Embryonic stem (ES) cells are of great interest because of their capability of unlimited self-renewal and multilineage differentiation, thus serving as a potentially unlimited source for tissue replacement in regenerative medicine. ES cells possess factors that maintain and induce pluripotency, as demonstrated by successful reprogramming of somatic cells by fusion with ES cells. Understanding the complex molecular mechanisms underlying ES cell pluripotency should illuminate fundamental properties of stem cells and the process of reprogramming. Proteomics has proven to be a powerful approach to gain insight into key intracellular signals governing ES cell self-renewal and differentiation. We have recently employed a proteomics approach to explore the regulatory protein networks in which Nanog, a fundamental ES cell transcription factor, operates and have constructed the first protein interaction network in mouse ES cells. The network is highly enriched for factors known to be critical in ES cell biology and appears to function as a module for pluripotency. Here we will review current ES cell proteomic studies and provide insights into how a pluripotency protein network will advance recent efforts in cellular reprogramming.

1.
Avilion, A.A., S.K. Nicolis, L.H. Pevny, L. Perez, N. Vivian, R. Lovell-Badge (2003) Multipotent cell lineages in early mouse development depend on SOX2 function. Genes Dev 17: 126–140.
2.
Baharvand, H., A. Fathi, D. van Hoof, G.H. Salekdeh (2007) Concise review: trends in stem cell proteomics. Stem Cells 25: 1888–1903.
3.
Boyer, L.A., T.I. Lee, M.F. Cole, S.E. Johnstone, S.S. Levine, J.P. Zucker, M.G. Guenther, R.M. Kumar, H.L. Murray, R.G. Jenner, D.K. Gifford, D.A. Melton, R. Jaenisch, R.A. Young (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell 122: 947–956.
4.
Boyer, L.A., K. Plath, J. Zeitlinger, T. Brambrink, L.A. Medeiros, T.I. Lee, S.S. Levine, M. Wernig, A. Tajonar, M.K. Ray, G.W. Bell, A.P. Otte, M. Vidal, D.K. Gifford, R.A. Young, R. Jaenisch (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349–353.
5.
Chambers, I., D. Colby, M. Robertson, J. Nichols, S. Lee, S. Tweedie, A. Smith (2003) Functional expression cloning of Nanog, a pluripotency sustaining factor in embryonic stem cells. Cell 113: 643–655.
6.
Chazaud, C., Y. Yamanaka, T. Pawson, J. Rossant (2006) Early lineage segregation between epiblast and primitive endoderm in mouse blastocysts through the Grb2-MAPK pathway. Dev Cell 10: 615–624.
7.
Collins, S.R., K.M. Miller, N.L. Maas, A. Roguev, J. Fillingham, C.S. Chu, M. Schuldiner, M. Gebbia, J. Recht, M. Shales, H. Ding, H. Xu, J. Han, K. Ingvarsdottir, B. Cheng, B. Andrews, C. Boone, S.L. Berger, P. Hieter, Z. Zhang, G.W. Brown, C.J. Ingles, A. Emili, C.D. Allis, D.P. Toczyski, J.S. Weissman, J.F. Greenblatt, N.J. Krogan (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature 446: 806–810.
8.
Cowan, C.A., J. Atienza, D.A. Melton, K. Eggan (2005) Nuclear reprogramming of somatic cells after fusion with human embryonic stem cells. Science 309: 1369–1373.
9.
Crook, J.M., N.R. Dunn, A. Colman (2006) Repressed by a NuRD. Nat Cell Biol 8: 212–214.
10.
de Boer, E., P. Rodriguez, E. Bonte, J. Krijgsveld, E. Katsantoni, A. Heck, F. Grosveld, J. Strouboulis (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci USA 100: 7480–7485.
11.
Eggan, K., K. Baldwin, M. Tackett, J. Osborne, J. Gogos, A. Chess, R. Axel, R. Jaenisch (2004) Mice cloned from olfactory sensory neurons. Nature 428: 44–49.
12.
Egli, D., J. Rosains, G. Birkhoff, K. Eggan (2007) Developmental reprogramming after chromosome transfer into mitotic mouse zygotes. Nature 447: 679–685.
13.
Elliott, S.T., D.G. Crider, C.P. Garnham, K.R. Boheler, J.E. Van Eyk (2004) Two-dimensional gel electrophoresis database of murine R1 embryonic stem cells. Proteomics 4: 3813–3832.
14.
Evans, M.J., M.H. Kaufman (1981) Establishment in culture of pluripotential cells from mouse embryos. Nature 292: 154–156.
15.
Fortunel, N.O., H.H. Otu, H.H. Ng, J. Chen, X. Mu, T. Chevassut, X. Li, M. Joseph, C. Bailey, J.A. Hatzfeld, A. Hatzfeld, F. Usta, V.B. Vega, P.M. Long, T.A. Libermann, B. Lim (2003) Comment on ‘“Stemness”: transcriptional profiling of embryonic and adult stem cells’ and ‘a stem cell molecular signature’. Science 302: 393.
16.
Graf, T., K. McNagny, G. Brady, J. Frampton (1992) Chicken ‘erythroid’ cells transformed by the Gag-Myb-Ets-encoding E26 leukemia virus are multipotent. Cell 70: 201–213.
17.
Guan, K., K. Nayernia, L.S. Maier, S. Wagner, R. Dressel, J.H. Lee, J. Nolte, F. Wolf, M. Li, W. Engel, G. Hasenfuss (2006) Pluripotency of spermatogonial stem cells from adult mouse testis. Nature 440: 1199–1203.
18.
Hatano, S.Y., M. Tada, H. Kimura, S. Yamaguchi, T. Kono, T. Nakano, H. Suemori, N. Nakatsuji, T. Tada (2005) Pluripotential competence of cells associated with Nanog activity. Mech Dev 122: 67–79.
19.
Hochedlinger, K., R. Jaenisch (2002) Monoclonal mice generated by nuclear transfer from mature B and T donor cells. Nature 415: 1035–1038.
20.
Hochedlinger, K., R. Blelloch, C. Brennan, Y. Yamada, M. Kim, L. Chin, R. Jaenisch (2004) Reprogramming of a melanoma genome by nuclear transplantation. Genes Dev 18: 1875–1885.
21.
Hochedlinger, K., R. Jaenisch (2006) Nuclear reprogramming and pluripotency. Nature 441: 1061–1067.
22.
Ivanova, N.B., J.T. Dimos, C. Schaniel, J.A. Hackney, K.A. Moore, I.R. Lemischka (2002) A stem cell molecular signature. Science 298: 601–604.
23.
Ivanova, N., R. Dobrin, R. Lu, I. Kotenko, J. Levorse, C. DeCoste, X. Schafer, Y. Lun, I.R. Lemischka (2006) Dissecting self-renewal in stem cells with RNA interference. Nature 442: 533–538.
24.
Kaji, K., I.M. Caballero, R. MacLeod, J. Nichols, V.A. Wilson, B. Hendrich (2006) The NuRD component Mbd3 is required for pluripotency of embryonic stem cells. Nat Cell Biol 8: 285–292.
25.
Kanatsu-Shinohara, M., K. Inoue, J. Lee, M. Yoshimoto, N. Ogonuki, H. Miki, S. Baba, T. Kato, Y. Kazuki, S. Toyokuni, M. Toyoshima, O. Niwa, M. Oshimura, T. Heike, T. Nakahata, F. Ishino, A. Ogura, T. Shinohara (2004) Generation of pluripotent stem cells from neonatal mouse testis. Cell 119: 1001–1012.
26.
Kim, K., P. Lerou, A. Yabuuchi, C. Lengerke, K. Ng, J. West, A. Kirby, M.J. Daly, G.Q. Daley (2007) Histocompatible embryonic stem cells by parthenogenesis. Science 315: 482–486.
27.
Kuroda, T., M. Tada, H. Kubota, H. Kimura, S.Y. Hatano, H. Suemori, N. Nakatsuji, T. Tada (2005) Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression. Mol Cell Biol 25: 2475–2485.
28.
Li, J., T. Ishii, P. Feinstein, P. Mombaerts (2004) Odorant receptor gene choice is reset by nuclear transfer from mouse olfactory sensory neurons. Nature 428: 393–399.
29.
Li, L., M.C. Connelly, C. Wetmore, T. Curran, J.I. Morgan (2003) Mouse embryos cloned from brain tumors. Cancer Res 63: 2733–2736.
30.
Lin, T., C. Chao, S. Saito, S.J. Mazur, M.E. Murphy, E. Appella, Y. Xu (2005) p53 induces differentiation of mouse embryonic stem cells by suppressing Nanog expression. Nat Cell Biol 7: 165–171.
31.
Loh, Y.H., Q. Wu, J.L. Chew, V.B. Vega, W. Zhang, X. Chen, G. Bourque, J. George, B. Leong, J. Liu, K.Y. Wong, K.W. Sung, C.W. Lee, X.D. Zhao, K.P. Chiu, L. Lipovich, V.A. Kuznetsov, P. Robson, L.W. Stanton, C.L. Wei, Y. Ruan, B. Lim, H.H. Ng (2006) The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet 38: 431–440.
32.
Maherali, N., R. Sridharan, W. Xie, J. Utikal, S. Eminli, K. Arnold, M. Stadtfeld, R. Yachechko, J. Tchieu, R. Jaenisch, K. Plath, K. Hochedlinger (2007) Directly reprogrammed fibroblasts show global epigenetic remodeling and widespread tissue contribution. Cell Stem Cell 1: 55–70.
33.
Martin, G.R. (1981) Isolation of a pluripotent cell line from early mouse embryos cultured in medium conditioned by teratocarcinoma stem cells. Proc Natl Acad Sci USA 78: 7634–7638.
34.
Masui, S., Y. Nakatake, Y. Toyooka, D. Shimosato, R. Yagi, K. Takahashi, H. Okochi, A. Okuda, R. Matoba, A.A. Sharov, M.S. Ko, H. Niwa (2007) Pluripotency governed by Sox2 via regulation of Oct3/4 expression in mouse embryonic stem cells. Nat Cell Biol 9: 625–635.
35.
Mitsui, K., Y. Tokuzawa, H. Itoh, K. Segawa, M. Murakami, K. Takahashi, M. Maruyama, M. Maeda, S. Yamanaka (2003) The homeoprotein Nanog is required for maintenance of pluripotency in mouse epiblast and ES cells. Cell 113: 631–642.
36.
Nagano, K., M. Taoka, Y. Yamauchi, C. Itagaki, T. Shinkawa, K. Nunomura, N. Okamura, N. Takahashi, T. Izumi, T. Isobe (2005) Large-scale identification of proteins expressed in mouse embryonic stem cells. Proteomics 5: 1346–1361.
37.
Nichols, J., B. Zevnik, K. Anastassiadis, H. Niwa, D. Klewe-Nebenius, I. Chambers, H. Scholer, A. Smith (1998) Formation of pluripotent stem cells in the mammalian embryo depends on the POU transcription factor Oct4. Cell 95: 379–391.
38.
Niwa, H., J. Miyazaki, A.G. Smith (2000) Quantitative expression of Oct-3/4 defines differentiation, dedifferentiation or self-renewal of ES cells. Nat Genet 24: 372–376.
39.
Niwa, H., Y. Toyooka, D. Shimosato, D. Strumpf, K. Takahashi, R. Yagi, J. Rossant (2005) Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation. Cell 123: 917–929.
40.
Okita, K., T. Ichisaka, S. Yamanaka (2007) Generation of germline-competent induced pluripotent stem cells. Nature 448: 313–317.
41.
Orkin, S.H. (2000) Diversification of haematopoietic stem cells to specific lineages. Nat Rev Genet 1: 57–64.
42.
Ramalho-Santos, M., S. Yoon, Y. Matsuzaki, R.C. Mulligan, D.A. Melton (2002) ‘Stemness’: transcriptional profiling of embryonic and adult stem cells. Science 298: 597–600.
43.
Rodda, D.J., J.L. Chew, L.H. Lim, Y.H. Loh, B. Wang, H.H. Ng, P. Robson (2005) Transcriptional regulation of nanog by OCT4 and SOX2. J Biol Chem 280: 24731–24737.
44.
Rowland, B.D., R. Bernards, D.S. Peeper (2005) The KLF4 tumour suppressor is a transcriptional repressor of p53 that acts as a context-dependent oncogene. Nat Cell Biol 7: 1074–1082.
45.
Silva, J., I. Chambers, S. Pollard, A. Smith (2006) Nanog promotes transfer of pluripotency after cell fusion. Nature 441: 997–1001.
46.
Tada, M., Y. Takahama, K. Abe, N. Nakatsuji, T. Tada (2001) Nuclear reprogramming of somatic cells by in vitro hybridization with ES cells. Curr Biol 11: 1553–1558.
47.
Takahashi, K., S. Yamanaka (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663–676.
48.
Van Hoof, D., R. Passier, D. Ward-Van Oostwaard, M.W. Pinkse, A.J. Heck, C.L. Mummery, J. Krijgsveld (2006) A quest for human and mouse embryonic stem cell-specific proteins. Mol Cell Proteomics 5: 1261–1273.
49.
Wang, J., S. Rao, J. Chu, X. Shen, D.N. Levasseur, T.W. Theunissen, S.H. Orkin (2006) A protein interaction network for pluripotency of embryonic stem cells. Nature 444: 364–368.
50.
Wernig, M., A. Meissner, R. Foreman, T. Brambrink, M. Ku, K. Hochedlinger, B.E. Bernstein, R. Jaenisch (2007) In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature 448: 318–324.
51.
Yamanaka, S. (2007) Strategies and new developments in the generation of patient-specific pluripotent stem cells. Cell Stem Cell 1: 39–49.
Copyright / Drug Dosage / Disclaimer
Copyright: All rights reserved. No part of this publication may be translated into other languages, reproduced or utilized in any form or by any means, electronic or mechanical, including photocopying, recording, microcopying, or by any information storage and retrieval system, without permission in writing from the publisher.
Drug Dosage: The authors and the publisher have exerted every effort to ensure that drug selection and dosage set forth in this text are in accord with current recommendations and practice at the time of publication. However, in view of ongoing research, changes in government regulations, and the constant flow of information relating to drug therapy and drug reactions, the reader is urged to check the package insert for each drug for any changes in indications and dosage and for added warnings and precautions. This is particularly important when the recommended agent is a new and/or infrequently employed drug.
Disclaimer: The statements, opinions and data contained in this publication are solely those of the individual authors and contributors and not of the publishers and the editor(s). The appearance of advertisements or/and product references in the publication is not a warranty, endorsement, or approval of the products or services advertised or of their effectiveness, quality or safety. The publisher and the editor(s) disclaim responsibility for any injury to persons or property resulting from any ideas, methods, instructions or products referred to in the content or advertisements.
You do not currently have access to this content.