Time Course of Gene Expression in the Substantia Nigra in Response to Intrastriatal 6-hydroxydopamine in the rat.
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ABSTRACT:
ORGANISM(S): Rattus norvegicus
PROVIDER: GSE58710 | GEO | 2014/06/21
SECONDARY ACCESSION(S): PRJNA253211
REPOSITORIES: GEO
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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
Project description:The mesencephalic dopaminergic (mDA) cell system is composed by two major groups of projecting cells in the Substantia Nigra (A9 neurons) and the Ventral Tegmental Area (A10 cells). A9 neurons form the nigrostriatal pathway and are involved in regulating voluntary movements and postural reflexes. Their selective degeneration leads to Parkinson’s disease (PD). We used cDNA microarrays and nanoCAGE technology coupled with Laser Capture Microdissection (LCM) to characterize the intrinsic physiological properties of A9 DA neurons. Surprisingly, we found that these cells express alpha- and beta- chains of haemoglobin. Here we report that globin-immunoreactivity decorates the majority of A9 DA neurons, a subpopulation of cortical and hippocampal astrocytes as well as mature oligodendrocytes. This pattern of expression was confirmed in different mouse strains, in rat and human. This is the first report showing that haemoglobin is expressed in the Substantia Nigra of human post mortem brain. Our data suggest that the most famed oxygen-carrying globin is not exclusively restricted to the blood, but it may play a role in the normal physiology of the brain as well as in neurodegenerative disorders.
2009-08-04 | GSE16192 | GEO
Project description:Genetic variation modulating risk of sporadic Parkinson’s disease (PD) has been primarily explored through genome wide association studies (GWAS). However, like many other common genetic diseases, the impacted genes remain largely unknown. Here, we used single-cell RNA-seq to characterize dopaminergic (DA) neuron populations in the mouse brain at embryonic and early postnatal timepoints. These data facilitated unbiased identification of DA neuron subpopulations through their unique transcriptional profiles, including a novel postnatal neuroblast population and substantia nigra (SN) DA neurons. We use these population-specific data to develop a scoring system to prioritize candidate genes in all 49 GWAS intervals implicated in PD risk, including known PD genes and many with extensive supporting literature. As proof of principle, we confirm that the nigrostriatal pathway is compromised in Cplx1 null mice. Ultimately, this systematic approach establishes biologically pertinent candidates and testable hypotheses for sporadic PD, informing a new era of PD genetic research.
2018-01-31 | GSE108020 | GEO
Project description:Our goal was to develop a list of genes that could be used effectively to highlight the genomic profiling of human embryonic neural stem cells (hENSCs), and to identify genes involved in the process of their differentiation to dopaminergic (DA) neurons. Our results showed that Agilent's Whole Human Genome Oligonucleotide Microarray permits the monitoring of at least 41000 genes as cells differentiate. In this study, we identified 13525 genes to be differentially expressed between undifferentiated hENSC and DA cells isolated from human substansia nigra. Approximately 3737 genes were up-regulated in the embryonic NSC, and 4116 genes were up-regulated in DA cells. Careful analysis of the emerged data using the web-accessible program named Database for Annotation, Visualization and Integrated Discovery (DAVID) has permitted us to distinguish several genes and pathways that are involved in dopaminergic differentiation, and to identify the crucial signaling pathways that direct the process of differentiation. Our study elucidated that genes related to midbrain development, such as Nr4a2 (nuclear receptor subfamily 4, group A, member 2, Nurr1) and En1 (engrailed 1), were increased to 3.76- and 6.41-folds, respectively. In addition, the transcriptions of the genes for DA neuron phenotype, such as Ddc (doapmine decarboxylase, AADC), Slc6a3 (solute carrier family 6, member 3, DAT), and Th (tyrosine hydroxylase), were significantly increased to 8.08, 4.01, and 5.91, respectively. As data accumulate with different populations and different methods of differentiation, one will perhaps be able to identify the key regulators and biomarkers that may allow selective selection of limited number of genes or transcription factors to be used for direct reprogramming of NSC into DA cells, with an ultimate goal of obtaining different types of allogenic neurons including personalized DA neurons to be used in replacement therapy for neurodegenerative diseases such as Parkinson's disease (PD). Two-condition experiment: hENSC S vs. DA cells. Biological replicates: 2 hENSC, and 2 DA neuron samples from human substantia nigra cells.
2011-10-26 | E-GEOD-25931 | biostudies-arrayexpress
Project description:WNT1/beta-catenin signaling plays a crucial role in the generation of mesodiencephalic dopaminergic (mdDA) neurons including the Substantia nigra pars compacta (SNc) subpopulation, whose degeneration is a hallmark of Parkinson’s Disease (PD). However, the precise functions of WNT/beta-catenin signaling in this context remain unknown. Using mutant mice, primary ventral midbrain (VM) cells and pluripotent stem cells (mouse embryonic stem cells and induced pluripotent stem cells), we show that Dickkopf 3 (DKK3), a secreted glycoprotein that modulates WNT/beta-catenin signaling, is specifically required for the correct differentiation of a rostrolateral mdDA precursor subset into SNc DA neurons. Dkk3 transcription in the murine VM coincides with the onset of mdDA neurogenesis and is required for the maintenance of LMX1A and consequently PITX3 expression in rostrolateral mdDA precursors, without affecting the proliferation or specification of their progenitors. Treatment of primary VM cells or differentiating pluripotent stem cells with recombinant WNT1 and/or DKK3 proteins consistently increases the proportion of mdDA cells with SNc DA neuron identity and promotes their survival in vitro. The SNc DA pro-differentiation and pro-survival properties of DKK3, together with its known anti-tumorigenic effect, therefore make it an ideal candidate for the improvement of regenerative and neuroprotective strategies in the treatment of PD.
2015-08-22 | GSE58813 | GEO
Project description:The mesencephalic dopaminergic (mDA) cell system is composed by two major groups of projecting cells in the Substantia Nigra (A9 neurons) and the Ventral Tegmental Area (A10 cells). A9 neurons form the nigrostriatal pathway and are involved in regulating voluntary movements and postural reflexes. Their selective degeneration leads to Parkinsons disease (PD). We used cDNA microarrays and nanoCAGE technology coupled with Laser Capture Microdissection (LCM) to characterize the intrinsic physiological properties of A9 DA neurons. Surprisingly, we found that these cells express alpha- and beta- chains of haemoglobin. Here we report that globin-immunoreactivity decorates the majority of A9 DA neurons, a subpopulation of cortical and hippocampal astrocytes as well as mature oligodendrocytes. This pattern of expression was confirmed in different mouse strains, in rat and human. This is the first report showing that haemoglobin is expressed in the Substantia Nigra of human post mortem brain. Our data suggest that the most famed oxygen-carrying globin is not exclusively restricted to the blood, but it may play a role in the normal physiology of the brain as well as in neurodegenerative disorders. To investigate the biological effects of globin expression, alpha- and beta- chains of mouse hemoglobin were overexpressed in MN9D dopaminergic neuroblastoma cell lines. RNA from 4 replicates each of over-expressing cells and of control samples, for a total of 8 samples, were hybridized on Affymetrix GeneChip Mouse Genome 430A 2.0 Arrays. Hybridization of one of the control samples did not pass quality assessment and the sample was therefore excluded from further analysis.
2010-02-25 | E-GEOD-16192 | biostudies-arrayexpress
Project description:We report RNA sequencing results of human substantia nigra and putamen samples from Parkinson's disease patients and controls. Each substantia nigra sample is the result of pooling brain tissue from two individuals with the same , while each putamen sample is the result of pooling brain tissue from three individuals. We found 354 differentially expressed genes (DEGs) in the SN of PD patients compared to age-matched controls, while we observed 261 DEGs in the putamen samples. The top-enriched pathways from the SN were associated with “protein folding” and “neurotransmitter transport”, and the putamen DEGs with “synapse organization”. In summary, our data confirms the key role of protein folding and neuronal degeneration in the pathology of PD, and highlights new genes and pathways that have not yet been explored in the context of PD.
2020-09-02 | GSE136666 | GEO
Project description:WNT1/beta-catenin signaling plays a crucial role in the generation of mesodiencephalic dopaminergic (mdDA) neurons including the Substantia nigra pars compacta (SNc) subpopulation, whose degeneration is a hallmark of Parkinson’s Disease (PD). However, the precise functions of WNT/beta-catenin signaling in this context remain unknown. Using mutant mice, primary ventral midbrain (VM) cells and pluripotent stem cells (mouse embryonic stem cells and induced pluripotent stem cells), we show that Dickkopf 3 (DKK3), a secreted glycoprotein that modulates WNT/beta-catenin signaling, is specifically required for the correct differentiation of a rostrolateral mdDA precursor subset into SNc DA neurons. Dkk3 transcription in the murine VM coincides with the onset of mdDA neurogenesis and is required for the maintenance of LMX1A and consequently PITX3 expression in rostrolateral mdDA precursors, without affecting the proliferation or specification of their progenitors. Treatment of primary VM cells or differentiating pluripotent stem cells with recombinant WNT1 and/or DKK3 proteins consistently increases the proportion of mdDA cells with SNc DA neuron identity and promotes their survival in vitro. The SNc DA pro-differentiation and pro-survival properties of DKK3, together with its known anti-tumorigenic effect, therefore make it an ideal candidate for the improvement of regenerative and neuroprotective strategies in the treatment of PD. We performed gene expression microarray analysis on iPSC-derived and FACS-sorted GFP-positive Pitx3GFP/+ mdDA neurons, differentiated in the presence or absence of recombinant human WNT1 and recombinant human DKK3. In addition, we analysed primary and FACS-sorted GFP-positive Pitx3+/GFP mdDA neurons isolated from the E13.5 and E14.5 ventral midbrain of Pitx3+/GFP embryos
2015-08-22 | E-GEOD-58813 | biostudies-arrayexpress
Project description:Advances in large-scale proteomics analysis have been very useful in understanding pathogenesis of diseases and elaborating therapeutic strategies. Proteomics has been employed to study Parkinson’s disease (PD), however, sparse studies reported proteome investigation after cell therapy approaches. In this study, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify differentially expressed proteins in a mouse model of PD after cell therapy. Proteins were extracted from five nigrostriatal-related brain regions of mice previously lesioned with 6-hydroxydopamine (6-OHDA) in the substantia nigra (SN). Protein expression was compared in non-grafted brain to 1 and 7 days after intranigral grafting of E12.5 embryonic ventral mesencephalon (VM). We found a total of 277 deregulated proteins after transplantation, which are known to be involved in lipid metabolism, oxidative phosphorylation and PD; thus, confirming that our animal model is similar to human PD and that the presence of grafted cells modulates the expression of these proteins. Notably, 7 proteins were commonly downregulated in all selected brain regions after engraftment, including Acta1, Atp6v1e1, Eci3, Lypla2, Pip4k2a, Sccpdh and Sh3gl2. These are known to be involved in the formation of lipids and recycling of dopamine (DA) vesicle at the synapse. Moreover, intranigral transplantation of VM cells decreased the expression of proteins related to oxidative stress, especially in the nigrostriatal pathway containing the DA grafted neurons. In the same regions, an upregulation of several proteins including alpha-synuclein and tyrosine hydroxylase were observed, whereas expression of tetraspanin 7 was shut down. Overall, these results suggest that intranigral transplantation of VM tissue in an animal model of PD may induce a decrease of oxidative stress in the nigrostriatal pathway and a restoration of the machinery of neurotransmitters, particularly dopamine release to promote DA transmission through a decrease of D2 dopamine receptors endocytosis. Identification of new mechanistic elements involved in the nigrostriatal reconstruction process is a promising approach to enhance the repair of this pathway in PD patients undergoing cell therapy.
2021-03-08 | PXD022193 | Pride
Project description:A hallmark of Parkinson’s disease is the specific degeneration of dopaminergic neurons in the substantia nigra pars compacta. Interestingly, not all of these neurons are equally affected. Studies revealed that neurons located more ventrally within the substantia nigra pars compacta have a higher prevalence to degenerate than those located in the dorsal tier. Reasons for this selective neuronal vulnerability are still unknown. The objective of the present study was to gain a better understanding of molecular differences between these two neuronal subpopulations that can explain the selective neuronal vulnerability within the substantia nigra. For this, both neuronal subpopulations were specifically isolated with laser microdissection. Following, their proteome was analyzed via data independent acquisition mass spectrometry. The results of this study revealed a minor number of proteins that were either specific or differentially expressed in one of the examined neuronal subpopulations within the substantia nigra. These proteins are associated with the cytoskeleton, neuronal plasticity, or calcium homeostasis. With these findings a deeper understanding can be gained of the selective neuronal vulnerability within the substantia nigra and of protective mechanisms against neurodegeneration in specific neuronal subpopulations.
2024-08-09 | PXD037696 | Pride