Patterning pluripotency in embryonic stem cells

Authors

  • Yue Shelby Zhang,

    1. Department for Biomedical Engineering, Columbia University, New York, USA
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  • Ana Sevilla,

    1. Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA
    2. New York Stem Cell Foundation Research Institute, New York, USA
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  • Leo Q. Wan,

    1. Department for Biomedical Engineering, Columbia University, New York, USA
    2. Rensselaer Polytechnic Institute, Troy, New York, USA
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  • Ihor R. Lemischka,

    Corresponding author
    1. Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York, New York, USA
    • Correspondence: Gordana Vunjak-Novakovic, Ph.D., Department of Biomedical Engineering, 622 West 168th Street, New York, New York 10032, USA. Telephone: +1-212-305-2304; Fax: +1-212-305-4692; e-mail: gv2131@columbia.edu; or Ihor R. Lemischka, Ph.D., Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York 10029, New York, USA. Telephone: 212-659-8228; Fax: 212-803-6740; e-mail: ihor.lemischka@mssm.edu

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  • Gordana Vunjak-Novakovic

    Corresponding author
    1. Department for Biomedical Engineering, Columbia University, New York, USA
    • Correspondence: Gordana Vunjak-Novakovic, Ph.D., Department of Biomedical Engineering, 622 West 168th Street, New York, New York 10032, USA. Telephone: +1-212-305-2304; Fax: +1-212-305-4692; e-mail: gv2131@columbia.edu; or Ihor R. Lemischka, Ph.D., Department of Developmental and Regenerative Biology, The Black Family Stem Cell Institute, Mount Sinai School of Medicine, New York 10029, New York, USA. Telephone: 212-659-8228; Fax: 212-803-6740; e-mail: ihor.lemischka@mssm.edu

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  • Author contributions: Y.Z. and A.S.: conception and design, collection and assembly of data, data analysis and interpretation, and manuscript writing; L.Q.W.: data analysis and interpretation; I.R.L.: conception and design, data analysis and interpretation, manuscript writing, and final approval of manuscript; G.V.-N.: conception and design, data analysis and interpretation, manuscript writing, financial support, and final approval of manuscript. Y.Z. and A.S. contributed equally to this article.

Abstract

Developmental gradients of morphogens and the formation of boundaries guide the choices between self-renewal and differentiation in stem cells. Still, surprisingly little is known about gene expression signatures of differentiating stem cells at the boundaries between regions. We thus combined inducible gene expression with a microfluidic technology to pattern gene expression in murine embryonic stem cells. Regional depletion of the Nanog transcriptional regulator was achieved through the exposure of cells to microfluidic gradients of morphogens. In this way, we established pluripotency-differentiation boundaries between Nanog expressing cells (pluripotency zone) and Nanog suppressed cells (early differentiation zone) within the same cell population, with a gradient of Nanog expression across the individual cell colonies, to serve as a mimic of the developmental process. Using this system, we identified strong interactions between Nanog and its target genes by constructing a network with Nanog as the root and the measured levels of gene expression in each region. Gene expression patterns at the pluripotency-differentiation boundaries recreated in vitro were similar to those in the developing blastocyst. This approach to the study of cellular commitment at the boundaries between gene expression domains, a phenomenon critical for understanding of early development, has potential to benefit fundamental research of stem cells and their application in regenerative medicine. Stem Cells 2013;31:1806-1815

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