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

Abstract

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.

High-throughput screen for genes predominantly expressed in the ICM of mouse blastocysts by whole mount in situ hybridization

“…We then attempted to identify candidate genes that are expressed more highly in the ICM than in TE cells. Due to difficulty of collecting the ICM and TE from blastocysts separately, we exploited the cultured cells derived from these cell types in our previous study (Tanaka et al, 2002). Mouse ES cells are cultured from the ICM (Evans and Kaufman, 1981;Martin, 1981), whereas mouse TS cells are cultured from the TE (Tanaka et al, 1998) (Fig.…”

“…To supplement the data (Tanaka et al, 2002) and update to the latest microarray platform, we performed hybridizations of ES and TS RNAs onto the NIA 22K 60-mer oligonucleotide microarrays in triplicate (Carter et al, 2003a). This glass-slide microarray platform contains genes from preimplantation and stem cells (for experimental design, see ref (Tanaka et al, 2002); for all the array data set, see http://lgsun.grc.nia.nih.gov/data, and also Supplementary Material 3).…”

“…This glass-slide microarray platform contains genes from preimplantation and stem cells (for experimental design, see ref (Tanaka et al, 2002); for all the array data set, see http://lgsun.grc.nia.nih.gov/data, and also Supplementary Material 3). By this criterion, we identified 1388 genes that were expressed more highly in ES cells than in TS cells.…”

Analysis of Esg1 Expression in Pluripotent Cells and the Germline Reveals Similarities with Oct4 and Sox2 and Differences Between Human Pluripotent Cell Lines

“…Although previous reports have suggested that Esg1 is not expressed after the preimplantation and peri-implantation stages [11,12], we examined Esg1 expression during germ cell development. A unique quality of segregating PGCs is the expression of many pluripotency-associated genes, which are downregulated in somatic cells.…”

A Conserved Organization of Transcription during Embryonic Stem Cell Differentiation and in Cells with High C Value

“…For example, during erythropoiesis nuclei become smaller and heterochromatic as many genes are silenced; concurrently, globin genes become active by associating with specific nuclear sites known as "factories" or "active chromatin hubs" (Cook, 1999(Cook, , 2002de Laat and Grosveld, 2003;Osborne et al, 2004). Although microarrays provide detailed information on changes in steady-state mRNA levels during differentiation (Kelly and Rizzino, 2000;Harris and Childs, 2002;Tanaka et al, 2002;Sperger et al, 2003), there is little information on how primary rates of transcription change. For example, we do not know by how much global rates vary as any mammalian cell differentiates.…”