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The Journal of Neuroscience, September 27, 2006, 26(39):9956-9966; doi:10.1523/JNEUROSCI.0468-06.2006

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Cellular/Molecular
Global Transcriptome Analysis of Genetically Identified Neurons in the Adult Cortex

Moritz J. Rossner,^1,2 Johannes Hirrlinger,^1,3 Sven P. Wichert,¹ Christine Boehm,² Dieter Newrzella,² Holger Hiemisch,² Gisela Eisenhardt,² Carolin Stuenkel,¹ Oliver von Ahsen,² and Klaus-Armin Nave¹

¹Max-Planck-Institute of Experimental Medicine, 37075 Göttingen, Germany, ²Axaron Bioscience, 69120 Heidelberg, Germany, and ³Deutsche Forschungsgemeinschaft-Research Center for Molecular Physiology of the Brain, 37073 Göttingen, Germany

Correspondence should be addressed to Dr. Moritz J. Rossner at the above address. Email: rossner{at}em.mpg.de

The enormous cellular complexity of the brain is a major obstacle for gene expression profiling of neurological disease models, because physiologically relevant changes of transcription in a specific neuronal subset are likely to be lost in the presence of other neurons and glia. We solved this problem in transgenic mice by labeling genetically defined cells with a nuclear variant of GFP. When combined with laser-directed microdissection, intact RNA from unfixed, freeze-dried sections can be isolated, which is a prerequisite for high-quality global transcriptome analysis. Here, we compared gene expression profiles between pyramidal motor neurons and pyramidal somatosensory neurons captured from layer V of the adult neocortex. One striking feature of motor neurons is the elevated expression of ribosomal genes and genes involved in ATP synthesis. This suggests a molecular adaptation of the upper motor neurons to longer axonal projections and higher electrical activity. These molecular signatures were not detected when cortical layers and microareas were analyzed in toto.

Additionally, we used microarrays to determine the global mRNA expression profiles of microdissected Purkinje cells and cellularly complex cerebellar cortex microregions. In summary, our analysis shows that cellularly complex targets lead to averaged gene expression profiles that lack substantial amounts of cell type-specific information. Thus, cell type-restricted sampling strategies are mandatory in the CNS. The combined use of a genetic label with laser-microdissection offers an unbiased approach to map patterns of gene expression onto practically any cell type of the brain.

Key words: cortex; cerebellum; microarrays; transcriptome; microdissection; GFP

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Received Feb. 1, 2006; revised Aug. 16, 2006; accepted Aug. 20, 2006.

Correspondence should be addressed to Dr. Moritz J. Rossner at the above address. Email: rossner{at}em.mpg.de

This article has been cited by other articles:

				E. Sanz, L. Yang, T. Su, D. R. Morris, G. S. McKnight, and P. S. Amieux Cell-type-specific isolation of ribosome-associated mRNA from complex tissues PNAS, August 18, 2009; 106(33): 13939 - 13944. [Abstract] [Full Text] [PDF]

				U. Lalo, Y. Pankratov, S. P. Wichert, M. J. Rossner, R. A. North, F. Kirchhoff, and A. Verkhratsky P2X1 and P2X5 Subunits Form the Functional P2X Receptor in Mouse Cortical Astrocytes J. Neurosci., May 21, 2008; 28(21): 5473 - 5480. [Abstract] [Full Text] [PDF]

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