Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model.
Identification of an epigenetic signature in human induced pluripotent stem cells using a linear machine learning model.
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DOI：
10.1007/s13577-020-00446-3
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发表时间：
2021-01
期刊：
影响因子：
4.3
通讯作者：
Umezawa A
中科院分区：
文献类型：
--
作者：
Nishino K;Takasawa K;Okamura K;Arai Y;Sekiya A;Akutsu H;Umezawa A
使用人类诱导的多能干细胞(IPSCs)作为人类胚胎干细胞(ESCs)的替代品，是应对免疫排斥等挑战的潜在解决方案，而且不涉及将ESCs用于再生医学的伦理问题，从而使生物学研究得以发展。然而，以前研究的比较分析并没有表明IPSCs与ESCs有任何具体的区别。因此，在本研究中，我们建立了一个基于线性分类的学习模型，以区分ESCs、iPSCs、胚胎癌细胞(ECCs)和体细胞。学习的模型识别细胞类型的最高准确率为94.23%。此外，通过对所学模型的成分分析，确定了IPSCs的表观遗传学特征，这与ESCs的表观遗传学特征不同。在第7、8、12和22号染色体上，存在甲基化波动的IPSC特异性区域非常丰富。本研究开发的方法数据全面，可广泛应用于分子生物学研究的多个方面。本文的在线版本(10.1007/s13577-020-00446-3)包含向授权用户提供的补充材料。
The use of human induced pluripotent stem cells (iPSCs), used as an alternative to human embryonic stem cells (ESCs), is a potential solution to challenges, such as immune rejection, and does not involve the ethical issues concerning the use of ESCs in regenerative medicine, thereby enabling developments in biological research. However, comparative analyses from previous studies have not indicated any specific feature that distinguishes iPSCs from ESCs. Therefore, in this study, we established a linear classification-based learning model to distinguish among ESCs, iPSCs, embryonal carcinoma cells (ECCs), and somatic cells on the basis of their DNA methylation profiles. The highest accuracy achieved by the learned models in identifying the cell type was 94.23%. In addition, the epigenetic signature of iPSCs, which is distinct from that of ESCs, was identified by component analysis of the learned models. The iPSC-specific regions with methylation fluctuations were abundant on chromosomes 7, 8, 12, and 22. The method developed in this study can be utilized with comprehensive data and widely applied to many aspects of molecular biology research. The online version of this article (10.1007/s13577-020-00446-3) contains supplementary material, which is available to authorized users.
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影响因子：
10.3
作者：
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通讯作者：
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