An analysis of the gene expression program of mammalian neural progenitor cells - PubMed (original) (raw)

An analysis of the gene expression program of mammalian neural progenitor cells

F J Livesey et al. Proc Natl Acad Sci U S A. 2004.

Abstract

A diverse range of neural cell types is generated from a pool of dividing stem and progenitor cells in an orderly manner during development. Little is known of the molecular and cellular biology underpinning the intrinsic control of this process. We have used a nonbiased method to purify populations of neural progenitor cells from the murine CNS to characterize the gene expression program of mammalian retinal progenitor cells. Analysis of these data led to the identification of a core set of >800 transcripts enriched in retinal progenitor cells compared to both their immediate postmitotic progeny and to differentiated neurons. This core set was found to be shared by progenitors in other regions of the developing CNS, with important regional differences in key functional families. In addition to providing an expression fingerprint of this cell type, this set highlights several key aspects of progenitor biology.

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Figures

Fig. 1.

Fig. 1.

Strategy adopted to identify of retinal progenitor cell-enriched transcripts. Cycling cells of the developing retina were FACS-purified based on DNA content, yielding one population enriched in progenitor cells (4N cells) and a second composed of progenitor cells and postmitotic neurons (2N cells). Gene expression was compared directly between the 2N and 4N populations, and also between the 4N population and adult brain (see text for details). Reproducible differences between progenitor cells and the reference used in each case were identified by using the significance analysis of microarrays algorithm (see text for details), and genes that passed this filter were then hierarchically clustered to visualize the data and confirm differential expression.

Fig. 2.

Fig. 2.

Identification of a set of transcripts enriched in FACS-purified retinal progenitor cells. (A) Significance analysis of microarrays plot of the distribution of expected and observed values for gene expression ratios. Genes found to be reproducibly enriched in expression in 4N (progenitor) cells compared to brain and retinal 2N cells (neurons and progenitors) are highlighted in red, those expressed at a lower level in 4N cells are in green. (B) Hierarchical clustering of the results from A. (C) Detail of the hierarchical cluster analysis from A, showing genes enriched in expression in 4N cells compared to both brain and 2N cells. Note that, in addition to 4N/2N and 4N/brain hybridizations, brain/4N or dye-swap hybridizations were also included both as technical replicates and to control for dye-dependent biases within the hybridizations. In this and subsequent cluster diagrams, each row illustrates the gene expression ratios for a single gene, and each column represents a single array hybridization. The samples used for each hybridization are shown at the top of each column, with the Cy5-labeled sample listed first. By convention, the intensity of the color of each gene expression representation is proportional to the magnitude of the gene expression ratio, with red representing genes expressed at higher levels in the Cy5-labeled sample, green those expressed at a higher level in the Cy3-labeled sample, and black those expressed equally between the samples. (D) Detail of the hierarchical clustering of the results from A, showing genes enriched in expression in brain and 2N cells compared to 4N cells. This cluster includes several genes encoding synapse-associated proteins.

Fig. 3.

Fig. 3.

Expression of genes identified as progenitor cell-enriched. In situ hybridization studies of the expression of a subset of the core set of retinal progenitor cell-enriched transcripts. All sections are from the E14.5 mouse retina. (A_–_L) Low-power views of expression of this subset of genes. Gene identifiers are as shown on each panel. Retinal progenitor cells occupy over three-quarters of the radial thickness of the neural retina at this stage with the innermost cells being ganglion cells, as shown by the neuron-specific GAP-43 staining in L. Note that although most genes are expressed in progenitor cells (for example, in A, B, and D), some genes are expressed in both progenitor cells and neurons (for example, in C and G). (M_–_R) High-power views of the progenitor cell-specific expression of a selection of genes, as labeled in each panel. Note the lack of expression of five of the six genes on the inner (vitreal) side of the retina populated by ganglion and amacrine cells, with CDK4 expressed at a low level within this region. Examples are also shown of genes with heterogeneous expression within progenitor cells, including Otx2 (M) and NOPE (Q).

Fig. 4.

Fig. 4.

Identification of a core progenitor cell expression program expressed in diverse regions of the CNS. (A_–_D) Hierarchical cluster analysis of gene expression in progenitor (4N) cells from three regions of the developing CNS, compared to adult brain: retina, cerebral cortex, and cerebellum. The complete cluster analysis is shown in A. Examples are shown of genes enriched in retinal progenitor cells (B), genes commonly enriched in progenitor cells from all three regions (C), and enriched in brain (D). (E_–_H) In situ hybridization studies of the developmental expression within the forebrain of a subset of the core set of retinal progenitor cell-enriched transcripts also found enriched in cortical and cerebellar progenitor cells. All images are of coronal sections the E14.5 mouse forebrain. Genes are as marked on each panel. Note the high level of expression of each gene within the ventricular zone (VZ) of the developing cortex (arrowheads) and the sharply localized expression of SFRP2 at the junction between the cortical and subcortical VZs. MARCKS is expressed within postmitotic neurons in the cortical plate, in addition to its expression within cortical VZ progenitor cells.

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