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Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes

  • Authors:
    • Rui Lin
    • Yufeng Wang
    • Kun Ji
    • Zhongyan Liu
    • Shuai Xiao
    • Dehua Zhou
    • Quanning Chen
    • Baomin Shi
  • View Affiliations / Copyright

    Affiliations: Department of General Surgery, Tongji Hospital, School of Medicine, Tongji University Medical School, Shanghai 200065, P.R. China
    Copyright: © Lin et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 4351-4359
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    Published online on: January 5, 2018
       https://doi.org/10.3892/mmr.2018.8385
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Abstract

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.
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Copy and paste a formatted citation
Spandidos Publications style
Lin R, Wang Y, Ji K, Liu Z, Xiao S, Zhou D, Chen Q and Shi B: Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes. Mol Med Rep 17: 4351-4359, 2018.
APA
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D. ... Shi, B. (2018). Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes. Molecular Medicine Reports, 17, 4351-4359. https://doi.org/10.3892/mmr.2018.8385
MLA
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D., Chen, Q., Shi, B."Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes". Molecular Medicine Reports 17.3 (2018): 4351-4359.
Chicago
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D., Chen, Q., Shi, B."Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes". Molecular Medicine Reports 17, no. 3 (2018): 4351-4359. https://doi.org/10.3892/mmr.2018.8385
Copy and paste a formatted citation
x
Spandidos Publications style
Lin R, Wang Y, Ji K, Liu Z, Xiao S, Zhou D, Chen Q and Shi B: Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes. Mol Med Rep 17: 4351-4359, 2018.
APA
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D. ... Shi, B. (2018). Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes. Molecular Medicine Reports, 17, 4351-4359. https://doi.org/10.3892/mmr.2018.8385
MLA
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D., Chen, Q., Shi, B."Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes". Molecular Medicine Reports 17.3 (2018): 4351-4359.
Chicago
Lin, R., Wang, Y., Ji, K., Liu, Z., Xiao, S., Zhou, D., Chen, Q., Shi, B."Bioinformatics analysis to screen key genes implicated in the differentiation of induced pluripotent stem cells to hepatocytes". Molecular Medicine Reports 17, no. 3 (2018): 4351-4359. https://doi.org/10.3892/mmr.2018.8385
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