Nuclei and subnuclei gene expression profiling in mammalian brain

Bonaventure, Pascal; Guo, Hongqing; Tian, Bin; Liu, Xuejun; Bittner, Anton; Roland, Barbara; Salunga, Ranelle; Xiao, Jun; Kamme, Fredrik; Meurers, Bernhard H.; Bakker, Margot H.M.; Jurzak, Mirek; Leysen, Josée E.; Erlander, Mark G.

doi:10.1016/s0006-8993(02)02504-0

Cited by 151 publications

(90 citation statements)

References 27 publications

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“…cDNA microarrays containing Ϸ13,000 mouse cDNA clones on three physically different slides were used in this study as described (31,32). cDNA clones were obtained commercially from Research Genetics (Huntsville, AL) (I.M.A.G.E.…”

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confidence: 99%

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

Nedvetzki

Gonen

Assayag

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

182

175

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We report here that joint inflammation in collagen-induced arthritis is more aggravated in CD44-knockout mice than in WT mice, and we provide evidence for molecular redundancy as a causal factor. Furthermore, we show that under the inflammatory cascade, RHAMM (receptor for hyaluronan-mediated motility), a hyaluronan receptor distinct from CD44, compensates for the loss of CD44 in binding hyaluronic acid, supporting cell migration, up-regulating genes involved with inflammation (as assessed by microarrays containing 13,000 cDNA clones), and exacerbating collagen-induced arthritis. Interestingly, we further found that the compensation for loss of the CD44 gene does not occur because of enhanced expression of the redundant gene (RHAMM), but rather because the loss of CD44 allows increased accumulation of the hyaluronic acid substrate, with which both CD44 and RHAMM engage, thus enabling augmented signaling through RHAMM. This model enlightens several aspects of molecular redundancy, which is widely discussed in many scientific circles, but the processes are still ill defined

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confidence: 99%

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

Nedvetzki

Gonen

Assayag

et al. 2004

Proc. Natl. Acad. Sci. U.S.A.

182

175

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“…Such differential responses to nicotine support the concept that various brain regions participate in different cellular and physiological functions. Indeed, a gene expression profiling study demonstrated similar profiles in subnuclei of the same brain region (i.e., Ca1 and Ca3 of the hippocampus) but very different profiles in different brain regions (i.e., hypothalamus and hippocampus) [6]. Because different regions of the brain are divergent in their cellular compositions (i.e., neurotransmitter release, receptor expression, intracellular signaling cascades) to manage specific physiological activities, a region-specific transcriptional response of ubiquitin-proteasome signaling to nicotine treatment would be expected.…”

Section: Discussionmentioning

confidence: 99%

Nicotine coregulates multiple pathways involved in protein modification/degradation in rat brain

Kane

Konu

Jennie

et al. 2004

Molecular Brain Research

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Previously, we used cDNA microarrays to demonstrate that the phosphatidylinositol and MAP kinase signaling pathways are regulated by nicotine in different rat brain regions. In the present report, we show that, after exposure to nicotine for 14 days, ubiquitin, ubiquitinconjugating enzymes, 20S and 19S proteasomal subunits, and chaperonin-containing TCP-1 protein (CCT) complex members are upregulated in rat prefrontal cortex (PFC) while being downregulated in the medial basal hypothalamus (MBH). In particular, relative to saline controls, ubiquitins B and C were upregulated by 33% and 47% ( Pb0.01), respectively, in the PFC. The proteasome beta subunit 1 (PSMB1) and 26S ATPase 3 (PSMC3) genes were upregulated in the PFC by 95% and 119% ( Pb0.001), respectively. In addition to the protein degradation pathway of the ubiquitin-proteasome complexes, we observed in the PFC an increase in the expression of small, ubiquitin-related modifiers (SUMO) 1 and 2 by 80% and 33%, respectively ( Pb0.001), and in 3 of 6 CCT subunits by up to 150% ( Pb0.0001). To a lesser extent, a change in the opposite direction was obtained in the expression of the same gene families in the MBH. Quantitative real-time RT-PCR was used to validate the microarray results obtained with some representative genes involved in these pathways. Taken together, our results suggest that, in response to systemic nicotine administration, the ubiquitin-proteasome, SUMO, and chaperonin complexes provide an intricate control mechanism to maintain cellular homeostasis, possibly by regulating the composition and signaling of target neurons in a region-specific manner. D

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“…This approach has been used to measure gene expression patterns in particular regions, subregions, or cell populations in the brain (6)(7)(8)(9)(10)(11). Two previous studies have analyzed gene expression differences across multiple regions of the mammalian brain by using multiple strains or species (12,13).…”

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confidence: 99%

Adult mouse brain gene expression patterns bear an embryologic imprint

Zapala

Hovatta²,

Ellison³

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

177

162

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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...

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Nuclei and subnuclei gene expression profiling in mammalian brain

Cited by 151 publications

References 27 publications

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

RHAMM, a receptor for hyaluronan-mediated motility, compensates for CD44 in inflamed CD44-knockout mice: A different interpretation of redundancy

Nicotine coregulates multiple pathways involved in protein modification/degradation in rat brain

Adult mouse brain gene expression patterns bear an embryologic imprint

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