CiteULike: giovanni's Johnson

Rosiglitazone treatment prevents mitochondrial dysfunction in mutant huntingtin expressing cells: Possible role of PPARgamma in the pathogenesis of huntington disease

Rodrigo Quintanilla — 2008-07-19T02:23:05-00:00

J. Biol. Chem. (18 July 2008), M804291200.

Peroxisome Proliferator-Activated Receptor- (PPAR) is a member of the PPAR family of transcription factors. Synthetic PPAR- agonists are used as oral anti-hyperglycemic drugs for the treatment of non-insulin-dependent diabetes mellitus. However, emerging evidence indicates that PPAR activators can also prevent or attenuate neurodegeneration. Given these previous findings, the focus of this paper is on the potential neuroprotective role of PPAR activation in preventing the loss of mitochondrial function in Huntington's Disease (HD). For these studies we used striatal cells that express wild type (STHdhQ7/Q7) or mutant (STHdhQ111/Q111) huntingtin protein at physiological levels. Treatment of mutant cells with thapsigargin resulted in a pronounced decrease in mitochondrial calcium uptake, an increase in reactive oxygen species (ROS) production, and a significant decrease in mitochondrial membrane potential. PPAR activation by rosiglitazone totally prevented the mitochondrial dysfunction and oxidative stress that occurred when mutant striatal cells were challenged with pathological increases in calcium. The beneficial effects of rosiglitazone were mediated by activation of the PPAR[gamma] receptor, as all protective effects were prevented by the PPAR[gamma] receptor antagonist GW9662. Additionally, the PPAR[gamma] signaling pathway was significantly impaired in the mutant striatal cells with decreases in PPAR[gamma] expression and reduced PPAR[gamma] transcriptional activity. Treatment with rosiglitazone increased mitochondrial mass levels, suggesting a role for the PPAR[gamma] pathway in mitochondrial function in striatal cells. Altogether, this evidence indicates that PPAR activation by rosiglitazone attenuates mitochondrial dysfunction in mutant huntingtin-expressing striatal cells, and this could be an important therapeutic avenue to ameliorate the mitochondrial dysfunction that occurs in HD. 10.1074/jbc.M804291200

Mapping the Genetic Architecture of Gene Expression in Human Liver

Eric Schadt — 2008-05-06T17:50:07-00:00

PLoS Biology, Vol. 6, No. 5. (1 May 2008), e107.

Genetic variants that are associated with common human diseases do not lead directly to disease, but instead act on intermediate, molecular phenotypes that in turn induce changes in higher-order disease traits. Therefore, identifying the molecular phenotypes that vary in response to changes in DNA and that also associate with changes in disease traits has the potential to provide the functional information required to not only identify and validate the susceptibility genes that are directly affected by changes in DNA, but also to understand the molecular networks in which such genes operate and how changes in these networks lead to changes in disease traits. Toward that end, we profiled more than 39,000 transcripts and we genotyped 782,476 unique single nucleotide polymorphisms (SNPs) in more than 400 human liver samples to characterize the genetic architecture of gene expression in the human liver, a metabolically active tissue that is important in a number of common human diseases, including obesity, diabetes, and atherosclerosis. This genome-wide association study of gene expression resulted in the detection of more than 6,000 associations between SNP genotypes and liver gene expression traits, where many of the corresponding genes identified have already been implicated in a number of human diseases. The utility of these data for elucidating the causes of common human diseases is demonstrated by integrating them with genotypic and expression data from other human and mouse populations. This provides much-needed functional support for the candidate susceptibility genes being identified at a growing number of genetic loci that have been identified as key drivers of disease from genome-wide association studies of disease. By using an integrative genomics approach, we highlight how the gene RPS26 and not ERBB3 is supported by our data as the most likely susceptibility gene for a novel type 1 diabetes locus recently identified in a large-scale, genome-wide association study. We also identify SORT1 and CELSR2 as candidate susceptibility genes for a locus recently associated with coronary artery disease and plasma low-density lipoprotein cholesterol levels in the process.

Association of GSK3B with Alzheimer's Disease and Frontotemporal Dementia

B Schaffer — 2008-04-03T21:57:02-00:00

Archives of Neurology (in press)

Novel transcriptional activities of vitamin e: inhibition of cholesterol biosynthesis.

S Valastyan — 2008-01-09T04:45:06-00:00

Biochemistry, Vol. 47, No. 2. (15 January 2008), pp. 744-752.

Vitamin E is a dietary lipid that is essential for vertebrate health and fertility. The biological activity of vitamin E is thought to reflect its ability to quench oxygen- and carbon-based free radicals and thus to protect the organism from oxidative damage. However, recent reports suggest that vitamin E may also display other biological activities. Here, to examine possible mechanisms that may underlie such nonclassical activities of vitamin E, we investigated the possibility that it functions as a specific modulator of gene expression. We show that treatment of cultured hepatocytes with (RRR)-alpha-tocopherol alters the expression of multiple genes and that these effects are distinct from those elicited by another antioxidant. Genes modulated by vitamin E include those that encode key enzymes in the cholesterol biosynthetic pathway. Correspondingly, vitamin E caused a pronounced inhibition of de novo cholesterol biosynthesis. The transcriptional activities of vitamin E were mediated by attenuating the post-translational processing of the transcription factor SREBP-2 that, in turn, led to a decreased transcriptional activity of sterol-responsive elements in the promoters of target genes. These observations indicate that vitamin E possesses novel transcriptional activities that affect fundamental biological processes. Cross talk between tocopherol levels and cholesterol status may be an important facet of the biological activities of vitamin E.

Genome-Wide Mapping of in Vivo Protein-DNA Interactions

David Johnson — 2007-06-04T11:05:50-00:00

Science (31 May 2007), 1141319.

In vivo protein-DNA interactions connect each transcription factor with its direct targets to form a gene network scaffold. To map these protein-DNA interactions comprehensively across entire mammalian genomes, we developed a large-scale chromatin immunoprecipitation assay (ChIPSeq) based on direct ultra-high-throughput DNA sequencing. This sequence census method was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST, for repressor element-1 silencing transcription factor) to 1946 locations in the human genome. The data display sharp resolution of binding position [+/-50 base pairs (bp)], which facilitated our finding motifs and allowed us to identify noncanonical NRSF-binding motifs. These ChIPSeq data also have high sensitivity and specificity [ROC (receiver operator characteristic) area =0.96] and statistical confidence (P <10-4), properties that were important for inferring new candidate interactions. These include key transcription factors in the gene network that regulates pancreatic islet cell development. 10.1126/science.1141319

Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes

Harald Goring — 2007-09-27T14:44:10-00:00

Nat Genet, Vol. 39, No. 10. (October 2007), pp. 1208-1216.

Relationship Between Mitochondrial Electron Transport Chain Dysfunction, Development, and Life Extension in Caenorhabditis elegans.

Shane L Rea — 2007-10-05T20:43:19-00:00

PLoS Biol, Vol. 5, No. 10. (2 October 2007)

Prior studies have shown that disruption of mitochondrial electron transport chain (ETC) function in the nematode Caenorhabditis elegans can result in life extension. Counter to these findings, many mutations that disrupt ETC function in humans are known to be pathologically life-shortening. In this study, we have undertaken the first formal investigation of the role of partial mitochondrial ETC inhibition and its contribution to the life-extension phenotype of C. elegans. We have developed a novel RNA interference (RNAi) dilution strategy to incrementally reduce the expression level of five genes encoding mitochondrial proteins in C. elegans: atp-3, nuo-2, isp-1, cco-1, and frataxin (frh-1). We observed that each RNAi treatment led to marked alterations in multiple ETC components. Using this dilution technique, we observed a consistent, three-phase lifespan response to increasingly greater inhibition by RNAi: at low levels of inhibition, there was no response, then as inhibition increased, lifespan responded by monotonically lengthening. Finally, at the highest levels of RNAi inhibition, lifespan began to shorten. Indirect measurements of whole-animal oxidative stress showed no correlation with life extension. Instead, larval development, fertility, and adult size all became coordinately affected at the same point at which lifespan began to increase. We show that a specific signal, initiated during the L3/L4 larval stage of development, is sufficient for initiating mitochondrial dysfunction-dependent life extension in C. elegans. This stage of development is characterized by the last somatic cell divisions normally undertaken by C. elegans and also by massive mitochondrial DNA expansion. The coordinate effects of mitochondrial dysfunction on several cell cycle-dependent phenotypes, coupled with recent findings directly linking cell cycle progression with mitochondrial activity in C. elegans, lead us to propose that cell cycle checkpoint control plays a key role in specifying longevity of mitochondrial mutants.

Clearance of amyloid-β by circulating lipoprotein receptors

Abhay Sagare — 2007-09-08T22:04:49-00:00

Nature Medicine, Vol. 13, No. 9. (12 August 2007), pp. 1029-1031.

Mutations in progranulin are a major cause of ubiquitin-positive frontotemporal lobar degeneration

Jennifer Gass — 2006-10-02T08:35:19-00:00

Hum. Mol. Genet., Vol. 15, No. 20. (15 October 2006), pp. 2988-3001.

Null mutations in the progranulin gene (PGRN) were recently reported to cause tau-negative frontotemporal dementia linked to chromosome 17. We assessed the genetic contribution of PGRN mutations in an extended population of patients with frontotemporal lobar degeneration (FTLD) (N=378). Mutations were identified in 10% of the total FTLD population and 23% of patients with a positive family history. This mutation frequency dropped to 5% when analysis was restricted to an unbiased FTLD subpopulation (N=167) derived from patients referred to Alzheimer's Disease Research Centers (ADRC). Among the ADRC patients, PGRN mutations were equally frequent as mutations in the tau gene (MAPT). We identified 23 different pathogenic PGRN mutations, including a total of 21 nonsense, frameshift and splice-site mutations that cause premature termination of the coding sequence and degradation of the mutant RNA by nonsense-mediated decay. We also observed an unusual splice-site mutation in the exon 1 5' splice site, which leads to loss of the Kozac sequence, and a missense mutation in the hydrophobic core of the PGRN signal peptide. Both mutations revealed novel mechanisms that result in loss of functional PGRN. One mutation, c.1477C>T (p.Arg493X), was detected in eight independently ascertained familial FTLD patients who were shown to share a common extended haplotype over the PGRN genomic region. Clinical examination of patients with PGRN mutations revealed highly variable onset ages with language dysfunction as a common presenting symptom. Neuropathological examination showed FTLD with ubiquitin-positive cytoplasmic and intranuclear inclusions in all PGRN mutation carriers. 10.1093/hmg/ddl241

Adjusting batch effects in microarray expression data using empirical Bayes methods

Johnson — 2007-01-21T05:33:25-00:00

Biostatistics, Vol. 8, No. 1. (January 2007), pp. 118-127.

FRAT-2 preferentially increases GSK3beta -mediated phosphorylation of primed sites which results in enhanced tau phosphorylation

WH Stoothoff — 2006-10-18T01:45:21-00:00

J Biol Chem (2004)

Tau is a microtubule-associated protein found primarily in neurons and its function is regulated by site-specific phosphorylation. Although it is well-established that tau is phosphorylated at both primed and unprimed epitopes by glycogen synthase kinase 3beta (GSK3beta), how specific proteins that interact with GSK3beta regulate tau phosphorylation has not been thoroughly examined. Members of the frequently rearranged in advanced T-cell lymphoma (FRAT) protein family have been shown to interact with GSK3beta, and FRAT-1 has been shown to modulate GSK3beta's activity towards tau and other substrates. However, the effects of FRAT-2 on GSK3beta activity and tau phosphorylation have not been examined. Therefore in this study the effects of FRAT-2 on GSK3beta activity and tau phosphorylation were examined. In situ, FRAT-2 significantly increased GSK3beta-mediated phosphorylation of tau at a primed epitope, while not significantly affecting the phosphorylation of unprimed sites. Co-immunoprecipitation studies revealed that association of FRAT-2 with GSK3beta resulted in a significant increase in phosphorylation of a primed substrate, but did not alter phosphorylation of an unprimed substrate. Further, in vitro assays using recombinant proteins directly demonstrated that FRAT-2 enhances GSK3beta mediated phosphorylation of a primed substrate to a greater extent than an unprimed substrate. In addition, FRAT-2 is phosphorylated by GSK3beta. This is the first demonstration of a protein differentially regulating the activity of GSK3beta towards primed and unprimed epitopes.

Axin negatively affects tau phosphorylation by glycogen synthase kinase 3beta

WH Stoothoff — 2006-10-18T01:45:21-00:00

J Neurochem, Vol. 83, No. 4. (2002), pp. 904-13.

Glycogen synthase kinase 3beta (GSK3beta) is an essential protein kinase that regulates numerous functions within the cell. One critically important substrate of GSK3beta is the microtubule-associated protein tau. Phosphorylation of tau by GSK3beta decreases tau-microtubule interactions. In addition to phosphorylating tau, GSK3beta is a downstream regulator of the wnt signaling pathway, which maintains the levels of beta-catenin. Axin plays a central role in regulating beta-catenin levels by bringing together GSK3beta and beta-catenin and facilitating the phosphorylation of beta-catenin, targeting it for ubiquitination and degradation by the proteasome. Although axin clearly facilitates the phosphorylation of beta-catenin, its effects on the phosphorylation of other GSK3beta substrates are unclear. Therefore in this study the effects of axin on GSK3beta-mediated tau phosphorylation were examined. The results clearly demonstrate that axin is a negative regulator of tau phosphorylation by GSK3beta. This negative regulation of GSK3beta-mediated tau phosphorylation is due to the fact that axin efficiently binds GSK3beta but not tau and thus sequesters GSK3beta away from tau, as an axin mutant that does not bind GSK3beta did not inhibit tau phosphorylation by GSK3beta. This is the first demonstration that axin negatively affects the phosphorylation of a GSK3beta substrate, and provides a novel mechanism by which tau phosphorylation and function can be regulated within the cell.

Possible association of the tau H1/H1 genotype with primary progressive aphasia

MJ Sobrido — 2006-10-18T01:45:21-00:00

Neurology, Vol. 60, No. 5. (2003), pp. 862-4.

The authors screened for tau gene mutations and polymorphisms to determine whether genetic variation at or near the tau locus contributes to the development of primary progressive aphasia (PPA). No mutations were detected in 25 patients with PPA. However, a significant overrepresentation of the tau H1/H1 genotype, also found in progressive supranuclear palsy and corticobasal degeneration, was found in the PPA group. Whether tau haplotypes have a primary causal role or whether they affect the topology of neurodegeneration remains to be determined.

Cyclin-dependent kinase-5 in neurodegeneration

SB Shelton — 2006-10-18T01:45:20-00:00

J Neurochem, Vol. 88, No. 6. (2004), pp. 1313-26.

Cyclin-dependent kinase-5 (CDK5) is predominantly active in the nervous system and it is well established that CDK5 is essential in neuronal development. In addition to its recognized role in development, there is increasing evidence that CDK5 may be involved in the pathogenesis of several neurodegenerative disorders. Although studies have shown that CDK5 can modulate cell death and survival, controversy still exists as to the exact role CDK5 may play in neurodegenerative processes. This review will highlight recent data on the possible roles of CDK5 in neurodegeneration.

Sequencing complex diseases With HapMap

T Liu — 2006-10-18T01:45:13-00:00

Genetics, Vol. 168, No. 1. (2004), pp. 503-11.

Determining the patterns of DNA sequence variation in the human genome is a useful first step toward identifying the genetic basis of a common disease. A haplotype map (HapMap), aimed at describing these variation patterns across the entire genome, has been recently developed by the International HapMap Consortium. In this article, we present a novel statistical model for directly characterizing specific sequence variants that are responsible for disease risk based on the haplotype structure provided by HapMap. Our model is developed in the maximum-likelihood context, implemented with the EM algorithm. We perform simulation studies to investigate the statistical properties of this disease-sequencing model. A worked example from a human obesity study with 155 patients was used to validate this model. In this example, we found that patients carrying a haplotype constituted by allele Gly16 at codon 16 and allele Gln27 at codon 27 genotyped within the beta2AR candidate gene display significantly lower body mass index than patients carrying the other haplotypes. The implications and extensions of our model are discussed.

Tau complexes with phospholipase C-gamma in situ

SM Jenkins — 2006-10-18T01:45:10-00:00

Neuroreport, Vol. 9, No. 1. (1998), pp. 67-71.

Based on the results of recent in vitro studies, tau has been proposed to be involved in regulating signal transduction through the phospholipase C-gamma (PLC-gamma) signaling pathway. The present study provides support for the physiological relevance of this hypothesis by demonstrating the existence of a tau-PLC-gamma complex in situ in a human neuroblastoma cell line. Both PLC-gamma and PLC-delta, but not PLC-beta, co-purified with microtubule-associated proteins. PLC-gamma, but neither PLC-delta nor PLC-beta, co-immunoprecipitated with tau, and the PLC co-precipitating with tau was enzymatically active. Additionally, both tau and MAP-2 co-precipitated with PLC-gamma. These studies indicate that tau associates, either directly or indirectly, with PLC-gamma in situ, suggesting that tau may be appropriately localized to participate in the regulation of signal transduction through the PLC-gamma pathway in vivo.

Modulation of the phosphorylation state of tau in situ: the roles of calcium and cyclic AMP

LM Fleming — 2006-10-18T01:45:06-00:00

Biochem J, Vol. 309 (Pt 1) (1995), pp. 41-7.

Alterations in situ in the phosphorylation state of the microtubule-associated protein tau were examined in response to increasing intracellular levels of Ca2+ through N-methyl-D-aspartate (NMDA)-receptor activation, or activating cyclic AMP (cAMP)-dependent protein kinase (cAMP-PK), in rat cerebral-cortical slices. Increasing intracellular concentrations of Ca2+ by treatment of the brain slices with the glutamate analogue NMDA in depolarizing conditions (55 mM KCl) resulted in dephosphorylation of tau. Addition of KCl+NMDA to the slices resulted in a 40% decrease in 32P incorporation into tau, whereas addition of KCl or NMDA alone had no effect on tau phosphorylation. The KCl+NMDA-induced dephosphorylation of tau was blocked by the non-competitive NMDA-receptor antagonist MK801. Determine the involvement of the Ca2+/calmodulin-dependent phosphatase, calcineurin, in the KCl+NMDA-induced dephosphorylation of tau, slices were pretreated with the calcineurin inhibitor Cyclosporin A. Pretreatment of the rat brain slices with Cyclosporin A completely abolished the dephosphorylation of tau induced by the addition of KCl+NMDA. The dephosphorylation of tau in situ was site-selective, as indicated by the loss of 32P label from only a few select peptides. Activation of cAMP-PK by stimulating adenylate cyclase in rat cerebral-cortical slices with forskolin resulted in a 73% increase over control levels in 32P incorporation into immunoprecipitated tau. Two-dimensional phosphopeptide mapping revealed that most of the sites on tau phosphorylated in brain slices in response to increased cAMP levels were the same as those phosphorylated on isolated tau by purified cAMP-PK. Although the state of tau phosphorylation is certainly regulated by many protein phosphatases and kinases in vivo, to our knowledge this study provides the first direct evidence of a specific protein phosphatase and kinase that modulate the phosphorylation state of tau in situ.

Glycogen synthase kinase 3beta (GSK3beta) induces caspase cleaved tau aggregation in situ

JH Cho — 2006-10-18T01:45:03-00:00

J Biol Chem (2004)

Tau is a substrate of caspases, and caspase cleaved tau has been detected in Alzheimer's disease brain, but not in control brain. Further, in vitro studies have revealed that caspase cleaved tau is more fibrillogenic than full-length tau. Considering these previous findings, the purpose of this study was to determine how the caspase cleavage of tau affected tau function and aggregation in a cell model system. The effects of glycogen synthase kinase 3beta (GSK3beta), a well-established tau kinase, on these processes also were examined. Tau or tau that had been truncated at Asp421 to mimic caspase cleavage (Tau-D421) was transfected into cells with or without GSK3beta and phosphorylation, microtubule binding and tau aggregation were examined. Tau-D421 was not as efficiently phosphorylated by GSK3beta as full-length tau. Tau-D421 efficiently bound microtubules, and in contrast to the full-length tau, co-expression with GSK3beta did not result in a reduction in the ability of Tau-D421 to bind microtubules. In the absence of GSK3beta, neither Tau-D421 nor full-length tau formed sarkosyl insoluble inclusions. However, in the presence of GSK3beta Tau-D421, but not full-length tau, was present in the sarkosyl insoluble fraction and formed Thioflavin-S positive inclusions in the cell. Nonetheless, co-expression of GSK3beta and Tau-D421 did not result in an enhancement of cell death. These data suggest that a combination of phosphorylation events and caspase activation contribute to the tau oligomerization process in Alzheimer's disease, with GSK3b-mediated tau phosphorylation preceding caspase cleavage.