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Comparative Gene Expression Signature of Pig, Human and Mouse Induced Pluripotent Stem Cell Lines Reveals Insight into Pig Pluripotency Gene Networks

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Abstract

Reported pig induced pluripotent stem cells (piPSCs) have shown either a bFGF-dependent state with human embryonic stem cell (ESC) and mouse epiblast stem cell (EpiSC) morphology and molecular features or piPSCs exist in a LIF-dependent state and resemble fully reprogrammed mouse iPSCs. The features of authentic piPSCs and molecular events during the reprogramming are largely unknown. In this study, we assessed the transcriptome profile of multiple piPSC lines derived from different laboratories worldwide and compared to mouse and human iPSCs to determine the molecular signaling pathways that might play a central role in authentic piPSCs. The results demonstrated that the up-regulation of endogenous epithelial cells adhesion molecule (EpCAM) was correlated with the pluripotent state of pig pluripotent cells, which could be utilized as a marker for evaluating pig cell reprogramming. Comparison of key signaling pathways JAK-STAT, NOTCH, TGFB1, WNT and VEGF in pig, mouse and human iPSCs showed that the core transcriptional network to maintain pluripotency and self-renewal in pig were different from that in mouse, but had significant similarities to human. Pig iPSCs, which lacked expression of specific naïve state markers KLF2/4/5 and TBX3, but expressed the primed state markers of Otx2 and Fabp7, share defining features with human ESCs and mouse EpiSCs. The cluster of imprinted genes delineated by the delta-like homolog 1 gene and the type III iodothyronine deiodinase gene (DLK1-DIO3) were silenced in piPSCs as previously seen in mouse iPSCs that have limited ability to contribute to chimaeras. These key differences in naïve state gene and imprinting gene expression suggests that so far known piPSC lines may be more similar to primed state cells. The primed state of these cells may potentially explain the rare ability of piPSCS to generate chimeras and cloned offspring.

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References

  1. Vassiliev, I., Vassilieva, S., Truong, K. P., Beebe, L. F., McIlfatrick, S. M., Harrison, S. J., & Nottle, M. B. (2011). Isolation and in vitro characterization of putative porcine embryonic stem cells from cloned embryos treated with trichostatin A. Cellular Reprogramming, 13(3), 205–213.

    Article  PubMed  CAS  Google Scholar 

  2. West, F. D., Uhl, E. W., Liu, Y., Stowe, H., Lu, Y., Yu, P., Gallegos-Cardenas, A., Pratt, S. L., & Stice, S. L. (2011). Brief report: chimeric pigs produced from induced pluripotent stem cells demonstrate germline transmission and no evidence of tumor formation in young pigs. Stem Cells, 10, 1640–1643.

    Article  CAS  Google Scholar 

  3. Fujishiro, S. H., Nakano, K., Mizukami, Y., Azami, T., Arai, Y., Matsunari, H., Ishino, R., Nishimura, T., Watanabe, M., Abe, T., Furukawa, Y., Umeyama, K., Yamanaka, S., Ema, M., Nagashima, H., & Hanazono, Y. (2013). Generation of naive-like porcine-induced pluripotent stem cells capable of contributing to embryonic and fetal development. Stem Cells and Development, 22(3), 473–482.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  4. Takahashi, K., & Yamanaka, S. (2006). Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell, 126, 663–676.

    Article  PubMed  CAS  Google Scholar 

  5. Ezashi, T., Telugu, B. P., Alexenko, A. P., Sachdev, S., Sinha, S., & Roberts, R. M. (2009). Derivation of induced pluripotent stem cells from pig somatic cells. Proceedings of the National Academy of Sciences of the United States of America, 106, 10993–10998.

    Article  PubMed Central  PubMed  Google Scholar 

  6. Wu, Z., Chen, J., Ren, J., Bao, L., Liao, J., Cui, C., Rao, L., Li, H., Gu, Y., Dai, H., et al. (2009). Generation of pig induced pluripotent stem cells with a drug-inducible system. Journal of Molecular Cell Biology, 1, 46–54.

    Article  PubMed  CAS  Google Scholar 

  7. Cheng, D., Guo, Y., Li, Z., Liu, Y., Gao, X., Gao, Y., Cheng, X., Hu, J., & Wang, H. (2012). Porcine induced pluripotent stem cells require LIF and maintain their developmental potential in early stage of embryos. PLoS One, 7, e51778.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  8. Esteban, M. A., Xu, J., Yang, J., Peng, M., Qin, D., Li, W., Jiang, Z., Chen, J., Deng, K., Zhong, M., et al. (2009). Generation of induced pluripotent stem cell lines from Tibetan miniature pig. Journal of Biological Chemistry, 284, 17634–17640.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  9. West, F. D., Terlouw, S. L., Kwon, D. J., Mumaw, J. L., Dhara, S. K., Hasneen, K., Dobrinsky, J. R., & Stice, S. L. (2010). Porcine induced pluripotent stem cells produce chimeric offspring. Stem Cells and Development, 19, 1211–1220.

    Article  PubMed  CAS  Google Scholar 

  10. Fan, N., Chen, J., Shang, Z., Dou, H., Ji, G., Zou, Q., Wu, L., He, L., Wang, F., Liu, K., et al. (2013). Piglets cloned from induced pluripotent stem cells. Cell Research, 23, 162–166.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  11. Chen, X., Xu, H., Yuan, P., Fang, F., Huss, M., Vega, V. B., Wong, E., Orlov, Y. L., Zhang, W., Jiang, J., et al. (2008). Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106–1117.

    Article  PubMed  CAS  Google Scholar 

  12. Smith, A.G. (2001). Embryo-derived stem cells: of mice and men. Annual review of cell and developmental biology, 17, 435–462

    Google Scholar 

  13. Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., et al. (2005). Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947–956.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  14. Wei, C. L., Miura, T., Robson, P., Lim, S. K., Xu, X. Q., Lee, M. Y., Gupta, S., Stanton, L., Luo, Y., Schmitt, J., et al. (2005). Transcriptome profiling of human and murine ESCs identifies divergent paths required to maintain the stem cell state. Stem Cells, 23, 166–185.

    Article  PubMed  CAS  Google Scholar 

  15. Richards, M., Tan, S. P., Tan, J. H., Chan, W. K., & Bongso, A. (2004). The transcriptome profile of human embryonic stem cells as defined by SAGE. Stem Cells, 22, 51–64.

    Article  PubMed  CAS  Google Scholar 

  16. Brandenberger, R., Khrebtukova, I., Thies, R. S., Miura, T., Jingli, C., Puri, R., Vasicek, T., Lebkowski, J., & Rao, M. (2004). MPSS profiling of human embryonic stem cells. BMC Developmental Biology, 4, 10.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  17. Brandenberger, R., Wei, H., Zhang, S., Lei, S., Murage, J., Fisk, G. J., Li, Y., Xu, C., Fang, R., Guegler, K., et al. (2004). Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nature Biotechnology, 22, 707–716.

    Article  PubMed  Google Scholar 

  18. Xue, Z., Huang, K., Cai, C., Cai, L., Jiang, C. Y., Feng, Y., Liu, Z., Zeng, Q., Cheng, L., Sun, Y. E., et al. (2013). Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. doi:10.1038/nature12364.

    PubMed Central  Google Scholar 

  19. Telugu, B. P., Ezashi, T., Sinha, S., Alexenko, A. P., Spate, L., Prather, R. S., & Roberts, R. M. (2011). Leukemia inhibitory factor (LIF)-dependent, pluripotent stem cells established from inner cell mass of porcine embryos. Journal of Biological Chemistry, 286, 28948–28953.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  20. Chen, J., Liu, J., Yang, J., Chen, Y., Ni, S., Song, H., Zeng, L., Ding, K., & Pei, D. (2011). BMPs functionally replace Klf4 and support efficient reprogramming of mouse fibroblasts by Oct4 alone. Cell Research, 21, 205–212.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  21. Mikkelsen, T. S., Hanna, J., Zhang, X., Ku, M., Wernig, M., Schorderet, P., Bernstein, B. E., Jaenisch, R., Lander, E. S., & Meissner, A. (2008). Dissecting direct reprogramming through integrative genomic analysis. Nature, 454, 49–55.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  22. Liu, L., Luo, G. Z., Yang, W., Zhao, X., Zheng, Q., Lv, Z., Li, W., Wu, H. J., Wang, L., Wang, X. J., et al. (2010). Activation of the imprinted Dlk1-Dio3 region correlates with pluripotency levels of mouse stem cells. Journal of Biological Chemistry, 285, 19483–19490.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  23. Hanna, J., Markoulaki, S., Mitalipova, M., Cheng, A. W., Cassady, J. P., Staerk, J., Carey, B. W., Lengner, C. J., Foreman, R., Love, J., et al. (2009). Metastable pluripotent states in NOD-mouse-derived ESCs. Cell Stem Cell, 4, 513–524.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  24. Warren, L., Manos, P. D., Ahfeldt, T., Loh, Y. H., Li, H., Lau, F., Ebina, W., Mandal, P. K., Smith, Z. D., Meissner, A., et al. (2010). Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA. Cell Stem Cell, 7, 618–630.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  25. Tsai, S., Cassady, J. P., Freking, B. A., Nonneman, D. J., Rohrer, G. A., & Piedrahita, J. A. (2006). Annotation of the Affymetrix porcine genome microarray. Animal Genetics, 37, 423–424.

    Article  PubMed  CAS  Google Scholar 

  26. da Huang, W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nature Protocols, 4, 44–57.

    Article  CAS  Google Scholar 

  27. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000). Gene ontology: tool for the unification of biology. The gene ontology consortium. Nature Genetics, 25, 25–29.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  28. Hu, J., Cheng, D., Gao, X., Bao, J., Ma, X., & Wang, H. (2012). Vitamin C enhances the in vitro development of porcine pre-implantation embryos by reducing oxidative stress. Reproduction in Domestic Animals, 47(6), 873–879.

    Article  PubMed  CAS  Google Scholar 

  29. Chen, J., Lu, Z., Cheng, D., Peng, S., & Wang, H. (2011). Isolation and characterization of porcine amniotic fluid-derived multipotent stem cells. PLoS One, 6, e19964.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  30. Zhou, L., Wang, W., Liu, Y., de Castro, J. F., Ezashi, T., Telugu, B. P., Roberts, R. M., Kaplan, H. J., & Dean, D. C. (2011). Differentiation of induced pluripotent stem cells of Swine into rod photoreceptors and their integration into the retina. Stem Cells, 29, 972–980.

    Article  PubMed  CAS  Google Scholar 

  31. Lee, M. R., Prasain, N., Chae, H. D., Kim, Y. J., Mantel, C., Yoder, M. C., & Broxmeyer, H. E. (2013). Epigenetic regulation of NANOG by miR-302 cluster-MBD2 completes induced pluripotent stem cell reprogramming. Stem Cells, 31, 666–681.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  32. Stoyanova, T., Goldstein, A. S., Cai, H., Drake, J. M., Huang, J., & Witte, O. N. (2012). Regulated proteolysis of Trop2 drives epithelial hyperplasia and stem cell self-renewal via β-catenin signaling. Genes and Development, 26(20), 2271–2285.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  33. Jouneau, A., Ciaudo, C., Sismeiro, O., Brochard, V., Jouneau, L., Vandormael-Pournin, S., Coppee, J. Y., Zhou, Q., Heard, E., Antoniewski, C., et al. (2012). Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles. RNA, 18, 253–264.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  34. Stadler, B., Ivanovska, I., Mehta, K., Song, S., Nelson, A., Tan, Y., Mathieu, J., Darby, C., Blau, C. A., Ware, C., et al. (2010). Characterization of microRNAs involved in embryonic stem cell states. Stem Cells and Development, 19, 935–950.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  35. Stadtfeld, M., Apostolou, E., Akutsu, H., Fukuda, A., Follett, P., Natesan, S., Kono, T., Shioda, T., & Hochedlinger, K. (2010). Aberrant silencing of imprinted genes on chromosome 12qF1 in mouse induced pluripotent stem cells. Nature, 465, 175–181.

    Article  PubMed  CAS  PubMed Central  Google Scholar 

  36. Cheng, D., Li, Z., Liu, Y., Gao, Y., & Wang, H. (2012). Kinetic analysis of porcine fibroblast reprogramming toward pluripotency by defined factors. Cellular Reprogramming, 14, 312–323.

    PubMed  CAS  Google Scholar 

  37. Lu, T. Y., Lu, R. M., Liao, M. Y., Yu, J., Chung, C. H., Kao, C. F., & Wu, H. C. (2010). Epithelial cell adhesion molecule regulation is associated with the maintenance of the undifferentiated phenotype of human embryonic stem cells. Journal of Biological Chemistry, 285, 8719–8732.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  38. Chen, H. F., Chuang, C. Y., Lee, W. C., Huang, H. P., Wu, H. C., Ho, H. N., Chen, Y. J., & Kuo, H. C. (2011). Surface marker epithelial cell adhesion molecule and E-cadherin facilitate the identification and selection of induced pluripotent stem cells. Stem Cell Reviews, 7, 722–735.

    Article  PubMed  CAS  Google Scholar 

  39. Polo, J. M., Anderssen, E., Walsh, R. M., Schwarz, B. A., Nefzger, C. M., Lim, S. M., Borkent, M., Apostolou, E., Alaei, S., Cloutier, J., et al. (2012). A molecular roadmap of reprogramming somatic cells into iPS cells. Cell, 151, 1617–1632.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  40. McConnell, B. B., Ghaleb, A. M., Nandan, M. O., & Yang, V. W. (2007). The diverse functions of Kruppel-like factors 4 and 5 in epithelial biology and pathobiology. Bioessays, 29, 549–557.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  41. Guo, G., Yang, J., Nichols, J., Hall, J. S., Eyres, I., Mansfield, W., & Smith, A. (2009). Klf4 reverts developmentally programmed restriction of ground state pluripotency. Development, 136, 1063–1069.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  42. Han, J. Y., Yuan, P., Yang, H., Zhang, J. Q., Soh, B. S., Li, P., Lim, S. L., Cao, S. Y., Tay, J. L., Orlov, Y. L., et al. (2010). Tbx3 improves the germ-line competency of induced pluripotent stem cells. Nature, 463, 1096–1100.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  43. Acampora, D., Di Giovannantonio, L. G., & Simeone, A. (2012). Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition. Development, 140(1), 43–55.

    Article  PubMed  CAS  Google Scholar 

  44. Rais, Y., Zviran, A., Geula, S., Gafni, O., Chomsky, E., Viukov, S., Mansour, A. A., Caspi, I., Krupalnik, V., Zerbib, M., et al. (2013). Deterministic direct reprogramming of somatic cells to pluripotency. Nature, 502, 65–70.

    Article  PubMed  CAS  Google Scholar 

  45. Gafni, O., Weinberger, L., Mansour, A. A., Manor, Y. S., Chomsky, E., Ben-Yosef, D., Kalma, Y., Viukov, S., Maza, I., Zviran, A., et al. (2013). Derivation of novel human ground state naive pluripotent stem cells. Nature. doi:10.1038/nature12745.

    Google Scholar 

  46. Niwa, H., Ogawa, K., Shimosato, D., & Adachi, K. (2009). A parallel circuit of LIF signalling pathways maintains pluripotency of mouse ES cells. Nature, 460, 118–122.

    Article  PubMed  CAS  Google Scholar 

  47. Rodriguez, A., Allegrucci, C., & Alberio, R. (2012). Modulation of pluripotency in the porcine embryo and iPS cells. PLoS One, 7, e49079.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  48. Da Rocha, S. T., Edwards, C. A., Ito, M., Ogata, T., & Ferguson-Smith, A. C. (2008). Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends in Genetics, 24, 306–316.

    Article  PubMed  CAS  Google Scholar 

  49. Chen, J., Liu, H., Liu, J., Qi, J., Wei, B., Yang, J., Liang, H., Chen, Y., Wu, Y., Guo, L., et al. (2013). H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nature Genetics, 45, 34–42.

    Article  PubMed  CAS  Google Scholar 

  50. Stadtfeld, M., Apostolou, E., Ferrari, F., Choi, J., Walsh, R. M., Chen, T., Ooi, S. S., Kim, S. Y., Bestor, T. H., Shioda, T., et al. (2012). Ascorbic acid prevents loss of Dlk1-Dio3 imprinting and facilitates generation of all-iPS cell mice from terminally differentiated B cells. Nature Genetics, 44, 398–405.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  51. Edwards, C. A., Mungall, A. J., Matthews, L., Ryder, E., Gray, D. J., Pask, A. J., Shaw, G., Graves, J. A., Rogers, J., Consortium, S., et al. (2008). The evolution of the DLK1-DIO3 imprinted domain in mammals. PLoS Biology, 6, e135.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  52. Esmailpour, T., & Huang, T. (2012). TBX3 promotes human embryonic stem cell proliferation and neuroepithelial differentiation in a differentiation stage-dependent manner. Stem Cells, 30, 2152–2163.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

  53. Wang, J., Gu, Q., Hao, J., Jia, Y., Xue, B., Jin, H., Ma, J., Wei, R., Hai, T., Kong, Q., et al. (2013). Tbx3 and Nr5alpha2 play important roles in pig pluripotent stem cells. Stem Cell Reviews, 9(5), 700–708.

    Article  PubMed  CAS  Google Scholar 

  54. Hanna, J., Cheng, A. W., Saha, K., Kim, J., Lengner, C. J., Soldner, F., Cassady, J. P., Muffat, J., Carey, B. W., & Jaenisch, R. (2010). Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs. Proceedings of the National Academy of Sciences of the United States of America, 107, 9222–9227.

    Article  PubMed Central  PubMed  CAS  Google Scholar 

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Acknowledgments

We thank Dr. X. Lei (College of Animal Sciences, Zhejiang University, Hangzhou, China) for providing us pig iPS cell line iPF4-2. We also thank Dr. M. Roberts for allowing us to process the data from their lab. We thank S. Zhang, M. Qing and Y. Gao for their technical supports and comments. This work was supported by the National Basic Research Program of China (2011CBA01002) and the National Natural Science Foundation of China (No.31371505).

Conflict of Interest

The authors indicate no potential conflicts of interest. The authors have received research grants from the National Basic Research Program of China (2011CBA01002) and the National Natural Science Foundation of China (No.31371505).

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Authors and Affiliations

  1. College of Veterinary Medicine, Shaanxi Center for Stem Cell Engineering and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China

    Yajun Liu, Yangyang Ma, De Cheng, Xiaopeng Liu, Xiaoling Ma & Huayan Wang

  2. Regenerative Bioscience Center, University of Georgia, Athens, GA, USA

    Jeong-Yeh Yang & Franklin D. West

  3. Department of Animal and Dairy Science, University of Georgia, Rhodes Center for Animal and Dairy Science, 425 River Road, Athens, GA, 30602-2771, USA

    Jeong-Yeh Yang & Franklin D. West

  4. Department of Cellular and Molecular Physiology, College of Medicine, Pennsylvania State University, 500 University Drive, Hershey, PA, 17033, USA

    De Cheng

  5. Department of Animal Biotechnology, College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, China

    Huayan Wang

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  1. Yajun Liu
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Liu, Y., Ma, Y., Yang, JY. et al. Comparative Gene Expression Signature of Pig, Human and Mouse Induced Pluripotent Stem Cell Lines Reveals Insight into Pig Pluripotency Gene Networks. Stem Cell Rev and Rep 10, 162–176 (2014). https://doi.org/10.1007/s12015-013-9485-9

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