Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University Medical School, Shanghai 200065, P.R. China.
Mol Med Rep. 2018 Mar;17(3):4351-4359. doi: 10.3892/mmr.2018.8385. Epub 2018 Jan 5.
Due to the lack of potential organs, hepatocellular transplantation has been considered for treating end-stage liver disease. Induced pluripotent stem cells (iPSCs) are reverted from somatic cells and are able to differentiate into hepatocytes. The present study aimed to investigate the mechanisms underlying iPSC differentiation to hepatocytes. GSE66076 was downloaded from the Gene Expression Omnibus; this database includes data from 3 undifferentiated (T0), 3 definitive endoderm (T5), and 3 early hepatocyte (T24) samples across hepatic‑directed differentiation of iPSCs. Differentially expressed genes (DEGs) between T0 and T5 or T24 samples were identified using the linear models for microarray data package in Bioconductor, and enrichment analyses were performed. Using the weighted correlation network analysis package in R, clusters were identified for the merged DEGs. Cytoscape was used to construct protein‑protein interaction (PPI) networks for DEGs identified to belong to significant clusters. Using the ReactomeFI plugin in Cytoscape, functional interaction (FI) networks were constructed for the common genes. A total of 433 and 1,342 DEGs were identified in the T5 and T24 samples respectively, compared with the T0 samples. Blue and turquoise clusters were identified as significant gene clusters. In the PPI network for DEGs in the blue cluster, the key node fibroblast growth factor 2 (FGF2) could interact with bone morphogenetic protein 2 (BMP2). Cyclin‑dependent kinase 1 (CDK1) was demonstrated to have the highest degree (degree=71) in the PPI network for DEGs in the turquoise cluster. Enrichment analysis for the common genes, including hepatocyte nuclear factor 4α (HNF4A) and epidermal growth factor (EGF), in the FI network indicated that EGF and FGF2 were enriched in the Ras and Rap1 signaling pathways. The present results suggest that FGF2, BMP2, CDK1, HNF4A and EGF may participate in the differentiation of iPSCs into hepatocytes.
由于潜在器官的缺乏，肝细胞移植已被用于治疗终末期肝病。诱导多能干细胞（iPSCs）是从体细胞中逆转而来的，能够分化为肝细胞。本研究旨在探讨 iPSC 向肝细胞分化的机制。从基因表达综合数据库（GEO）中下载 GSE66076 数据集；该数据库包含了 3 个未分化（T0）、3 个确定内胚层（T5）和 3 个早期肝细胞（T24）样本，这些样本是通过 iPSC 向肝系定向分化得到的。使用 Bioconductor 中的线性模型微阵列数据包识别 T0 和 T5 或 T24 样本之间的差异表达基因（DEGs），并进行富集分析。使用 R 中的加权相关网络分析包识别合并的 DEGs 的聚类。使用 Cytoscape 构建属于显著聚类的 DEGs 的蛋白质-蛋白质相互作用（PPI）网络。使用 Cytoscape 中的 ReactomeFI 插件构建共同基因的功能相互作用（FI）网络。与 T0 样本相比，T5 和 T24 样本分别鉴定出 433 个和 1342 个 DEGs。鉴定出蓝色和绿松石色聚类为显著基因聚类。在蓝色聚类中 DEGs 的 PPI 网络中，关键节点成纤维细胞生长因子 2（FGF2）可以与骨形态发生蛋白 2（BMP2）相互作用。细胞周期蛋白依赖性激酶 1（CDK1）在绿松石聚类中 DEGs 的 PPI 网络中具有最高的度数（度数=71）。FI 网络中共同基因（包括肝细胞核因子 4α（HNF4A）和表皮生长因子（EGF））的富集分析表明，EGF 和 FGF2 富集在 Ras 和 Rap1 信号通路中。本研究结果表明，FGF2、BMP2、CDK1、HNF4A 和 EGF 可能参与 iPSC 向肝细胞的分化。
