A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors
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DOI：
10.1038/s41591-020-0844-1
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发表时间：
2020-05-01
期刊：
影响因子：
82.9
通讯作者：
Regev, Aviv
中科院分区：
文献类型：
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作者：
Slyper, Michal;Porter, Caroline B. M.;Regev, Aviv
单细胞基因组学对于绘制肿瘤生态系统至关重要。尽管单细胞RNA测序（scRNA - Seq）可对从新鲜肿瘤中分离的细胞的RNA进行分析，但单核RNA测序（snRNA - Seq）对于分析冷冻的或难以分离的肿瘤是必需的。每种方法都需要针对不同的组织和肿瘤类型进行定制，这对其应用造成了障碍。在此，我们分别针对使用scRNA - Seq分析新鲜临床肿瘤样本以及使用snRNA - Seq分析冷冻临床肿瘤样本开发了一套系统的工具包。我们分析了来自23个样本的40个样本中的216,490个细胞和细胞核，这些样本涵盖了8种具有不同组织和样本特征的肿瘤类型。我们通过细胞和细胞核质量、回收率以及细胞组成来评估实验方案。来自匹配样本的scRNA - Seq和snRNA - Seq检测到了相同的细胞类型，但比例不同。我们的工作为广泛的肿瘤研究提供了指导，包括针对其他肿瘤从工具包中测试和选择方法的标准，从而为绘制肿瘤图谱铺平了道路。
Single-cell genomics is essential to chart tumor ecosystems. Although single-cell RNA-Seq (scRNA-Seq) profiles RNA from cells dissociated from fresh tumors, single-nucleus RNA-Seq (snRNA-Seq) is needed to profile frozen or hard-to-dissociate tumors. Each requires customization to different tissue and tumor types, posing a barrier to adoption. Here, we have developed a systematic toolbox for profiling fresh and frozen clinical tumor samples using scRNA-Seq and snRNA-Seq, respectively. We analyzed 216,490 cells and nuclei from 40 samples across 23 specimens spanning eight tumor types of varying tissue and sample characteristics. We evaluated protocols by cell and nucleus quality, recovery rate and cellular composition. scRNA-Seq and snRNA-Seq from matched samples recovered the same cell types, but at different proportions. Our work provides guidance for studies in a broad range of tumors, including criteria for testing and selecting methods from the toolbox for other tumors, thus paving the way for charting tumor atlases.