Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation

Nature Biotechnology volume 22, pages 707–716 (2004)Cite this article

Abstract

Human embryonic stem (hES) cells hold promise for generating an unlimited supply of cells for replacement therapies. To characterize hES cells at the molecular level, we obtained 148,453 expressed sequence tags (ESTs) from undifferentiated hES cells and three differentiated derivative subpopulations. Over 32,000 different transcripts expressed in hES cells were identified, of which more than 16,000 do not match closely any gene in the UniGene public database. Queries to this EST database revealed 532 significantly upregulated and 140 significantly downregulated genes in undifferentiated hES cells. These data highlight changes in the transcriptional network that occur when hES cells differentiate. Among the differentially regulated genes are several components of signaling pathways and transcriptional regulators that likely play key roles in hES cell growth and differentiation. The genomic data presented here may facilitate the derivation of clinically useful cell types from hES cells.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Identification of transcripts from human embryonic stem cells.
Figure 2: Expression of Leukemia Inhibitory Factor (LIF) gene family genes and their receptors in human ES cells based on EST frequencies (see Table 1b).
Figure 3: WNT pathway.
Figure 4: NODAL pathway summary.

Similar content being viewed by others

Accession codes

Accessions

GenBank/EMBL/DDBJ

References

  1. Reubinoff, B., Pera, M.F., Fong, C.-Y., Trounson, A. & Bongso, A. Embryonic stem cell lines from human blastocysts: somatic differentiation in vitro. Nat. Biotechnol. 18, 399–404 (2000).

    Article  CAS  Google Scholar 

  2. Thomson, J.A. et al. Embryonic stem cell lines derived from human blastocysts. Science 282, 1145–1147 (1998).

    Article  CAS  Google Scholar 

  3. Xu, C. et al. Feeder-free growth of undifferentiated human embryonic stem cells on defined matrices with conditioned medium. Nat. Biotechnol. 19, 971–974 (2001).

    Article  CAS  Google Scholar 

  4. Rambhatla, L., Chiu, C.P., Kundu, P., Peng, Y. & Carpenter, M.K. Generation of hepatocyte-like cells from human embryonic stem cells. Cell Transplant. 12, 1–11 (2003).

    Article  Google Scholar 

  5. Carpenter, M.K. et al. Enrichment of neurons and neural precursors from human embryonic stem cells. Exp. Neurol. 172, 383–397 (2001).

    Article  CAS  Google Scholar 

  6. Lebkowski, J.S. et al. Human embryonic stem cells: culture, differentiation, and genetic modification for regenerative medicine applications. Cancer J. 7 (Suppl.), S83–S93 (2001).

    PubMed  Google Scholar 

  7. Schuler, G.D. et al. A gene map of the human genome. Science 274, 540–546 (1996).

    Article  CAS  Google Scholar 

  8. Boguski, M.S., Lowe, T.M. & Tolstoshev, C.M. dbEST–database for “expressed sequence tags.” Nat. Genet. 4, 332–333 (1993).

    Article  CAS  Google Scholar 

  9. Okubo, K. et al. Large scale cDNA sequencing for analysis of quantitative and qualitative aspects of gene expression. Nat. Genet. 2, 173–179 (1992).

    Article  CAS  Google Scholar 

  10. Siegel, S. & Castellan, N. Nonparametric Statistics for the Behavioral Sciences edn. 2 (McGraw-Hill, London, 1988).

    Google Scholar 

  11. Yoshida, K. et al. Maintenance of the pluripotential phenotype of embryonic stem cells through direct activation of gp130 signalling pathways. Mech. Dev. 45, 163–171 (1994).

    Article  CAS  Google Scholar 

  12. Schuringa, J.J. van der Schaaf, S., Vellenga, E., Eggen, B.J. & Kruijer, W. LIF-induced STAT3 signaling in murine versus human embryonal carcinoma (EC) cells. Exp. Cell Res. 274, 119–129 (2002).

    Article  CAS  Google Scholar 

  13. Metcalf, D. The unsolved enigmas of leukemia inhibitory factor. Stem Cells 21, 5–14 (2003).

    Article  CAS  Google Scholar 

  14. Bravo, J. & Heath, J.K. Receptor recognition by gp130 cytokines. EMBO J. 19, 2399–2411 (2000).

    Article  CAS  Google Scholar 

  15. Aaronson, D.S. & Horvath, C.M. A road map for those who know JAK-STAT. Science 296, 1653–1655 (2002).

    Article  CAS  Google Scholar 

  16. Schindler, C.W. Series introduction. JAK-STAT signaling in human disease. J. Clin. Invest. 109, 1133–1137 (2002).

    Article  CAS  Google Scholar 

  17. Duval, D., Reinhardt, B., Kedinger, C. & Boeuf, H. Role of suppressors of cytokine signaling (Socs) in leukemia inhibitory factor (LIF)-dependent embryonic stem cell survival. FASEB J. 14, 1577–1584 (2000).

    Article  CAS  Google Scholar 

  18. Carpenter, M.K. et al. Properties of four human embryonic stem cell lines maintained in a feeder-free culture system. Dev. Dyn. 229, 243–258 (2004).

    Article  CAS  Google Scholar 

  19. Ornitz, D.M. & Itoh, N. Fibroblast growth factors. Genome Biol. 2, R3005 (2001).

    Article  Google Scholar 

  20. Ornitz, D.M. et al. Receptor specificity of the fibroblast growth factor family. J. Biol. Chem. 271, 15292–15297 (1996).

    Article  CAS  Google Scholar 

  21. Goldfarb, M. Signaling by fibroblast growth factors: the inside story. Science STKE 2001, PE37 (2001).

    CAS  Google Scholar 

  22. Taipale, J. & Beachy, P.A. The Hedgehog and Wnt signalling pathways in cancer. Nature 411, 349–354 (2001).

    Article  CAS  Google Scholar 

  23. Reya, T. et al. A role for Wnt signalling in self-renewal of haematopoietic stem cells. Nature 423, 409–414 (2003).

    Article  CAS  Google Scholar 

  24. Willert, K. et al. Wnt proteins are lipid-modified and can act as stem cell growth factors. Nature 423, 448–452 (2003).

    Article  CAS  Google Scholar 

  25. Tang, K. et al. Wnt-1 promotes neuronal differentiation and inhibits gliogenesis in P19 cells. Biochem. Biophys. Res. Commun. 293, 167–173 (2002).

    Article  CAS  Google Scholar 

  26. Aubert, J., Dunstan, H., Chambers, I. & Smith, A. Functional gene screening in embryonic stem cells implicates Wnt antagonism in neural differentiation. Nat. Biotechnol. 20, 1240–1245 (2002).

    Article  CAS  Google Scholar 

  27. Ding, S. et al. Synthetic small molecules that control stem cell fate. Proc. Natl. Acad. Sci. USA 100, 7632–7637 (2003).

    Article  CAS  Google Scholar 

  28. Gregory, C.A., Singh, H., Perry, A.S. & Prockop, D.J. The Wnt signaling inhibitor dick-kopf-1 is required for reentry into the cell cycle of human adult stem cells from bone marrow. J. Biol. Chem. 278, 28067–28078 (2003).

    Article  CAS  Google Scholar 

  29. Li, X., Yost, H.J., Virshup, D.M. & Seeling, J.M. Protein phosphatase 2A and its B56 regulatory subunit inhibit Wnt signaling in Xenopus. EMBO J. 20, 4122–4131 (2001).

    Article  CAS  Google Scholar 

  30. Schier, A.F. & Shen, M.M. Nodal signalling in vertebrate development. Nature 403, 385–389 (2000).

    Article  CAS  Google Scholar 

  31. Purandare, S.M. et al. A complex syndrome of left-right axis, central nervous system and axial skeleton defects in Zic3 mutant mice. Development 129, 2293–2302 (2002).

    CAS  PubMed  Google Scholar 

  32. Gebbia, M. et al. X-linked situs abnormalities result from mutations in ZIC3. Nat. Genet. 17, 305–308 (1997).

    Article  CAS  Google Scholar 

  33. Cavaleri, F. & Scholer, H.R. Nanog. A new recruit to the embryonic stem cell orchestra. Cell 113, 551–552 (2003).

    Article  CAS  Google Scholar 

  34. Botquin, V. et al. New POU dimer configuration mediates antagonistic control of an osteopontin preimplantation enhancer by Oct-4 and Sox-2. Genes Dev. 12, 2073–2090 (1998).

    Article  CAS  Google Scholar 

  35. Yuan, H., Corbi, N., Basilico, C. & Dailey, L. Developmental-specific activity of the FGF-4 enhancer requires the synergistic action of Sox2 and Oct-3. Genes Dev. 9, 2635–2645 (1995).

    Article  CAS  Google Scholar 

  36. Schoorlemmer, J. et al. Characterization of a negative retinoic acid response element in the murine Oct4 promoter. Mol. Cell. Biol. 14, 1122–1136 (1994).

    Article  CAS  Google Scholar 

  37. Ben-Shushan, E., Sharir, H., Pikarsky, E. & Bergman, Y. A dynamic balance between ARP-1/COUP-TFII, EAR-3/COUP-TFI, and retinoic acid receptor:retinoid X receptor heterodimers regulates Oct-3/4 expression in embryonal carcinoma cells. Mol. Cell. Biol. 15, 1034–1048 (1995).

    Article  CAS  Google Scholar 

  38. Audic, S. & Claverie, J.M. The significance of digital gene expression profiles. Genome Res. 7, 986–995 (1997).

    Article  CAS  Google Scholar 

  39. Ewing, R.M. et al. Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression. Genome Res. 9, 950–959 (1999).

    Article  CAS  Google Scholar 

  40. Claverie, J.M. Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet. 8, 1821–1832 (1999).

    Article  CAS  Google Scholar 

  41. Ko, M.S. et al. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Development 127, 1737–1749 (2000).

    PubMed  Google Scholar 

  42. Strausberg, R.L., Dahl, C.A. & Klausner, R.D. New opportunities for uncovering the molecular basis of cancer. Nat. Genet. 15 (Suppl.), 415–416 (1997).

    Article  CAS  Google Scholar 

  43. Rohlf, F.K., Sokal, R.R. & Freeman, W.H. Statistical Tables, Edn. 3. (WH Freeman & Co., New York; 1994).

    Google Scholar 

  44. Ramalho-Santos, M., Yoon, S., Matsuzaki, Y., Mulligan, R.C. & Melton, D.A. “Stemness”: transcriptional profiling of embryonic and adult stem cells. Science 298, 597–600 (2002).

    Article  CAS  Google Scholar 

  45. Ivanova, N.B. et al. A stem cell molecular signature. Science 298, 601–604 (2002).

    Article  CAS  Google Scholar 

  46. Adams, M.D. et al. Sequence identification of 2,375 human brain genes. Nature 355, 632–634 (1992).

    Article  CAS  Google Scholar 

  47. Smith, T.P., Godtel, R.A. & Lee, R.T. PCR-based setup for high-throughput cDNA library sequencing on the ABI 3700 automated DNA sequencer. Biotechniques 29, 698–700 (2000).

    Article  CAS  Google Scholar 

  48. Pop, M. & Kosack, D. Using the TIGR assembler in shotgun sequencing projects. Methods Mol. Biol. 255, 279–294 (2004).

    CAS  PubMed  Google Scholar 

  49. Altschul, S.F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402 (1997).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank Ellen Beasley, Melissa Carpenter, Dennis Gilbert, Joseph D. Gold, Calvin Harley, Greg Fisk, Gregg Morin and Catherine Priest for valuable discussions and Michael G. Walker for help with the statistical analysis. We acknowledge Jakyoung Agnew, Jerrod Denham, Kathaleen Golds, Robert Holt, Margaret Inokuma, Karen Ketchum, Michael Mok, Steven Rabkin and Tim Stockwell for expert technical assistance.

Author information

Author notes

  1. Sally Zhang

    Present address: Transplantation Immunology, Department of Cardiothoracic Surgery, Stanford University, Stanford, California, 94305, USA

  2. Shirley Lei

    Present address: UCSF School of Dentistry, 513 Parnassus Avenue, S-630, San Francisco, California, 94143-0430, USA

  3. Jaji Murage

    Present address: Molecular Pharmacology, Stanford University, 269 Campus Drive, CCSR 3230, Stanford, California, 94305, USA

  4. Rixun Fang & Karl Guegler

    Present address: Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California, 94404, USA

  5. Lawrence W Stanton

    Present address: Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672

Authors and Affiliations

  1. Geron Corporation, 230 Constitution Drive, Menlo Park, California, 94025, USA

    Ralph Brandenberger, Henry Wei, Sally Zhang, Shirley Lei, Jaji Murage, Gregory J Fisk, Yan Li, Chunhui Xu, Ramumkar Mandalam, Jane Lebkowski & Lawrence W Stanton

  2. Celera Genomics, 45 West Gude Drive, Rockville, 20850, Maryland, USA

    Rixun Fang & Karl Guegler

  3. National Institute on Aging, 5600 Nathan Shock Drive, Baltimore, 21224, Maryland, USA

    Mahendra S Rao

  4. Transplantation Immunology, Department of Cardiothoracic Surgery, Stanford University, Stanford, California, 94305, USA

    Shirley Lei, Jaji Murage, Rixun Fang, Karl Guegler & Lawrence W Stanton

  5. UCSF School of Dentistry, 513 Parnassus Avenue, S-630, San Francisco, California, 94143-0430, USA

    Sally Zhang, Jaji Murage, Rixun Fang, Karl Guegler & Lawrence W Stanton

  6. Molecular Pharmacology, Stanford University, 269 Campus Drive, CCSR 3230, Stanford, California, 94305, USA

    Sally Zhang, Shirley Lei, Rixun Fang, Karl Guegler & Lawrence W Stanton

  7. Applied Biosystems, 850 Lincoln Centre Drive, Foster City, California, 94404, USA

    Sally Zhang, Shirley Lei, Jaji Murage & Lawrence W Stanton

  8. Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672

    Sally Zhang, Shirley Lei, Jaji Murage, Rixun Fang & Karl Guegler

Authors
  1. Ralph Brandenberger
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Henry Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sally Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shirley Lei
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jaji Murage
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Gregory J Fisk
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Yan Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Chunhui Xu
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Rixun Fang
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Karl Guegler
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Mahendra S Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Ramumkar Mandalam
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Jane Lebkowski
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Lawrence W Stanton
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Ralph Brandenberger.

Ethics declarations

Competing interests

Several of the authors are or were employees of Geron Corporation or Celera Genomics.

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Cite this article

Brandenberger, R., Wei, H., Zhang, S. et al. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. Nat Biotechnol 22, 707–716 (2004). https://doi.org/10.1038/nbt971

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nbt971

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing