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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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MicroRNA profiling by high-throughput sequencing in the substantia nigra and striatum of Multiple System Atrophy (MSA) transgenic mice and wild type controls

ABSTRACT: Multiple system atrophy (MSA) is a fatal rapidly progressive Ia-synucleinopathy, characterized by prominent Ia-synuclein accumulation in oligodendrocytes. In this study we investigated miRNA expression in the substantia nigra and striatum of MSA transgenic mice (Tg(Plp1-SNCA)1Haa) and wild type controls. This forms part of a larger study in which we investigated miRNA-mRNA regulatory network in substantia nigra and striatum of MSA transgenic mice in pre-motor stage of neurodegenration.

INSTRUMENT(S): Ion Torrent Proton

ORGANISM(S): Mus musculus

SUBMITTER: Rimpi Khurana

PROVIDER: E-MTAB-3993 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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miRNA microarray analysis of the substantia nigra and stratum in a mouse model of multiple system atrophy

Project description:Multiple system atrophy (MSA) is a fatal rapidly progressive Î±-synucleinopathy, characterized by prominent Î±-synuclein accumulation in oligodendrocytes. In this study we used Exiqon microarrays to investigate micro RNA expression in substantia nigra and striatum of MSA transgenic mice (Tg(Plp1-SNCA)1Haa) and wild type controls. This forms part of a larger study in which we investigated miRNA-mRNA regulatory network in substantia nagra and striatum of MSA transgenic mice in pre-motor stage of neurodegenration.

2016-03-15 | E-MTAB-3986 | biostudies-arrayexpress

mRNA microarray analysis of the substantia nigra in a mouse model of multiple system atrophy

Project description:Multiple system atrophy (MSA) is a fatal rapidly progressive Î±-synucleinopathy, characterized by prominent Î±-synuclein accumulation in oligodendrocytes. In this study we investigated mRNA expression in substantia nigra of MSA transgenic mice (Tg(Plp1-SNCA)1Haa) and wild type controls. This forms part of a larger study in which we investigated miRNA-mRNA regulatory network in substantia nagra and striatum of MSA transgenic mice in pre-motor stage of neurodegenration.

2016-03-15 | E-MTAB-3985 | biostudies-arrayexpress

Glycomic and Proteomic changes in aging brain nigrostriatal pathway

Project description:This study identifies the age related changes in glycan receptors of heparan sulfate (HS) proteoglycan (receptor for rAAV2), and/or N-glycans with terminal galactose (receptor for rAAV9) and proteomics for receptors and co-receptors of adeno-associated virus in the nigro-striatal region of the brain. We analyzed the striatum and substantia nigra for changes in HS, N-glycans and proteomic signatures in young versus aged rat brain nigro-striatum from histological sections. These studies provide insight into age- and brain region-specific changes in glycan receptors and proteomics that will inform design of improved viral vectors for Parkinson’s disease gene therapy.

2018-06-27 | PXD008990 | Pride

Spiked human substantia nigra proteome data set for use as a spectral library for protein modelling and protein mapping

Project description:This article describes a mass spectrometry data set generated from human substantia nigra tissue that was spiked with iRT peptides. The data set can be used as a spectral library for analysis of the human brain, especially human substantia nigra, for example, in the context of Parkinson’s disease. Obtaining a sufficient amount of high-quality substantia nigra tissue is the key limiting factor for establishing a brain region-specific spectral library. Hence, combining existing spectral libraries for data-independent acquisition analysis (DIA) can overcome this major limitation. Moreover, these data can be used to map brain region-specific proteins and to model brain region-specific pathways. Both can improve our understanding of the functioning of the brain in greater depth. In addition, these data can also be used to determine the optimal settings for measuring proteins and peptides of interest. To create the substantia nigra-specific spectral library, the tissue was first homogenized and then fractionated via different types of SDS gel electrophoresis, resulting in 18 fractions. These fractions were analysed in triplicate by nanoHPLC-ESI-MS/MS, resulting in 54 data files.

2019-08-15 | PXD011076 | Pride

Whole Transcriptome Analysis of Substantia Nigra in Mice with MPTP-Induced Parkinsonism Bearing Defective Glucocerebrosidase Activity

Project description:We characterized the transcriptomic profiles of cells from the substantia nigra (SN) of mice with co-injection with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) and selective inhibitor of GCase activity (conduritol-β-epoxide, (CBE)) to mimic PD bearing GCase dysfunction (MPTP+CBE), mice treated with MPTP, mice treated with CBE and control mice treated with injec-tion of sodium chloride (NaCl) (vehicle).

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Time Course of Gene Expression in the Substantia Nigra in Response to Intrastriatal 6-hydroxydopamine in the rat.

Project description:The 6-hydroxydopamine (6OHDA) rat model of parkinsonism is among the first, and most commonly used, animal models of Parkinson’s disease. It provides insight into the compensatory changes that occur in the brain after dopamine (DA) neuron degeneration. In order to better define the consequences of substantia nigra DA neuron loss on the neural and glial populations during and following nigrostriatal degeneration, tissue was collected and evaluated from the substantia nigra of 6OHDA or vehicle treated, or naïve rats at 1, 2, 4, 6 & 16 weeks. Comprehensive gene expression analysis was conducted to detect significant differences in gene expression. Comparisons were conducted within the same treatment groups over time as well as across treatments within the same post-treatment interval. Longitudinal expression patterns were parsed using a k-means clustering algorithm as a method for finding patterns indicative of neuronal loss, upregulation in response to lesion or surgical damage exclusive of lesion. Tissue was collected from the substantia nigra of 6OHDA treated, sham and naïve rats at 1, 2, 4, 6 & 16 weeks post-treatment. A unilateral striatal lesion was employed that results in a 99% striatal DA reduction and an 80% loss of DA neurons in the substantia nigra. 6OHDA lesions were confirmed via catecholamine quantitation by HPLC. RNA integrity was assessed with an Agilent 2100 Bioanalyzer with minimum RIN acceptance criteria of 8.0. Multidimensional plots and Pearson Correlations were used to establish group/treatment homogeneity. Tissue was subjected to comprehensive gene expression analysis using the Affymetrix Rat Gene 1.0ST array.

2014-06-21 | E-GEOD-58710 | biostudies-arrayexpress

Characterization of cerebrospinal fluid via data-independent acquisition mass spectrometry

Project description:Cerebrospinal fluid (CSF) is in direct contact with the brain and serves as a valuable specimen to examine diseases of the central nervous system through analyzing its components. These include the analysis of metabolites, cells as well as proteins. For identifying new suitable diagnostic protein biomarkers bottom-up data-dependent acquisition (DDA) mass spectrometry-based approaches are most popular. Drawbacks of this method are stochastic and irreproducible precursor ion selection. Recently, data-independent acquisition (DIA) emerged as an alternative method. It overcomes several limitations of DDA, since it combines the benefits of DDA and targeted methods like selected reaction monitoring (SRM). We established a DIA method for in-depth proteome analysis of CSF. For this, four spectral libraries were generated with samples from native CSF (n=5) CSF fractionation (15 in total) and substantia nigra fractionation (54 in total) applying to CSF DIA of three replicates. The DDA and DIA methods for CSF were conducted with the same nanoLC parameters using a 180 minute gradient. Compared to a conventional DDA method, our DIA approach both increased the number of identified protein groups with 1574 compared to DDA with 648 over 50 % with a comprehensive spectral library (generated with DDA measurements from five native CSF and 54 substantia nigra fractions) and decreased the coefficient of variation to 6 %, compared to 11 % with a DDA method. We also could show that a sample specific spectral library generated only from native CSF increased the identification reproducibility from three DIA replicates to 90 % (77 % with a DDA method). Moreover, by utilizing a substantia nigra specific spectral library for CSF DIA over 60 brain-originated proteins could be identified compared to only eleven with DDA. In conclusion, the here presented optimized DIA method substantially outperforms DDA and could develop into a powerful tool for biomarker discovery in CSF.

2018-09-17 | PXD010690 | Pride

Proteomic characterization of neuromelanin granules isolated from human substantia nigra by laser-microdissection

Project description:Neuromelanin is a complex polymer pigment found primarily in the dopaminergic neurons of human substantia nigra. Neuromelanin pigment is stored in granules including a protein matrix and lipid droplets. Neuromelanin granules are yet only partially characterised regarding their structure and function. To clarify the exact function of neuromelanin granules in humans, their enrichment and in-depth characterization from human substantia nigra is necessary. Previously published global proteome studies of neuromelanin granules in human substantia nigra required high tissue amounts. Due to the limited availability of human brain tissue we established a new method based on laser microdissection combined with mass spectrometry for the isolation and analysis of neuromelanin granules. With this method it is possible for the first time to isolate a sufficient amount of neuromelanin granules for global proteomics analysis from ten 10 µm tissue sections. In total 1,000 proteins were identified associated with neuromelanin granules. More than 68% of those proteins were also identified in previously performed studies. Our results confirm and further extend previously described findings, supporting the connection of neuromelanin granules to iron homeostasis and lysosomes, respectively endosomes. Hence, this method is suitable for the donor specific enrichment and proteomic analysis of neuromelanin granules.

2016-12-22 | PXD004987 | Pride

Transcription profiling of melanized domamine neurons isolated from male and female patients with Parkinson disease to investigate gender differences

Project description:We used 500 melanized dopamine neurons isolated from post-mortem human substantia nigra pars compacta of each sample with laser capture microdissection. Total RNA was extracted with Arcturus PicoPure RNA extraction kit and amplified two times with Arcturus RiboAmp RNA amplification kit. the samples were then sent to the Partners Center for Genetics and Genomics (HPCGG.org) for labeling, hybridization and scanning according to standard Affymetrix protocols. Samples from a total of 16 human brains, 8 PDs (4 male and 4 female) and 8 controls (4 male and 4 female) were studied. These were selected from available material after screening total RNA extracted from a small region of the SN for integrity of 18S and 28S species using an Agilent bioanalyzer. We also matched the cases for age and post mortem interval (PMI) (PD Female age, 75 ± 4.4, PMI, 20.5 ± 2.5; PD Male age 77 ± 6.3, PMI 13.85 ± 1.7; Con Female age 68 ± 3.3, PMI 21.8 ± 0.8; Con Male age 70.2 ± 6.3, PMI 18.11 ± 3.6). Vital Statistics of the cases used in this study. PD= Parkinson disease, C= Control, F=Female, M=Male: Case Age Sex PMI Cel file Pdf1 81 F 17 459F cf1 61 f <24 515H Pdf2 84 F 24.08 515K cf2 n/a f >48 515I Pdf3 69 F <24 515J cf3 74 f 23.00 459D Pdf4 66 F <24 515F cf4 69 f 20.70 459A pdm1 68 m 17.16 515E Cm1 67 m 22.33 459C pdm2 67 m 14.5 515D Cm2 63 m 21.50 459B pdm3 94 m 9.25 515G Cm3 62 m 21.20 515L pdm4 78 m 14.50 515B Cm4 89 m 7.42 515C

2008-01-19 | E-MEXP-1416 | biostudies-arrayexpress

Transcriptional interaction network analyses in dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra in Parkinson's disease

Project description:We analyzed the transcriptomic profile of post-mortem explants from dorsal nucleus of vagus nerve, locus coeruleus and substantia nigra obtained from controls and Braak 4 (BK4) and 5 (BK5) stages of Parkinson’s disease (PD) patients in order to investigate how gene-gene interaction patterns vary along different anatomical regions in patients and controls. The comparative transcriptional networks analyses indicate that the main hubs in PD networks are related to ubquitin/proteasome, oxidative stress, neuroprotection, neurogenesis and PD associated proteins. Transcriptomic profiles of controls and Parkinson’s disease patients were compared using SAM test for LC or Wilcoxon Mann-Whitney test for SN and VA (p<0.005 and p<0.01, respectively) in order to identify differentially expressed transcripts.

2015-01-11 | E-GEOD-43490 | biostudies-arrayexpress

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