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Regulatory networks define phenotypic classes of human stem cell lines

Author

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  • Franz-Josef Müller

    (Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    Center for Psychiatry, ZIP-Kiel, University Hospital Schleswig Holstein, Niemannsweg 147, D-24105 Kiel, Germany)

  • Louise C. Laurent

    (Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    University of California, San Diego, 200 West Arbor Drive, San Diego, California 92035, USA)

  • Dennis Kostka

    (Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany
    Present address: Genome and Biomedical Sciences Facility and Department of Statistics, University of California, Davis 451 Health Sciences Drive, Davis, California 95616, USA.)

  • Igor Ulitsky

    (School of Computer Science, Tel Aviv University)

  • Roy Williams

    (The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, USA)

  • Christina Lu

    (Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA)

  • In-Hyun Park

    (Children’s Hospital Boston and Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA)

  • Mahendra S. Rao

    (Invitrogen Co, 3705 Executive Way, Frederick, Maryland 21704, USA
    Center for Stem Cell Biology, Buck Institute on Aging, 8001 Redwood Boulevard, Novato, California 94945, USA)

  • Ron Shamir

    (School of Computer Science, Tel Aviv University)

  • Philip H. Schwartz

    (Center for Neuroscience Research, Children’s Hospital of Orange County Research Institute, 455 South Main Street, Orange, California 92868, USA
    Developmental Biology Center, University of California, Irvine, 4205 McGaugh Hall, Irvine, California 92697, USA)

  • Nils O. Schmidt

    (Martinistrasse 52, D-20246 Hamburg, Germany)

  • Jeanne F. Loring

    (Center for Regenerative Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
    The Burnham Institute for Medical Research, 10901 North Torrey Pines Road, La Jolla, California 92037, USA)

Abstract

Human stem cells: surfing the PluriNet Hundreds of different human cell lines are grouped under the catch-all term 'stem cells'. They can be from embryos, fetuses or adults. And they can be pluripotent — able to produce a broad range of cells — or fated to produce a limited repertoire of cell types. Müller et al. set out to establish a 'stem cell diagnostic' to bring order to the characterization and classification of human stem cells, based on a database of transcriptional profiles derived from more than 150 cell samples. Bioinformatic analyses revealed that pluripotent stem cell lines share many properties and all possess a characteristic protein–protein network, dubbed 'PluriNet'. Other cell types, including brain-derived neural stem cell lines, are much more diverse. These results offer a new strategy for classifying stem cells and support the idea that pluripotency and self-renewal are under tight control by specific molecular networks.

Suggested Citation

  • Franz-Josef Müller & Louise C. Laurent & Dennis Kostka & Igor Ulitsky & Roy Williams & Christina Lu & In-Hyun Park & Mahendra S. Rao & Ron Shamir & Philip H. Schwartz & Nils O. Schmidt & Jeanne F. Lor, 2008. "Regulatory networks define phenotypic classes of human stem cell lines," Nature, Nature, vol. 455(7211), pages 401-405, September.
    • Handle: RePEc:nat:nature:v:455:y:2008:i:7211:d:10.1038_nature07213
    DOI: 10.1038/nature07213
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    Cited by:

    1. Anyou Wang & Ying Du & Qianchuan He & Chunxiao Zhou, 2013. "A Quantitative System for Discriminating Induced Pluripotent Stem Cells, Embryonic Stem Cells and Somatic Cells," PLOS ONE, Public Library of Science, vol. 8(2), pages 1-10, February.
    2. Kakajan Komurov & Michael A White & Prahlad T Ram, 2010. "Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data," PLOS Computational Biology, Public Library of Science, vol. 6(8), pages 1-10, August.

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