Comments on 'Molecular architecture of lineage allocation and tissue organization in early mouse embryo'.
Comments on 'Molecular architecture of lineage allocation and tissue organization in early mouse embryo'.
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对“早期小鼠胚胎中谱系分配和组织组织的分子结构”的评论。
DOI：
10.1093/jmcb/mjz101
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Guangdun Peng
中科院分区：
文献类型：
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作者：
Guizhong Cui;Naihe Jing;Guangdun Peng
单细胞RNA-seq能够通过伪时间重建对连续改变状态的细胞进行比对，极大地改变了对胚胎发育过程中细胞命运转变的理解(Shapiro等人，2013；Hoppe等人，2014)。虽然仍然缺乏单细胞空间分析，空间差异对细胞排列有贡献，但可以进行伪空间分析，也可以推断细胞组织(Cheng等人，2019年；Nowotschin等人，2019)。然而，实时时间和空间的转录切割分析不是通过计算重建来揭示空间或发育轨迹，而是为解剖细胞组织、分子结构和谱系分配提供了一个可信的基准。识别复杂生物系统中空间基因表达差异的能力对于我们理解发育生物学和疾病的进展至关重要。在最近发表的题为《小鼠早期胚胎谱系分配和组织的分子体系结构》(Peng等人，2019年)中，我们对跨越E5的植入后小鼠胚胎的空间结构进行了系统的调查。5至E7。5个阶段。与移植后阶段小鼠早期胚胎的传统单细胞RNA-SEQ相比，现在相当多(Pijuan-Sala等人，2019；Nowotschin等人，2019)，保留了细胞的固有位置和细胞之间的关系，从而为探索胚胎中祖细胞的动态分子结构提供了独特的属性。考虑到这么多激光显微解剖的胚胎组织被测序，这是一项数据量很大的工作。虽然空间域的2D显示和识别基本上遵循了以前的努力(Peng等人，2016；han等人，2018)，但细胞群体在时间和空间上的组织谱系和连通性需要独特的分析方法，与单细胞轨迹方案有很大不同。相对稀疏的数据覆盖不适合伪时间或伪空间重建的连续变化模型。此外，还介绍了不同程度的批次效应。
Single-cell RNA-seq, with its capability to align cells of continuously changed status by pseudo-time reconstruction, has greatly revolutionized the understanding of cell fate transition during embryo development (Shapiro et al., 2013; Hoppe et al., 2014). While there is still a lack of single-cell spatial analysis, with the spatial variance contributing to the cell alignment, pseudo-space analysis might be conducted and the cell organization could be inferred as well (Cheng et al., 2019; Nowotschin et al., 2019). However, rather than revealing spatial or developmental trajectory by computational reconstruction, transcriptomic analysis of real time and space provides an authentic benchmark for dissecting the cell organization, molecular architecture, and lineage allocation. The ability to discern spatial gene expression differences in complex biological systems is critical to our understanding of developmental biology and the progression of disease.In the recent publication entitled ‘Molecular architecture of lineage allocation and tissue organization in early mouse embryo’(Peng et al., 2019), we performed a systematic survey of spatial architecture of post-implantation mouse embryos spanning E5. 5 to E7. 5 stages. In contrast to conventional single-cell RNA-seq of early mouse embryos at the postimplantation stages, which is quite a few now (Pijuan-Sala et al., 2019; Nowotschin et al., 2019), the native location of cells and the relationship between cells were retained, thus providing unique attributes to probe the dynamic molecular structure of progenitor cells in the embryo. This is a data-heavy work, considering that so many pieces of laser microdissected embryonic tissues were sequenced. Although the 2D display and identification of spatial domains were basically following the previous endeavors (Peng et al., 2016; Han et al., 2018), the tissue lineage and connectivity of cell populations in time and space demand unique analytic methodologies that differ greatly with single-cell trajectory protocol. The relatively sparse data coverage does not fit a continuous change model for pseudo-time or pseudospace reconstruction. Besides, various degrees of batch effects were introduced