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Vol. 12, Issue 12, 1921-1928, December 2002

LETTER
Gene Expression Profiling of Embryo-Derived Stem Cells Reveals Candidate Genes Associated With Pluripotency and Lineage Specificity

Tetsuya S. Tanaka,1 Tilo Kunath,2 Wendy L. Kimber,1 Saied A. Jaradat,1 Carole A. Stagg,1 Masayuki Usuda,3 Takashi Yokota,3 Hitoshi Niwa,4 Janet Rossant,2 and Minoru S.H. Ko1,5

1 Laboratory of Genetics, National Institute on Aging, National Institutes of Health, Baltimore, Maryland, 21224-6820, USA; 2 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, Ontario, Canada; 3 Department of Stem Cell Regulation, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan; 4 Laboratory for Pluripotent Cell Studies, RIKEN Center for Developmental Biology, Kobe, Hyogo, Japan

Large-scale gene expression profiling was performed on embryo-derived stem cell lines to identify molecular signatures of pluripotency and lineage specificity. Analysis of pluripotent embryonic stem (ES) cells, extraembryonic-restricted trophoblast stem (TS) cells, and terminally-differentiated mouse embryo fibroblast (MEF) cells identified expression profiles unique to each cell type, as well as genes common only to ES and TS cells. Whereas most of the MEF-specific genes had been characterized previously, the majority (67%) of the ES-specific genes were novel and did not include known differentiated cell markers. Comparison with microarray data from embryonic material demonstrated that ES-specific genes were underrepresented in all stages sampled, whereas TS-specific genes included known placental markers. Investigation of four novel TS-specific genes showed trophoblast-restricted expression in cell lines and in vivo, whereas one uncharacterized ES-specific gene, Esg-1, was found to be exclusively associated with pluripotency. We suggest that pluripotency requires a set of genes not expressed in other cell types, whereas lineage-restricted stem cells, like TS cells, express genes predictive of their differentiated lineage.

[Supplemental material is available online at www.genome.org and http://lgsun.grc.nia.nih.gov/microarray/data.html]

5 Corresponding author.

12:1921-1928 ©2002 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/02 $5.00
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