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a Genome Institute of Singapore, Singapore;
b National Institute of Ageing; Stem Cell, Laboratory of Neuroscience, Baltimore, Maryland, USA;
c Division of Cancer Biology, Beth Israel Deaconess Medical Center, Harvard Institutes of Medicine, Boston, Massachusetts, USA;
d Department of Biological Sciences, National University of Singapore, Singapore;
e Lynx Therapeutics Inc., Hayward, California, USA;
f Embryo Stem Cell International, Singapore;
g Geron Corporation, Menlo Park, California, USA
Key Words. Embryonic stem cells, murine and human • Transcriptome • Massively parallel signature sequencing (MPSS)
Correspondence: Bing Lim, M.D., Ph.D., Genome Institute of Singapore, 60 Biopolis Street, Genome#02-01, Singapore 138672. Telephone: 65-6478-8000; Fax: 65-6478-9005; e-mail: limb1{at}gis.a-star.edu.sg; and Mahendra Rao, M.D., Ph.D., National Institute of Ageing: Stem Cell, LNS, GRC, 333 Cassell Drive, Baltimore, MD 21224. Telephone: 410-558-8204; Fax: 410-558-8249; e-mail: raomah{at}grc.nia.nih.gov
Human embryonic stem cells (hESCs) are an important source of stem cells in regenerative medicine, and much remains unknown about their molecular characteristics. To develop a detailed genomic profile of ESC lines in two different species, we compared transcriptomes of one murine and two different hESC lines by massively parallel signature sequencing (MPSS). Over 2 million signature tags from each line and their differentiating embryoid bodies were sequenced. Major differences and conserved similarities between species identified by MPSS were validated by reverse transcription polymerase chain reaction (RT-PCR) and microarray. The two hESC lines were similar overall, with differences that are attributable to alleles and propagation. Human–mouse comparisons, however, identified only a small (core) set of conserved genes that included genes known to be important in ESC biology, as well as additional novel genes. Identified were major differences in leukemia inhibitory factor, transforming growth factor-beta, and Wnt and fibroblast growth factor signaling pathways, as well as the expression of genes encoding metabolic, cytoskeletal, and matrix proteins, many of which were verified by RT-PCR or by comparing them with published databases. The study reported here underscores the importance of cross-species comparisons and the versatility and sensitivity of MPSS as a powerful complement to current array technology.
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