Activin and BMP4 synergistically promote formation of definitive endoderm in human embryonic stem cells.

Human embryonic stem cells (hESCs) herald tremendous promise for the production of clinically useful cell types for the treatment of injury and disease. Numerous reports demonstrate their differentiation into definitive endoderm (DE) cells, the germ layer from which pancreatic ß cells and hepatocytes arise, solely from exposure to a high dose of recombinant Activin/Nodal. We show that combining a second related ligand, BMP4, in combination with Activin A yields 15%-20% more DE as compared with Activin A alone. The addition of recombinant BMP4 accelerates the downregulation of pluripotency genes, particularly SOX2, and results in upregulation of endogenous BMP2 and BMP4, which in turn leads to elevated levels of phospho-SMAD1/5/8. Combined Activin A and BMP4 treatment also leads to an increase in the expression of DE genes CXCR4, SOX17, and FOXA2 when compared with Activin A addition alone. Comparative microarray studies between DE cells harvested on day 3 of differentiation further reveal a novel set of genes upregulated in response to initial BMP4 exposure. Several of these, including APLNR, LRIG3, MCC, LEPREL1, ROR2, and LZTS1, are expressed in the mouse primitive streak, the site of DE formation. Thus, this synergism between Activin A and BMP4 during the in vitro differentiation of hESC into DE suggests a complex interplay between BMP and Activin/Nodal signaling during the in vivo allocation and expansion of the endoderm lineage.

Modeling co-expression across species for complex traits: insights to the difference of human and mouse embryonic stem cells.

Complex interactions between genes or proteins contribute substantially to phenotypic evolution. We present a probabilistic model and a maximum likelihood approach for cross-species clustering analysis and for identification of conserved as well as species-specific co-expression modules. This model enables a "soft" cross-species clustering (SCSC) approach by encouraging but not enforcing orthologous genes to be grouped into the same cluster. SCSC is therefore robust to obscure orthologous relationships and can reflect different functional roles of orthologous genes in different species. We generated a time-course gene expression dataset for differentiating mouse embryonic stem (ES) cells, and compiled a dataset of published gene expression data on differentiating human ES cells. Applying SCSC to analyze these datasets, we identified conserved and species-specific gene regulatory modules. Together with protein-DNA binding data, an SCSC cluster specifically induced in murine ES cells indicated that the KLF2/4/5 transcription factors, although critical to maintaining the pluripotent phenotype in mouse ES cells, were decoupled from the OCT4/SOX2/NANOG regulatory module in human ES cells. Two of the target genes of murine KLF2/4/5, LIN28 and NODAL, were rewired to be targets of OCT4/SOX2/NANOG in human ES cells. Moreover, by mapping SCSC clusters onto KEGG signaling pathways, we identified the signal transduction components that were induced in pluripotent ES cells in either a conserved or a species-specific manner. These results suggest that the pluripotent cell identity can be established and maintained through more than one gene regulatory network.

Dissecting early differentially expressed genes in a mixture of differentiating embryonic stem cells.

The differentiation of embryonic stem cells is initiated by a gradual loss of pluripotency-associated transcripts and induction of differentiation genes. Accordingly, the detection of differentially expressed genes at the early stages of differentiation could assist the identification of the causal genes that either promote or inhibit differentiation. The previous methods of identifying differentially expressed genes by comparing different cell types would inevitably include a large portion of genes that respond to, rather than regulate, the differentiation process. We demonstrate through the use of biological replicates and a novel statistical approach that the gene expression data obtained without prior separation of cell types are informative for detecting differentially expressed genes at the early stages of differentiation. Applying the proposed method to analyze the differentiation of murine embryonic stem cells, we identified and then experimentally verified Smarcad1 as a novel regulator of pluripotency and self-renewal. We formalized this statistical approach as a statistical test that is generally applicable to analyze other differentiation processes.

A gene regulatory network in mouse embryonic stem cells.

We analyze new and existing expression and transcription factor-binding data to characterize gene regulatory relations in mouse ES cells (ESC). In addition to confirming the key roles of Oct4, Sox2, and Nanog, our analysis identifies several genes, such as Esrrb, Stat3, Tcf7, Sall4, and LRH-1, as statistically significant coregulators. The regulatory interactions among 15 core regulators are used to construct a gene regulatory network in ESC. The network encapsulates extensive cross-regulations among the core regulators, highlights how they may control epigenetic processes, and reveals the surprising roles of nuclear receptors. Our analysis also provides information on the regulation of a large number of putative target genes of the network.

Directed differentiation of human embryonic stem cells into the pancreatic endocrine lineage.

Human embryonic stem (hES) cells represent a potentially unlimited source of transplantable beta-cells for the treatment of diabetes. Here we describe a differentiation strategy that reproducibly directs HES3, an National Institutes of Health (NIH)-registered hES cell line, into cells of the pancreatic endocrine lineage. HES3 cells are removed from their feeder layer and cultured as embryoid bodies in a three-dimensional matrix in the presence of Activin A and Bmp4 to induce definitive endoderm. Next, growth factors known to promote the proliferation and differentiation of pancreatic ductal epithelial cells to glucose-sensing, insulin-secreting beta-cells are added. Pdx1 expression, which identifies pancreatic progenitors, is detected as early as day 12 of differentiation. By day 34, Pdx1+ cells comprise between 5% and 20% of the total cell population and Insulin gene expression is up-regulated, with release of C-peptide into the culture medium. Unlike another recent report of the induction of insulin+ cells in differentiated hES cell populations, we are unable to detect the expression of other pancreatic hormones in insulin+ cells. When transplanted into severe combined immunodeficiency (SCID) mice, differentiated cell populations retain their endocrine identity and synthesize insulin.

Gene expression in the preimplantation embryo: in-vitro developmental changes.

The regulation of early embryo development and the mechanism of implantation remains poorly understood, due to the large number of genes and the complexity of the systems involved. The effect of in-vitro culture on embryos also remains unclear, which raises concerns about the safety of assisted reproductive technology. Changes in the expression of several individual genes in cultured embryos have been reported previously, but a large-scale comparison has not yet been performed to investigate the effects of in-vitro culture systems on embryo development. This study investigated established gene expression profiles of more that 20,000 genes from in-vitro cultured mouse embryos at eight different stages (oocytes, zygote, 2-, 4-, 8-cell embryo, compacting embryo, morula and blastocyst) using microarray technology, and compared these profiles with in-vivo embryos. In most stages of development there was little significant difference in overall expression patterns between in-vitro and in-vivo embryos. In addition, the expression patterns of developmentally important genes from several different categories, such as apoptosis, glycolysis, adhesion and methylation, were examined and compared between in-vitro and in-vivo embryos. Among the genes examined, DNA methyltransferase 1 (DNMT1) shows a significantly higher (P < 0.05) expression level in cultured embryos. Cadherin-11 also demonstrates a slightly different pattern, although the difference is not statistically significant. All the other genes have remarkably similar expression patterns between in-vitro and in-vivo embryos throughout preimplantation stages.

Adult CNS explants as a source of neural progenitors.

Adult neural progenitors have been isolated from diverse regions of the CNS using methods which primarily involve the enzymatic digestion of tissue pieces; however, interpretation of these experiments can be complicated by the loss of anatomical resolution during the isolation procedures. We have developed a novel, explant-based technique for the isolation of neural progenitors. Living CNS regions were sectioned using a vibratome and small, well-defined discs of tissue punched out. When cultured, explants from the cortex, hippocampus, cerebellum, spinal cord, hypothalamus, and caudate nucleus all robustly gave rise to proliferating progenitors. These progenitors were similar in behaviour and morphology to previously characterised multipotent hippocampal progenitor lines. Clones from all regions examined could proliferate from single cells and give rise to secondary neurospheres at a low but consistent frequency. Immunostaining demonstrated that clonal cortical progenitors were able to differentiate into both neurons and glial cells, indicating their multipotent characteristics. These results demonstrate it is possible to isolate anatomically resolved adult neural progenitors from small amounts of tissue throughout the CNS, thus, providing a tool for investigating the frequency and characteristics of progenitor cells from different regions.

Functional maturation of isolated neural progenitor cells from the adult rat hippocampus.

Although neural progenitor cells (NPCs) may provide a source of new neurons to alleviate neural trauma, little is known about their electrical properties as they differentiate. We have previously shown that single NPCs from the adult rat hippocampus can be cloned in the presence of heparan sulphate chains purified from the hippocampus, and that these cells can be pushed into a proliferative phenotype with the mitogen FGF2 [Chipperfield, H., Bedi, K.S., Cool, S.M. & Nurcombe, V. (2002) Int. J. Dev. Biol., 46, 661-670]. In this study, the active and passive electrical properties of both undifferentiated and differentiated adult hippocampal NPCs, from 0 to 12 days in vitro as single-cell preparations, were investigated. Sparsely plated, undifferentiated NPCs had a resting membrane potential of approximately -90 mV and were electrically inexcitable. In > 70%, ATP and benzoylbenzoyl-ATP evoked an inward current and membrane depolarization, whereas acetylcholine, noradrenaline, glutamate and GABA had no detectable effect. In Fura-2-loaded undifferentiated NPCs, ATP and benzoylbenzoyl-ATP evoked a transient increase in the intracellular free Ca(2+) concentration, which was dependent on extracellular Ca(2+) and was inhibited reversibly by pyridoxalphosphate-6-azophenyl-2'-4'-disulphonic acid (PPADS), a P2 receptor antagonist. After differentiation, NPC-derived neurons became electrically excitable, expressing voltage-dependent TTX-sensitive Na(+) channels, low- and high-voltage-activated Ca(2+) channels and delayed-rectifier K(+) channels. Differentiated cells also possessed functional glutamate, GABA, glycine and purinergic (P2X) receptors. Appearance of voltage-dependent and ligand-gated ion channels appears to be an important early step in the differentiation of NPCs.

Heparan sulfates isolated from adult neural progenitor cells can direct phenotypic maturation.

Multipotent progenitor stem cells that generate both neurons and glia are components of the hippocampus, subventricular zone and olfactory system of adult mammalian nervous system. The lineage choices any stem cell makes are known to be greatly dependent on the constitution of the extracellular matrix to which they are exposed during their development. Here, the adult rat hippocampus was used as a source of cells for clonal culture in order to investigate the effects of the extracellular glycosaminoglycan heparan sulfate (HS). Neurospheres were readily generated from adult tissue and could be used as a source of cells for further experiments. HS species that promote the actions of fibroblast growth factor-2 (FGF2) for embryonic neural progenitors were found to inhibit the actions of this mitogen for adult progenitors. Only HS fractions that promoted the actions of FGF1 had mitogenic effects on these adult cells. The adult cells proved difficult to clone from single cells. However, when endogenous HS was purified from these cells and added back at high concentration to single cells, the clones were capable of generating plentiful neuronal and glial progeny. The adult hippocampal progenitor (AHP) HS is composed of 32 kDa chains bearing 3 sulfated domains. A proportion of primary osteoblast stem cells exposed to the hippocampal HS adopt neuronal phenotypes. Hence, there appears to be a combination of HS-binding extracellular molecules that predispose cells to particular lineages.