Gene Expression Signatures of Seven Individual Human Embryonic Stem Cell Lines

Authors

  • Heli Skottman Ph.D.,

    Corresponding author
    1. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
    2. Department of Clinical Science, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
    • Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, POB 123, 0520 Turku, Finland. Telephone: 358-02-3338622; Fax: 358-02-3338000
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  • Milla Mikkola,

    1. Biomedicum Helsinki, Program of Developmental and Reproductive Biology, University of Helsinki, Helsinki, Finland
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  • Karolina Lundin,

    1. Biomedicum Helsinki, Program of Developmental and Reproductive Biology, University of Helsinki, Helsinki, Finland
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  • Cia Olsson,

    1. Biomedicum Helsinki, Program of Developmental and Reproductive Biology, University of Helsinki, Helsinki, Finland
    2. Family Federation of Finland, Helsinki, Finland
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  • Anne-Marie Strömberg,

    1. Department of Clinical Science, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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  • Timo Tuuri,

    1. Biomedicum Helsinki, Program of Developmental and Reproductive Biology, University of Helsinki, Helsinki, Finland
    2. Family Federation of Finland, Helsinki, Finland
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  • Timo Otonkoski,

    1. Biomedicum Helsinki, Program of Developmental and Reproductive Biology, University of Helsinki, Helsinki, Finland
    2. Hospital for Children and Adolescents, University of Helsinki, Helsinki, Finland
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    • These authors contributed equally to this study.

  • Outi Hovatta,

    1. Department of Clinical Science, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm, Sweden
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    • These authors contributed equally to this study.

  • Riitta Lahesmaa

    1. Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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    • These authors contributed equally to this study.


Abstract

Identification of molecular components that define a pluripotent human embryonic stem cell (hESC) provides the basis for understanding the molecular mechanisms regulating the maintenance of pluripotency and induction of differentiation. We compared the gene expression profiles of seven genetically independent hESC lines with those of nonlineage-differentiated cells derived from each line. A total of 8,464 transcripts were expressed in all hESC lines. More than 45% of them have no yet-known biological function, which indicates that a high number of unknown factors contribute to hESC pluripotency. Among these 8,464 transcripts, 280 genes were specific for hESCs and 219 genes were more than twofold differentially expressed in all hESC lines compared with nonlineage-differentiated cells. They represent genes implicated in the maintenance of pluripotency and those involved in early differentiation. The chromosomal distribution of these hESC-enriched genes showed over-representation in chromosome 19 and under-representation in chromosome 18. Although the overall gene expression profiles of the seven hESC lines were markedly similar, each line also had a subset of differentially expressed genes reflecting their genetic variation and possibly preferential differentiation potential. Limited overlap between gene expression profiles illustrates the importance of cross-validation of results between different ESC lines.

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