Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.
Single-cell analysis of mixed-lineage states leading to a binary cell fate choice.
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DOI：
10.1038/nature19348
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发表时间：
2016-09-29
期刊：
影响因子：
64.8
通讯作者：
Grimes, H. Leighton
中科院分区：
文献类型：
--
作者：
Olsson, Andre;Venkatasubramanian, Meenakshi;Chaudhri, Viren K.;Aronow, Bruce J.;Salomonis, Nathan;Singh, Harinder;Grimes, H. Leighton
描述细胞的分层状态，包括罕见的中间体和协调细胞类型规范的调控基因网络，是发育生物学的持续挑战。单细胞RNA测序极大地加快了这类研究的速度，因为它能够提供对基因组状态及其假定调节因子的全面描述。造血多潜能祖细胞以及双潜能中间体在单细胞水平上表现出基因表达的混合谱系模式。这种混合谱系状态可能反映了不同发育潜力的分子启动，即共表达的另类谱系决定因素，即转录因子。尽管已经提出了一个双稳定的基因调控网络来调控中性粒细胞或巨噬细胞的规格，但体内过渡态的性质以及细胞命运决定因素的潜在动力学仍然难以捉摸。在这里，我们使用单细胞RNA测序结合一种新的分析工具，迭代聚类和引导基因选择，以及克隆形成试验来描绘最终导致小鼠中性粒细胞或巨噬细胞指定的分级基因组和调控状态。我们表明，这项分析捕获了普遍存在的混合血统中间体，这些中间体表现出造血干细胞/祖细胞和髓系祖细胞基因的同时表达。它还发现了罕见的亚稳中间体，破坏了造血干细胞/祖细胞基因表达计划，转而表达低水平的髓系决定因素IRF8和Gfi1(Refs，，，)。遗传扰动和染色质免疫沉淀，然后测序显示，IRF8和Gfi1是对抗髓系基因调控网络的关键组件。这两个决定因素的共同损失“捕获”了亚稳中间体。我们认为，混合谱系状态在细胞命运指定过程中是必需的，由于其动态不稳定性而表现出不同的频率，并由相反的基因调控网络决定。
Delineating hierarchical cellular states, including rare intermediates and the networks of regulatory genes that orchestrate cell-type specification, are continuing challenges for developmental biology. Single-cell RNA sequencing is greatly accelerating such research, given its power to provide comprehensive descriptions of genomic states and their presumptive regulators,,,,. Haematopoietic multipotential progenitor cells, as well as bipotential intermediates, manifest mixed-lineage patterns of gene expression at a single-cell level,. Such mixed-lineage states may reflect the molecular priming of different developmental potentials by co-expressed alternative-lineage determinants, namely transcription factors. Although a bistable gene regulatory network has been proposed to regulate the specification of either neutrophils or macrophages,, the nature of the transition states manifestedin vivo, and the underlying dynamics of the cell-fate determinants, have remained elusive. Here we use single-cell RNA sequencing coupled with a new analytic tool, iterative clustering and guide-gene selection, and clonogenic assays to delineate hierarchical genomic and regulatory states that culminate in neutrophil or macrophage specification in mice. We show that this analysis captured prevalent mixed-lineage intermediates that manifested concurrent expression of haematopoietic stem cell/progenitor and myeloid progenitor cell genes. It also revealed rare metastable intermediates that had collapsed the haematopoietic stem cell/progenitor gene expression programme, instead expressing low levels of the myeloid determinants, Irf8 and Gfi1 (refs , , , , ). Genetic perturbations and chromatin immunoprecipitation followed by sequencing revealed Irf8 and Gfi1 as key components of counteracting myeloid-gene-regulatory networks. Combined loss of these two determinants ‘trapped’ the metastable intermediate. We propose that mixed-lineage states are obligatory during cell-fate specification, manifest differing frequencies because of their dynamic instability and are dictated by counteracting gene-regulatory networks.
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影响因子：
48
作者：
Huber W;Carey VJ;Gentleman R;Anders S;Carlson M;Carvalho BS;Bravo HC;Davis S;Gatto L;Girke T;Gottardo R;Hahne F;Hansen KD;Irizarry RA;Lawrence M;Love MI;MacDonald J;Obenchain V;Oleś AK;Pagès H;Reyes A;Shannon P;Smyth GK;Tenenbaum D;Waldron L;Morgan M
通讯作者：
Morgan M
影响因子：
11.4
作者：
Brass, AL;Zhu, AQ;Singh, H
通讯作者：
Singh, H
影响因子：
46.9
作者：
Nagai, T;Ibata, K;Miyawaki, A
通讯作者：
Miyawaki, A
影响因子：
64.5
作者：
Laslo, Peter;Spooner, Chauncey J.;Singh, Harinder
通讯作者：
Singh, Harinder
影响因子：
5.3
作者：
Jung, S;Aliberti, J;Littman, DR
通讯作者：
Littman, DR