Ghosheh Nidal, Küppers-Munther Barbara, Asplund Annika, Andersson Christian X, Björquist Petter, Andersson Tommy B, Carén Helena, Simonsson Stina, Sartipy Peter, Synnergren Jane
School of Bioscience, Systems Biology Research Center, University of Skövde, 541 28 Skövde, Sweden.
Takara Bio Europe AB, Arvid Wallgrens Backe 20, 413 46 Gothenburg, Sweden.
ACS Omega. 2020 Mar 2;5(10):4816-4827. doi: 10.1021/acsomega.9b03514. eCollection 2020 Mar 17.
Human pluripotent stem cell-derived hepatocytes (hPSC-HEP) display many properties of mature hepatocytes, including expression of important genes of the drug metabolizing machinery, glycogen storage, and production of multiple serum proteins. To this date, hPSC-HEP do not, however, fully recapitulate the complete functionality of in vivo mature hepatocytes. In this study, we applied versatile bioinformatic algorithms, including functional annotation and pathway enrichment analyses, transcription factor binding-site enrichment, and similarity and correlation analyses, to datasets collected from different stages during hPSC-HEP differentiation and compared these to developmental stages and tissues from fetal and adult human liver. Our results demonstrate a high level of similarity between the in vitro differentiation of hPSC-HEP and in vivo hepatogenesis. Importantly, the transcriptional correlation of hPSC-HEP with adult liver (AL) tissues was higher than with fetal liver (FL) tissues (0.83 and 0.70, respectively). Functional data revealed mature features of hPSC-HEP including cytochrome P450 enzymes activities and albumin secretion. Moreover, hPSC-HEP showed expression of many genes involved in drug absorption, distribution, metabolism, and excretion. Despite the high similarities observed, we identified differences of specific pathways and regulatory players by analyzing the gene expression between hPSC-HEP and AL. These findings will aid future intervention and improvement of in vitro hepatocyte differentiation protocol in order to generate hepatocytes displaying the complete functionality of mature hepatocytes. Finally, on the transcriptional level, our results show stronger correlation and higher similarity of hPSC-HEP to AL than to FL. In addition, potential targets for further functional improvement of hPSC-HEP were also identified.
人多能干细胞衍生的肝细胞（hPSC-HEP）表现出成熟肝细胞的许多特性，包括药物代谢机制重要基因的表达、糖原储存以及多种血清蛋白的产生。然而，迄今为止，hPSC-HEP尚未完全重现体内成熟肝细胞的完整功能。在本研究中，我们将多种生物信息学算法，包括功能注释和通路富集分析、转录因子结合位点富集以及相似性和相关性分析，应用于hPSC-HEP分化不同阶段收集的数据集，并将这些数据集与胎儿和成人肝脏的发育阶段及组织进行比较。我们的结果表明，hPSC-HEP的体外分化与体内肝脏发生之间具有高度相似性。重要的是，hPSC-HEP与成人肝脏（AL）组织的转录相关性高于与胎儿肝脏（FL）组织的转录相关性（分别为0.83和0.70）。功能数据揭示了hPSC-HEP的成熟特征，包括细胞色素P450酶活性和白蛋白分泌。此外，hPSC-HEP显示出许多参与药物吸收、分布、代谢和排泄的基因的表达。尽管观察到高度相似性，但我们通过分析hPSC-HEP与AL之间的基因表达，确定了特定通路和调控因子的差异。这些发现将有助于未来对体外肝细胞分化方案进行干预和改进，以生成具有成熟肝细胞完整功能的肝细胞。最后，在转录水平上，我们的结果表明hPSC-HEP与AL的相关性和相似性比与FL更强。此外，还确定了hPSC-HEP进一步功能改进的潜在靶点。
