Correlation of Murine Embryonic Stem Cell Gene Expression Profiles with Functional Measures of Pluripotency

Abstract

Global gene expression profiling was performed on murine embryonic stem cells (ESCs) induced to differentiate by removal of leukemia inhibitory factor (LIF) to identify genes whose change in expression correlates with loss of pluripotency. To identify appropriate time points for the gene expression analysis, the dynamics of loss of pluripotency were investigated using three functional assays: chimeric mouse formation, embryoid body generation, and colony-forming ability. A rapid loss of pluripotency was detected within 24 hours, with very low residual activity in all assays by 72 hours. Gene expression profiles of undifferentiated ESCs and ESCs cultured for 18 and 72 hours in the absence of LIF were determined using the Affymetrix GeneChip U74v2. In total, 473 genes were identified as significantly differentially expressed, with approximately one third having unknown biological function. Among the 275 genes whose expression decreased with ESC differentiation were several factors previously identified as important for, or markers of, ESC pluripotency, including Stat3, Rex1, Sox2, Gbx2, and Bmp4. A significant number of the decreased genes also overlap with previously published mouse and human ESC data. Furthermore, several membrane proteins were among the 48 decreased genes correlating most closely with the functional assays, including the stem cell factor receptor c-Kit. Through identification of genes whose expression closely follows functional properties of ESCs during early differentiation, this study lays the foundation for further elucidating the molecular mechanisms regulating the maintenance of ESC pluripotency and facilitates the identification of more reliable molecular markers of the undifferentiated state. Stem Cells 2005;23:663-680

A Cassette System to Study Embryonic Stem Cell Differentiation by Inducible RNA Interference

“…2, 3A). These results are consistent with DNA microarray data of others who reported Brf1 (Zfp36L1) downregulation after LIF removal [41,42]. That the effect in some clones was less intense than that following LIF removal suggests that not all effects on gene expression by LIF removal are mediated by Stat3.…”

Bcl2, a transcriptional target of p38α, is critical for neuronal commitment of mouse embryonic stem cells

“…However, our study also revealed a specific SB-dependent downregulation of pluripotent ES cell markers such as Rex1, Fbox15 and Pdgfa. 36 Although SB could accelerate cell differentiation and boost apoptosis, by abruptly repressing pluripotent cell markers. At the opposite side, the antiapoptotic PD compound increases expression of survival genes, such as Spp1 gene, recently characterized as a critical self-renewal gene expressed in undifferentiated ES cells.…”

Tumorigenic Role of Orphan Nuclear Receptor NR0B1 in Lung Adenocarcinoma

“…23 A recent study on the embryonic stem cells showed that NR0B1 is abundantly expressed in an undifferentiated status, but its expression level is down-regulated on differentiation. 24 Knocked down of NR0B1 expression resulted in differentiation of embryonic stem cells, suggesting a role of NR0B1 for the maintenance of undifferentiated state. 25 NR0B1 is expressed in several kinds of cancers, such as endometrial carcinoma, ovarian carcinoma, prostatic carcinoma, and Ewing's sarcoma.…”