利用单细胞测序技术追踪胚胎发育中细胞的演变过程

Tracing embryonic development through single-cell sequencing analysis

在生命形成过程中,如何从单一的受精卵产生多种细胞类型、组织以及器官,并且将它们组装在一起形成一个完整的个体是生物学最重要的奥秘之一.在胚胎发育过程中,细胞的分裂和逐步分化是最基本的生物学事件,揭示这一过程中不同细胞类型的产生方式将对深刻理解个体发育具有重要的意义.过去几十年来,研究人员利用遗传标记的方法对部分器官中特定细胞类型的形成过程进行了深入的分析,然而由于技术方面的限制,在大时间尺度上对整个胚胎的发育进程进行全面的追踪仍然十分困难.近年来,以单细胞测序技术、基因编辑技术以及计算生物学为代表的新兴生物学方法,为研究人员提供了新的工具,极大地拓展了我们对不同生物学问题的可操作性,使得我们对于胚胎发育过程中的重要生物学事件有了更加清晰的认识.现在,一种将单细胞测序技术与基因编辑技术以及计算工具相结合的方法,正在向人们展现到目前为止关于脊椎动物胚胎发育最为详细的细胞命运转变图谱.2018年4月,Science[1]杂志以新闻报道的形式对当月在该杂志上发表的3篇文章进行了深度介绍,展现了这些新技术在研究胚胎发育过程中的巨大应用前景.在这3篇文章中,研究人员报道了他们对大多数发育中的斑马鱼或青蛙胚胎细胞内的基因表达进行多个时间点测序分析的结果.他们将这些以几分钟到几小时间隔获得的数据拼接在一起,通过构建细胞命运转变图谱,揭示了不同类型细胞的形成过程,完整地展现了脊椎动物胚胎发育过程.

The gradual formation of varies tissues and organs from a single fertilized egg is precisely regulated in spatial and temporal manner during the embryonic development. A comprehensive understanding about the cell fate decision of different cell types is one of the key questions in developmental biology. However, limitations in biotechnology have severely restricted us to well understand the whole process of embryonic development in the past decades, leading to many unresolved questions that still need further exploration. In the last few years, rapid development of emerging technologies, which are represented by single-cell sequencing, gene editing and computational biology have immensely expanded our accessibility to many challenging questions that could hardly be resolved in the past. Continuous modifications of these methods also make it possible for us to reveal the key regulatory processes in embryonic development and disease progression more comprehensively. Meanwhile, the combination of these different biotechnologies is providing us a more flexible way to carry out in-depth investigations of many basic problems in embryonic development and even the occurrence of diseases. Recently, researchers from three different groups applied high throughput single-cell RNA sequencing methods combined with computational tools to trace the transcriptional changes during vertebrate embryo development. In a study on zebrafish embryo development, through analyzing more than 90000 single cells, researchers highlighted the cell transition process during body axis patterning, different germ layer formation as well as organogenesis. Meanwhile, another zebrafish study constructed a branching tree based on large scale single-cell RNA-seq data, revealing the transcriptome trajectories during the formation of the 25 different cell types, highlighting how progenitor cells gradually differentiate to specific cell types. Besides, another group applied microfluidics based single-cell sequencing method and analyzed above 130000 cells from whole frog embryo. They identified 259 gene expression clusters that were corresponded to 10 different time points, providing a landscape of cell states during the formation of all cell lineages. These studies combined single-cell sequencing and computation tools or gene editing tools to track the cell fate transition in zebrafish and frog embryo development. By recording the gene expression atlas of each single cell that collected from multiple fetal stages, they tracked the cell type formation and cell fate decision cell-by-cell, constructing entire cell lineages in embryonic development. In recent years, the emerging of new technologies greatly expanded our insights in many key biological events, leading us a more comprehensive understanding of development and human disease. The constantly development of single-cell RNA-seq and computational tools play very important roles in life science, especially in embryo development and cell differentiation, identifying novel sub-cell types as well as their function in development. In disease pathology analysis, especially in cancer studies, applying single-cell RNA-seq immensely revealed the heterogeneity of cancer cells, highlighted the molecular features of these disease related cells, paving new ways to better understand the pathogenesis of human disease. These studies revealed the great potential of single-cell sequencing in solving important biological questions, and they also provided a novel approach to investigate the onset and progression of many diseases.