were unbiasedly selected by calculating an eigengene score derived from analysis of genome-wide DNA methylations. With 30 biomarkers, or even with as few as 3 top biomarkers, this system can discriminate SCs from pluripotent cells (PCs, including ESCs and iPSCs) with almost 100% accuracy. With approximately 100 biomarkers, the system can distinguish ESCs from iPSCs with an accuracy of 95%. This robust system performs precisely with raw data without normalization as well as with converted data in which the continuous methylation levels are accounted. Strikingly, this system can even accurately predict new samples generated from different microarray platforms and the next-generation sequencing. The subtypes of cells, such as female and male iPSCs and fetal and adult SCs, can also be discriminated with this method. Thus, this novel quantitative system works as an accurate framework for discriminating the three cell types, iPSCs, ESCs, and SCs. This strategy also supports the notion that DNA-methylation generally varies among the three cell types.Anyou WangYing DuQianchuan HeChunxiao ZhouPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 8, Iss 2, p e56095 (2013)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Anyou Wang Ying Du Qianchuan He Chunxiao Zhou A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
description	Induced pluripotent stem cells (iPSCs) derived from somatic cells (SCs) and embryonic stem cells (ESCs) provide promising resources for regenerative medicine and medical research, leading to a daily identification of new cell lines. However, an efficient system to discriminate the different types of cell lines is lacking. Here, we develop a quantitative system to discriminate the three cell types, iPSCs, ESCs, and SCs. The system consists of DNA-methylation biomarkers and mathematical models, including an artificial neural network and support vector machines. All biomarkers were unbiasedly selected by calculating an eigengene score derived from analysis of genome-wide DNA methylations. With 30 biomarkers, or even with as few as 3 top biomarkers, this system can discriminate SCs from pluripotent cells (PCs, including ESCs and iPSCs) with almost 100% accuracy. With approximately 100 biomarkers, the system can distinguish ESCs from iPSCs with an accuracy of 95%. This robust system performs precisely with raw data without normalization as well as with converted data in which the continuous methylation levels are accounted. Strikingly, this system can even accurately predict new samples generated from different microarray platforms and the next-generation sequencing. The subtypes of cells, such as female and male iPSCs and fetal and adult SCs, can also be discriminated with this method. Thus, this novel quantitative system works as an accurate framework for discriminating the three cell types, iPSCs, ESCs, and SCs. This strategy also supports the notion that DNA-methylation generally varies among the three cell types.
format	article
author	Anyou Wang Ying Du Qianchuan He Chunxiao Zhou
author_facet	Anyou Wang Ying Du Qianchuan He Chunxiao Zhou
author_sort	Anyou Wang
title	A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
title_short	A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
title_full	A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
title_fullStr	A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
title_full_unstemmed	A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
title_sort	quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.
publisher	Public Library of Science (PLoS)
publishDate	2013
url	https://doaj.org/article/7862593a54be44579970263d08203210
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A quantitative system for discriminating induced pluripotent stem cells, embryonic stem cells and somatic cells.

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