Expression profiling of mouse embryonic and tissue stem cells

在我们早期的工作中，我们比较了小鼠ES细胞和滋养层干细胞（TS）的DNA微阵列的全球表达谱。我们研究了Esg 1，这是一个在ES细胞中特异性表达的基因，发现该基因编码一种RNA结合蛋白，可以与许多RNA靶点结合。我们还比较了小鼠ES细胞在体外进行神经分化和成人神经干祖细胞（NS）的表达谱。结果表明，ES细胞在体外向神经细胞分化的过程再现了体内神经细胞的发育过程。我们还推断出一组4,000个基因，其表达随着神经定向分化而增加;它可以用作神经定向分化程度的尺度。我们还进行了小鼠胚胎生殖（EG）细胞和多能成体干细胞（MAPCs）的全球基因表达谱分析。我们已经进行了高通量原位杂交检测ES细胞培养的244个基因。我们发现三个基因（Zscan 4，Whsc 2和Rhox 9）显示出斑点表达模式（斑点集落模式）。我们还发现9个基因表现出相对异质性的表达模式（菌落中的镶嵌模式：Zfp 42/Rex 1、Rest、Atf 4、Pa 2g 4、E2 f2、Nanog、Dppa 3/Pgc 7/Stella、Esrrb和Fscn 1）。这表明在未分化的ES细胞培养物中存在异质细胞群。作为了解ES细胞基因表达调控的基础信息，我们使用DNA微阵列测量了基本上所有小鼠基因的mRNA半衰期。最近，我们也证明了，全球基因表达谱的主成分分析地图细胞在多维转录本档案空间和分化细胞的位置进展，在一个逐步的方式沿着轨迹从未分化的胚胎干细胞（ES）位于顶点。我们提出了三个“细胞谱系分化”，代表了ES细胞在哺乳动物发育中分化为前三个谱系：原始内胚层、滋养层和原始外胚层/神经外胚层。细胞沿着这些轨迹的位置似乎反映了细胞的发育潜能，并且可以用作细胞潜能的尺度。事实上，我们已经表明，胚胎生殖细胞和诱导多能（iPS）细胞被映射的轨迹的起源附近，而小鼠胚胎成纤维细胞和成纤维细胞系被映射的轨迹的远端附近。我们研究了与这些细胞谱系轨迹相关的分子过程，通过基于微阵列的基因表达谱的成纤维细胞转化为iPS细胞。我们发现许多早期胚胎基因在小鼠成纤维细胞形成iPS细胞的早期阶段被重新激活。

In our earlier work, we compared the global expression profiles of mouse ES cells and trophoblast stem (TS) cells by DNA microarrays. We studied Esg1, one of the genes identified as a gene expressed specifically in ES cells, and found that the gene encodes an RNA-binding protein that binds to many RNA targets. We have also compared the expression profiles of mouse ES cells undergoing neural differentiation in vitro and those of adult neural stem progenitor (NS) cells. The results suggested that ES cells undergoing neural differentiation in vitro recapitulate the development of neural lineages in vivo. We also inferred a set of 4,000 genes, the expression of which increased with neural commitment differentiation; it can be used as a scale for the degree of commitment to neural differentiation. We also carried out global gene expression profiling of mouse embryonic germ (EG) cells and multipotent adult stem cells (MAPCs). We have carried out high-throughput in situ hybridization assays on ES cell cultures for 244 genes. We found that three genes (Zscan4, Whsc2, and Rhox9) showed a spotty expression pattern (spot-in-colony pattern). We also found nine genes that showed a relatively heterogeneous expression pattern (mosaic-in-colony pattern: Zfp42/Rex1, Rest, Atf4, Pa2g4, E2f2, Nanog, Dppa3/Pgc7/Stella, Esrrb, and Fscn1). This indicates the presence of a heterogeneous cell population in undifferentiated ES cell cultures. As the baseline information to understand the gene expression regulation in ES cells, we have measured the mRNA half-life of essentially all mouse genes by using DNA microarrays. Recently, we have also demonstrated that principal component analysis of global gene expression profiles map cells in multidimensional transcript profile space and the positions of differentiating cells progress in a stepwise manner along trajectories starting from undifferentiated embryonic stem (ES) cells located in the apex. We have presented three 'cell lineage trajectories', which represent the differentiation of ES cells into the first three lineages in mammalian development: primitive endoderm, trophoblast and primitive ectoderm/neural ectoderm. The positions of the cells along these trajectories seem to reflect the developmental potency of cells and can be used as a scale for the potential of cells. Indeed, we have shown that embryonic germ cells and induced pluripotent (iPS) cells are mapped near the origin of the trajectories, whereas mouse embryo fibroblast and fibroblast cell lines are mapped near the far end of the trajectories. We studied the molecular processes that are associated with these cell lineage trajectories by microarray-based gene expression profiling of the fibroblast cells being converted to the iPS cells. We found that many early embryonic genes are reactivated during the early phase of iPS cell formation from mouse fibroblast cells.