Somatic mutations and cell identity linked by Genotyping of Transcriptomes
Somatic mutations and cell identity linked by Genotyping of Transcriptomes
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DOI：
10.1038/s41586-019-1367-0
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发表时间：
2019-07-18
期刊：
影响因子：
64.8
通讯作者：
Landau, Dan A.
中科院分区：
文献类型：
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作者：
Nam, Anna S.;Kim, Kyu-Tae;Landau, Dan A.
在缺乏区分癌症克隆彼此或混合的非肿瘤细胞的表面标志物的情况下，定义恶性细胞的转录组身份具有挑战性。为了应对这一挑战，我们开发了转录组基因分型（GoT），这是一种将基因分型与高通量基于液滴的单细胞RNA测序相结合的方法。我们应用GoT分析了来自CALR突变的骨髓增生性肿瘤患者的38，290个CD 34（+）细胞，以研究体细胞突变如何破坏人类造血的复杂过程。恶性与正常造血祖细胞的高分辨率映射显示，具有突变CALR的细胞的髓样分化具有增加的适应性优势。我们确定未折叠蛋白反应是CALR突变的主要结果，对细胞特性有相当大的依赖性，以及在未定型干细胞中特异性上调NF-κ B通路。我们进一步扩展了GoT工具包，以对远离转录物末端的多个靶标和基因座进行基因分型。总之，这些发现揭示了骨髓增生性肿瘤中体细胞突变的转录输出依赖于天然细胞身份。
Defining the transcriptomic identity of malignant cells is challenging in the absence of surface markers that distinguish cancer clones from one another, or from admixed non-neoplastic cells. To address this challenge, here we developed Genotyping of Transcriptomes (GoT), a method to integrate genotyping with high-throughput droplet-based single-cell RNA sequencing. We apply GoT to profile 38,290 CD34(+) cells from patients with CALR-mutated myeloproliferative neoplasms to study how somatic mutations corrupt the complex process of human haematopoiesis. High-resolution mapping of malignant versus normal haematopoietic progenitors revealed an increasing fitness advantage with myeloid differentiation of cells with mutated CALR. We identified the unfolded protein response as a predominant outcome of CALR mutations, with a considerable dependency on cell identity, as well as upregulation of the NF-kappa B pathway specifically in uncommitted stem cells. We further extended the GoT toolkit to genotype multiple targets and loci that are distant from transcript ends. Together, these findings reveal that the transcriptional output of somatic mutations in myeloproliferative neoplasms is dependent on the native cell identity.