Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells.
Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells.
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DOI：
10.1016/j.jhep.2015.05.013
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发表时间：
2015-10
影响因子：
25.7
通讯作者：
Hengstler JG
中科院分区：
文献类型：
--
作者：
Godoy P;Schmidt-Heck W;Natarajan K;Lucendo-Villarin B;Szkolnicka D;Asplund A;Björquist P;Widera A;Stöber R;Campos G;Hammad S;Sachinidis A;Chaudhari U;Damm G;Weiss TS;Nüssler A;Synnergren J;Edlund K;Küppers-Munther B;Hay DC;Hengstler JG
干细胞向肝细胞样细胞（HLC）的分化为人类肝细胞的无限供应提供了前景。然而，hcc的分化程度仍存在争议。为了获得无偏定性，我们使用来自三个不同实验室的人胚胎和诱导干细胞（ESC, hiPSC）的hplc进行了转录组学研究。将ESC和hcc的全基因组基因表达谱与新鲜分离的和培养达14天的原代人肝细胞进行比较。确定了代表成功和失败的肝细胞分化的基因网络，以及参与其调节的转录因子。基因调控网络分析表明，HLC是一种具有肝、肠、成纤维细胞和干细胞特征的混合细胞类型。“不想要的”肠道特征与KLF5和CDX2转录网络有关。聚类分析发现，与成熟肝功能（n = 1057）和下调增殖相关基因（n = 1562）高度相关的基因群接近原代肝细胞的水平。然而，含有447、101和505基因的另外三个基因簇未能达到肝细胞的水平。其中两个集群的Key TF包括SOX11、FOXQ1和YBX3。第三个不成功的簇由HNF1、CAR、FXR和PXR控制，与新鲜分离的肝细胞相比，培养的肝细胞中被抑制的基因强烈重叠，这表明目前的体外条件缺乏维持肝细胞中基因表达所需的刺激，因此也解释了相应的hcc缺乏。目前的基因调控网络方法确定了需要调节的关键转录因子，以改善hplc分化。
The differentiation of stem cells to hepatocyte-like cells (HLC) offers the perspective of unlimited supply of human hepatocytes. However, the degree of differentiation of HLC remains controversial. To obtain an unbiased characterization, we performed a transcriptomic study with HLC derived from human embryonic and induced stem cells (ESC, hiPSC) from three different laboratories. Genome-wide gene expression profiles of ESC and HLC were compared to freshly isolated and up to 14 days cultivated primary human hepatocytes. Gene networks representing successful and failed hepatocyte differentiation, and the transcription factors involved in their regulation were identified. Gene regulatory network analysis demonstrated that HLC represent a mixed cell type with features of liver, intestine, fibroblast and stem cells. The “unwanted” intestinal features were associated with KLF5 and CDX2 transcriptional networks. Cluster analysis identified highly correlated groups of genes associated with mature liver functions (n = 1057) and downregulated proliferation associated genes (n = 1562) that approach levels of primary hepatocytes. However, three further clusters containing 447, 101, and 505 genes failed to reach levels of hepatocytes. Key TF of two of these clusters include SOX11, FOXQ1, and YBX3. The third unsuccessful cluster, controlled by HNF1, CAR, FXR, and PXR, strongly overlaps with genes repressed in cultivated hepatocytes compared to freshly isolated hepatocytes, suggesting that current in vitro conditions lack stimuli required to maintain gene expression in hepatocytes, which consequently also explains a corresponding deficiency of HLC. The present gene regulatory network approach identifies key transcription factors which require modulation to improve HLC differentiation.