Identifying Cell-Type-Specific Metabolic Signatures Using Transcriptome and Proteome Analyses.
Identifying Cell-Type-Specific Metabolic Signatures Using Transcriptome and Proteome Analyses.
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利用转录组和蛋白质组分析鉴定细胞类型特异性代谢特征
DOI：
10.1002/cpz1.245
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发表时间：
2021-09
期刊：
影响因子：
--
通讯作者：
Cheng CW
中科院分区：
文献类型：
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作者：
Gebert N;Rahman S;Lewis CA;Ori A;Cheng CW
在各种组织中的研究已经揭示了代谢途径在调节成体干细胞在组织再生和肿瘤起始中的功能中的中心作用。因此，成体干细胞独特的代谢依赖性或偏好性正在成为一类新的治疗靶点。最近，包括高分辨率代谢组学、蛋白质组学和转录组学在内的先进方法已经被开发出来以解决对干细胞代谢日益增长的兴趣。一个实用的框架，整合组学分析，需要系统地进行代谢特性的细胞类型特异性的方式。在这里，我们利用转录组学和蛋白质组学研究的最新进展，通过使用基因和参与主要代谢途径的编码酶重建细胞身份来识别细胞类型特异性代谢特征。我们提供细胞分离、转录组和蛋白质组分析以及代谢物分析和测量的方案。这里提出的映射细胞类型特异性代谢特征的工作流程，虽然最初是为肠隐窝细胞开发的，但可以很容易地实现其他组织中的细胞群，并且与大多数公共数据集高度兼容。
Studies in various tissues have revealed a central role of metabolic pathways in regulating adult stem cell function in tissue regeneration and tumor initiation. The unique metabolic dependences or preferences of adult stem cells, therefore, are emerging as a new category of therapeutic target. Recently, advanced methods including high-resolution metabolomics, proteomics, and transcriptomics have been developed to address the growing interest in stem cell metabolism. A practical framework integrating the omics analyses is needed to systematically perform metabolic characterization in a cell-type-specific manner. Here, we leverage recent advances in transcriptomics and proteomics research to identify cell-type-specific metabolic features by reconstructing cell identity using genes and the encoded enzymes involved in major metabolic pathways. We provide protocols for cell isolation, transcriptome and proteome analyses, and metabolite profiling and measurement. The workflow for mapping cell-type-specific metabolic signatures presented here, although initially developed for intestinal crypt cells, can be easily implemented for cell populations in other tissues, and is highly compatible with most public datasets.