Whole-organism clone tracing using single-cell sequencing
Whole-organism clone tracing using single-cell sequencing
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DOI：
10.1038/nature25969
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发表时间：
2018-04-05
期刊：
影响因子：
64.8
通讯作者：
van Oudenaarden, Alexander
中科院分区：
文献类型：
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作者：
Alemany, Anna;Florescu, Maria;van Oudenaarden, Alexander
胚胎发育是多细胞生物生命中的关键时期，在此期间，有限的胚胎祖细胞产生成体中的所有细胞。确定这些祖细胞在成体组织中获得的命运需要同时测量克隆历史和单细胞分辨率的细胞身份，这一直是一个重大挑战。克隆历史传统上通过在发育期间显微镜下跟踪细胞（1，2），监测遗传编码的荧光蛋白的遗传表达（3），以及最近使用利用体细胞突变（4），微卫星不稳定性（5），转座子标签（6），病毒条形码（7），CRISPR-Cas（9）基因组编辑（8-13）和Cre-loxP重组（14）。单细胞转录组学（15）为无偏细胞类型分类提供了一个强大的平台。在这里，我们提出了ScarTrace，一种单细胞测序策略，可以同时定量从成年斑马鱼不同器官获得的数千个细胞的克隆历史和细胞类型。使用ScarTrace，我们发现一小组多能胚胎祖细胞在肾骨髓中产生所有造血细胞，并且许多祖细胞在眼睛和大脑中产生特定的细胞类型。此外，我们还研究了胚胎祖细胞何时发育到左眼或右眼。ScarTrace揭示了尾鳍中的表皮细胞和间充质细胞来自相同的祖细胞，并且成骨细胞限制的前体细胞可以在再生过程中产生间充质细胞。此外，我们确定常驻免疫细胞的鳍与其他血细胞类型的不同克隆起源。我们设想，类似的方法将在其他实验系统中有重要的应用，其中胚胎克隆起源与成人细胞类型的匹配将最终允许重建成人身体是如何从单细胞构建的。
Embryonic development is a crucial period in the life of a multicellular organism, during which limited sets of embryonic progenitors produce all cells in the adult body. Determining which fate these progenitors acquire in adult tissues requires the simultaneous measurement of clonal history and cell identity at single-cell resolution, which has been a major challenge. Clonal history has traditionally been investigated by microscopically tracking cells during development(1,2), monitoring the heritable expression of genetically encoded fluorescent proteins(3) and, more recently, using next-generation sequencing technologies that exploit somatic mutations(4), microsatellite instability(5), transposon tagging(6), viral barcoding(7), CRISPR-Cas(9) genome editing(8-13) and Cre-loxP recombination(14). Single-cell transcriptomics(15) provides a powerful platform for unbiased cell-type classification. Here we present ScarTrace, a single-cell sequencing strategy that enables the simultaneous quantification of clonal history and cell type for thousands of cells obtained from different organs of the adult zebrafish. Using ScarTrace, we show that a small set of multipotent embryonic progenitors generate all haematopoietic cells in the kidney marrow, and that many progenitors produce specific cell types in the eyes and brain. In addition, we study when embryonic progenitors commit to the left or right eye. ScarTrace reveals that epidermal and mesenchymal cells in the caudal fin arise from the same progenitors, and that osteoblast-restricted precursors can produce mesenchymal cells during regeneration. Furthermore, we identify resident immune cells in the fin with a distinct clonal origin from other blood cell types. We envision that similar approaches will have major applications in other experimental systems, in which the matching of embryonic clonal origin to adult cell type will ultimately allow reconstruction of how the adult body is built from a single cell.