Unique gene expression signatures of independently-derived human embryonic stem cell lines

Abstract

Human embryonic stem cells (hESCs) have the potential to differentiate to diverse cell types. This ability endows hESCs with promise for the development of novel therapeutics, as well as promise for the development of a rigorous genetic system to probe human gene function. However, in spite of the impending utility of hESCs for clinical and basic applications, little is known about their fundamental properties. Recent reports have documented transcriptional profiles of mouse embryonic stem cells (mESCs), adult stem cells and a single hESC line, H9. To date, however, the transcriptional profiles of independently-derived hESC lines have not been compared. In order to examine the similarities and differences in multiple hESC lines, we compared gene expression profiles of the HSF-1, HSF-6 and H9 lines. We found that the majority of genes examined were expressed in all three cell lines. However, we also observed that each line possessed a unique expression signature; the expression of many genes was limited to just one or two hESC lines. We suggest that the observed differences in gene expression between independently-derived hESC lines may reflect inherent differences in the initial culture of each line and/or the underlying genetics of the embryos from which the lines were derived.

Non-canonical TAF complexes regulate active promoters in human embryonic stem cells

“…Finally, we analyzed the ChIP-chip dataset in relation to previous genome-wide studies in hESCs (Abeyta et al, 2004; Boyer et al, 2005; Guenther et al, 2007) for features that might distinguish class I and class II genes and found two statistically significant differences (Figure 6E,F; Table 1). First, the promoters of class I genes had greater histone H3 lysine 4 trimethylation (H3K4me3) than those of class II genes (Figure 6E).…”

“…In a search of published expression datasets (Abeyta et al, 2004), we found that several TAFs of the canonical TFIID complex were apparently not expressed in hESCs. To investigate this possibility, we analyzed expression of 13 TAFs by immunoblotting lysates from H9 cells, a well-characterized hESC line.…”

Fourier transform infrared microspectroscopy reveals unique phenotypes for human embryonic and induced pluripotent stem cell lines and their progeny

“…Previous work suggests that different origins and culture conditions can lead to different hESC lines having distinct gene expression signatures [32]. Accordingly, our initial experiments involved determining the spectroscopic similarities between five independently derived hESC lines grown under standardized conditions.…”

Assessing Self-Renewal and Differentiation in Human Embryonic Stem Cell Lines

“…hESCs are also similar in their ability to proliferate and differentiate into cell types of the three germ layers in vitro and in vivo [9 -16]. Properties of hESCs have also been compared using microarray, expressed sequence tag (EST) scan, serial analysis of gene expression (SAGE), and massively parallel signature sequencing (MPSS) [4,[17][18][19][20][21][22][23][24][25][26][27]. These studies suggest that it is likely that markers shared by hESC lines, but absent in other cell populations, exist.…”