Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features

A meta-analysis of human embryonic stem cells transcriptome integrated into a web-based expression atlas

Microarray technology provides a unique opportunity to examine gene expression patterns in human embryonic stem cells (hESCs). We performed a meta-analysis of 38 original studies reporting on the transcriptome of hESCs. We determined that 1,076 genes were found to be overexpressed in hESCs by at least three studies when compared to differentiated cell types, thus composing a "consensus hESC gene list." Only one gene was reported by all studies: the homeodomain transcription factor POU5F1/OCT3/4. The list comprised other genes critical for pluripotency such as the transcription factors NANOG and SOX2, and the growth factors TDGF1/CRIPTO and Galanin. We show that CD24 and SEMA6A, two cell surface protein-coding genes from the top of the consensus hESC gene list, display a strong and specific membrane protein expression on hESCs. Moreover, CD24 labeling permits the purification by flow cytometry of hESCs cocultured on human fibroblasts. The consensus hESC gene list also included the FZD7 WNT receptor, the G protein-coupled receptor GPR19, and the HELLS helicase, which could play an important role in hESCs biology. Conversely, we identified 783 genes downregulated in hESCs and reported in at least three studies. This "consensus differentiation gene list" included the IL6ST/GP130 LIF receptor. We created an online hESC expression atlas, http://amazonia.montp.inserm.fr, to provide an easy access to this public transcriptome dataset. Expression histograms comparing hESCs to a broad collection of fetal and adult tissues can be retrieved with this web tool for more than 15,000 genes.

Trisomy 12 in HESC leads to no selective in vivo growth advantage in teratomas, but induces an increased abundance of renal development

The aim of this investigation was to examine the impact of chromosome 12 amplification (tri-12 cells) in human embryonic stem cells (HESC), following in vivo engraftment to an immunodeficient xeno-model. For this we used sublines from the HESC line HS181, spontaneously exhibiting either low or high frequencies of tri-12 cells. Fluorescent in situ hybridization (FISH) analysis revealed a random distribution of tri-12 cells in the HS181 colonies in vitro. Similarly, the contribution of tri-12 cells to the development of various tissues in teratomas in vivo seemed to be fully random with no particular preference regarding in vivo differentiation pathway of tri-12 HS181 cells compared to HS181 cells with disomy 12 (di-12 cells). On the other hand, following in vivo transplantation the ratio of tri-12/di-12 cells was significantly reduced (P < 0.001), indicating a negative selection for this trisomy in vivo. Moreover, injection of HS181 cultures containing tri-12 cells resulted in a significantly increased abundance of areas compatible with renal formation (P < 0.001), relative teratomas derived from injection of di-12 HS181 cells. However, such areas included no increased relative frequency of tri-12 cells, suggesting indirect mechanism(s) for the increased abundance of renal development. The reasons for such developmental bias are unknown and warrant further investigation.

The Regulation of Self-Renewal in Human Embryonic Stem Cells

Human embryonic stem (hES) cells have the ability to self-renew while maintaining their pluripotency. The ability of stem cells to self-renew expansively is essential in both development and maintenance of adult tissues. ES cell lines were first generated from mouse blastocysts, these lines provided much needed information regarding ES cell propagation, growth factor dependence, and marker expression. However, the application potential of murine models is restricted in value because many differences between mouse and human ES cells have since been identified. The process of hES cells self-renewal appears to be regulated by many different pathways; however, the molecular mechanisms enabling this process are not fully characterized. Further defining these mechanisms will enable growth of hES cells under defined conditions and aid controlled differentiation of cells into specified lineages, in turn providing cells suitable for therapeutic applications. This review provides a summary of the mechanisms known to control self-renewal and pluripotency in hES cells.

NANOG maintains self-renewal of primate ES cells in the absence of a feeder layer

Nanog is a homeodomain transcription factor that is expressed specifically in undifferentiated embryonic stem (ES) cells and has been shown to be essential in the maintenance of pluripotency in mouse ES cells. To examine the function of NANOG in primate ES cells, we generated transgenic monkey ES cell lines expressing three- to seven-fold higher levels of NANOG protein compared to wild-type ES cells. These NANOG over-expressing cell lines retained their undifferentiated state in the absence of a feeder layer, as shown by expression of undifferentiated ES cell markers such as alkaline phosphatase (ALP) and OCT-4. We also demonstrated that in vitro differentiation of transgenic cell lines was mostly restricted to the ectodermal lineage, as examined by reverse transcriptase-polymerase chain reaction (RT-PCR). Knockdown experiments using NANOG small interfering (si) RNA resulted in induction of differentiation markers such as AFP, GATA4 and GATA6 for the endoderm and CDX2 for the trophectoderm. These results suggest that NANOG plays a crucial role in maintaining the pluripotent state of primate ES cells.

Guiding embryonic stem cells towards differentiation: lessons from molecular embryology

Embryonic stem cells are uniquely endowed with the capacity of self-renewal and the potential to give rise to all possible cell types, including germ cells. These qualities have made mouse embryonic stem cells a valuable resource for genetic manipulation of the mouse genome. In addition, they present a powerful system for the in vitro dissection of mammalian embryonic development. The recent isolation of human embryonic stem cells has raised a lot of interest for the potential of transposing our knowledge of lineage-specific differentiation of embryonic stem cells to cell-based therapy of human disease. Recent reports have provided insights into the specific differentiation of embryonic stem cells to different cell types of the embryo. However, progress in this direction seems to depend on the knowledge of the mechanisms controlling lineage decisions during embryogenesis.

Transcriptional control of pluripotency: decisions in early development

The pathways controlling the maintenance and loss of pluripotency in cells of the early embryo regulate the formation of the tissues that will support development. Several transcription factors have been identified as being integral to the establishment and/or maintenance of pluripotency, coordinately regulating the expression of genes within pluripotent cells and acting as gene targets of these same processes. Recent advances in understanding the transcriptional regulation of these factors have revealed differences in the transcriptional complexes present within sub-populations of the pluripotent lineage and in the mechanisms regulating the loss of pluripotency on differentiation.

Transcriptional dynamics of the embryonic stem cell switch

Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the transcription factors OCT4, SOX2, and NANOG. In addition to regulating each other through feedback loops, these genes also regulate downstream target genes involved in the maintenance and differentiation of embryonic stem cells. A search for the OCT4-SOX2-NANOG network motif in other species reveals that it is unique to mammals. With a kinetic modeling approach, we ascribe function to the observed OCT4-SOX2-NANOG network by making plausible assumptions about the interactions between the transcription factors at the gene promoter binding sites and RNA polymerase (RNAP), at each of the three genes as well as at the target genes. We identify a bistable switch in the network, which arises due to several positive feedback loops, and is switched on/off by input environmental signals. The switch stabilizes the expression levels of the three genes, and through their regulatory roles on the downstream target genes, leads to a binary decision: when OCT4, SOX2, and NANOG are expressed and the switch is on, the self-renewal genes are on and the differentiation genes are off. The opposite holds when the switch is off. The model is extremely robust to parameter changes. In addition to providing a self-consistent picture of the transcriptional circuit, the model generates several predictions. Increasing the binding strength of NANOG to OCT4 and SOX2, or increasing its basal transcriptional rate, leads to an irreversible bistable switch: the switch remains on even when the activating signal is removed. Hence, the stem cell can be manipulated to be self-renewing without the requirement of input signals. We also suggest tests that could discriminate between a variety of feedforward regulation architectures of the target genes by OCT4, SOX2, and NANOG.

Human embryonic stem cells: the battle between self-renewal and differentiation

Human embryonic stem cells are pluripotent cells derived from the inner cell mass of blastocyst-stage embryos. These cells possess two unique properties: an indefinite self-renewal capacity and pluripotency, the ability to differentiate to cells from the three germ layers. The pathways governing self-renewal and pluripotency are currently under intensive research. Much effort is devoted to the establishment of feeder-free cultures by elucidation of the cytokines and growth factors required for cell propagation. These seem thus far, to be distinct from those required by mouse embryonic stem cells. In addition, transcriptional regulators unique to embryonic stem cells seem to govern the pluripotent state. These transcriptional regulators determine cell fate, and decide whether the cell will remain pluripotent or differentiate. Together, the understanding of the exogenous and endogenous factors determining cell fate will facilitate the use of these cells in cell-based therapies and will allow understanding of early developmental processes.