Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells

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• 作者：Patricio Godoy¹ ; ¹¹ ; Wolfgang Schmidt-Heck² ; Karthick Natarajan³ ; Baltasar Lucendo-Villarin⁴ ; Dagmara Szkolnicka⁴ ; Annika Asplund⁵ ; ⁶ ; Petter Bjö ; rquist⁷ ; Agata Widera¹ ; Regina Stö ; ber¹ ; Gisela Campos¹ ; Seddik Hammad¹ ; Agapios Sachinidis³ ; Umesh Chaudhari³ ; Georg Damm⁸ ; Thomas S. Weiss⁹ ; Andreas Nü ; ssler¹⁰ ; Jane Synnergren⁶ ; Karolina Edlund¹ ; Barbara Kü ; ppers-Munther⁵ ; David C. Hay⁴ ; ^{davehay@talktalk.net" class="auth_mail" title="E-mail the corresponding author} ; Jan G. Hengstler¹ ; ^{Hengstler@ifado.de" class="auth_mail" title="E-mail the corresponding author}
• 关键词：FH ; Freshly isolated hepatocytes ; CS ; collagen sandwich ; CM ; collagen monolayer ; SC ; stem cells ; HLC ; hepatocyte-like cells ; TF ; transcription factors
• 刊名：Journal of Hepatology
• 出版年：2015
• 出版时间：October 2015
• 年：2015
• 卷：63
• 期：4
• 页码：934-942
• 全文大小：2154 K

文摘

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.

Methods

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.

Results

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.

Conclusions

The present gene regulatory network approach identifies key transcription factors which require modulation to improve HLC differentiation.