Lu Shi-Jiang, Hipp Jennifer A, Feng Qiang, Hipp Jason D, Lanza Robert, Atala Anthony
Advanced Cell Technology, Worcester, MA 01605, USA.
Genome Biol. 2007;8(11):R240. doi: 10.1186/gb-2007-8-11-r240.
Microarrays are being used to understand human embryonic stem cell (hESC) differentiation. Most differentiation protocols use a multi-stage approach that induces commitment along a particular lineage. Therefore, each stage represents a more mature and less heterogeneous phenotype. Thus, characterizing the heterogeneous progenitor populations upon differentiation are of increasing importance. Here we describe a novel method of data analysis using a recently developed differentiation protocol involving the formation of functional hemangioblasts from hESCs. Blast cells are multipotent and can differentiate into multiple lineages of hematopoeitic cells (erythroid, granulocyte and macrophage), endothelial and smooth muscle cells.
Large-scale transcriptional analysis was performed at distinct time points of hESC differentiation (undifferentiated hESCs, embryoid bodies, and blast cells, the last of which generates both hematopoietic and endothelial progenies). Identifying genes enriched in blast cells relative to hESCs revealed a genetic signature indicative of erythroblasts, suggesting that erythroblasts are the predominant cell type in the blast cell population. Because of the heterogeneity of blast cells, numerous comparisons were made to publicly available data sets in silico, some of which blast cells are capable of differentiating into, to assess and characterize the blast cell population. Biologically relevant comparisons masked particular genetic signatures within the heterogeneous population and identified genetic signatures indicating the presence of endothelia, cardiomyocytes, and hematopoietic lineages in the blast cell population.
The significance of this microarray study is in its ability to assess and identify cellular populations within a heterogeneous population through biologically relevant in silico comparisons of publicly available data sets. In conclusion, multiple in silico comparisons were necessary to characterize tissue-specific genetic signatures within a heterogeneous hemangioblast population.
微阵列正被用于了解人类胚胎干细胞（hESC）的分化。大多数分化方案采用多阶段方法，诱导细胞沿着特定谱系定向分化。因此，每个阶段都代表着一种更成熟且异质性更低的表型。所以，表征分化过程中异质性祖细胞群体变得越来越重要。在此，我们描述了一种新的数据分析方法，该方法使用了最近开发的一种分化方案，该方案涉及从hESC形成功能性成血管细胞。成血管细胞具有多能性，可分化为造血细胞（红细胞、粒细胞和巨噬细胞）、内皮细胞和平滑肌细胞的多个谱系。
在hESC分化的不同时间点（未分化的hESC、胚状体和成血管细胞，其中成血管细胞可产生造血和内皮祖细胞）进行了大规模转录分析。鉴定相对于hESC在成血管细胞中富集的基因，揭示了一种指示成红细胞的基因特征，表明成红细胞是成血管细胞群体中的主要细胞类型。由于成血管细胞的异质性，在计算机上与公开可用的数据集进行了大量比较，其中一些是成血管细胞能够分化形成的细胞类型，以评估和表征成血管细胞群体。生物学上相关的比较掩盖了异质群体中的特定基因特征，并鉴定出表明成血管细胞群体中存在内皮细胞、心肌细胞和造血谱系的基因特征。
这项微阵列研究的意义在于其能够通过对公开可用数据集进行生物学上相关的计算机比较，来评估和识别异质群体中的细胞群体。总之，需要进行多次计算机比较，以表征异质性成血管细胞群体中的组织特异性基因特征。
