Gene expression tomography

Abstract

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.

Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease

“…Normalization used 18S RNA. Genomic contamination was excluded (Brown et al 2002b) by the use of primers that cross the intron of the housekeeping gene GdX (Filippi et al 1990) and no reverse transcriptase controls.…”

Genome scale mapping of brain gene expression

“…A considerable proportion of these genes will be of interest; however, inhomogeneity becomes less of a problem as voxel size decreases and hence resolution improves. For initial studies of voxelation and GET (Brown et al 2002a(Brown et al , 2002b(Brown et al , 2002c, simple approaches to registered harvesting of voxels and slices were sufficient and used available tools such as the cryostat; however, higher resolution maps will require dedicated instruments for semiautomated harvesting of miniaturized voxels and slices.…”

“…The method employs high-throughput analysis of spatially registered voxels harvested from the brain (Figure 1), followed by 3D reconstruction (Brown et al 2002a(Brown et al , 2002c. In contrast, GET employs analyses of sets of parallel slices or "views" obtained from the brain by progressive rotation about multiple independent axes (Figure 1) (Brown et al 2002b). Tomographic image reconstruction can then be employed for reconstruction of gene expression patterns.…”

“…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).…”

Identifying gene functions using functional expression profiles obtained by voxelation

“…Voxelation is a new approach that involves dicing the brain into spatially registered voxels (cubes). It produces multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems [5][6][7]. Related research suggests that voxelation is a useful approach for understanding how the genome constructs the brain.…”