A Meta-Analysis of Human Embryonic Stem Cells Transcriptome Integrated into a Web-Based Expression Atlas

Authors

  • Said Assou,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
    4. MacoPharma, Tourcoing, France
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  • Tanguy Le Carrour,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
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  • Sylvie Tondeur,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
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  • Susanne Ström,

    1. Department of Obstetrics and Gynecology, CLINTEC, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
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  • Audrey Gabelle,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
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  • Sophie Marty,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
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  • Laure Nadal,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
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  • Véronique Pantesco,

    1. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
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  • Thierry Réme,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
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  • Jean-Philippe Hugnot,

    1. Institut des Neurosciences de Montpellier, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U583, Montpellier, France
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  • Stéphan Gasca,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Centre Hospitalier Universitaire de Montpellier, Unité Biologie Clinique d'Assistance Médicale à la Procréation-Diagnostic Pré-Implantatoire, Hôpital Arnaud de Villeneuve, Montpellier, France
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  • Outi Hovatta,

    1. Department of Obstetrics and Gynecology, CLINTEC, Karolinska Institutet, Karolinska University Hospital, Huddinge, Stockholm, Sweden
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  • Samir Hamamah,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
    4. Centre Hospitalier Universitaire de Montpellier, Unité Biologie Clinique d'Assistance Médicale à la Procréation-Diagnostic Pré-Implantatoire, Hôpital Arnaud de Villeneuve, Montpellier, France
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  • Bernard Klein,

    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
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  • John De Vos M.D., Ph.D.

    Corresponding author
    1. Centre Hospitalier Universitaire de Montpellier, Institute for Research in Biotherapy, Hôpital Saint-Eloi, Montpellier, France
    2. Institut National de la Santé et de la Recherche Médicale, U847, Montpellier, France
    3. Université Montpellier, Unité de Formation et de Recherche de médecine, Montpellier, France
    • Institute for Research in Biotherapy, Hôpital Saint-Eloi, 80 Avenue Augustin Fliche, 34295 Montpellier Cedex 5, France. Telephone: 33-(0)4-67-33-01-91; Fax: 33-(0)4-67-33-01-13
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Abstract

Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a “consensus hESC gene list.” Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This “consensus differentiation gene list” included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, http://amazonia.montp.inserm.fr, to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.

Disclosure of potential conflicts of interest is found at the end of this article.

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