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The Journal of Neuroscience, January 2, 2008, 28(1):264-278; doi:10.1523/JNEUROSCI.4178-07.2008

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Cellular/Molecular
A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

John D. Cahoy,^1,2 * Ben Emery,^1 * Amit Kaushal,^3,4 * Lynette C. Foo,¹ Jennifer L. Zamanian,¹ Karen S. Christopherson,¹ Yi Xing,⁵ Jane L. Lubischer,⁶ Paul A. Krieg,⁷ Sergey A. Krupenko,⁸ Wesley J. Thompson,⁹ and Ben A. Barres^1,2

Departments of ¹Neurobiology and ²Developmental Biology, ³Stanford Genome Technology Center, and ⁴Stanford Center for Biomedical Informatics Research, Stanford University School of Medicine, Stanford, California 94305, ⁵Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, Iowa 52242, ⁶Department of Zoology and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, North Carolina 27695, ⁷Department of Cell Biology and Anatomy, University of Arizona College of Medicine, Tucson, Arizona 85724, ⁸Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, and ⁹Section of Neurobiology, Institute for Neuroscience, and Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712

Correspondence should be addressed to John D. Cahoy, Department of Neurobiology, Stanford University, D205 Fairchild Building, 299 Campus Drive, Stanford, CA 94305. Email: jcahoy{at}stanford.edu

Understanding the cell–cell interactions that control CNS development and function has long been limited by the lack of methods to cleanly separate neural cell types. Here we describe methods for the prospective isolation and purification of astrocytes, neurons, and oligodendrocytes from developing and mature mouse forebrain. We used FACS (fluorescent-activated cell sorting) to isolate astrocytes from transgenic mice that express enhanced green fluorescent protein (EGFP) under the control of an S100β promoter. Using Affymetrix GeneChip Arrays, we then created a transcriptome database of the expression levels of >20,000 genes by gene profiling these three main CNS neural cell types at various postnatal ages between postnatal day 1 (P1) and P30. This database provides a detailed global characterization and comparison of the genes expressed by acutely isolated astrocytes, neurons, and oligodendrocytes. We found that Aldh1L1 is a highly specific antigenic marker for astrocytes with a substantially broader pattern of astrocyte expression than the traditional astrocyte marker GFAP. Astrocytes were enriched in specific metabolic and lipid synthetic pathways, as well as the draper/Megf10 and Mertk/integrin _vβ₅ phagocytic pathways suggesting that astrocytes are professional phagocytes. Our findings call into question the concept of a "glial" cell class as the gene profiles of astrocytes and oligodendrocytes are as dissimilar to each other as they are to neurons. This transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes provides a resource to the neuroscience community by providing improved cell-type-specific markers and for better understanding of neural development, function, and disease.

Key words: astrocyte; neuron; oligodendrocyte; GeneChip; Aldh1L1; culture; gene profiling; microarray; transcriptome; phagocytosis; astroglia; Megf10; Mertk; Draper; Mfge8

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Received Sept. 12, 2007; revised Nov. 9, 2007; accepted Nov. 14, 2007.

Correspondence should be addressed to John D. Cahoy, Department of Neurobiology, Stanford University, D205 Fairchild Building, 299 Campus Drive, Stanford, CA 94305. Email: jcahoy{at}stanford.edu

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