Gene expression tomography

Department of Molecular and Medical Pharmacology, University of California, Los Angeles 90095, USA.
Physiological Genomics (Impact Factor: 2.37). 03/2002; 8(2):159-67. DOI: 10.1152/physiolgenomics.00090.2001
Source: PubMed


Gene expression tomography, or GET, is a new method to increase the speed of three-dimensional (3-D) gene expression analysis in the brain. The name is evocative of the method's dual foundations in high-throughput gene expression analysis and computerized tomographic image reconstruction, familiar from techniques such as positron emission tomography (PET) and X-ray computerized tomography (CT). In GET, brain slices are taken using a cryostat in conjunction with axial rotation about independent axes to create a series of "views" of the brain. Gene expression information obtained from the axially rotated views can then be used to recreate 3-D gene expression patterns. GET was used to successfully reconstruct images of tyrosine hydroxylase gene expression in the mouse brain, using both RNase protection and real-time quantitative reverse transcription PCR (QRT-PCR). A Monte-Carlo analysis confirmed the good quality of the GET image reconstruction. By speeding acquisition of gene expression patterns, GET may help improve our understanding of the genomics of the brain in both health and disease.

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Available from: Alexei Ossadtchi, Mar 07, 2014
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    • "We consider this a time-and-cost-effective strategy for acquiring comprehensive gene expression data in a spatial context. The mapping accuracy of the tomography technique depends on the number of data points [31]. These are dependent on the fraction width and the number of sectioning directions, such that by increasing the points over the brain regions one increases the regional accuracy. "
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    ABSTRACT: Increased information on the encoded mammalian genome is expected to facilitate an integrated understanding of complex anatomical structure and function based on the knowledge of gene products. Determination of gene expression-anatomy associations is crucial for this understanding. To elicit the association in the three-dimensional (3D) space, we introduce a novel technique for comprehensive mapping of endogenous gene expression into a web-accessible standard space: Transcriptome Tomography. The technique is based on conjugation of sequential tissue-block sectioning, all fractions of which are used for molecular measurements of gene expression densities, and the block- face imaging, which are used for 3D reconstruction of the fractions. To generate a 3D map, tissues are serially sectioned in each of three orthogonal planes and the expression density data are mapped using a tomographic technique. This rapid and unbiased mapping technique using a relatively small number of original data points allows researchers to create their own expression maps in the broad anatomical context of the space. In the first instance we generated a dataset of 36,000 maps, reconstructed from data of 61 fractions measured with microarray, covering the whole mouse brain (ViBrism: in one month. After computational estimation of the mapping accuracy we validated the dataset against existing data with respect to the expression location and density. To demonstrate the relevance of the framework, we showed disease related expression of Huntington's disease gene and Bdnf. Our tomographic approach is applicable to analysis of any biological molecules derived from frozen tissues, organs and whole embryos, and the maps are spatially isotropic and well suited to the analysis in the standard space (e.g. Waxholm Space for brain-atlas databases). This will facilitate research creating and using open-standards for a molecular-based understanding of complex structures; and will contribute to new insights into a broad range of biological and medical questions.
    Full-text · Article · Sep 2012 · PLoS ONE
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    • "Various transcript profiling tools and levels of spatial resolution can be employed for the high-throughput acquisition of brain gene expression patterns using voxelation. Gene expression tools that have been used include real-time PCR and microarrays, although serial analysis of gene expression (SAGE) (Velculescu et al. 1995) and RNase protection (Brown et al. 2002b) could also be employed. Voxelation has been performed at a number of different spatial levels of resolution. "
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    ABSTRACT: Voxelation is a new approach for genome scale acquisition of brain gene expression patterns. The method employs high-throughput analysis of spatially registered voxels (cubes) to create multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. The spatial resolution of voxelation depends on voxel size, with smaller voxels giving higher resolution. An important question is the applicability of different transcript profiling tools for the various levels of resolution that can be employed. Here, we describe the use of three methods to analyze voxel transcript abundance: real-time PCR, microarray analysis and linear amplification coupled with microarrays. We show statistically significant concordance between real-time PCR and microarray analysis for the myelin basic protein gene in human brain specimens at differing levels of spatial resolution. In addition, we also demonstrate the feasibility of using linear amplification coupled with microarray analysis to create voxelation maps from the mouse brain at high resolution, 1 microl. These data indicate the suitability of a number of transcript profiling tools for various levels of spatial resolution in voxelation.
    Preview · Article · Jun 2004 · Journal of Molecular Histology
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    • "Gene expression tomography has recently been used to reconstruct images of tyrosine hydroxylase (TH) gene expression in the mouse brain (Brown et al 2002b). Tyrosine hydroxylase transcript levels were quantitated in the harvested slices using real-time polymerase chain reaction (PCR) or RNase protection, and gene expression images reconstructed using filtered back projection (Figure 4). "
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    ABSTRACT: Two new approaches, voxelation and gene expression tomography (GET), permit multiplex acquisition of gene expression patterns in the brain. Both methods result in volumetric images of gene expression analogous to those produced in biomedical imaging systems. Voxelation employs analysis of spatially registered cubes from the brain, whereas GET entails analysis of parallel slices obtained by rotation about multiple axes. These methods have been used to investigate neurologic diseases and their models in both humans and mice. The results of these studies are discussed, as is the future of high-throughput gene expression mapping in the brain.
    Preview · Article · Jul 2003 · Biological Psychiatry
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