Human embryonic stem cells (hESCs) are pluripotent cells that maintain their ability to self-renew and give rise to differentiated progeny representing all three embryonic germ layers [1, 2]. Differentiation of hESCs in vitro into several cell types, such as cardiac, neural, hematopoietic, pancreatic, and hepatic lineages, has been described [3–7]. Derivatives of hESCs could thus potentially be used for cell transplantation therapies in various severe degenerative diseases [8, 9].
Several genes involved in maintaining the mouse ESC characteristics have been functionally characterized, but there is still little known about the molecular control of hESC pluripotency, self-renewal, and differentiation. To understand these mechanisms, it is essential to first identify genes and gene products important for pluripotency. Comparison of the transcriptional profiles of different hESC lines may advance the identification of a core set of molecular components that define pluripotent hESCs and could provide understanding of molecular mechanisms underlying these properties.
DNA microarray analysis allows large-scale gene expression profiling of several thousands of genes, also from very limited amounts of starting material. This is especially important with hESCs due to the fact that large-scale culturing of hESCs is still difficult. High-density arrays, containing most of the known human genes as well as thousands of unknown expressed sequence tags (ESTs), are especially useful tools for studying unknown phenomena in hESCs. During recent years, the first large-scale expression profiles of hESCs have been reported using DNA microarrays [10–13], EST sequencing , serial analysis of gene expression , and massively parallel signature sequencing [16–18]. In this paper, we describe for the first time comparative large-scale transcriptional analyses of seven new hESC lines using DNA microarrays. Comparison of gene expression profiles between different hESC lines has been difficult due to the dissimilar culture conditions. To overcome this problem, we have analyzed differences and similarities in gene expression profiles of seven individual hESC lines cultured in identical conditions. It is known that gene expression profiles differ between individuals of different genetic backgrounds . Each hESC line carries a unique human genome, and fundamental characteristics of each line may be determined by the unique genome. For this reason, it is unlikely that all hESCs are identical with their gene expression profiles. In this work, a high degree of correlation of gene expression in all seven hESC lines was found, but differences in the expression patterns between individual lines were also observed. In addition, all seven hESC lines expressed a panel of specific transcripts not expressed in nonlineage-differentiated cells or in fibroblasts, potentially representing genes responsible for pluripotency.