Oncode Institute, Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, 3584 CT Utrecht, The Netherlands.
Nature. 2018 Apr 5;556(7699):108-112. doi: 10.1038/nature25969. Epub 2018 Mar 28.
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, monitoring the heritable expression of genetically encoded fluorescent proteins and, more recently, using next-generation sequencing technologies that exploit somatic mutations, microsatellite instability, transposon tagging, viral barcoding, CRISPR-Cas9 genome editing and Cre-loxP recombination. Single-cell transcriptomics 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.
胚胎发育是多细胞生物生命中的一个关键时期，在此期间，有限数量的胚胎祖细胞产生成年体内的所有细胞。确定这些祖细胞在成年组织中获得什么样的命运，需要以单细胞分辨率同时测量克隆历史和细胞身份，这一直是一个主要挑战。克隆历史传统上是通过在发育过程中显微镜跟踪细胞来研究的，监测遗传编码荧光蛋白的可遗传表达，以及最近使用下一代测序技术，这些技术利用体细胞突变、微卫星不稳定性、转座子标记、病毒条形码、CRISPR-Cas9 基因组编辑和 Cre-loxP 重组。单细胞转录组学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，这是一种单细胞测序策略，可同时定量来自成年斑马鱼不同器官的数千个细胞的克隆历史和细胞类型。使用 ScarTrace，我们表明一小部分多能胚胎祖细胞产生肾脏骨髓中的所有造血细胞，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，我们研究胚胎祖细胞何时决定左眼或右眼。ScarTrace 表明，尾部鳍中的表皮和间充质细胞来自同一祖细胞，并且成骨细胞受限前体在再生过程中可以产生间充质细胞。此外，我们在 fins 中鉴定出具有与其他血细胞类型不同的克隆起源的常驻免疫细胞。我们设想类似的方法将在其他实验系统中有重要应用，其中胚胎克隆起源与成年细胞类型的匹配最终将允许从单个细胞重建成年体的构建方式。
