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Analysis of chaperone mRNA expression in the adult mouse brain by meta analysis of the Allen Brain Atlas.

Tebbenkamp AT, Borchelt DR - PLoS ONE (2010)

Bottom Line: Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain.The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families.Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, SantaFe Health Alzheimer's Disease Center, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America. atebbenk@ufl.edu

ABSTRACT
The pathology of many neurodegenerative diseases is characterized by the accumulation of misfolded and aggregated proteins in various cell types and regional substructures throughout the central and peripheral nervous systems. The accumulation of these aggregated proteins signals dysfunction of cellular protein homeostatic mechanisms such as the ubiquitin/proteasome system, autophagy, and the chaperone network. Although there are several published studies in which transcriptional profiling has been used to examine gene expression in various tissues, including tissues of neurodegenerative disease models, there has not been a report that focuses exclusively on expression of the chaperone network. In the present study, we used the Allen Brain Atlas online database to analyze chaperone expression levels. This database utilizes a quantitative in situ hybridization approach and provides data on 270 chaperone genes within many substructures of the adult mouse brain. We determined that 256 of these chaperone genes are expressed at some level. Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain. The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families. Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

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Related in: MedlinePlus

Immunoblot analysis of DnaJb1, DnaJb2, and Tomm70a.A. Immunoblots of different brain regions. Top Panel – A positive control sample for the antibody was loaded in the last late (labeled DnaJ1). Quantitation for DnaJb1, DnaJb2, and Tomm70a are shown in panels B–D, respectively.
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pone-0013675-g012: Immunoblot analysis of DnaJb1, DnaJb2, and Tomm70a.A. Immunoblots of different brain regions. Top Panel – A positive control sample for the antibody was loaded in the last late (labeled DnaJ1). Quantitation for DnaJb1, DnaJb2, and Tomm70a are shown in panels B–D, respectively.

Mentions: From our analysis of the chaperone expression data in ABA we can identify about 30 genes in the ABA that show a significant degree of variability in levels across different structures of the brain (Table 1, Figure 11, Table S3). Clearly it would be worthwhile to know whether the variability in mRNA levels across different brain structures translates into differing levels of protein. Most of the genes we identify as variable are poorly characterized in terms of function or protein levels. For many we could not identify validated antibody reagents that are required for accurate determination of protein levels. However, we identified antibodies for 3 genes that show a broad range of expression levels, from the lowest quintile to the highest quintile: DnaJb1, DnaJb2, and Tomm70a (Figure 11). Immunoblots of homogenates from different brain structures revealed some discrepancies between the ABA predictions based on mRNA levels and protein levels (Figure 12A). In contrast to predictions based on the ABA database, protein levels of DnaJb1 were not variable across brain structures (Figure 12B). For DnaJ2b we detected a statistically significant difference in protein levels between the cortex and the pons/medulla (Figure 12C), but ABA predicts these structures should have similar levels of expression (Figure 11). For Tomm70a the ABA contains expression data for two different probe sets, one of which predicts uniformly low levels of expression and one that predicts varied levels of expression (see Figure 4). Immunoblots for Tomm70a showed varied levels of expression with the variability closely matching what is predicted by the ABA (Figure 12D). The levels ofTomm70a were highest in striatum with statistically significant lower levels in hippocampus and pons/medulla. Thus, for 2 out of 3 of the chaperones in which we examined protein levels, we find differences from what is predicted by the ABA. It is possible that the inconsistencies between the levels of mRNA for DnaJb1 and DnaJb2 protein may be explained by subcellular localization of the proteins. The mRNA for these proteins is predominately localized to neuronal cell bodies, but these soluble cytosolic proteins are likely to be transported down axons possibly distributing the protein across many structures of the brain. In the case of Tomm70a, the protein is localized to the outer membrane of mitochondria [47], which are very abundant in cell bodies. From these data, it is hard to judge the extent to which the expression data in the ABA predicts protein levels in brain. It is possible that there is even less variability in the levels of chaperones across brain structures than is predicted by the ABA.


Analysis of chaperone mRNA expression in the adult mouse brain by meta analysis of the Allen Brain Atlas.

Tebbenkamp AT, Borchelt DR - PLoS ONE (2010)

Immunoblot analysis of DnaJb1, DnaJb2, and Tomm70a.A. Immunoblots of different brain regions. Top Panel – A positive control sample for the antibody was loaded in the last late (labeled DnaJ1). Quantitation for DnaJb1, DnaJb2, and Tomm70a are shown in panels B–D, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2965669&req=5

pone-0013675-g012: Immunoblot analysis of DnaJb1, DnaJb2, and Tomm70a.A. Immunoblots of different brain regions. Top Panel – A positive control sample for the antibody was loaded in the last late (labeled DnaJ1). Quantitation for DnaJb1, DnaJb2, and Tomm70a are shown in panels B–D, respectively.
Mentions: From our analysis of the chaperone expression data in ABA we can identify about 30 genes in the ABA that show a significant degree of variability in levels across different structures of the brain (Table 1, Figure 11, Table S3). Clearly it would be worthwhile to know whether the variability in mRNA levels across different brain structures translates into differing levels of protein. Most of the genes we identify as variable are poorly characterized in terms of function or protein levels. For many we could not identify validated antibody reagents that are required for accurate determination of protein levels. However, we identified antibodies for 3 genes that show a broad range of expression levels, from the lowest quintile to the highest quintile: DnaJb1, DnaJb2, and Tomm70a (Figure 11). Immunoblots of homogenates from different brain structures revealed some discrepancies between the ABA predictions based on mRNA levels and protein levels (Figure 12A). In contrast to predictions based on the ABA database, protein levels of DnaJb1 were not variable across brain structures (Figure 12B). For DnaJ2b we detected a statistically significant difference in protein levels between the cortex and the pons/medulla (Figure 12C), but ABA predicts these structures should have similar levels of expression (Figure 11). For Tomm70a the ABA contains expression data for two different probe sets, one of which predicts uniformly low levels of expression and one that predicts varied levels of expression (see Figure 4). Immunoblots for Tomm70a showed varied levels of expression with the variability closely matching what is predicted by the ABA (Figure 12D). The levels ofTomm70a were highest in striatum with statistically significant lower levels in hippocampus and pons/medulla. Thus, for 2 out of 3 of the chaperones in which we examined protein levels, we find differences from what is predicted by the ABA. It is possible that the inconsistencies between the levels of mRNA for DnaJb1 and DnaJb2 protein may be explained by subcellular localization of the proteins. The mRNA for these proteins is predominately localized to neuronal cell bodies, but these soluble cytosolic proteins are likely to be transported down axons possibly distributing the protein across many structures of the brain. In the case of Tomm70a, the protein is localized to the outer membrane of mitochondria [47], which are very abundant in cell bodies. From these data, it is hard to judge the extent to which the expression data in the ABA predicts protein levels in brain. It is possible that there is even less variability in the levels of chaperones across brain structures than is predicted by the ABA.

Bottom Line: Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain.The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families.Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

View Article: PubMed Central - PubMed

Affiliation: Department of Neuroscience, SantaFe Health Alzheimer's Disease Center, McKnight Brain Institute, University of Florida, Gainesville, Florida, United States of America. atebbenk@ufl.edu

ABSTRACT
The pathology of many neurodegenerative diseases is characterized by the accumulation of misfolded and aggregated proteins in various cell types and regional substructures throughout the central and peripheral nervous systems. The accumulation of these aggregated proteins signals dysfunction of cellular protein homeostatic mechanisms such as the ubiquitin/proteasome system, autophagy, and the chaperone network. Although there are several published studies in which transcriptional profiling has been used to examine gene expression in various tissues, including tissues of neurodegenerative disease models, there has not been a report that focuses exclusively on expression of the chaperone network. In the present study, we used the Allen Brain Atlas online database to analyze chaperone expression levels. This database utilizes a quantitative in situ hybridization approach and provides data on 270 chaperone genes within many substructures of the adult mouse brain. We determined that 256 of these chaperone genes are expressed at some level. Surprisingly, relatively few genes, only 30, showed significant variations in levels of mRNA across different substructures of the brain. The greatest degree of variability was exhibited by genes of the DnaJ co-chaperone, Tetratricopeptide repeat, and the HSPH families. Our analysis provides a valuable resource towards determining how variations in chaperone gene expression may modulate the vulnerability of specific neuronal populations of mammalian brain.

Show MeSH
Related in: MedlinePlus