Microarray analysis of selected genes in neural stem and progenitor cells Yongquan Luo,* Jingli Cai,* Ying Liu,* Haipeng Xue,* Francis J. Chrest, Robert P. Wersto and Mahendra Rao* *Laboratory of Neurosciences and  Research Resource Branch, Gerontology Research Center, National Institute on Aging, Room 4E02, 5600 Nathan Shock Drive, Baltimore, Maryland, USA Abstract To access and compare gene expression in fetal neuroepit- helial cells (NEPs) and progenitor cells, we have used microarrays containing approximately 500 known genes rela- ted to cell cycle regulation, apoptosis, growth and differenti- ation. We have identified 152 genes that are expressed in NEPs and 209 genes expressed by progenitor cells. The majority of genes (141) detected in NEPs are also present in progenitor populations. There are 68 genes specifically expressed in progenitors with little or no expression in NEPs, and a few genes that appear to be present exclusively in NEPs. Using cell sorting, RT–PCR, in situ hybridization or immunocytochemistry, we have examined the segregation of expression to neuronal and glial progenitors, and identified several that appeared to be enriched in neuronal (e.g. CDK5, neuropilin, EphrinB2, FGF11) or glial (e.g. CXCR4, RhoC, CD44, tenascin C) precursors. Our data provide a first report of gene expression profiles of neural stem and progenitor cells at early stages of development, and provide evidence for the potential roles of specific cell cycle regulators, chemokines, cytokines and extracellular matrix molecules in neural devel- opment and lineage segregation. Keywords: astrocyte, differentiation, glial restricted precur- sor, neuroepithelial cells, neuronal restricted precursor, pro- liferation. J. Neurochem. (2002) 83, 1481–1497. Neural stem cells (NSCs) are self-renewing multipotent precursors that generate neurons, astrocytes and oligodend- rocytes in the CNS (Gage et al. 1995; Weiss et al. 1996). Fetal NSCs have attracted attention not only for their role in normal development but also for their potential use for the treatment of neurodegenerative disorders (Studer et al. 1998; Sanchez-Pernaute et al. 2001; Kim et al. 2002). Our ability to regulate NSC differentiation and harness their potential for therapy is limited, however, and would be enhanced if we understood the process of NSC differentiation better. The genetic program for NSC differentiation may be similar to that of hematopoietic stem cell (HSC) differentiation where specific sets of genes regulate quiescence, self-renewal and differentiation (Geschwind et al. 2001; Terskikh et al. 2001), and either the Ôsame stem cell genesÕ or unique subsets of functionally similar genes may be used to regulate the neural development program. Alternatively, novel pathways regu- lating NSC differentiation may exist (Geschwind et al. 2001). Examination of gene expression patterns in NSC and comparison of genes expressed by NSCs with NSC- derived differentiated cells will probably promote our understanding of the process of NSC differentiation. NSCs present in the developing neural tube, termed neuroepithelial cells (NEPs), provide a useful system for the Received July 30, 2002; revised manuscript received September 27, 2002; accepted September 30, 2002. Address correspondence and reprint requests to M. Rao, Laboratory of Neurosciences, Gerontology Research Center, National Institute on Aging, Room 4E02, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA. E-mail: raomah@grc.nia.nih.gov Abbreviations used: BMP, bone morphogenetic protein; BSA, bovine serum albumin; CDK, cyclin-dependent kinase; CEE, chicken embryo extract; CXCR, chemokin (CXC motif) receptor; DAPI, bisbenzimide; ECM, extracellular matrix; EGFR, epidermal growth factor receptor; En, embryonic day n; E-NCAM, embryonic neural cell adhesion molecule; FGF, fibroblast growth factor; FGFR, fibroblast growth factor receptor; HSC, haemopoietic stem cell; GAPDH, glyceraldehyde-3-phosphate dehydrogenase; GFAP, glial acidic fibrillary protein; GRP, glial restricted precursor; IAP, inhibitor of apoptosis protein; LIF, leukaemia inhibitory factor; MMP, matrix metalloproteinase; NCAM, neural cell adhesion molecule; NEP, neuroepithelial cell; NRP, neuronal restricted precursor; NSC, neural stem cell; PBS, phosphate-buffered saline; PBST, phos- phate-buffered saline with Triton X-100; PDGF, platelet-derived growth factor; PTEN, phosphate and tensin homolog; SCF, stem cell factor; SDS, sodium dodecyl sulfate; SSC, saline sodium citrate buffer; TnC, tenascin C, TRAF, TNF receptor associated factor. Journal of Neurochemistry , 2002, 83, 1481–1497 Ó 2002 International Society for Neurochemistry, Journal of Neurochemistry , 83, 1481–1497 1481