Cell type-specific genes show striking and distinct patterns of spatial expression in the mouse brain

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 110; no. 8; pp. 3095 - 3100
• Main Authors: Ko, Younhee, Ament, Seth A., Eddy, James A., Caballero, Juan, Earls, John C., Hood, Leroy, Price, Nathan D.
• Format: Journal Article
• Language: English
• Published: Washington, DC National Academy of Sciences 19.02.2013; National Acad Sciences
• Subjects: adults; Animals; Astrocytes; Biological and medical sciences; Biological markers; Biological Sciences; biomarkers; Biomarkers - metabolism; Blood; Brain; Brain - cytology; Brain - metabolism; Cells; diagnostic techniques; Fundamental and applied biological sciences. Psychology; Gene expression; Gene Expression Profiling; gene expression regulation; Genes; In Situ Hybridization; Mice; Nervous system diseases; Neuroglia; Neurons; Neurons - metabolism; Oligodendroglia; ontogeny; Rodents; Transcriptome; transcriptomics; Vertebrates: nervous system and sense organs; Vertebrata; Mammalia; Mouse; Animal; Rodentia; Central nervous system; Encephalon
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1222897110

To characterize gene expression patterns in the regional subdivisions of the mammalian brain, we integrated spatial gene expression patterns from the Allen Brain Atlas for the adult mouse with panels of cell type-specific genes for neurons, astrocytes, and oligodendrocytes from previously published transcriptome profiling experiments. We found that the combined spatial expression patterns of 170 neuron-specific transcripts revealed strikingly clear and symmetrical signatures for most of the brain’s major subdivisions. Moreover, the brain expression spatial signatures correspond to anatomical structures and may even reflect developmental ontogeny. Spatial expression profiles of astrocyte- and oligodendrocyte-specific genes also revealed regional differences; these defined fewer regions and were less distinct but still symmetrical in the coronal plane. Follow-up analysis suggested that region-based clustering of neuron-specific genes was related to (i) a combination of individual genes with restricted expression patterns, (ii) region-specific differences in the relative expression of functional groups of genes, and (iii) regional differences in neuronal density. Products from some of these neuron-specific genes are present in peripheral blood, raising the possibility that they could reflect the activities of disease- or injury-perturbed networks and collectively function as biomarkers for clinical disease diagnostics.