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Results for “brain proteomics”

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PubMed2005

Proteomic determination of widespread detergent-insolubility including Abeta but not tau early in the pathogenesis of Alzheimer's disease.

Biochemical characterization of the major detergent-insoluble proteins that comprise hallmark histopathologic lesions initiated the molecular era of Alzheimer's disease (AD) research. Here, we reinvestigated detergent-insoluble proteins in AD using modern proteomic techniques. Using liquid chromatography (LC)-mass spectrometry (MS)-MS-based proteomics, we robustly identified 125 proteins in the detergent-insoluble fraction of late-onset AD (LOAD) temporal cortex that included several proteins critical to Abeta production, components of synaptic scaffolding, and products of genes linked to an increased risk of LOAD; we verified 15 of 15 of these proteins by Western blot. Following multiple analyses, we estimated that these represent ~80% of detergent-insoluble proteins in LOAD detectable by our method. Abeta, tau, and 7 of 8 other newly identified detergent-insoluble proteins were disproportionately increased in temporal cortex from patients with LOAD and AD derived from mutations in PSEN1 and PSEN2; all of these except tau were elevated in individuals with prodromal dementia, while none except Abeta were elevated in aged APPswe mice. These results are consistent with the amyloid hypothesis of AD and extend it to include widespread protein insolubility, not exclusively Abeta insolubility, early in AD pathogenesis even before the onset of clinical dementia.

Alzheimer Disease↗

PubMed2005

Redox proteomics identification of oxidized proteins in Alzheimer's disease hippocampus and cerebellum: an approach to understand pathological and biochemical alterations in AD.

Alzheimer's disease (AD) is characterized by the presence of neurofibrillary tangles, senile plaques and loss of synapses. There is accumulating evidence that oxidative stress plays an important role in AD pathophysiology. Previous redox proteomics studies from our laboratory on AD inferior parietal lobule led to the identification of oxidatively modified proteins that were consistent with biochemical or pathological alterations in AD. The present study was focused on the identification of specific targets of protein oxidation in AD and control hippocampus and cerebellum using a redox proteomics approach. In AD hippocampus, peptidyl prolyl cis-trans isomerase, phosphoglycerate mutase 1, ubiquitin carboxyl terminal hydrolase 1, dihydropyrimidinase related protein-2 (DRP-2), carbonic anhydrase II, triose phosphate isomerase, alpha-enolase, and gamma-SNAP were identified as significantly oxidized protein with reduced enzyme activities relative to control hippocampus. In addition, no significant excessively oxidized protein spots were identified in cerebellum compared to control, consistent with the lack of pathology in this brain region in AD. The identification of oxidatively modified proteins in AD hippocampus was verified by immunochemical means. The identification of common oxidized proteins in different brain regions of AD brain suggests a potential role for these oxidized proteins and thereby oxidative stress in the pathogenesis of Alzheimer's disease.

Aged↗

PubMed2026

Systematic proteomic analysis of neuroimaging metrics identifies therapeutic targets for pituitary neuroendocrine.

The relationship between proteomics and neuroimaging metrics (NIMs) is still not fully understood. By examining the specific proteins expressed in different NIMs, researchers can gain insights into how these NIMs contribute to pituitary neuroendocrine tumors (PitNETs), ultimately enabling the development of targeted interventions and treatments. We identified 15 significantly NIMs and 18 proteins that exhibit a noteworthy causal relationship with the risk of developing PitNETs by forward MR analysis. Additionally, 10 proteins and one distinct neuroimaging metric with PitNETs. Then, the MR results indicated the identification of 33 significant relationships, which connect proteins with NIMs across five distinct categories. Then, we discovered that NIMs are capable of mediating 63% of the inverse relationship observed between WNT3 and the phenotypic characteristics of PitNETs. The results also suggested that WNT3 was associated with hypothalamic function, pituitary function, thyroid function, adrenal function, and gonadal function. Additionally, WNT3 expression was higher in PitNETs and was verified in multiple datasets. This research effectively connects the roles of protein markers with the structures of the brain and the PitNETs that can affect it. By establishing this link, the study provides valuable insights that can help in understanding the complex mechanisms that contribute to PitNETs.

Proteomics↗

PubMed2006

Upregulation of dihydropyrimidinase-related protein 2, spectrin alpha II chain, heat shock cognate protein 70 pseudogene 1 and tropomodulin 2 after focal cerebral ischemia in rats--a proteomics approach.

In recent years, there are an increasing number of proteomics studies that investigated the alterations in the protein expression relevant to human diseases but none for stroke. We, therefore, attempted such a study in a paradigm of focal cerebral ischemia in rat. Rats were subjected to cerebral ischemia by unilateral occlusion of the middle cerebral artery. Global protein analysis was performed after 24h on the lesioned and sham-control cerebral cortex using two-dimensional gel electrophoresis. Protein spots with more than a 3-fold change in intensity were identified by mass spectrometry. Middle cerebral artery occlusion (MCAO) caused infarct volume of 18-22% predominantly in the cortex of the lesioned hemisphere. Two-dimensional gel electrophoresis resolved about 1500 protein spots of which only 12 were significantly upregulated by 3-46-fold. Three spots were identified to be dihydropyrimidinase-related protein 2 (DRP-2, also known as collapsin response mediator protein 2 (CRMP-2) or turned on after division, 64 kD protein (TOAD-64)). The spots varied in pI values only and this may reflect different phosphorylation status of the same protein. Two spots were identified as spectrin alpha II chain (rat fragment, also known as alpha-fodrin or non-erythroid alpha chain, SPNA-2); and one spot each for heat shock cognate protein 70 pseudogene 1 (HSC70-ps1, also known as heat shock protein 8 pseudogene 1), and tropomodulin 2 (Tmod2). The upregulation of protein expression was corroborated by observed upregulation of mRNA expression. The remaining five spots were not identified satisfactorily. As DRP-2, spectrin, and Tmod2 are involved in axonal and neurite growth as well as synaptic plasticity and maturation, the presently observed upregulation of the expression of these proteins may indicate active neuroregeneration and repair at 24h after the induction of cerebral ischemia.

Animals↗

PubMed2000

National Institute of Mental Health goals for behavioral science.

Because all health conditions for which the National Institute of Mental Health (NIMH) is responsible manifest at the level of behavior, and all interventions must have an impact at the behavioral level, NIMH is firmly committed to the support of behavioral science. In an era in which research in areas that some view as reductionist--for example, genomics, genetics, functional genomics and proteomics, and molecular science--is especially promising, NIMH is striving to maintain a balance in its portfolio with studies that explore integrative aspects of biology, including behavior. Without this perspective, new information about fundamental processes will prove ultimately to be shallow. This commentary discusses how understanding of brain and behavior in mental illness and health calls for integrating bottom-up research that studies brain and behavior through genes and molecules, with top-down research that examines the impact of environment.

Behavioral Sciences↗

PubMed2006

Exercise affects energy metabolism and neural plasticity-related proteins in the hippocampus as revealed by proteomic analysis.

Studies were conducted to evaluate the effect of a brief voluntary exercise period on the expression pattern and post-translational modification of multiple protein classes in the rat hippocampus using proteomics. An analysis of 80 protein spots of relative high abundance on two-dimensional gels revealed that approximately 90% of the proteins identified were associated with energy metabolism and synaptic plasticity. Exercise up-regulated proteins involved in four aspects of energy metabolism, i.e. glycolysis, ATP synthesis, ATP transduction and glutamate turnover. Specifically, we found increases in fructose-bisphosphate aldolase C, phosphoglycerate kinase 1, mitochondrial ATP synthase, ubiquitous mitochondrial creatine kinase and glutamate dehydrogenase 1. Exercise also up-regulated specific synaptic-plasticity-related proteins, the cytoskeletal protein alpha-internexin and molecular chaperones (chaperonin-containing TCP-1, neuronal protein 22, heat shock 60-kDa protein 1 and heat shock protein 8). Western blot was used to confirm the direction and magnitude of change in ubiquitous mitochondrial creatine kinase, an enzyme essential for transducing mitochondrial-derived ATP to sites of high-energy demand such as the synapse. Protein phosphorylation visualized by Pro-Q Diamond fluorescent staining showed that neurofilament light polypeptide, glial fibrillary acidic protein, heat shock protein 8 and transcriptional activator protein pur-alpha were more intensely phosphorylated with exercise as compared with sedentary control levels. Our results, together with the fact that most of the proteins that we found to be up-regulated have been implicated in cognitive function, support a mechanism by which exercise uses processes of energy metabolism and synaptic plasticity to promote brain health.

Animals↗

PubMed2001

Natural intramolecular isotope measurements in physiology: elements of the case for an effort toward high-precision position-specific isotope analysis.

Chemical information available in organisms can be categorized into three major domains, macromolecular, small molecules, and isotope ratios. Information about physiological state is commonly obtained by qualitative and quantitative analysis in the macromolecular and small molecule domains. Genomics and proteomics are emerging approaches to analysis of macromolecules, and both areas yield definitive information on present physiological state. There is relatively little record of past physiological states of the individual available in these domains. Natural isotopic variability, particularly on an intramolecular level, is likely to retain more physiological history. Because of ubiquitous isotopic fractionation, every stereochemically unique position in every molecule has an isotope ratio that reflects the processes of synthesis and degradation. This fact highlights a vast amount of organismal chemical information that is essentially unstudied. Isotope measurements can be classified according to the chemical complexity of the analyte into bulk, compound-specific, and position-specific or intramolecular levels. Recent advances in analysis of isotope ratios are transforming natural science, and particularly answering questions about ecosystems using bulk methods; however, they have had relatively little impact on physiology. This may be because the vast complexities of physiological questions demand very selective information available in position-specific isotope analysis (PSIA). The relatively few high-precision PSIA studies, based on isotope ratio mass spectrometry (IRMS), have revealed intramolecular isotope ratio differences in pivotal physiological compounds including amino acids, glucose, glycerol, acetate, fatty acids, and purines. The majority of these analyses have been accomplished by laborious offline methods; however, recent advances in instrumentation presage rapid PSIA that will be necessary to attack real physiological problems. Gas-phase pyrolysis has been shown to be an effective method to determine (13)C/(12)C at high precision for molecular fragments, and technologies to extend C-based PSIA to N and other organic elements are emerging. Two related efforts are warranted, (a) development of rapid, convenient, and sensitive methods for high-precision PSIA, a necessary precursor to (b) a concerted investigation into the relationship of metabolic state to intramolecular isotope ratio. Inherent in this latter goal is the need to identify long-lived molecules in long-lived cells that retain a record of early isotopic conditions, as has been shown for post-mortem human neuronal DNA. Using known metabolic precursor-product relationships between intramolecular positions, future studies of physiological isotope fractionation should reveal the relationship of diet and environment to observed isotope ratio. This science of isotope physiology, or simply isotopics, should add an important tool for elucidation of early factors that effect later health, probably the most difficult class of biomedical issues.

Acetates↗

PubMed2003

Reproduction phase-related expression of GnRH-like immunoreactivity in the olfactory receptor neurons, their projections to the olfactory bulb and in the nervus terminalis in the female Indian major carp Cirrhinus mrigala (Ham.).

The reproductive biology of the Indian major carp Cirrhinus mrigala is tightly synchronized with the seasonal changes in the environment. While the ovaries show growth from February through June, the fish spawn in July-August to coincide with the monsoon; thereafter the fish pass into the postspawning and resting phases. We investigated the pattern of GnRH immunoreactivity in the olfactory system at regular intervals extending over a period of 35 months. Although no signal was detected in the olfactory organ of fish collected from April through February following year, distinct GnRH-like immunoreactivity appeared in the fish collected in March. Intense immunoreactivity was noticed in several olfactory receptor neurons (ORNs) and their axonal fibers as they extend over the olfactory nerve, spread in the periphery of the olfactory bulb (OB), and terminate in the glomerular layer. Strong immunoreactivity was seen in some fascicles of the medial olfactory tracts extending from the OB to the telencephalon. Some neurons of the ganglion cells of nervus terminalis showed GnRH immunostaining during March; no immunoreactivity was detected at other times of the year. Plexus of GnRH immunoreactive fibers extending throughout the bulb represented a different component of the olfactory system; the fiber density showed a seasonal pattern that could be related to the status of gonadal maturity. While it was highest in the prespawning phase, significant reduction in the fiber density was noticed in the fish of spawning and the following regressive phases. Taken together the data suggest that the GnRH in the olfactory system of C. mrigala may play a major role in translation of the environmental cues and influence the downstream signals leading to the stimulation of the brain-pituitary-ovary axis.

Animals↗

PubMed2004

[A new approach to protein phosphorylation modification analysis for neuron].

OBJECTIVE: To develop a new method for analysis of protein phosphorylation modification in cultured neuron. METHODS: Cultured neurons were pre-incubated in DMEM without sodium phosphate for 15 min to deplete the metabolic pools. Neurons were then labeled with [32P] orthophosphate (2.78 x 10(6) Bq/ml) for 1.5 h and stimulated by either insulin (100 nmol/L), EGF (20 nm/L) or saline for 0, 5, 20, 60, 120 min. Reactions were terminated by freezing neurons in liquid nitrogen prior to the solubilizing of them in a lysis buffer containing 8 mol/L urea, 4% CHAPS, 2% Bio-lyte, pH 3-10, 2 mmol/L TBP. Protein concentrations were determined with Bio-Rad DC Protein Assay kit. The 32P-labled lysates isoelectrically focused on IPG Drystrip pH 3-10 or pH 4-7 Linear gels were subsequently separated in second-dimensional SDS-PAGE. The dried gel was autoradiographed for 5 days at -70 degrees C with an intensifying screen. Alternatively, the separated proteins were visualized by Coomassie Brilliant Blue (CBB) R250 straining. RESULTS: Autoradiography of the 2-DE-separated 32P-laebled neuron lysates revealed around 100 phosphoproteins. This phosphoprotein pattern was stable at 1.5 h after radiolabelling and did not vary significantly for up to 4 h further incubation in the absence of hormone. Most of the major proteins which are phosphorylated in response to insulin or EGF migrated with pH 4.6-6.5 and MW 20000-130000. Insulin and EGF induced similar but not identical patterns of protein phosphoryltion in neurons. Only a few phosphoproteins were abundant enough to be visualized by CBB straining, suggesting that abundance of these phosphoproteins is extremely low. Responses to both isulin and EGF are marked by more increased labeling of the constitutive phosphoproteins, compared with the appearance of new phosphoproteins. CONCLUSION: This approach co-application of 32P-labeled with 2-DE separation and autoradiography has proven to be specific and sensitive in phosphoprotein analysis for neuron. It was valuable in functional proteomic analysis for protein phosphorylation modification during cellular signal transduction.

Animals↗

PubMed2005

Comparative genomics on Wnt7a orthologs.

WNT and Hedgehog signaling pathways network together during carcinogenesis and embryogenesis. WNT7A mRNA is expressed in human gastric and pancreatic cancer cells. WNT7A mRNA expression is relatively high in the temporal, occipital and parietal lobes, paracentral gyrus of the cerebral cortex, caudate nucleus, hippocampus, medulla oblongata and putamen within the adult human brain. Here, we identified and characterized the rat Wnt7a gene using bioinformatics. The rat Wnt7a gene, consisting of four exons, was located within the AC106100.7 genome sequence. Rat Wnt7a (349 aa) with 24 Cys residues and 3 Asn-linked glycosylation sites showed 99.7, 99.1 and 93.7% total-amino- acid identity with mouse Wnt7a, human WNT7A and chicken wnt7a, respectively. The N-terminal signal peptide was not identified within the Wnt7a orthologs. Exonic regions, except the 3'-UTR, were conserved between the rat Wnt7a and human WNT7A genes; however, the 5'-flanking region was significantly divergent between the rat Wnt7a and human WNT7A genes. Although the COMP1- and ELK1-binding sites within exon 1 were conserved among mammalian Wnt7a promoters, transcriptional regulation of the rodent Wnt7a orthologs was predicted to be distinct from that of human WNT7A based on the divergence within the 5'-flanking promoter region. Therefore, biological functions of rodent Wnt7a are not always consistent with those of human WNT7A due to promoter evolution. This is the first report on the rat Wnt7a gene and comparative genomics for Wnt7a orthologs.

Animals↗

PubMed2006

Proteomics of polyglutamine aggregates.

In nine members of polyglutamine (polyQ) diseases, CAG repeat expansions of their responsible genes are observed. The disease is considered to be caused by the formation of polyQ aggregates that sequester proteins essential for cell viability. To understand the pathological process of polyQ diseases, a proteomic approach was used to identify aggregate interacting proteins (AIPs). Constructs were designed to express EGFP-fused, CAG-expanded (150 Q) huntingtin exon1 under the control of an ecdysone-inducible promoter and either lacking or containing a nuclear localization signal (NLS). After induction of a stably transfected Neuro 2A cell line with ecdysone, aggregates form in either the cytoplasm or the nucleus. The aggregates in these two different compartments were isolated with different methods. Cytoplasmic aggregate particles were purified using a fluorescence-activated cell sorter (FACS) by monitoring EGFP fluorescence, whereas nuclear aggregates were purified by using the detergent insoluble nature of aggregates. The resulting highly pure aggregates were subjected to SDS-PAGE followed by Coomassie blue staining. Bands containing AIP candidates were excised, and, after in-gel digestion with trypsin, were analyzed by mass spectrometry to identify the proteins. Novel candidates were confirmed as AIPs by immunocytological analysis to observe colocalization with polyQ aggregates. This chapter describes methods for the establishment of stable mutant cells, the purification of polyQ aggregates, and sample preparation for mass spectrometry analysis in detail.

Animals↗

PubMed2002

Identification and characterization of teicoplanin-intermediate Staphylococcus aureus blood culture isolates in NE Scotland.

The study objective was to screen both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) isolates from blood cultures for reduced susceptibility to vancomycin and teicoplanin. A total of 72 MRSA and 143 MSSA isolates were screened on brain-heart infusion agar containing either 4 mg/L vancomycin or 8 mg/L teicoplanin, using an inoculum of approximately 10(6) organisms. MICs were determined by Etest, broth microdilution and agar incorporation. Isolates were characterized by PFGE, mecA and nuc PCR, transmission electron microscopy (TEM) and analysis of cell proteins (proteomics). Based on British Society for Antimicrobial Chemotherapy (BSAC) breakpoints, seven MRSAs and seven MSSAs were teicoplanin resistant, with MICs of up to 16 and 24 mg/L respectively, but were vancomycin sensitive. Based on higher NCCLS breakpoints, five MRSAs and six MSSAs were teicoplanin intermediate, vancomycin sensitive. All the MRSAs belonged to the EMRSA-16 clone and subdivided into two groups. The MSSAs belonged to five different clones. TEM showed the resistant variants to have slightly thicker cell walls than sensitive variants. Most notably, the resistant variants possessed characteristic dark, granular material concentrated in the middle of the cells, believed to be chromosome. Proteomics showed the resistant variants to overexpress phosphoglycerate kinase. Both MRSA and MSSA with reduced teicoplanin susceptibility may remain vancomycin sensitive by NCCLS and BSAC criteria and it is important to screen clinical isolates of MRSA and MSSA for reduced susceptibility to both agents.

Blood↗

PubMed2005

Corcoran Lecture. Cardiovascular genomics and oxidative stress.

The majority of modifiable cardiovascular risk factors are complex, polygenic, or at least oligogenic traits, with genetic and environmental determinants playing important roles in disease risk and its phenotypic expression. The Human Genome Project and subsequent mouse and rat genome data have provided powerful tools to commence the dissection of genetic determinants of hypertension and other cardiovascular risk factors. Despite several new methodologies such as genome-wide scans, genome-wide gene expression profiling, and proteomic screens, it is fair to say that the progress of genetic studies designed as nonhypothesis driven has been relatively slow. On the other hand, several interesting candidate pathways have been identified, where investigators allowed for hypothesis-driven functional studies. One example of such pathway is vascular oxidative stress with its extensive network of genes and proteins, many with proven contributions to cardiovascular disease. Therefore, in parallel to genome-wide or proteome-wide studies, it will be constructive to pursue "pathwayomics" defined here as functional studies of a candidate pathway for disease pathogenesis.

Animals↗

PubMed2003

Identification of differentially expressed proteins in human glioblastoma cell lines and tumors.

An in-frame deletion of 801 bp in exons 2-7 (type III mutation) of the epidermal growth factor receptor (EGFR) is detected at high incidence in primary glioblastoma tumors. A proteomic approach was used to generate differential protein expression maps of fetal human astrocytes (FHA), human glioblastoma cell lines U87MG and U87MG expressing type III EGFR deletion (U87MGdeltaEGFR) that confers high malignancy to tumor cells. Two-dimensional gel electrophoresis followed by in-gel digestion of separated spots and protein identification by LC-MS-MS and matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) identified 23 proteins expressed at higher levels or exclusively in FHA and 29 proteins expressed at higher levels or exclusively in U87MG cells. Three proteins, ubiquitin, cystatin B, and tissue transglutaminase (TTG), were upregulated in U87MGdeltaEGFR relative to U87MG. Four proteins highly expressed by U87MG cells, Hsp27, major vault protein, TTG, and cystatin B, were analyzed by Western blot, ELISA, or RT-PCR in cell extracts and in tissue samples of glioblastoma multiforme (GBM; grade IV), low-grade astrocytomas (grades I and II), and nonmalignant brain lesions. All four proteins were highly expressed in GBM tissues compared to nonmalignant brain. These proteins may be used as diagnostic or functional (e.g., multiple drug resistance, invasiveness) markers for glioblastoma tumors.

Astrocytes↗

PubMed2001

Identification of the apolipoprotein E4 isoform in cerebrospinal fluid with preparative two-dimensional electrophoresis and matrix assisted laser desorption/ionization-time of flight-mass spectrometry.

Apolipoprotein E (apoE) was isolated from human cerebrospinal fluid (CSF) from control individuals and patients with Alzheimer's disease (AD). The purification was performed with preparative two-dimensional electrophoresis (2-DE), involving liquid-phase isoelectric focusing (IEF) in the Rotofor cell in combination with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and electroelution in the Mini Whole Gel Eluter. ApoE was characterized by matrix-assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) analysis of tryptic digests. The known change of Cys to Arg in position 112 of the apoE4 isoform was identified. This was detected in CSF from AD patients, reflecting the increased frequency of the apoE4 allele in this population. This peptide was not detected in CSF samples from healty control individuals. The use of this rapid electrophoretic separation in proteomic studies of CSF proteins provides single proteins, such as apoE, of high purity in yields sufficient for characterization by MALDI-TOF-MS. Characterization of proteins and their modifications (amino acid substitutions, glycosylation or phosphorylation) in CSF will be a useful tool in the investigation of the pathophysiology of brain disorders such as AD.

Adult↗

PubMed2006

Structure of the catalytic pore of gamma-secretase probed by the accessibility of substituted cysteines.

Several single-span membrane proteins are cleaved within their transmembrane domains (TMDs) by intramembrane-cleaving proteases, although the structure of the active site executing intramembrane cleavage remains unknown. Here we use the substituted cysteine accessibility method to examine the structure of presenilin-1, a catalytic subunit of gamma-secretase, involved in amyloid beta protein generation in Alzheimer's disease and Notch signaling. We show that TMD6 and TMD7 of presenilin-1 contribute to the formation of a hydrophilic pore within the membrane. Residues at the luminal portion of TMD6 are predicted to form a subsite for substrate or inhibitor binding on the alpha-helix facing a hydrophilic milieu, whereas those around the GxGD catalytic motif within TMD7 are highly water accessible, suggesting formation of a hydrophilic structure within the pore. Collectively, our data suggest that the active site of gamma-secretase resides in a catalytic pore filled with water within the lipid bilayer and is tapered around the catalytic aspartates.

Amino Acid Motifs↗

PubMed2003

Gene expression profiling and functional proteomic analysis reveal perturbed kinase-mediated signaling in genetic stroke susceptibility.

The stroke-prone spontaneously hypertensive rat (SHRSP) is a model of heritable hypertension-associated cerebrovascular injury. This study sought to compare SHRSP to the stroke-resistant SHR strain to identify genes and protein pathways whose expression and/or function was significantly altered between the strains prior to the onset of stroke. Cerebral cortex gene expression profiles from male SHRSPs and matched SHRs were examined by Affymetrix microarray analysis. mRNAs encoding the brain-derived neurotrophic factor receptor (TrkB) and multiple kinases of the MAPK/AKT signaling pathways, including JNK2, AKT2, and PI3K, were differentially expressed between SHRSP and SHR. Because these data suggest altered function in pathways involving MAP and AKT kinase activity, we performed Western blot using phosphorylation state-specific antibodies to characterize activity of MAP kinase and PI3K/AKT pathways. Changes in the levels of the phosphorylated forms of these kinases paralleled the changes in transcript levels observed between the strains. Two-dimensional gel electrophoresis and peptide fragment mass fingerprinting were used to identify altered protein substrates of these kinases. Protein profiling of kinase substrates further supported the notion of perturbed kinase-mediated signaling in SHRSP and identified adenylyl cyclase associated protein 2, TOAD-64, propionyl CoA carboxylase, APG-1, and valosin-containing protein as kinase targets whose phosphorylation state is altered between these strains. Altered gene and protein expression patterns in SHRSP are consistent with increased vulnerability of this strain to cerebrovascular injury.

Animals↗

PubMedDate not supplied

Organelle proteomics of rat synaptic proteins: correlation-profiling by isotope-coded affinity tagging in conjunction with liquid chromatography-tandem mass spectrometry to reveal post-synaptic density specific proteins.

Organelle proteomics is the method of choice for global analysis of cellular proteins. However, it is difficult to isolate organelles to homogeneity. Recently, correlation-profiling has been used to filter off the contaminants ad hoc and to disclose the genuine organelle-specific proteins. In the present study, we further extend the method to include subcellular compartments that contain proteins shared by multiple distinct subcellular domains. We performed correlation profiling of proteins contained in synaptic membrane and postsynaptic density (PSD) fractions isolated from rat brain. Proteins were labeled with isotope-coded affinity-tag reagents, digested with trypsin, and resulting peptides were resolved by cation exchange chromatography followed by reversed phase chromatography. Peptides were then subjected to mass spectrometry for quantification and identification. We confirm that the core PSD proteins were enriched in the PSD preparation. Other functional protein groups such as cytoskeleton-associated proteins, protein kinases and phosphatases, signaling components and regulators, as well as proteins involved in energy production partitioned to multiple organelles. When analyzed as groups, they were shown to accumulate to a lesser extent. Mitochondrial proteins and transporters were generally strongly depleted from the PSD fraction confirming that they were contaminants of the PSD preparation. Finally, immunoelectron microscopy was performed on selected proteins to validate the proteomics results, and confirm that synaptophysin that was highly depleted in the PSD preparation is localized in the presynaptic compartment, whereas LASP-1 that was slightly enriched in the PSD preparation is present in the PSD as well as other subdomains within the synapse.

Affinity Labels↗