Although protein phosphorylation has been characterized more extensively, modulation of the acetylation state of signaling molecules is now being recognized as a key means of signal transduction. The enzymes responsible for mediating these changes include histone acetyl transferases and histone deacetylases (HDACs). Members of the HDAC family of enzymes have been identified as potential therapeutic targets for diseases ranging from cancer to ischemia and neurodegeneration. We initiated a project to conduct comprehensive gene expression mapping of the 11 HDAC isoforms (HDAC1-11) (classes I, II, and IV) throughout the rat brain using high-resolution in situ hybridization (ISH) and imaging technology. Internal and external data bases were employed to identify the appropriate rat sequence information for probe selection. In addition, immunohistochemistry was performed on these samples to separately examine HDAC expression in neurons, astrocytes, oligodendrocytes, and endothelial cells in the CNS. This double-labeling approach enabled the identification of specific cell types in which the individual HDACs were expressed. The signals obtained by ISH were compared to radiolabeled standards and thereby enabled semiquantitative analysis of individual HDAC isoforms and defined relative levels of gene expression in >50 brain regions. This project produced an extensive atlas of 11 HDAC isoforms throughout the rat brain, including cell type localization, providing a valuable resource for examining the roles of specific HDACs in the brain and the development of future modulators of HDAC activity.

The current model to explain the organization of the mammalian nervous system is based on studies of anatomy, embryology, and evolution. To further investigate the molecular organization of the adult mammalian brain, we have built a gene expression-based brain map. We measured gene expression patterns for 24 neural tissues covering the mouse central nervous system and found, surprisingly, that the adult brain bears a transcriptional ''imprint'' consistent with both embryological origins and classic evolutionary relationships. Embryonic cellular position along the anteriorposterior axis of the neural tube was shown to be closely associated with, and possibly a determinant of, the gene expression patterns in adult structures. We also observed a significant number of embryonic patterning and homeobox genes with region-specific expression in the adult nervous system. The relationships between global expression patterns for different anatomical regions and the nature of the observed region-specific genes suggest that the adult brain retains a degree of overall gene expression established during embryogenesis that is important for regional specificity and the functional relationships between regions in the adult. The complete collection of extensively annotated gene expression data along with data mining and visualization tools have been made available on a publicly accessible web site (www.barlow-lockhartbrainmapnimhgrant.org).database ͉ development ͉ evolution ͉ gene expression profiling ͉ inbred strains of mice T he adult nervous system achieves its mature form as the result of neuroectodermal cells committing to a specific fate and then segregating into distinct regional collectives of neurons that become fully functional through establishment of connections to other neurons. Our current understanding of brain architecture and organization is based on studies of embryology, anatomy, and evolution in which direct observation of anatomic structures was the foundation for postulated models of brain structure (1). Recent models of brain development and maturation consider relationships between different regions based on the expression of specific genes in assigning developmental origins of adult structures (2, 3). Here, we have constructed a regional gene expression atlas of the adult mouse brain and analyzed the quantitative results by using molecular classification algorithms.Genome-wide gene expression profiling is a powerful technique for deriving information about specific brain regions (4, 5). This approach has been used to measure gene expression patterns in particular regions, subregions, or cell populations in the brain (6-11). Two previous studies have analyzed gene expression differences across multiple regions of the mammalian brain by using multiple strains or species (12,13). However, the current study is the most extensive to date in terms of the number of genes and the coverage of different neural tissues. Our goal was to create a publicly accessible gene-based brain map with data sets, metadata, datab...

Various transgenic mouse models of Alzheimer's disease (AD) have been developed that overexpress mutant forms of amyloid precursor protein in an effort to elucidate more fully the potential role of ␤-amyloid (A␤) in the etiopathogenesis of the disease. The present study represents the first complete 3D reconstruction of A␤ in the hippocampus and entorhinal cortex of PDAPP transgenic mice. A␤ deposits were detected by immunostaining and thioflavin fluorescence, and quantified by using high-throughput digital image acquisition and analysis. Quantitative analysis of amyloid load in hippocampal subfields showed a dramatic increase between 12 and 15 months of age, with little or no earlier detectable deposition. Three-dimensional reconstruction in the oldest brains visualized previously unrecognized sheets of A␤ coursing through the hippocampus and cerebral cortex. In contrast with previous hypotheses, compact plaques form before significant deposition of diffuse A␤, suggesting that different mechanisms are involved in the deposition of diffuse amyloid and the aggregation into plaques. The dentate gyrus was the hippocampal subfield with the greatest amyloid burden. Sublaminar distribution of A␤ in the dentate gyrus correlated most closely with the termination of afferent projections from the lateral entorhinal cortex, mirroring the selective vulnerability of this circuit in human AD. This detailed temporal and spatial analysis of A␤ and compact amyloid deposition suggests that specific corticocortical circuits express selective, but late, vulnerability to the pathognomonic markers of amyloid deposition, and can provide a basis for detecting prior vulnerability factors. A lzheimer's disease (AD), the most common form of dementia in the aging population, is characterized by the extracellular accumulation of ␤-amyloid (A␤), the intracellular appearance of neurofibrillary tangles, and synaptic and neuronal loss (1). Mounting evidence supports a causal role for A␤ in the pathophysiology of AD (2, 3). Various transgenic models have been developed which overexpress mutant forms of amyloid precursor protein (APP); these models mimic some aspects of AD pathology, including A␤ deposition and synaptic damage (4-9).In AD, amyloid deposition and neurofibrillary tangle formation occur in a spatially and temporally defined pattern in specific neocortical and hippocampal regions that reflects selective vulnerability of certain circuits, particularly corticocortical circuits in neocortex (10, 11) and the perforant path that projects from the entorhinal cortex (EC) to the dentate gyrus (DG) (12, 13). Transgenic mouse models that overexpress mutant APP show an age-dependent accumulation of A␤ (14); however, there has been no comprehensive quantitative analysis of the spatial and temporal progression of amyloid and A␤ accumulation, especially in the most vulnerable regions.Deposits of A␤ that form in AD have been morphologically classified into several types, such as diffuse, fibrillar, dense-cored or classic, compact, or ''burnt-out'' ...

High-resolution magnetic resonance microscopy (MRM) was used to determine regional brain volumetric changes in a mouse model of Alzheimer's disease. These transgenic (Tg) mice overexpress human mutant amyloid precursor protein (APP) V717F under control of platelet-derived growth factor promoter (PDAPP mice), and cortical and hippocampal ␤-amyloid (A␤) deposits accumulate in heterozygotes after 8 -10 mos. We used MRM to obtain 3D volumetric data on mouse brains imaged in their skulls to define genotype-and age-related changes. Hippocampal, cerebellar, and brain volumes and corpus callosum length were quantified in 40-, 100-, 365-, and 630-day-old mice. Measurements taken at age 100 days, before A␤ deposition, revealed a 12.3% reduction of hippocampus volume in Tg mice compared with WT controls. This reduction persisted without progression to age 21 mos. A significant 18% increase in hippocampal volume occurred between 40 and 630 days in WT mice, and no corresponding significant increase occurred in Tg mice. Cavalieri volume estimates of hippocampal subfields from 100-day-old Tg mice further localized a 28% volume deficit in the dentate gyrus. In addition, corpus callosum length was reduced by Ϸ25% in Tg mice at all ages analyzed. In summary, reduced hippocampal volume and corpus callosum length can be detected by MRM before A␤ deposition. We conclude that overexpression of APP and amyloid may initiate pathologic changes before the appearance of plaques, suggesting novel targets for the treatment of Alzheimer's disease and further reinforcing the need for early diagnosis and treatment.T he essential neuropathologic features of Alzheimer's disease (AD) include the progressive deposition of amyloid plaques and neurofibrillary tangles in neocortical and hippocampal structures and a parallel global decrease in cortical volume (1, 2). Extensive data from analysis of postmortem human brain and mouse models of AD associate the neuropathology of AD with alterations in the expression, distribution, and deposition of ␤ amyloid protein (A␤). In AD brains, A␤ levels are increased, and the protein can be found in fibrillar chains within compact plaques, aggregated in diffuse plaques, or as oligomers and monomers in regions outside of plaques (3-6). Some of the known human mutations associated with AD affect the processing or cleavage of amyloid precursor protein (APP) and can cause increased A␤ levels or increase the relative amount of the primary plaque component A␤ 1-42 compared with A␤ 1-40 (3, 5-10). Other human mutations have been identified within the coding region of A␤ 1-42 , which can increase A␤ neurotoxicity (11). Transgenic (Tg) mouse models have shown that high levels of A␤ can cause AD-like amyloid plaque pathology. Tg mice that overexpress APP have some but not all deficits observed in AD (12, 13). Other Tg mouse models that have mutations associated with AD resulting in up-regulation of A␤ production have many, but not all, of the observed deficits seen in AD, including reduced hippocampal volume, reduced synap...