Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer.
Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer.
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DOI：
10.1038/s41467-017-00244-w
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发表时间：
2017-08-09
影响因子：
16.6
通讯作者：
Navin N
中科院分区：
文献类型：
--
作者：
Gao R;Kim C;Sei E;Foukakis T;Crosetto N;Chan LK;Srinivasan M;Zhang H;Meric-Bernstam F;Navin N
单细胞RNA测序已成为解析肿瘤转录多样性的有力工具，但受到通量、成本以及处理存档冷冻组织样本能力的限制。在此，我们开发了一种高通量3′单细胞核RNA测序方法，该方法结合了纳米网格技术、自动成像和细胞选择，可并行对多达约1800个单核进行测序。我们将乳腺癌细胞系中485个单核的转录组与424个单细胞进行比较，结果显示在基因水平和丰度上具有高度一致性（93.34%）。我们还分析了来自冷冻乳腺癌肿瘤样本的416个核以及来自正常乳腺组织的380个核。这些数据揭示了癌细胞表型的异质性，包括血管生成、增殖和干性，以及一个具有许多过表达癌基因的小亚群（19%）。我们的研究证明了纳米网格单细胞核RNA测序在研究冷冻存档组织样本中肿瘤核转录程序方面的实用性。
单细胞RNA测序是理解细胞多样性的有力工具，但受到成本、通量和样本制备的限制。在此，作者利用集成成像的纳米网格技术，从新鲜或冷冻组织中并行对数千个肿瘤核进行测序。
Single cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop a high-throughput 3′ single-nucleus RNA sequencing approach that combines nanogrid technology, automated imaging, and cell selection to sequence up to ~1800 single nuclei in parallel. We compare the transcriptomes of 485 single nuclei to 424 single cells in a breast cancer cell line, which shows a high concordance (93.34%) in gene levels and abundance. We also analyze 416 nuclei from a frozen breast tumor sample and 380 nuclei from normal breast tissue. These data reveal heterogeneity in cancer cell phenotypes, including angiogenesis, proliferation, and stemness, and a minor subpopulation (19%) with many overexpressed cancer genes. Our studies demonstrate the utility of nanogrid single-nucleus RNA sequencing for studying the transcriptional programs of tumor nuclei in frozen archival tissue samples. Single cell RNA sequencing is a powerful tool for understanding cellular diversity but is limited by cost, throughput and sample preparation. Here the authors use nanogrid technology with integrated imaging to sequence thousands of cancer nuclei in parallel from fresh or frozen tissue.
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影响因子：
12.3
作者：
Bose S;Wan Z;Carr A;Rizvi AH;Vieira G;Pe'er D;Sims PA
通讯作者：
Sims PA
影响因子：
5.8
作者：
Carey, Lisa A.
通讯作者：
Carey, Lisa A.
影响因子：
2
作者：
Chen X;Li J;Gray WH;Lehmann BD;Bauer JA;Shyr Y;Pietenpol JA
通讯作者：
Pietenpol JA
影响因子：
48
作者：
Kharchenko, Peter V.;Silberstein, Lev;Scadden, David T.
通讯作者：
Scadden, David T.
DOI：
10.1126/science.aad7038
发表时间：
2016-08-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Habib N;Li Y;Heidenreich M;Swiech L;Avraham-Davidi I;Trombetta JJ;Hession C;Zhang F;Regev A
通讯作者：
Regev A