Abstract
Factor-based induced reprogramming approaches have tremendous potential for human regenerative medicine, but the efficiencies of these approaches are still low. In this study, we analyzed the global transcriptional profiles of mouse induced pluripotent stem cells (miPSCs) and mouse embryonic stem cells (mESCs) from seven different labs and present here the first successful clustering according to cell type, not by lab of origin. We identified 2131 different expression genes (DEs) as candidate pluripotency-associated genes by comparing mESCs/miPSCs with somatic cells and 720 DEs between miPSCs and mESCs. Interestingly, there was a significant overlap between the two DE sets. Therefore, we defined the overlap DEs as “consensus DEs” including 313 miPSC-specific genes expressed at a higher level in miPSCs versus mESCs and 184 mESC-specific genes in total and reasoned that these may contribute to the differences in pluripotency between mESCs and miPSCs. A classification of “consensus DEs” according to their different expression levels between somatic cells and mESCs/miPSCs shows that 86% of the miPSC-specific genes are more highly expressed in somatic cells, while 73% of mESC-specific genes are highly expressed in mESCs/miPSCs, indicating that the miPSCs have not efficiently silenced the expression pattern of the somatic cells from which they are derived and failed to completely induce the genes with high expression levels in mESCs. We further revealed a strong correlation between oocyte-enriched factors and insufficiently induced mESC-specific genes and identified 11 hub genes via network analysis. In light of these findings, we postulated that these key hub genes might not only drive somatic cell nuclear transfer (SCNT) reprogramming but also augment the efficiency and quality of miPSC reprogramming.
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References
Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126(4), 663–676.
Takahashi, K., Tanabe, K., Ohnuki, M., et al. (2007). Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell, 131(5), 861–872.
Yu, J., Vodyanik, M. A., Smuga-Otto, K., et al. (2007). Induced pluripotent stem cell lines derived from human somatic cells. Science, 318(5858), 1917–1920.
Park, I. H., Arora, N., Huo, H., et al. (2008). Disease-specific induced pluripotent stem cells. Cell, 134(5), 877–886.
Hu, B. Y., Weick, J. P., Yu, J., et al. (2010). Neural differentiation of human induced pluripotent stem cells follows developmental principles but with variable potency. Proceedings of the National Academy of Sciences of the United States of America, 107(9), 4335–4340.
Wernig, M., Meissner, A., Foreman, R., et al. (2007). In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature, 448(7151), 318–324.
Kim, J. B., Zaehres, H., Wu, G., et al. (2008). Pluripotent stem cells induced from adult neural stem cells by reprogramming with two factors. Nature, 454(7204), 646–650.
Hanna, J., Markoulaki, S., Schorderet, P., et al. (2008). Direct reprogramming of terminally differentiated mature B lymphocytes to pluripotency. Cell, 133(2), 250–264.
Chin, M. H., Mason, M. J., Xie, W., et al. (2009). Induced pluripotent stem cells and embryonic stem cells are distinguished by gene expression signatures. Cell Stem Cell, 5(1), 111–123.
Sharma, A., & Wu, J. C. (2013). MicroRNA expression profiling of human-induced pluripotent and embryonic stem cells. Methods in Molecular Biology, 936, 247–256.
Pick, M., Stelzer, Y., Bar-Nur, O., Mayshar, Y., Eden, A., & Benvenisty, N. (2009). Clone- and gene-specific aberrations of parental imprinting in human induced pluripotent stem cells. Stem Cells, 27(11), 2686–2690.
Deng, J., Shoemaker, R., Xie, B., et al. (2009). Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming. Nature Biotechnology, 27(4), 353–360.
Brambrink, T., Hochedlinger, K., Bell, G., & Jaenisch, R. (2006). ES cells derived from cloned and fertilized blastocysts are transcriptionally and functionally indistinguishable. Proceedings of the National Academy of Sciences of the United States of America, 103(4), 933–938.
Wakayama, S., Jakt, M. L., Suzuki, M., et al. (2006). Equivalency of nuclear transfer-derived embryonic stem cells to those derived from fertilized mouse blastocysts. Stem Cells, 24(9), 2023–2033.
Gurdon, J. B., & Melton, D. A. (2008). Nuclear reprogramming in cells. Science, 322(5909), 1811–1815.
Hong, F., & Breitling, R. (2008). A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments. Bioinformatics, 24(3), 374–382.
Assou, S., Le Carrour, T., Tondeur, S., et al. (2007). A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas. Stem Cells, 25(4), 961–973.
Liu, Y., Cheng, D., Li, Z., Gao, X., & Wang, H. (2012). The gene expression profiles of induced pluripotent stem cells (iPSCs) generated by a non-integrating method are more similar to embryonic stem cells than those of iPSCs generated by an integrating method. Genetics and Molecular Biology, 35(3), 693–700.
Duan, L., Wang, Z., Shen, J., et al. (2014). Comparison of reprogramming genes in induced pluripotent stem cells and nuclear transfer cloned embryos. Stem Cell Reviews, 10(4), 548–560.
Mayshar, Y., Ben-David, U., Lavon, N., et al. (2010). Identification and classification of chromosomal aberrations in human induced pluripotent stem cells. Cell Stem Cell, 7(4), 521–531.
Chin, M. H., Pellegrini, M., Plath, K., & Lowry, W. E. (2010). Molecular analyses of human induced pluripotent stem cells and embryonic stem cells. Cell Stem Cell, 7(2), 263–269.
Newman, A. M., & Cooper, J. B. (2010). Lab-specific gene expression signatures in pluripotent stem cells. Cell Stem Cell, 7(2), 258–262.
Guenther, M. G., Frampton, G. M., Soldner, F., et al. (2010). Chromatin structure and gene expression programs of human embryonic and induced pluripotent stem cells. Cell Stem Cell, 7(2), 249–257.
Irizarry, R. A., Hobbs, B., Collin, F., et al. (2003). Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4(2), 249–264.
Lockstone, H. E. (2011). Exon array data analysis using Affymetrix power tools and R statistical software. Briefings in Bioinformatics, 12(6), 634–644.
Diboun, I., Wernisch, L., Orengo, C. A., & Koltzenburg, M. (2006). Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC Genomics, 7, 252.
Breitling, R., Armengaud, P., Amtmann, A., & Herzyk, P. (2004). Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Letters, 573(1–3), 83–92.
Hong, F., Breitling, R., McEntee, C. W., Wittner, B. S., Nemhauser, J. L., & Chory, J. (2006). RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis. Bioinformatics, 22(22), 2825–2827.
Falcon, S., & Gentleman, R. (2007). Using GOstats to test gene lists for GO term association. Bioinformatics, 23(2), 257–258.
Breuer, K., Foroushani, A. K., Laird, M. R., et al. (2013). InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Research, 41(Database issue), D1228–D1233.
Orchard, S., Kerrien, S., Abbani, S., et al. (2012). Protein interaction data curation: the International Molecular Exchange (IMEx) consortium. Nature Methods, 9(4), 345–350.
Licata, L., Briganti, L., Peluso, D., et al. (2012). MINT, the molecular interaction database: 2012 update. Nucleic Acids Research, 40(Database issue), D857–D861.
Orchard, S., Ammari, M., Aranda, B., et al. (2014). The MIntAct project--IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Research, 42(Database issue), D358–D363.
Chatr-Aryamontri, A., Breitkreutz, B. J., Heinicke, S., et al. (2013). The BioGRID interaction database: 2013 update. Nucleic Acids Research, 41(Database issue), D816–D823.
Salwinski, L., Miller, C. S., Smith, A. J., Pettit, F. K., Bowie, J. U., & Eisenberg, D. (2004). The Database of Interacting Proteins: 2004 update. Nucleic Acids Research, 32(Database issue), D449–D451.
Shannon, P., Markiel, A., Ozier, O., et al. (2003). Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11), 2498–2504.
Shan, Z. Y., Wu, Y. S., Li, X., et al. (2014). Continuous passages accelerate the reprogramming of mouse induced pluripotent stem cells. Cellular Reprogramming, 16(1), 77–83.
Zheng, Z., Jia, J. L., Bou, G., et al. (2012). rRNA genes are not fully activated in mouse somatic cell nuclear transfer embryos. The Journal of Biological Chemistry, 287(24), 19949–19960.
Jimenez, R., Melo, E. O., Davydenko, O., et al. (2015). Maternal SIN3A regulates reprogramming of gene expression during mouse preimplantation development. Biology of Reproduction, 93(4), 89.
Ang, Y. S., Tsai, S. Y., Lee, D. F., et al. (2011). Wdr5 mediates self-renewal and reprogramming via the embryonic stem cell core transcriptional network. Cell, 145(2), 183–197.
Rao, R. A., Dhele, N., Cheemadan, S., et al. (2015). Ezh2 mediated H3K27me3 activity facilitates somatic transition during human pluripotent reprogramming. Scientific Reports, 5, 8229.
Acknowledgements
This work was supported by the National Natural Science Foundation of China(J1210069).
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Fang Gao and Jingyu Li contributed equally to this work.
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Supplementary Figure 1
Flow chart of dataset selection. (PSD 111 kb)
Supplementary Table 1
Microarray studies in cell reprogramming used for meta-analysis. (DOCX 25 kb)
Supplementary Table 2
The DEs list identified between stem cells and donor cells from meta-analysis. (XLSX 122 kb)
Supplementary Table 3
The DEs list identified between miPSCs and mESCs from meta-analysis. (XLSX 47 kb)
Supplementary Table 4
mESC-specific genes and miPSC-specific genes. (XLSX 15 kb)
Supplementary Table 5
The up-regulated genes in MII oocytes compared to MEFs. (XLSX 418 kb)
Supplementary Table 6
The primer sequences used for qPCR analysis of the hub genes. (XLSX 10 kb)
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Gao, F., Li, J., Zhang, H. et al. Identifying Candidate Reprogramming Genes in Mouse Induced Pluripotent Stem Cells. Stem Cell Rev and Rep 13, 532–541 (2017). https://doi.org/10.1007/s12015-016-9704-2
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DOI: https://doi.org/10.1007/s12015-016-9704-2