Correlation of Murine Embryonic Stem Cell Gene Expression Profiles with Functional Measures of Pluripotency

Authors

  • Lars Palmqvist,

    1. Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
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  • Clive H. Glover,

    1. Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
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  • Lien Hsu,

    1. Department of Cancer Endocrinology, BC Cancer Agency, Vancouver, British Columbia, Canada
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  • Min Lu,

    1. Department of Cancer Endocrinology, BC Cancer Agency, Vancouver, British Columbia, Canada
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  • Bolette Bossen,

    1. Department of Cancer Endocrinology, BC Cancer Agency, Vancouver, British Columbia, Canada
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  • James M. Piret,

    1. Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
    2. Departments of Chemical and Biological Engineering, University of British Columbia, Vancouver, British Columbia, Canada
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  • R. Keith Humphries,

    1. Terry Fox Laboratory, BC Cancer Agency, Vancouver, British Columbia, Canada
    2. Departments of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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  • Cheryl D. Helgason Ph.D.

    Corresponding author
    1. Department of Cancer Endocrinology, BC Cancer Agency, Vancouver, British Columbia, Canada
    2. Departments of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
    • Department of Cancer Endocrinology, BC Cancer Agency, 675 West 10th Avenue, Vancouver, BC, Canada, V5Z 1L3. Telephone: 604-675-8011; Fax: 604-675-8183
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Abstract

Global gene expression profiling was performed on murine embryonic stem cells (ESCs) induced to differentiate by removal of leukemia inhibitory factor (LIF) to identify genes whose change in expression correlates with loss of pluripotency. To identify appropriate time points for the gene expression analysis, the dynamics of loss of pluripotency were investigated using three functional assays: chimeric mouse formation, embryoid body generation, and colony-forming ability. A rapid loss of pluripotency was detected within 24 hours, with very low residual activity in all assays by 72 hours. Gene expression profiles of undifferentiated ESCs and ESCs cultured for 18 and 72 hours in the absence of LIF were determined using the Affymetrix GeneChip U74v2. In total, 473 genes were identified as significantly differentially expressed, with approximately one third having unknown biological function. Among the 275 genes whose expression decreased with ESC differentiation were several factors previously identified as important for, or markers of, ESC pluripotency, including Stat3, Rex1, Sox2, Gbx2, and Bmp4. A significant number of the decreased genes also overlap with previously published mouse and human ESC data. Furthermore, several membrane proteins were among the 48 decreased genes correlating most closely with the functional assays, including the stem cell factor receptor c-Kit. Through identification of genes whose expression closely follows functional properties of ESCs during early differentiation, this study lays the foundation for further elucidating the molecular mechanisms regulating the maintenance of ESC pluripotency and facilitates the identification of more reliable molecular markers of the undifferentiated state.

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