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Yao Z, Jia F, Wang S, Jiao Q, Du X, Chen X, Jiang H. The involvement of IRP2-induced ferroptosis through the p53-SLC7A11-ALOX12 pathway in Parkinson's disease. Free Radic Biol Med 2024; 222:386-396. [PMID: 38936518 DOI: 10.1016/j.freeradbiomed.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 05/17/2024] [Accepted: 06/24/2024] [Indexed: 06/29/2024]
Abstract
Disturbance in iron homeostasis has been described in Parkinson's disease (PD), in which iron regulatory protein 2 (IRP2) plays a crucial role. IRP2 deletion resulted in the misregulation of iron metabolism and subsequent neurodegeneration. However, growing evidence showed that the levels of IRP2 were increased in the substantia nigra (SN) in MPTP-induced PD mice. To further clarify the role of increased IRP2 in PD, we developed IRP2-overexpressed mice by microinjecting AAV-Ireb2 in the SN. These mice showed decreased motor ability, abnormal gait and anxiety. Iron deposits induced by increased TFR1 and dopaminergic neuronal loss were observed in the SN. When these mice were treated with MPTP, exacerbated dyskinesia and dopaminergic neuronal loss were observed. In addition, TP53 was post-transcriptionally upregulated by IRP2 binding to the iron regulated element (IRE) in its 3' untranslated region. This resulted in increased lipid peroxidation levels and induced ferroptosis through the SLC7A11-ALOX12 pathway, which was independent of GPX4. This study revealed that IRP2 homeostasis in the SN was critical for PD progression and clarified the molecular mechanism of ferroptosis caused by IRP2.
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Affiliation(s)
- Zhengyang Yao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Fengju Jia
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Shuhua Wang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Qian Jiao
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Xixun Du
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Xi Chen
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China
| | - Hong Jiang
- Department of Physiology, Shandong Provincial Key Laboratory of Pathogenesis and Prevention of Neurological Disorders and State Key Disciplines, Physiology, School of Basic Medicine, Qingdao University, Qingdao 266071, China; School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao, 266500, China.
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Kolacheva A, Pavlova E, Bannikova A, Bogdanov V, Ugrumov M. Initial Molecular Mechanisms of the Pathogenesis of Parkinson's Disease in a Mouse Neurotoxic Model of the Earliest Preclinical Stage of This Disease. Int J Mol Sci 2024; 25:1354. [PMID: 38279354 PMCID: PMC10816442 DOI: 10.3390/ijms25021354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/17/2024] [Accepted: 01/18/2024] [Indexed: 01/28/2024] Open
Abstract
Studying the initial molecular mechanisms of the pathogenesis of Parkinson's disease (PD), primarily in the nigrostriatal dopaminergic system, is one of the priorities in neurology. Of particular interest is elucidating these mechanisms in the preclinical stage of PD, which lasts decades before diagnosis and is therefore not available for study in patients. Therefore, our main goal was to study the initial molecular mechanisms of the pathogenesis of PD in the striatum, the key center for dopamine regulation in motor function, in a mouse model of the earliest preclinical stage of PD, from 1 to 24 h after the administration of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). It was shown that the content of tyrosine hydroxylase (TH), the first enzyme in dopamine synthesis, does not change within 6 h after the administration of MPTP, but decreases after 24 h. In turn, TH activity increases after 1 h, decreases after 3 h, remains at the control level after 6 h, and decreases 24 h after the administration of MPTP. The concentration of dopamine in the striatum gradually decreases after MPTP administration, despite a decrease in its degradation. The identified initial molecular mechanisms of PD pathogenesis are considered as potential targets for the development of preventive neuroprotective treatment.
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Affiliation(s)
| | | | | | | | - Michael Ugrumov
- Laboratory of Neural and Neuroendocrine Regulations, Koltzov Institute of Developmental Biology of the Russian Academy of Sciences, 119334 Moscow, Russia; (A.K.); (E.P.); (A.B.); (V.B.)
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Serrano-Martínez I, Pedreño M, Castillo-González J, Ferraz-de-Paula V, Vargas-Rodríguez P, Forte-Lago I, Caro M, Campos-Salinas J, Villadiego J, Peñalver P, Morales JC, Delgado M, González-Rey E. Cortistatin as a Novel Multimodal Therapy for the Treatment of Parkinson's Disease. Int J Mol Sci 2024; 25:694. [PMID: 38255772 PMCID: PMC10815070 DOI: 10.3390/ijms25020694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 12/29/2023] [Accepted: 12/31/2023] [Indexed: 01/24/2024] Open
Abstract
Parkinson's disease (PD) is a complex disorder characterized by the impairment of the dopaminergic nigrostriatal system. PD has duplicated its global burden in the last few years, becoming the leading neurological disability worldwide. Therefore, there is an urgent need to develop innovative approaches that target multifactorial underlying causes to potentially prevent or limit disease progression. Accumulating evidence suggests that neuroinflammatory responses may play a pivotal role in the neurodegenerative processes that occur during the development of PD. Cortistatin is a neuropeptide that has shown potent anti-inflammatory and immunoregulatory effects in preclinical models of autoimmune and neuroinflammatory disorders. The goal of this study was to explore the therapeutic potential of cortistatin in a well-established preclinical mouse model of PD induced by acute exposure to the neurotoxin 1-methil-4-phenyl1-1,2,3,6-tetrahydropyridine (MPTP). We observed that treatment with cortistatin mitigated the MPTP-induced loss of dopaminergic neurons in the substantia nigra and their connections to the striatum. Consequently, cortistatin administration improved the locomotor activity of animals intoxicated with MPTP. In addition, cortistatin diminished the presence and activation of glial cells in the affected brain regions of MPTP-treated mice, reduced the production of immune mediators, and promoted the expression of neurotrophic factors in the striatum. In an in vitro model of PD, treatment with cortistatin also demonstrated a reduction in the cell death of dopaminergic neurons that were exposed to the neurotoxin. Taken together, these findings suggest that cortistatin could emerge as a promising new therapeutic agent that combines anti-inflammatory and neuroprotective properties to regulate the progression of PD at multiple levels.
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Affiliation(s)
- Ignacio Serrano-Martínez
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Marta Pedreño
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Julia Castillo-González
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Viviane Ferraz-de-Paula
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Pablo Vargas-Rodríguez
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Irene Forte-Lago
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Marta Caro
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Jenny Campos-Salinas
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Javier Villadiego
- Institute of Biomedicine of Seville (IBiS), Hospital Universitario Virgen del Rocío, CSIC, Universidad de Sevilla, 41013 Sevilla, Spain;
- Department of Medical Physiology and Biophysics, Faculty of Medicine, University of Seville, 41009 Sevilla, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
| | - Pablo Peñalver
- Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (P.P.); (J.C.M.)
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (P.P.); (J.C.M.)
| | - Mario Delgado
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
| | - Elena González-Rey
- Department of Cell Biology and Immunology, Institute of Parasitology and Biomedicine Lopez-Neyra (IPBLN), CSIC, PT Salud, 18016 Granada, Spain; (I.S.-M.); (M.P.); (J.C.-G.); (V.F.-d.-P.); (P.V.-R.); (I.F.-L.); (M.C.); (J.C.-S.); (M.D.)
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Li L, Ho PWL, Liu H, Pang SYY, Chang EES, Choi ZYK, Malki Y, Kung MHW, Ramsden DB, Ho SL. Transcriptional Regulation of the Synaptic Vesicle Protein Synaptogyrin-3 (SYNGR3) Gene: The Effects of NURR1 on Its Expression. Int J Mol Sci 2022; 23:ijms23073646. [PMID: 35409005 PMCID: PMC8998927 DOI: 10.3390/ijms23073646] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Synaptogyrin-3 (SYNGR3) is a synaptic vesicular membrane protein. Amongst four homologues (SYNGR1 to 4), SYNGR1 and 3 are especially abundant in the brain. SYNGR3 interacts with the dopamine transporter (DAT) to facilitate dopamine (DA) uptake and synaptic DA turnover in dopaminergic transmission. Perturbed SYNGR3 expression is observed in Parkinson’s disease (PD). The regulatory elements which affect SYNGR3 expression are unknown. Nuclear-receptor-related-1 protein (NURR1) can regulate dopaminergic neuronal differentiation and maintenance via binding to NGFI-B response elements (NBRE). We explored whether NURR1 can regulate SYNGR3 expression using an in silico analysis of the 5′-flanking region of the human SYNGR3 gene, reporter gene activity and an electrophoretic mobility shift assay (EMSA) of potential cis-acting sites. In silico analysis of two genomic DNA segments (1870 bp 5′-flanking region and 1870 + 159 bp of first exon) revealed one X Core Promoter Element 1 (XCPE1), two SP1, and three potential non-canonical NBRE response elements (ncNBRE) but no CAAT or TATA box. The longer segment exhibited gene promoter activity in luciferase reporter assays. Site-directed mutagenesis of XCPE1 decreased promoter activity in human neuroblastoma SH-SY5Y (↓43.2%) and human embryonic kidney HEK293 cells (↓39.7%). EMSA demonstrated NURR1 binding to these three ncNBRE. Site-directed mutagenesis of these ncNBRE reduced promoter activity by 11–17% in SH-SY5Y (neuronal) but not in HEK293 (non-neuronal) cells. C-DIM12 (Nurr1 activator) increased SYNGR3 protein expression in SH-SY5Y cells and its promoter activity using a real-time luciferase assay. As perturbed vesicular function is a feature of major neurodegenerative diseases, inducing SYNGR3 expression by NURR1 activators may be a potential therapeutic target to attenuate synaptic dysfunction in PD.
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Affiliation(s)
- Lingfei Li
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Philip Wing-Lok Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Huifang Liu
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Shirley Yin-Yu Pang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Eunice Eun-Seo Chang
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Zoe Yuen-Kiu Choi
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Yasine Malki
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - Michelle Hiu-Wai Kung
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
| | - David Boyer Ramsden
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham B15 2TT, UK
- Correspondence: (D.B.R.); (S.-L.H.)
| | - Shu-Leong Ho
- Division of Neurology, Department of Medicine, University of Hong Kong, Hong Kong SAR, China; (L.L.); (P.W.-L.H.); (H.L.); (S.Y.-Y.P.); (E.E.-S.C.); (Z.Y.-K.C.); (Y.M.); (M.H.-W.K.)
- Correspondence: (D.B.R.); (S.-L.H.)
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Identifying the hub gene and immune infiltration of Parkinson’s disease using bioinformatical methods. Brain Res 2022; 1785:147879. [DOI: 10.1016/j.brainres.2022.147879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/01/2022] [Accepted: 03/07/2022] [Indexed: 11/22/2022]
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Vlasov IN, Alieva AK, Novosadova EV, Arsenyeva EL, Rosinskaya AV, Partevian SA, Grivennikov IA, Shadrina MI. Transcriptome Analysis of Induced Pluripotent Stem Cells and Neuronal Progenitor Cells, Derived from Discordant Monozygotic Twins with Parkinson's Disease. Cells 2021; 10:3478. [PMID: 34943986 PMCID: PMC8700621 DOI: 10.3390/cells10123478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/13/2022] Open
Abstract
Parkinson's Disease (PD) is a widespread severe neurodegenerative disease that is characterized by pronounced deficiency of the dopaminergic system and disruption of the function of other neuromodulator systems. Although heritable genetic factors contribute significantly to PD pathogenesis, only a small percentage of sporadic cases of PD can be explained using known genetic risk factors. Due to that, it could be inferred that changes in gene expression could be important for explaining a significant percentage of PD cases. One of the ways to investigate such changes, while minimizing the effect of genetic factors on experiment, are the study of PD discordant monozygotic twins. In the course of the analysis of transcriptome data obtained from IPSC and NPCs, 20 and 1906 differentially expressed genes were identified respectively. We have observed an overexpression of TNF in NPC cultures, derived from twin with PD. Through investigation of gene interactions and gene involvement in biological processes, we have arrived to a hypothesis that TNF could play a crucial role in PD-related changes occurring in NPC derived from twins with PD, and identified INHBA, WNT7A and DKK1 as possible downstream effectors of TNF.
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Affiliation(s)
- Ivan N. Vlasov
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Anelya Kh. Alieva
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Ekaterina V. Novosadova
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Elena L. Arsenyeva
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Anna V. Rosinskaya
- State Public Health Institution Primorsk Regional Clinical Hospital No. 1, 57 Aleutskaya St., 690091 Vladivostok, Russia;
| | - Suzanna A. Partevian
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Igor A. Grivennikov
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
| | - Maria I. Shadrina
- Institute of Molecular Genetics of National Research Centre, Kurchatov Institute, 2 Kurchatova Sq., 123182 Moscow, Russia; (A.K.A.); (E.V.N.); (E.L.A.); (S.A.P.); (I.A.G.); (M.I.S.)
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Abdik E, Çakır T. Systematic investigation of mouse models of Parkinson's disease by transcriptome mapping on a brain-specific genome-scale metabolic network. Mol Omics 2021; 17:492-502. [PMID: 34370801 DOI: 10.1039/d0mo00135j] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genome-scale metabolic networks enable systemic investigation of metabolic alterations caused by diseases by providing interpretation of omics data. Although Mus musculus (mouse) is one of the most commonly used model organisms for neurodegenerative diseases, a brain-specific metabolic network model of mice has not yet been reconstructed. Here we reconstructed the first brain-specific metabolic network model of mice, iBrain674-Mm, by a homology-based approach, which consisted of 992 reactions controlled by 674 genes and distributed over 48 pathways. We validated the newly reconstructed network model by showing that it predicts healthy resting-state metabolic phenotypes of mouse brain compatible with the literature. We later used iBrain674-Mm to interpret various experimental mouse models of Parkinson's Disease (PD) at the transcriptome level. To this end, we applied a constraint-based modelling based biomarker prediction method called TIMBR (Transcriptionally Inferred Metabolic Biomarker Response) to predict altered metabolite production from transcriptomic data. Systemic analysis of seven different PD mouse models by TIMBR showed that the neuronal levels of glutamate, lactate, creatine phosphate, neuronal acetylcholine, bilirubin and formate increased in most of the PD mouse models, whereas the levels of melatonin, epinephrine, astrocytic formate and astrocytic bilirubin decreased. Although most of the predictions were consistent with the literature, there were some inconsistencies among different PD mouse models, signifying that there is no perfect experimental model to reflect PD metabolism. The newly reconstructed brain-specific genome-scale metabolic network model of mice can make important contributions to the interpretation and development of experimental mouse models of PD and other neurodegenerative diseases.
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Affiliation(s)
- Ecehan Abdik
- Department of Bioengineering, Gebze Technical University, Kocaeli, Turkey.
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Kao CY, Xu M, Wang L, Lin SC, Lee HJ, Duraine L, Bellen HJ, Goldstein DS, Tsai SY, Tsai MJ. Elevated COUP-TFII expression in dopaminergic neurons accelerates the progression of Parkinson's disease through mitochondrial dysfunction. PLoS Genet 2020; 16:e1008868. [PMID: 32579581 PMCID: PMC7340320 DOI: 10.1371/journal.pgen.1008868] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 07/07/2020] [Accepted: 05/18/2020] [Indexed: 11/19/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder featuring progressive loss of midbrain dopaminergic (DA) neurons that leads to motor symptoms. The etiology and pathogenesis of PD are not clear. We found that expression of COUP-TFII, an orphan nuclear receptor, in DA neurons is upregulated in PD patients through the analysis of public datasets. We show here that through epigenetic regulation, COUP-TFII contributes to oxidative stress, suggesting that COUP-TFII may play a role in PD pathogenesis. Elevated COUP-TFII expression specifically in DA neurons evokes DA neuronal loss in mice and accelerates the progression of phenotypes in a PD mouse model, MitoPark. Compared to control mice, those with elevated COUP-TFII expression displayed reduced cristae in mitochondria and enhanced cellular electron-dense vacuoles in the substantia nigra pars compacta. Mechanistically, we found that overexpression of COUP-TFII disturbs mitochondrial pathways, resulting in mitochondrial dysfunction. In particular, there is repressed expression of genes encoding cytosolic aldehyde dehydrogenases, which could enhance oxidative stress and interfere with mitochondrial function via 3,4-dihydroxyphenylacetaldehyde (DOPAL) buildup in DA neurons. Importantly, under-expression of COUP-TFII in DA neurons slowed the deterioration in motor functions of MitoPark mice. Taken together, our results suggest that COUP-TFII may be an important contributor to PD development and a potential therapeutic target.
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Affiliation(s)
- Chung-Yang Kao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mafei Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Leiming Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Molecular Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Physiology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Hui-Ju Lee
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Lita Duraine
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
| | - Hugo J. Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas, United States of America
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas, United States of America
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, United States of America
| | - David S. Goldstein
- Clinical Neurocardiology Section, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sophia Y. Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ming-Jer Tsai
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
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9
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Kakoty V, K C S, Tang RD, Yang CH, Dubey SK, Taliyan R. Fibroblast growth factor 21 and autophagy: A complex interplay in Parkinson disease. Biomed Pharmacother 2020; 127:110145. [PMID: 32361164 DOI: 10.1016/j.biopha.2020.110145] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Revised: 03/27/2020] [Accepted: 04/04/2020] [Indexed: 12/22/2022] Open
Abstract
Parkinson disease (PD) is the second common neurodegenerative disorder after Alzheimer's disease (AD). The predominant pathological hallmark is progressive loss of dopaminergic (DA) neurones in the substantia nigra (SN) complicated by aggregation of misfolded forms of alpha-synuclein (α-syn). α-syn is a cytosolic synaptic protein localized in the presynaptic neuron under normal circumstances. What drives misfolding of this protein is largely unknown. However, recent studies suggest that autophagy might be an important risk factor for contributing towards PD. Autophagy is an evolutionarily conserved mechanism that causes the clearance or degradation of misfolded, mutated and damaged proteins, organelles etc. However, in an aging individual this process might deteriorate which could possibly lead to the accumulation of damaged proteins. Hence, autophagy modulation might provide some interesting cues for the treatment of PD. Additionally, Fibroblast growth factor 21 (FGF21) which is known for its role as a potent regulator of glucose and energy metabolism has also proved to be neuroprotective in various neurodegenerative conditions possibly via mediation of autophagy.
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Affiliation(s)
- Violina Kakoty
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India.
| | - Sarathlal K C
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India.
| | - Ruei-Dun Tang
- Department of Pharmacology, Taipei Medical University, Taipei, Taiwan.
| | - Chih Hao Yang
- Department of Pharmacology, Taipei Medical University, Taipei, Taiwan.
| | - Sunil Kumar Dubey
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India.
| | - Rajeev Taliyan
- Department of Pharmacy, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India.
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10
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Liu H, Huang Y, Li J. Bioinformatic analysis for the identification of key candidate genes and pathways in the substantia nigra in Parkinson's disease. J Integr Neurosci 2018; 17:619-631. [PMID: 30010140 DOI: 10.3233/jin-180091] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease is one of the most common diseases in the elderly population, and the substantia nigra is generally involved in the disease process; however, the signaling pathways and related genes underlying Parkinson's disease remain unclear. This study integrated three cohorts of profile datasets to elucidate the potential key candidate genes and pathways in Parkinson's disease. The expression profiles of GSE8397, GSE20186 and GSE49036 were included 55 available substantia nigra tissue samples from individuals diagnosed with Parkinson's disease and 33 substantia nigra tissue samples from healthy controls. These samples were integrated and thoroughly analyzed. Differentially expressed genes (DEGs) were sorted, and candidate genes and pathway enrichments were analyzed. A DEG-associated protein-protein interaction network analysis was performed. 27 shared downregulated DEGs were identified from the three GSE datasets. The DEGs were clustered based on function and signaling pathway with significant enrichment analysis. 52 edges were identified from the DEG protein-protein interaction network complex, which included dopamine metabolism, nerve conduction, reduced neuronal toxicity and proliferation pathways. Using integrated bioinformatic analysis, we identified candidate genes and pathways in Parkinson's disease that could improve our understanding of underlying molecular events, which could be potential therapeutic targets for Parkinson's disease.
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Affiliation(s)
- Hongbin Liu
- The Department of Internal Neurology, Beijing Geriatric Hospital, Beijing, China
| | - Yongjun Huang
- The Department of Internal Neurology, Beijing Geriatric Hospital, Beijing, China
| | - Jinyi Li
- The Department of Urology, Mount Sinai Hospital, New York, US
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11
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Hunt RJ, Bateman JM. Mitochondrial retrograde signaling in the nervous system. FEBS Lett 2017; 592:663-678. [PMID: 29086414 DOI: 10.1002/1873-3468.12890] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 01/12/2023]
Abstract
Mitochondria generate the majority of cellular ATP and are essential for neuronal function. Loss of mitochondrial activity leads to primary mitochondrial diseases and may contribute to neurodegenerative diseases such as Alzheimer's and Parkinson's disease. Mitochondria communicate with the cell through mitochondrial retrograde signaling pathways. These signaling pathways are triggered by mitochondrial dysfunction and allow the organelle to control nuclear gene transcription. Neuronal mitochondrial retrograde signaling pathways have been identified in disease model systems and targeted to restore neuronal function and prevent neurodegeneration. In this review, we describe yeast and mammalian cellular models that have paved the way in the investigation of mitochondrial retrograde mechanisms. We then discuss the evidence for retrograde signaling in neurons and our current knowledge of retrograde signaling mechanisms in neuronal model systems. We argue that targeting mitochondrial retrograde pathways has the potential to lead to novel treatments for neurological diseases.
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Affiliation(s)
- Rachel J Hunt
- Wolfson Centre for Age-Related Diseases, King's College London, UK
| | - Joseph M Bateman
- Wolfson Centre for Age-Related Diseases, King's College London, UK
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12
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Oerton E, Bender A. Concordance analysis of microarray studies identifies representative gene expression changes in Parkinson's disease: a comparison of 33 human and animal studies. BMC Neurol 2017; 17:58. [PMID: 28335819 PMCID: PMC5364698 DOI: 10.1186/s12883-017-0838-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/13/2017] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND As the popularity of transcriptomic analysis has grown, the reported lack of concordance between different studies of the same condition has become a growing concern, raising questions as to the representativeness of different study types, such as non-human disease models or studies of surrogate tissues, to gene expression in the human condition. METHODS In a comparison of 33 microarray studies of Parkinson's disease, correlation and clustering analyses were used to determine the factors influencing concordance between studies, including agreement between different tissue types, different microarray platforms, and between neurotoxic and genetic disease models and human Parkinson's disease. RESULTS Concordance over all studies is low, with correlation of only 0.05 between differential gene expression signatures on average, but increases within human patients and studies of the same tissue type, rising to 0.38 for studies of human substantia nigra. Agreement of animal models, however, is dependent on model type. Studies of brain tissue from Parkinson's disease patients (specifically the substantia nigra) form a distinct group, showing patterns of differential gene expression noticeably different from that in non-brain tissues and animal models of Parkinson's disease; while comparison with other brain diseases (Alzheimer's disease and brain cancer) suggests that the mixed study types display a general signal of neurodegenerative disease. A meta-analysis of these 33 microarray studies demonstrates the greater ability of studies in humans and highly-affected tissues to identify genes previously known to be associated with Parkinson's disease. CONCLUSIONS The observed clustering and concordance results suggest the existence of a 'characteristic' signal of Parkinson's disease found in significantly affected human tissues in humans. These results help to account for the consistency (or lack thereof) so far observed in microarray studies of Parkinson's disease, and act as a guide to the selection of transcriptomic studies most representative of the underlying gene expression changes in the human disease.
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Affiliation(s)
- Erin Oerton
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Andreas Bender
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Cambridge, UK.
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13
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Mingazov ER, Ugrumov MV. Gene expression of proteins of the vesicle cycle in the striatum and motor cortex under functional failure of nigrostriatal system. DOKL BIOCHEM BIOPHYS 2016; 470:313-315. [PMID: 27817030 DOI: 10.1134/s160767291605001x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 11/23/2022]
Abstract
Degeneration of dopaminergic neurons in the substantia nigra and the decrease in the dopamine level in the striatum lead to dysfunctions of motor behavior. This is accompanied by dysregulation of neuro-transmission in glutamatergic neurons of the motor cortex and GABA-ergic neurons of the striatum. It is shown that dysregulation of the gene expression of vesicle cycle proteins in neurons of the motor cortex occurs at an early (presymptomatic) stage of degeneration of the nigrostriatal system, and in more severe degeneration (symptomatic stage) the level of gene expression of vesicle cycle proteins in the striatum decreases.
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Affiliation(s)
- E R Mingazov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334, Russia.
| | - M V Ugrumov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334, Russia
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14
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Selenotranscriptomic Analyses Identify Signature Selenoproteins in Brain Regions in a Mouse Model of Parkinson's Disease. PLoS One 2016; 11:e0163372. [PMID: 27656880 PMCID: PMC5033372 DOI: 10.1371/journal.pone.0163372] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/06/2016] [Indexed: 01/22/2023] Open
Abstract
Genes of selenoproteome have been increasingly implicated in various aspects of neurobiology and neurological disorders, but remain largely elusive in Parkinson’s disease (PD). In this study, we investigated the selenotranscriptome (24 selenoproteins in total) in five brain regions (cerebellum, substantia nigra, cortex, pons and hippocampus) by real time qPCR in a two-phase manner using a mouse model of chronic PD. A wide range of changes in selenotranscriptome was observed in a manner depending on selenoproteins and brain regions. While Selv mRNA was not detectable and Dio1& 3 mRNA levels were not affected, 1, 11 and 9 selenoproteins displayed patterns of increase only, decrease only, and mixed response, respectively, in these brain regions of PD mice. In particular, the mRNA expression of Gpx1-4 showed only a decreased trend in the PD mouse brains. In substantia nigra, levels of 17 selenoprotein mRNAs were significantly decreased whereas no selenoprotein was up-regulated in the PD mice. In contrast, the majority of selenotranscriptome did not change and a few selenoprotein mRNAs that respond displayed a mixed pattern of up- and down-regulation in cerebellum, cortex, hippocampus, and/or pons of the PD mice. Gpx4, Sep15, Selm, Sepw1, and Sepp1 mRNAs were most abundant across all these five brain regions. Our results showed differential responses of selenoproteins in various brain regions of the PD mouse model, providing critical selenotranscriptomic profiling for future functional investigation of individual selenoprotein in PD etiology.
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15
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Qi X, Davis B, Chiang YH, Filichia E, Barnett A, Greig NH, Hoffer B, Luo Y. Dopaminergic neuron-specific deletion of p53 gene is neuroprotective in an experimental Parkinson's disease model. J Neurochem 2016; 138:746-57. [PMID: 27317935 DOI: 10.1111/jnc.13706] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 01/06/2023]
Abstract
p53, a stress response gene, is involved in diverse cell death pathways and its activation has been implicated in the pathogenesis of Parkinson's disease (PD). However, whether the neuronal p53 protein plays a direct role in regulating dopaminergic (DA) neuronal cell death is unknown. In this study, in contrast to the global inhibition of p53 function by pharmacological inhibitors and in traditional p53 knock-out (KO) mice, we examined the effect of DA specific p53 gene deletion in DAT-p53KO mice. These DAT-p53KO mice did not exhibit apparent changes in the general structure and neuronal density of DA neurons during late development and in aging. However, in DA-p53KO mice treated with the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), we found that the induction of Bax and p53 up-regulated modulator of apoptosis (PUMA) mRNA and protein levels by MPTP were diminished in both striatum and substantia nigra of these mice. Notably, deletion of the p53 gene in DA neurons significantly reduced dopaminergic neuronal loss in substantia nigra, dopaminergic neuronal terminal loss at striatum and, additionally, decreased motor deficits in mice challenged with MPTP. In contrast, there was no difference in astrogliosis between WT and DAT-p53KO mice in response to MPTP treatment. These findings demonstrate a specific contribution of p53 activation in DA neuronal cell death by MPTP challenge. Our results further support the role of programmed cell death mediated by p53 in this animal model of PD and identify Bax, BAD and PUMA genes as downstream targets of p53 in modulating DA neuronal death in the in vivo MPTP-induced PD model. We deleted p53 gene in dopaminergic neurons in late developmental stages and found that DA specific p53 deletion is protective in acute MPTP animal model possibly through blocking MPTP-induced BAX and PUMA up-regulation. Astrocyte activation measured by GFAP positive cells and GFAP gene up-regulation in the striatum shows no difference between wt and DA-p53 ko mice.
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Affiliation(s)
- Xin Qi
- Department of Physiology & Biophysics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Brandon Davis
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yung-Hsiao Chiang
- Division of Neurosurgery, Department of Surgery, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Emily Filichia
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
| | - Austin Barnett
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute of Aging, Baltimore, Maryland, USA
| | - Barry Hoffer
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
| | - Yu Luo
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio, USA
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16
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Mingazov ER, Ugrumov MV. Gene expression of proteins of the vesicle cycle in dopaminergic neurons in modeling of Parkinson's disease. DOKL BIOCHEM BIOPHYS 2016; 468:206-8. [PMID: 27417722 DOI: 10.1134/s1607672916030133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Indexed: 11/22/2022]
Abstract
It is assumed that one of the causes of the degeneration of dopaminergic neurons is the dysregulation of the vesicle cycle, which is ensured by a number of proteins including syntaxin I, synaptotagmin I, complexins I and II, and Rab5. It was shown that there is a compensatory increase in gene expression of proteins responsible for exocytosis at the preclinical stage of Parkinson's disease (PD) in the in substantia nigra (SN) in mice. Conversely, in the model of the clinical stage of PD, the decreases of gene expression of proteins responsible for exocytosis, endocytosis, and neuronal survival, which may be among the triggers of motor dysfunctions.
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Affiliation(s)
- E R Mingazov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334, Russia.
| | - M V Ugrumov
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, ul. Vavilova 26, Moscow, 119334, Russia
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17
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Gene dysregulation is restored in the Parkinson's disease MPTP neurotoxic mice model upon treatment of the therapeutic drug Cu(II)(atsm). Sci Rep 2016; 6:22398. [PMID: 26928495 PMCID: PMC4772163 DOI: 10.1038/srep22398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 02/15/2016] [Indexed: 12/04/2022] Open
Abstract
The administration of MPTP selectively targets the dopaminergic system resulting in Parkinsonism-like symptoms and is commonly used as a mice model of Parkinson’s disease. We previously demonstrated that the neuroprotective compound CuII(atsm) rescues nigral cell loss and improves dopamine metabolism in the MPTP model. The mechanism of action of CuII(atsm) needs to be further defined to understand how the compound promotes neuronal survival. Whole genome transcriptomic profiling has become a popular method to examine the relationship between gene expression and function. Substantia nigra samples from MPTP-lesioned mice were evaluated using whole transcriptome sequencing to investigate the genes altered upon CuII(atsm) treatment. We identified 143 genes affected by MPTP lesioning that are associated with biological processes related to brain and cognitive development, dopamine synthesis and perturbed synaptic neurotransmission. Upon CuII(atsm) treatment, the expression of 40 genes involved in promoting dopamine synthesis, calcium signaling and synaptic plasticity were restored which were validated by qRT-PCR. The study provides the first detailed whole transcriptomic analysis of pathways involved in MPTP-induced Parkinsonism. In addition, we identify key therapeutic pathways targeted by a potentially new class of neuroprotective agents which may provide therapeutic benefits for other neurodegenerative disorders.
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18
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Sauer JM, Kleensang A, Peitsch MC, Hayes AW. Advancing Risk Assessment through the Application of Systems Toxicology. Toxicol Res 2016; 32:5-8. [PMID: 26977253 PMCID: PMC4780234 DOI: 10.5487/tr.2016.32.1.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 01/12/2016] [Accepted: 01/13/2016] [Indexed: 11/20/2022] Open
Abstract
Risk assessment is the process of quantifying the probability of a harmful effect to individuals or populations from human activities. Mechanistic approaches to risk assessment have been generally referred to as systems toxicology. Systems toxicology makes use of advanced analytical and computational tools to integrate classical toxicology and quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Three presentations including two case studies involving both in vitro and in vivo approaches described the current state of systems toxicology and the potential for its future application in chemical risk assessment.
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Affiliation(s)
- John Michael Sauer
- Predictive Safety Testing Consortium, Critical Path Institute, Tucson, AZ, USA
| | - André Kleensang
- Johns Hopkins University, Center for Alternatives to Animal Testing (CAAT), Bloomberg School of Public Health, Baltimore, MD USA
| | | | - A Wallace Hayes
- Harvard University and Michigan State University Institute for Integrative Toxicology, Andover, MA 01810
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19
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Ding H, Underwood R, Lavalley N, Yacoubian TA. 14-3-3 inhibition promotes dopaminergic neuron loss and 14-3-3θ overexpression promotes recovery in the MPTP mouse model of Parkinson's disease. Neuroscience 2015; 307:73-82. [PMID: 26314634 DOI: 10.1016/j.neuroscience.2015.08.042] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 07/25/2015] [Accepted: 08/18/2015] [Indexed: 01/15/2023]
Abstract
14-3-3s are a highly conserved protein family that plays important roles in cell survival and interact with several proteins implicated in Parkinson's disease (PD). Disruption of 14-3-3 expression and function has been implicated in the pathogenesis of PD. We have previously shown that increasing the expression level of 14-3-3θ is protective against rotenone and 1-methyl-4-phenylpyridinium (MPP(+)) in cultured cells. Here, we extend our studies to examine the effects of 14-3-3s in the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of PD. We first investigated whether targeted nigral 14-3-3θ overexpression mediated by adeno-associated virus offers neuroprotection against MPTP-induced toxicity. 14-3-3θ overexpression using this approach did not reduce MPTP-induced dopaminergic cell loss in the substantia nigra nor the depletion of dopamine (DA) and its metabolites in the striatum at three weeks after MPTP administration. However, 14-3-3θ-overexpressing mice showed a later partial recovery in striatal DA metabolites at eight weeks after MPTP administration compared to controls, suggesting that 14-3-3θ overexpression may help in the functional recovery of those dopaminergic neurons that survive. Conversely, we investigated whether disrupting 14-3-3 function in transgenic mice expressing the pan 14-3-3 inhibitor difopein exacerbates MPTP-induced toxicity. We found that difopein expression promoted dopaminergic cell loss in response to MPTP treatment. Together, these findings suggest that 14-3-3θ overexpression promotes recovery of DA metabolites whereas 14-3-3 inhibition exacerbates neuron loss in the MPTP mouse model of PD.
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Affiliation(s)
- H Ding
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, USA
| | - R Underwood
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, USA
| | - N Lavalley
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, USA
| | - T A Yacoubian
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, USA.
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20
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Rahnenführer J, Leist M. From smoking guns to footprints: mining for critical events of toxicity pathways in transcriptome data. Arch Toxicol 2015; 89:813-7. [PMID: 25851820 PMCID: PMC4396704 DOI: 10.1007/s00204-015-1497-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Accepted: 02/25/2015] [Indexed: 12/23/2022]
Affiliation(s)
| | - Marcel Leist
- Doerenakmp-Zbinden Chair for In Vitro Toxicology and Biomedicine, University of Konstanz, PO Box M657, 78457 Konstanz, Germany
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21
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Maertens A, Luechtefeld T, Kleensang A, Hartung T. MPTP's pathway of toxicity indicates central role of transcription factor SP1. Arch Toxicol 2015; 89:743-55. [PMID: 25851821 DOI: 10.1007/s00204-015-1509-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 03/16/2015] [Indexed: 01/15/2023]
Abstract
Deriving a Pathway of Toxicity from transcriptomic data remains a challenging task. We explore the use of weighted gene correlation network analysis (WGCNA) to extract an initial network from a small microarray study of MPTP toxicity in mice. Five modules were statistically significant; each module was analyzed for gene signatures in the Chemical and Genetic Perturbation subset of the Molecular Signatures Database as well as for over-represented transcription factor binding sites and WGCNA clustered probes by function and captured pathways relevant to neurodegenerative disorders. The resulting network was analyzed for transcription factor candidates, which were narrowed down via text-mining for relevance to the disease model, and then combined with the large-scale interaction FANTOM4 database to generate a genetic regulatory network. Modules were enriched for transcription factors relevant to Parkinson's disease. Transcription factors significantly improved the number of genes that could be connected in a given component. For each module, the transcription factor that had, by far, the highest number of interactions was SP1, and it also had substantial experimental evidence of interactions. This analysis both captures much of the known biology of MPTP toxicity and suggests several candidates for further study. Furthermore, the analysis strongly suggests that SP1 plays a central role in coordinating the cellular response to MPTP toxicity.
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Affiliation(s)
- Alexandra Maertens
- Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
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22
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Developing tools for defining and establishing pathways of toxicity. Arch Toxicol 2015; 89:809-12. [PMID: 25851822 PMCID: PMC4396705 DOI: 10.1007/s00204-015-1512-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 03/19/2015] [Indexed: 11/21/2022]
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23
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Carrieri C, Forrest ARR, Santoro C, Persichetti F, Carninci P, Zucchelli S, Gustincich S. Expression analysis of the long non-coding RNA antisense to Uchl1 (AS Uchl1) during dopaminergic cells' differentiation in vitro and in neurochemical models of Parkinson's disease. Front Cell Neurosci 2015; 9:114. [PMID: 25883552 PMCID: PMC4381646 DOI: 10.3389/fncel.2015.00114] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 03/12/2015] [Indexed: 01/04/2023] Open
Abstract
Antisense (AS) transcripts are RNA molecules that are transcribed from the opposite strand to sense (S) genes forming S/AS pairs. The most prominent configuration is when a lncRNA is antisense to a protein coding gene. Increasing evidences prove that antisense transcription may control sense gene expression acting at distinct regulatory levels. However, its contribution to brain function and neurodegenerative diseases remains unclear. We have recently identified AS Uchl1 as an antisense to the mouse Ubiquitin carboxy-terminal hydrolase L1 (Uchl1) gene (AS Uchl1), the synthenic locus of UCHL1/PARK5. This is mutated in rare cases of early-onset familial Parkinson's Disease (PD) and loss of UCHL1 activity has been reported in many neurodegenerative diseases. Importantly, manipulation of UchL1 expression has been proposed as tool for therapeutic intervention. AS Uchl1 induces UchL1 expression by increasing its translation. It is the representative member of SINEUPs (SINEB2 sequence to UP-regulate translation), a new functional class of natural antisense lncRNAs that activate translation of their sense genes. Here we take advantage of FANTOM5 dataset to identify the transcription start sites associated to S/AS pair at Uchl1 locus. We show that AS Uchl1 expression is under the regulation of Nurr1, a major transcription factor involved in dopaminergic cells' differentiation and maintenance. Furthermore, AS Uch1 RNA levels are strongly down-regulated in neurochemical models of PD in vitro and in vivo. This work positions AS Uchl1 RNA as a component of Nurr1-dependent gene network and target of cellular stress extending our understanding on the role of antisense transcription in the brain.
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Affiliation(s)
- Claudia Carrieri
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
| | - Alistair R R Forrest
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Claudio Santoro
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Francesca Persichetti
- Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Piero Carninci
- Division of Genomic Technologies, RIKEN Center for Life Science Technologies Yokohama, Japan
| | - Silvia Zucchelli
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy ; Dipartimento di Scienze della Salute, Universita' del Piemonte Orientale Novara, Italy
| | - Stefano Gustincich
- Area of Neuroscience, International School for Advanced Studies (SISSA) Trieste, Italy
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Method designed to respect molecular heterogeneity can profoundly correct present data interpretations for genome-wide expression analysis. PLoS One 2015; 10:e0121154. [PMID: 25793610 PMCID: PMC4368820 DOI: 10.1371/journal.pone.0121154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/20/2015] [Indexed: 11/27/2022] Open
Abstract
Although genome-wide expression analysis has become a routine tool for gaining insight into molecular mechanisms, extraction of information remains a major challenge. It has been unclear why standard statistical methods, such as the t-test and ANOVA, often lead to low levels of reproducibility, how likely applying fold-change cutoffs to enhance reproducibility is to miss key signals, and how adversely using such methods has affected data interpretations. We broadly examined expression data to investigate the reproducibility problem and discovered that molecular heterogeneity, a biological property of genetically different samples, has been improperly handled by the statistical methods. Here we give a mathematical description of the discovery and report the development of a statistical method, named HTA, for better handling molecular heterogeneity. We broadly demonstrate the improved sensitivity and specificity of HTA over the conventional methods and show that using fold-change cutoffs has lost much information. We illustrate the especial usefulness of HTA for heterogeneous diseases, by applying it to existing data sets of schizophrenia, bipolar disorder and Parkinson’s disease, and show it can abundantly and reproducibly uncover disease signatures not previously detectable. Based on 156 biological data sets, we estimate that the methodological issue has affected over 96% of expression studies and that HTA can profoundly correct 86% of the affected data interpretations. The methodological advancement can better facilitate systems understandings of biological processes, render biological inferences that are more reliable than they have hitherto been and engender translational medical applications, such as identifying diagnostic biomarkers and drug prediction, which are more robust.
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Validity of the MPTP-Treated Mouse as a Model for Parkinson's Disease. Mol Neurobiol 2015; 53:1625-1636. [PMID: 25676140 PMCID: PMC4789200 DOI: 10.1007/s12035-015-9103-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 01/15/2015] [Indexed: 11/03/2022]
Abstract
Parkinson's disease (PD) is characterized by dopaminergic (DA) neuron death in the substantia nigra (SN) and subsequent striatal adaptations. Mice treated with the neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyrimidine (MPTP) are widely used as a model for PD. To assess the validity of the MPTP mouse model for PD pathogenesis, we here identify the biological processes that are dysregulated in both human PD and MPTP-treated mice. Gene enrichment analysis of published differentially expressed messenger RNAs (mRNAs) in the SN of PD patients and MPTP-treated mice revealed an enrichment of gene categories related to motor dysfunction and neurodegeneration. In the PD striatum, a similar enrichment was found, whereas in the striatum of MPTP mice, acute processes linked to epilepsy were selectively enriched shortly following MPTP treatment. More importantly, we integrated the proteins encoded by the differentially expressed mRNAs into molecular landscapes showing PD pathogenesis-implicated processes only in the SN, including vesicular trafficking, exocytosis, mitochondrial apoptosis, and DA neuron-specific transcription, but not in the striatum. We conclude that the current use of the MPTP mouse as a model for studying the molecular processes in PD pathogenesis is more valid for SN than striatal mechanisms in PD. This novel insight has important practical implications for future studies using this model to investigate PD pathogenesis and evaluate the efficacy of new treatments.
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Selvakumar GP, Janakiraman U, Essa MM, Justin Thenmozhi A, Manivasagam T. Escin attenuates behavioral impairments, oxidative stress and inflammation in a chronic MPTP/probenecid mouse model of Parkinson's disease. Brain Res 2014; 1585:23-36. [PMID: 24657313 DOI: 10.1016/j.brainres.2014.03.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 01/24/2014] [Accepted: 03/07/2014] [Indexed: 11/17/2022]
Abstract
Parkinson's disease (PD) is a progressive neurodegenerative disorder that results mainly due to the death of dopaminergic neurons in the substantia nigra (SN), and subsequently has an effect on one's motor function and coordination. The current investigation explored the neuroprotective potential of escin, a natural triterpene-saponin on chronic 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine/probenecid (MPTP/p) induced mouse model of PD. Administration of MPTP led to the depleted striatal dopamine content, impaired patterns of behavior, enhanced oxidative stress and diminished expression of tyrosine hydroxylase (TH), dopamine transporter (DAT) and vesicular monoamine transporter-2 (VMAT-2). The expressions of interleukin-6 and -10, glial fibrillary acidic protein (GFAP), ionized calcium-binding adaptor protein-1 (IBA-1), tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase (iNOS) in SN were also enhanced. Oral treatment of escin significantly attenuated MPTP/p induced dopaminergic markers depletion, physiological abnormalities, oxidative stress and inhibit neuroinflammatory cytokine expressions in SN. The result of our study confirmed that escin mediated its protection against experimental PD through its antioxidant and anti-inflammatory properties.
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Affiliation(s)
| | - Udaiyappan Janakiraman
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar 608002, Tamilnadu, India
| | - Musthafa Mohamed Essa
- Department of Food Science and Nutrition, CAMS, Sultan Qaboos University, Muscat, Oman
| | | | - Thamilarasan Manivasagam
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalainagar 608002, Tamilnadu, India.
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Ding H, Fineberg NS, Gray M, Yacoubian TA. α-Synuclein overexpression represses 14-3-3θ transcription. J Mol Neurosci 2013; 51:1000-9. [PMID: 23912650 DOI: 10.1007/s12031-013-0086-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 07/25/2013] [Indexed: 10/26/2022]
Abstract
Previous gene microarray studies have shown that expression of 14-3-3θ is significantly decreased in an α-synuclein transgenic mouse model. In this study, we tested whether α-synuclein can regulate 14-3-3θ transcription. We demonstrate that the 14-3-3θ mRNA level is decreased in SH-SY5Y cells overexpressing α-synuclein. Luciferase activity under the control of the 14-3-3θ promoter is reduced both in stable SH-SY5Y cells constitutively overexpressing α-synuclein and in doxycycline-inducible SH-SY5Y cells upon α-synuclein induction, suggesting that the regulation of 14-3-3θ by α-synuclein occurs at the transcriptional level. Knockdown of α-synuclein by RNA interference does not increase the 14-3-3θ mRNA level. These findings suggest that α-synuclein represses 14-3-3θ transcription under pathologic conditions, but that regulation of 14-3-3θ expression is not a function of endogenous α-synuclein at baseline.
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Affiliation(s)
- Huiping Ding
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Civitan International Research Center 560D, 1719 6th Avenue South, Birmingham, AL, 35294, USA
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Kelmansky DM. Where statistics and molecular microarray experiments biology meet. Methods Mol Biol 2013; 972:15-35. [PMID: 23385529 DOI: 10.1007/978-1-60327-337-4_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This review chapter presents a statistical point of view to microarray experiments with the purpose of understanding the apparent contradictions that often appear in relation to their results. We give a brief introduction of molecular biology for nonspecialists. We describe microarray experiments from their construction and the biological principles the experiments rely on, to data acquisition and analysis. The role of epidemiological approaches and sample size considerations are also discussed.
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Affiliation(s)
- Diana M Kelmansky
- Instituto de Cálculo, Ciudad Universitaria, Buenos Aires, Argentina.
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Ginkgo biloba extract (EGb 761) modulates the expression of dopamine-related genes in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced Parkinsonism in mice. Neuroscience 2012; 223:246-57. [PMID: 22885234 DOI: 10.1016/j.neuroscience.2012.08.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 07/31/2012] [Accepted: 08/01/2012] [Indexed: 02/07/2023]
Abstract
1-Methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) causes nigrostriatal dopaminergic neurotoxicity and behavioral impairment in rodents similar to Parkinson's disease. The MPTP mouse model is widely used to evaluate new protective agents. EGb 761 is a well-defined mixture of active compounds extracted from Ginkgo biloba leaves according to a standardized procedure. We have shown that EGb 761 attenuates the loss of striatal dopamine levels and prevents the neurodegeneration of the nigrostriatal pathway induced by MPTP. This finding shows that neuroprotective effects of EGb 761 act, in part, on the dopamine system. Therefore, this study investigates whether EGb 761 exerts dopaminergic neuroprotection through the regulation of dopamine-related gene expression in MPTP-induced Parkinsonism. Male C57BL/6J mice were injected with MPTP (30 mg/kg, i.p.) for 5 days and later with EGb 761 (40 mg/kg, i.p.) daily for 18 days. The expression of selected genes was evaluated in the striatum and midbrain by quantitative PCR. The genes for tyrosine hydroxylase (Th), vesicular monoamine transporter 2 (Vmat2), dopamine transporter (Dat), dopamine D2 receptor (Da-d2r), and transcription factors (Pitx3 and Nurr1) related to dopamine neurotransmission were selected for the analysis. EGb 761 administration to MPTP-treated mice protected Th (41%), Vmat2 (15%), Dat (102%), Da-d2r (46%), Pitx3 (63%), and Nurr1 (148%) mRNA levels in the midbrain, all of which were up-regulated. However, EGb 761 partially reversed the MPTP effect exclusively for Th (48%) and Nurr1 (96%) mRNA in the striatum. Only Th and Nurr1 mRNA and protein levels were regulated by EGb 761 in both regions of the nigrostriatal pathway. This result could be related to the regulation of their transcription. Our results suggest that EGb 761-associated neuroprotection against MPTP neurotoxicity is related to the regulation of the dopamine genes. Moreover, this neuroprotection also involves the regulation of transcription factors such as Nurr1 that are important for the functional maintenance of dopaminergic neurons.
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LICAMELE LOUIS, GETOOR LISE. A METHOD FOR THE DETECTION OF MEANINGFUL AND REPRODUCIBLE GROUP SIGNATURES FROM GENE EXPRESSION PROFILES. J Bioinform Comput Biol 2011; 9:431-51. [DOI: 10.1142/s0219720011005598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 04/11/2011] [Accepted: 04/18/2011] [Indexed: 11/18/2022]
Abstract
Gene expression microarrays are commonly used to detect the biological signature of a disease or to gain a better understanding of the underlying mechanism of how a group of drugs treat a specific disease. The outcome of such experiments, e.g. the signature, is a list of differentially expressed genes. Reproducibility across independent experiments remains a challenge. We are interested in creating a method that can detect the shared signature of a group of expression profiles, e.g. a group of samples from individuals with the same disease or a group of drugs that treat the same therapeutic indication. We have developed a novel Weighted Influence — Rank of Ranks (WIMRR) method, and we demonstrate its ability to produce both meaningful and reproducible group signatures.
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Affiliation(s)
- LOUIS LICAMELE
- Computer Science Department, University of Maryland, AV Williams Bldg, Rm 3228, College Park, Maryland 20742, USA
- Informatics Department, Vanda Pharmaceuticals Inc, 9605 Medical Center Drive, Suite 300, Rockville, Maryland 20850, USA
| | - LISE GETOOR
- Computer Science Department, University of Maryland, AV Williams Bldg, Rm 3228, College Park, Maryland 20742, USA
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Benmoyal-Segal L, Soreq L, Ben-Shaul Y, Ben-Ari S, Ben-Moshe T, Aviel S, Bergman H, Soreq H. Adaptive alternative splicing correlates with less environmental risk of parkinsonism. NEURODEGENER DIS 2011; 9:87-98. [PMID: 22042332 DOI: 10.1159/000331328] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2011] [Accepted: 07/27/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND/OBJECTIVE Environmental exposure to anti-acetylcholinesterases (AChEs) aggravates the risk of Parkinsonism due to currently unclear mechanism(s). We explored the possibility that the brain's capacity to induce a widespread adaptive alternative splicing response to such exposure may be involved. METHODS Following exposure to the dopaminergic neurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP), brain region transcriptome profiles were tested. RESULTS Changes in transcript profiles, alternative splicing patterns and splicing-related gene categories were identified. Engineered mice over-expressing the protective AChE-R splice variant showed less total changes but more splicing-related ones than hypersensitive AChE-S over-expressors with similarly increased hydrolytic activities. Following MPTP exposure, the substantia nigra and prefrontal cortex (PFC) of both strains showed a nuclear increase in the splicing factor ASF/SF2 protein. Furthermore, intravenous injection with highly purified recombinant human AChE-R changed transcript profiles in the striatum. CONCLUSIONS Our findings are compatible with the working hypothesis that inherited or acquired alternative splicing deficits may promote parkinsonism, and we propose adaptive alternative splicing as a strategy for attenuating its progression.
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Affiliation(s)
- Liat Benmoyal-Segal
- Department of Biological Chemistry, Life Sciences Institute, Hebrew University of Jerusalem, Jerusalem, Israel
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Lauridsen JB, Johansen JL, Rekling JC, Thirstrup K, Moerk A, Sager TN. Regulation of the Bcas1 and Baiap3 transcripts in the subthalamic nucleus in mice recovering from MPTP toxicity. Neurosci Res 2011; 70:269-76. [PMID: 21514331 DOI: 10.1016/j.neures.2011.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 03/25/2011] [Accepted: 03/28/2011] [Indexed: 12/20/2022]
Abstract
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) exposure leads to significant and irreversible damage to dopaminergic neurons in both mice and humans. While MPTP exposure in humans causes permanent symptoms of Parkinson's disease, MPTP treated mice will recover behaviorally over a 3-week period. This mouse specific recovery might be linked to transcriptional changes in the basal ganglia enabling mice to maintain normal motor function in spite of low striatal dopamine levels. Laser microdissection was used to isolate the subthalamic nucleus from mice 7 and 28 days following MPTP exposure. High quality RNA was recovered and expressional analysis was performed on whole mouse genome microarrays. Identified regulated transcripts were validated in a separate batch of animals using quantitative PCR. Two transcripts with a significant regulation from days 7 to 28 in the MPTP treated groups, were identified: the brain specific angiogenesis inhibitor associated protein 3 (Baiap3) and the breast carcinoma amplified sequence 1 (Bcas1). Further studies of the molecular pathways involving these two transcripts may uncover processes in the subthalamic nucleus associated with the behavioral recovery observed after MPTP exposure.
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Affiliation(s)
- J B Lauridsen
- Department of Neuroscience and Pharmacology, Faculty of Health Sciences, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen, Denmark.
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Barr TL, Alexander S, Conley Y. Gene expression profiling for discovery of novel targets in human traumatic brain injury. Biol Res Nurs 2010; 13:140-53. [PMID: 21112922 DOI: 10.1177/1099800410385671] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Several clinical trials have failed to demonstrate a significant effect on outcome following human traumatic brain injury (TBI) despite promising results obtained in preclinical animal studies. These failures may be due in part to a misinterpretation of the findings obtained in preclinical animal models of TBI, a misunderstanding of the complexity of the human response to TBI, limited knowledge about the biological pathways that interact to contribute to good and bad outcomes after brain injury, and the effects of genomic variability and environment on individual recovery. Recent publications suggest that data obtained from gene expression profiling studies of complex neurological diseases such as stroke, multiple sclerosis (MS), Alzheimer's and Parkinson's may contribute to a more informed understanding of what affects outcome following TBI. These data may help to bridge the gap between successful preclinical studies and negative clinical trials in humans to reveal novel targets for therapy. Gene expression profiling has the capability to identify biomarkers associated with response to TBI, elucidate complex genetic interactions that may play a role in outcome following TBI, and reveal biological pathways related to brain health. This review highlights the current state of the literature on gene expression profiling for neurological disease and discusses its ability to aid in unraveling the variable human response to TBI and the potential for it to offer treatment strategies in an area where we currently have limited therapeutic options primarily based on supportive care.
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Affiliation(s)
- Taura L Barr
- West Virginia University School of Nursing & Center for Neuroscience, Morgantown, WV, USA.
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34
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Neuroprotective changes of striatal degeneration-related gene expression by acupuncture in an MPTP mouse model of Parkinsonism: microarray analysis. Cell Mol Neurobiol 2010; 31:377-91. [PMID: 21107677 DOI: 10.1007/s10571-010-9629-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2010] [Accepted: 11/02/2010] [Indexed: 01/02/2023]
Abstract
Acupuncture at acupoints GB34 and LR3 has been reported to inhibit nigrostriatal degeneration in Parkinsonism models, yet the genes related to this preventive effect of acupuncture on the nigrostriatal dopaminergic system remain elusive. This study investigated gene expression profile changes in the striatal region of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced Parkinsonism models after acupuncture at the acupoints GB34 and LR3 using a whole transcript genechip microarray (Affymetrix genechip mouse gene 1.0 ST array). It was confirmed that acupuncture at these acupoints could inhibit the decrease of tyrosine hydroxylase and dopamine transporter in the nigrostriatal region of the MPTP model while acupuncture at the non-acupoints could not counteract this decrease. Genechip gene array analysis (fold change cutoff 1.3 and P < 0.05) showed that 12 of the 69 probes up-regulated in MPTP when compared to the control were down-regulated by acupuncture at the acupoints. Of these 12 probes, 11 probes (nine annotated genes) were exclusively down-regulated by acupuncture only at the acupoints; the Gfral gene was excluded because it was commonly down-regulated by acupuncture at both the acupoints and the non-acupoints. In addition, 28 of the 189 probes down-regulated in MPTP when compared to the control were up-regulated by acupuncture at the acupoints. Of these 28 probes, 19 probes (seven annotated genes) were exclusively up-regulated by acupuncture only at the acupoints while nine probes were commonly up-regulated by acupuncture at both the acupoints and the non-acupoints. The regulation patterns of representative genes in real-time RT-PCR correlated with those of the genes in the microarray. These results suggest that the 30 probes (16 annotated genes), which are affected by MPTP and acupuncture only at the acupoints, are responsible for exerting in the striatal regions the inhibitory effect of acupuncture at the acupoints on MPTP-induced striatal degeneration.
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35
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Greene JG. Current status and future directions of gene expression profiling in Parkinson's disease. Neurobiol Dis 2010; 45:76-82. [PMID: 21056669 DOI: 10.1016/j.nbd.2010.10.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Revised: 10/25/2010] [Accepted: 10/27/2010] [Indexed: 12/31/2022] Open
Abstract
Parkinson's disease (PD) is a common age-associated neurodegenerative disorder. Motor symptoms are the cardinal component of PD, but non-motor symptoms, such as dementia, depression, and autonomic dysfunction are being increasingly recognized. Motor symptoms are primarily caused by selective degeneration of substantia nigra dopamine (SNDA) neurons in the midbrain; non-motor symptoms may be referable to well-described pathology at multiple levels of the neuraxis. Development of symptomatic and disease-modifying therapies is dependent on an accurate and comprehensive understanding of the pathogenesis and pathophysiology of PD. Gene expression profiling has been recently employed to assess function on a broad level in the hopes of gaining greater knowledge concerning how individual mechanisms of disease fit together as a whole and to generate novel hypotheses concerning PD pathogenesis, diagnosis, and progression. So far, the majority of studies have been performed on postmortem brain samples from PD patients, but more recently, studies have targeted enriched populations of dopamine neurons and have begun to explore extra-nigral neurons and even peripheral tissues. This review will provide a brief synopsis of gene expression profiling in parkinsonism and its pitfalls to date and propose several potential future directions and uses for the technique. It will focus on the use of microarray experiments to stimulate hypotheses concerning mechanisms of neurodegeneration in PD, since the majority of studies thus far have addressed that complicated issue.
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Affiliation(s)
- James G Greene
- Department of Neurology and the Center for Neurodegenerative Disease, Emory University School of Medicine, Atlanta, GA 30322, USA.
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Wen Z, Wang C, Shi Q, Huang Y, Su Z, Hong H, Tong W, Shi L. Evaluation of gene expression data generated from expired Affymetrix GeneChip® microarrays using MAQC reference RNA samples. BMC Bioinformatics 2010; 11 Suppl 6:S10. [PMID: 20946593 PMCID: PMC3026357 DOI: 10.1186/1471-2105-11-s6-s10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Affymetrix GeneChip® system is a commonly used platform for microarray analysis but the technology is inherently expensive. Unfortunately, changes in experimental planning and execution, such as the unavailability of previously anticipated samples or a shift in research focus, may render significant numbers of pre-purchased GeneChip® microarrays unprocessed before their manufacturer's expiration dates. Researchers and microarray core facilities wonder whether expired microarrays are still useful for gene expression analysis. In addition, it was not clear whether the two human reference RNA samples established by the MAQC project in 2005 still maintained their transcriptome integrity over a period of four years. Experiments were conducted to answer these questions. RESULTS Microarray data were generated in 2009 in three replicates for each of the two MAQC samples with either expired Affymetrix U133A or unexpired U133Plus2 microarrays. These results were compared with data obtained in 2005 on the U133Plus2 microarray. The percentage of overlap between the lists of differentially expressed genes (DEGs) from U133Plus2 microarray data generated in 2009 and in 2005 was 97.44%. While there was some degree of fold change compression in the expired U133A microarrays, the percentage of overlap between the lists of DEGs from the expired and unexpired microarrays was as high as 96.99%. Moreover, the microarray data generated using the expired U133A microarrays in 2009 were highly concordant with microarray and TaqMan® data generated by the MAQC project in 2005. CONCLUSIONS Our results demonstrated that microarray data generated using U133A microarrays, which were more than four years past the manufacturer's expiration date, were highly specific and consistent with those from unexpired microarrays in identifying DEGs despite some appreciable fold change compression and decrease in sensitivity. Our data also suggested that the MAQC reference RNA samples, stored at -80°C, were stable over a time frame of at least four years.
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Affiliation(s)
- Zhining Wen
- Division of Systems Biology, National Center for Toxicological Research (NCTR), US Food and Drug Administration (FDA), 3900 NCTR Road, Jefferson, AR 72079, USA
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Courtney E, Kornfeld S, Janitz K, Janitz M. Transcriptome profiling in neurodegenerative disease. J Neurosci Methods 2010; 193:189-202. [PMID: 20800617 DOI: 10.1016/j.jneumeth.2010.08.018] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2010] [Revised: 07/29/2010] [Accepted: 08/20/2010] [Indexed: 02/02/2023]
Abstract
Changes in gene expression and splicing patterns (that occur prior to the onset and during the progression of complex diseases) have become a major focus of neurodegenerative disease research. These signature patterns of gene expression provide clues about the mechanisms involved in the molecular pathogenesis of neurodegenerative disease and may facilitate the discovery of novel therapeutic drugs. With the development of array technologies and the very recent RNA-seq technique, our understanding of the pathogenesis of neurodegenerative disease is expanding exponentially. Here, we review the technologies involved in gene expression and splicing analysis and the related literature on three common neurodegenerative diseases: Alzheimer's disease, Parkinson's disease and Huntington's disease.
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Affiliation(s)
- Eliza Courtney
- School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
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Ohnuki T, Nakamura A, Okuyama S, Nakamura S. Gene expression profiling in progressively MPTP-lesioned macaques reveals molecular pathways associated with sporadic Parkinson's disease. Brain Res 2010; 1346:26-42. [PMID: 20513370 DOI: 10.1016/j.brainres.2010.05.066] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2009] [Revised: 05/01/2010] [Accepted: 05/24/2010] [Indexed: 12/26/2022]
Abstract
Parkinson's disease (PD) is a common neurodegenerative disease characterized by progressive loss of midbrain dopaminergic neurons. To gain an insight into the mechanisms underlying the progression of PD, gene expression analysis was performed using two different brain regions, the substantia nigra pars compacta (SN) and the striatum (STR), of 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned monkey model of PD. 230 genes were differentially expressed in the MPTP-treated SN compared to control, whereas 452 genes showed altered expression in the MPTP-treated STR, implying that MPTP elicits more damages in the striatal gene expression than in the SN. Comparative data analysis of the transcription profiles on the PD patients and MPTP monkey models, and pathway analysis indicated several signaling pathways as possible routes to MPTP-induced neurodegeneration. Interestingly, the networks which associated with cytoskeletal stability, ubiquitin-proteasome system (UPS) and Wnt signaling gained prominence in our study. Further transcriptional regulatory network analysis suggested the association of the neuronal repressor REST (RE1-silencing transcription factor; NRSF) and androgen receptor with the dysregulation of the striatal genes. Our study suggests the possibility that the dysfunction of multi-network signaling may induce abnormalities in a diverse range of biological processes, such as synaptic function, cytoskeletal stability, survival and differentiation.
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Affiliation(s)
- Tatsuya Ohnuki
- Molecular Function and Pharmacology Laboratories, Taisho Pharmaceutical Co., Ltd., Saitama, 331-9530, Japan.
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Stamelou M, de Silva R, Arias-Carrión O, Boura E, Höllerhage M, Oertel WH, Müller U, Höglinger GU. Rational therapeutic approaches to progressive supranuclear palsy. Brain 2010; 133:1578-90. [PMID: 20472654 DOI: 10.1093/brain/awq115] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Progressive supranuclear palsy is a sporadic and progressive neurodegenerative disease, most often presenting as a symmetric, akinetic-rigid syndrome with postural instability, vertical supranuclear gaze palsy and frontal lobe deficits. It belongs to the family of tauopathies and involves both cortical and subcortical structures. Although the exact pathophysiology is not yet fully understood, several lines of evidence point to a crucial contribution from both genetic predisposition and mitochondrial dysfunction. Recently gained insights into the pathophysiology of this disease have led to several hypothesis-driven therapeutic approaches aiming at disease-modification rather than mere symptomatic neurotransmitter-replacement therapy. Agents targeting mitochondrial dysfunction have already shown a positive effect in a phase II study and further studies to verify and expand these results are ongoing. Clinical studies with agents targeting tau dysfunction such as tau-kinase inhibitors, tau-aggregation inhibitors and microtubule stabilizers are in preparation or ongoing. This review presents the current pathophysiological concepts driving these exciting therapeutic developments.
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Affiliation(s)
- Maria Stamelou
- Department of Neurology, Philipps University, Rudolf-Bultmann Str. 8, D-35033 Marburg, Germany
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Phani S, Gonye G, Iacovitti L. VTA neurons show a potentially protective transcriptional response to MPTP. Brain Res 2010; 1343:1-13. [PMID: 20462502 DOI: 10.1016/j.brainres.2010.04.061] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 03/16/2010] [Accepted: 04/22/2010] [Indexed: 10/19/2022]
Abstract
Parkinson's disease and its characteristic symptoms are thought to arise from the progressive degeneration of specific midbrain dopamine (DA) neurons. In humans, DA neurons of the substantia nigra (SN) and their projections to the striatum show selective vulnerability, while neighboring DA neurons of the ventral tegmental area (VTA) are relatively spared from degeneration. This pattern of cell loss is mimicked in humans, primates, and certain rodents by the neurotoxin MPTP. In this study, we aimed to test the hypothesis that there are factors in the VTA that are potentially neuroprotective against MPTP and that these factors change over time. We have found a dynamic transcriptional response within the cells of the VTA to sustained exposure to a low dose of MPTP. Specifically, the VTA has increased expression of 148 genes as an early response to MPTP and 113 genes as a late response to MPTP toxicity. This response encompasses many areas of cellular function, including protein regulation (Phf6) and ion/metal regulation (PANK2 and Car4). Notably, these responses were largely absent from the cells of the SN. Our data show a clear dynamic response in maintaining the homeostasis and viability of the neurons in the VTA that is lacking in the SN after neurotoxin challenge.
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Affiliation(s)
- Sudarshan Phani
- Farber Institute for Neurosciences, Thomas Jefferson University, Philadelphia, PA, USA
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Storvik M, Arguel MJ, Schmieder S, Delerue-Audegond A, Li Q, Qin C, Vital A, Bioulac B, Gross CE, Wong G, Nahon JL, Bezard E. Genes regulated in MPTP-treated macaques and human Parkinson's disease suggest a common signature in prefrontal cortex. Neurobiol Dis 2010; 38:386-94. [PMID: 20206263 DOI: 10.1016/j.nbd.2010.02.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2009] [Revised: 02/11/2010] [Accepted: 02/13/2010] [Indexed: 11/20/2022] Open
Abstract
The presymptomatic phase of Parkinson's disease (PD) is now recognized as a prodromal phase, with compensatory mechanism masking its progression and non-motor early manifestations, such as depression, cognitive disturbances and apathy. Those mechanisms were thought to be strictly dopamine-mediated until recent advances have shed light upon involvement of putative outside-basal ganglia, i.e. cortical, structures. We took advantage of our progressive 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-treated macaque model to monitor whole genome transcriptional changes in several brain areas. Our data reveals that transcriptomic activity changes take place from early stages, suggesting very early compensatory mechanisms or pathological activity outside the basal ganglia, including the PFC. Specific transcriptomic changes occurring in the PFC of fully parkinsonian MPTP-treated macaques have been identified. Interestingly, a large part of these transcriptomic changes were also observed in human post-mortem samples of patients with neurodegenerative diseases analysed by quantitative PCR. These results suggest that the PFC is able to detect the progression of dopamine denervation even at very early time points. There are therefore mechanisms, within the PFC, leading to compensatory alterations and/or participating to pathophysiology of prodromal PD manifestations.
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Affiliation(s)
- Markus Storvik
- Department of Biosciences, Department of Neurobiology, Department of Pharmacology and Toxicology, University of Kuopio, Kuopio, Finland
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Abnormal gene expression in cerebellum of Npc1-/- mice during postnatal development. Brain Res 2010; 1325:128-40. [PMID: 20153740 DOI: 10.1016/j.brainres.2010.02.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2009] [Revised: 01/31/2010] [Accepted: 02/04/2010] [Indexed: 11/21/2022]
Abstract
Niemann-Pick Type C (NPC) disease is an autosomal recessive neurodegenerative disorder with abnormal lipid storage as the major cellular pathologic hallmark. Genetic analyses have identified mutations in NPC1 gene in the great majority of cases, while mutations in NPC2 account for the remainders. Yet little is known regarding the cellular mechanisms responsible for NPC pathogenesis, especially for neurodegeneration, which is the usual cause of death. To identify critical steps that could account for the pathological manifestations of the disease in one of the most affected brain structures, we performed global gene expression analysis in the cerebellum from 3-week old Npc1+/+ and Npc1-/- mice with two different microarray platforms (Agilent and Illumina). Differentially expressed genes identified by both microarray platforms were then subjected to KEGG pathway analysis. Expression of genes in six pathways was significantly altered in Npc1-/- mice; functionally, these signaling pathways belong to the following three categories: (1) steroid and terpenoid biosynthesis, (2) immune response, and (3) cell adhesion/motility. In addition, the expression of several proteins involved in lipid transport was significantly altered in Npc1-/- mice. Our results provide novel molecular insight regarding the mechanisms of pathogenesis in NPC disease and reveal potential new therapeutic targets.
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Höllerhage M, Matusch A, Champy P, Lombès A, Ruberg M, Oertel WH, Höglinger GU. Natural lipophilic inhibitors of mitochondrial complex I are candidate toxins for sporadic neurodegenerative tau pathologies. Exp Neurol 2009; 220:133-42. [PMID: 19682988 DOI: 10.1016/j.expneurol.2009.08.004] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Revised: 07/22/2009] [Accepted: 08/05/2009] [Indexed: 12/21/2022]
Abstract
Annonacin, a natural lipophilic inhibitor of mitochondrial complex I has been implicated in the etiology of a sporadic neurodegenerative tauopathy in Guadeloupe. We therefore studied further compounds representing the broad biochemical spectrum of complex I inhibitors to which humans are potentially exposed. We determined their lipophilicity, their effect on complex I activity in submitochondrial particles, and their effect on cellular ATP levels, neuronal cell death and somatodendritic redistribution of phosphorylated tau protein (AD2 antibody against pS396/pS404-tau) in primary cultures of fetal rat striatum. The 24 compounds tested were lipophilic (logP range 0.9-8.5; exception: MPP(+) logP=-1.35) and potent complex I inhibitors (IC(50) range 0.9 nM-2.6 mM). They all decreased ATP levels (EC(50) range 1.9 nM-54.2 microM), induced neuronal cell death (EC(50) range 1.1 nM-54.5 microM) and caused the redistribution of AD2(+) tau from axons to the cell body (EC(5) range 0.6 nM-33.3 microM). The potency of the compounds to inhibit complex I correlated with their potency to induce tau redistribution (r=0.80, p<0.001). In conclusion, we propose that the widely distributed lipophilic complex I inhibitors studied here might be implicated in the induction of tauopathies with global prevalence.
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Abstract
Gene expression changes in neuropsychiatric and neurodegenerative disorders, and gene responses to therapeutic drugs, provide new ways to identify central nervous system (CNS) targets for drug discovery. This review summarizes gene and pathway targets replicated in expression profiling of human postmortem brain, animal models, and cell culture studies. Analysis of isolated human neurons implicates targets for Alzheimer's disease and the cognitive decline associated with normal aging and mild cognitive impairment. In addition to tau, amyloid-beta precursor protein, and amyloid-beta peptides (Abeta), these targets include all three high-affinity neurotrophin receptors and the fibroblast growth factor (FGF) system, synapse markers, glutamate receptors (GluRs) and transporters, and dopamine (DA) receptors, particularly the D2 subtype. Gene-based candidates for Parkinson's disease (PD) include the ubiquitin-proteosome system, scavengers of reactive oxygen species, brain-derived neurotrophic factor (BDNF), its receptor, TrkB, and downstream target early growth response 1, Nurr-1, and signaling through protein kinase C and RAS pathways. Increasing variability and decreases in brain mRNA production from middle age to old age suggest that cognitive impairments during normal aging may be addressed by drugs that restore antioxidant, DNA repair, and synaptic functions including those of DA to levels of younger adults. Studies in schizophrenia identify robust decreases in genes for GABA function, including glutamic acid decarboxylase, HINT1, glutamate transport and GluRs, BDNF and TrkB, numerous 14-3-3 protein family members, and decreases in genes for CNS synaptic and metabolic functions, particularly glycolysis and ATP generation. Many of these metabolic genes are increased by insulin and muscarinic agonism, both of which are therapeutic in psychosis. Differential genomic signals are relatively sparse in bipolar disorder, but include deficiencies in the expression of 14-3-3 protein members, implicating these chaperone proteins and the neurotransmitter pathways they support as possible drug targets. Brains from persons with major depressive disorder reveal decreased expression for genes in glutamate transport and metabolism, neurotrophic signaling (eg, FGF, BDNF and VGF), and MAP kinase pathways. Increases in these pathways in the brains of animals exposed to electroconvulsive shock and antidepressant treatments identify neurotrophic and angiogenic growth factors and second messenger stimulation as therapeutic approaches for the treatment of depression.
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Prasad AA, Pasterkamp RJ. Axon guidance in the dopamine system. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 651:91-100. [PMID: 19731554 DOI: 10.1007/978-1-4419-0322-8_9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Meso-diencephalic dopamine neurons (mdDA) neurons are located in the retrorubral field (RRF), substantia nigra pars compacta (SNc) and ventral tegmental area (VTA) and give rise to prominent ascending axon projections. These so-called mesotelencephalic projections are organized into three main pathways: the mesostriatal, mesocortical and mesolimbic pathways. Mesotelencephalic pathways in the adult nervous system have been studied in much detail as a result of their important physiological functions and their implication in psychiatric, neurological and neurodegenerative disease. In comparison, relatively little is known about the formation of these projection systems during embryonic and postnatal development. However, understanding the formation of mdDA neurons and their projections is essential for the design of effective therapies for mdDA neuron-associated neurological and neurodegenerative disorders. Here we summarize our current knowledge of the ontogeny of mdDA axon projections in subsystems of the developing rodent central nervous system (CNS) and discuss the cellular and molecular mechanisms that mediate mdDA axon guidance in these CNS regions.
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Affiliation(s)
- Asheeta A Prasad
- Rudolf Magnus Institute of Neuroscience, Department of Neuroscience and Pharmacology, University Medical Center Utrecht, Utrecht, The Netherlands
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Simunovic F, Yi M, Wang Y, Macey L, Brown LT, Krichevsky AM, Andersen SL, Stephens RM, Benes FM, Sonntag KC. Gene expression profiling of substantia nigra dopamine neurons: further insights into Parkinson's disease pathology. ACTA ACUST UNITED AC 2008; 132:1795-809. [PMID: 19052140 DOI: 10.1093/brain/awn323] [Citation(s) in RCA: 266] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Parkinson's disease is caused by a progressive loss of the midbrain dopamine (DA) neurons in the substantia nigra pars compacta. Although the main cause of Parkinson's disease remains unknown, there is increasing evidence that it is a complex disorder caused by a combination of genetic and environmental factors, which affect key signalling pathways in substantia nigra DA neurons. Insights into pathogenesis of Parkinson's disease stem from in vitro and in vivo models and from postmortem analyses. Recent technological developments have added a new dimension to this research by determining gene expression profiles using high throughput microarray assays. However, many of the studies reported to date were based on whole midbrain dissections, which included cells other than DA neurons. Here, we have used laser microdissection to isolate single DA neurons from the substantia nigra pars compacta of controls and subjects with idiopathic Parkinson's disease matched for age and postmortem interval followed by microarrays to analyse gene expression profiling. Our data confirm a dysregulation of several functional groups of genes involved in the Parkinson's disease pathogenesis. In particular, we found prominent down-regulation of members of the PARK gene family and dysregulation of multiple genes associated with programmed cell death and survival. In addition, genes for neurotransmitter and ion channel receptors were also deregulated, supporting the view that alterations in electrical activity might influence DA neuron function. Our data provide a 'molecular fingerprint identity' of late-stage Parkinson's disease DA neurons that will advance our understanding of the molecular pathology of this disease.
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Affiliation(s)
- Filip Simunovic
- Department of Psychiatry, McLean Hospital, Harvard Medical School, Belmont, MA 02478, USA
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Meurers BH, Zhu C, Fernagut PO, Richter F, Hsia YC, Fleming SM, Oh M, Elashoff D, Dicarlo CD, Seaman RL, Chesselet MF. Low dose rotenone treatment causes selective transcriptional activation of cell death related pathways in dopaminergic neurons in vivo. Neurobiol Dis 2008; 33:182-92. [PMID: 19013527 DOI: 10.1016/j.nbd.2008.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 10/03/2008] [Accepted: 10/04/2008] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial complex I inhibition has been implicated in the degeneration of midbrain dopaminergic (DA) neurons in Parkinson's disease. However, the mechanisms and pathways that determine the cellular fate of DA neurons downstream of the mitochondrial dysfunction have not been fully identified. We conducted cell-type specific gene array experiments with nigral DA neurons from rats treated with the complex I inhibitor, rotenone, at a dose that does not induce cell death. The genome wide screen identified transcriptional changes in multiple cell death related pathways that are indicative of a simultaneous activation of both degenerative and protective mechanisms. Quantitative PCR analyses of a subset of these genes in different neuronal populations of the basal ganglia revealed that some of the changes are specific for DA neurons, suggesting that these neurons are highly sensitive to rotenone. Our data provide insight into potentially defensive strategies of DA neurons against disease relevant insults.
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Affiliation(s)
- B H Meurers
- Department of Neurology, UCLA, Los Angeles, CA 90095, USA.
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48
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Liu B, Shi Q, Ma S, Feng N, Li J, Wang L, Wang X. Striatal 19S Rpt6 deficit is related to alpha-synuclein accumulation in MPTP-treated mice. Biochem Biophys Res Commun 2008; 376:277-82. [PMID: 18782562 DOI: 10.1016/j.bbrc.2008.08.142] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 08/23/2008] [Indexed: 12/31/2022]
Abstract
Striatal mitochondrial proteins were investigated using proteomics in the 1-methyl 4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) mouse model of Parkinson's disease. Four proteins, 19S proteasome ATPase Rpt6 (19S Rpt6), Lectin-related nature killer cell receptor LY 49S, Zinc finger A20 domain containing 1, and the sodium channel-associated protein 1 isoform 2, were significantly decreased while alpha-synuclein was increased in MPTP-treated mice. The altered levels of 19S Rpt6 and alpha-synuclein were further verified by Western blot. Experiments using small interfering RNA (siRNA) showed that alpha-synuclein was increased by 50% in cultured striatal neurons when 19S Rpt6 was knocked down. Taken together, our results imply that a deficiency in 19S Rpt6 may be partially related to the MPTP-induced increase in alpha-synuclein in the striatum.
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Affiliation(s)
- Bin Liu
- Department of Pharmacology, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Xiannongtan Street, Xuanwu District, Beijing 100050, China
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49
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Shi L, Jones WD, Jensen RV, Harris SC, Perkins RG, Goodsaid FM, Guo L, Croner LJ, Boysen C, Fang H, Qian F, Amur S, Bao W, Barbacioru CC, Bertholet V, Cao XM, Chu TM, Collins PJ, Fan XH, Frueh FW, Fuscoe JC, Guo X, Han J, Herman D, Hong H, Kawasaki ES, Li QZ, Luo Y, Ma Y, Mei N, Peterson RL, Puri RK, Shippy R, Su Z, Sun YA, Sun H, Thorn B, Turpaz Y, Wang C, Wang SJ, Warrington JA, Willey JC, Wu J, Xie Q, Zhang L, Zhang L, Zhong S, Wolfinger RD, Tong W. The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies. BMC Bioinformatics 2008; 9 Suppl 9:S10. [PMID: 18793455 PMCID: PMC2537561 DOI: 10.1186/1471-2105-9-s9-s10] [Citation(s) in RCA: 183] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Reproducibility is a fundamental requirement in scientific experiments. Some recent publications have claimed that microarrays are unreliable because lists of differentially expressed genes (DEGs) are not reproducible in similar experiments. Meanwhile, new statistical methods for identifying DEGs continue to appear in the scientific literature. The resultant variety of existing and emerging methods exacerbates confusion and continuing debate in the microarray community on the appropriate choice of methods for identifying reliable DEG lists. RESULTS Using the data sets generated by the MicroArray Quality Control (MAQC) project, we investigated the impact on the reproducibility of DEG lists of a few widely used gene selection procedures. We present comprehensive results from inter-site comparisons using the same microarray platform, cross-platform comparisons using multiple microarray platforms, and comparisons between microarray results and those from TaqMan - the widely regarded "standard" gene expression platform. Our results demonstrate that (1) previously reported discordance between DEG lists could simply result from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion with a non-stringent P-value cutoff filtering, the DEG lists become much more reproducible, especially when fewer genes are selected as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability of the t-values; the more stringent the P-value threshold, the less reproducible the DEG list is. These observations are also consistent with results from extensive simulation calculations. CONCLUSION We recommend the use of FC-ranking plus a non-stringent P cutoff as a straightforward and baseline practice in order to generate more reproducible DEG lists. Specifically, the P-value cutoff should not be stringent (too small) and FC should be as large as possible. Our results provide practical guidance to choose the appropriate FC and P-value cutoffs when selecting a given number of DEGs. The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.
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Affiliation(s)
- Leming Shi
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Wendell D Jones
- Expression Analysis Inc., 2605 Meridian Parkway, Durham, NC 27713, USA
| | - Roderick V Jensen
- University of Massachusetts Boston, Department of Physics, 100 Morrissey Boulevard, Boston, MA 02125, USA
| | - Stephen C Harris
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Roger G Perkins
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Federico M Goodsaid
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Lei Guo
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Lisa J Croner
- Biogen Idec Inc., 5200 Research Place, San Diego, CA 92122, USA
| | - Cecilie Boysen
- ViaLogy Inc., 2400 Lincoln Avenue, Altadena, CA 91001, USA
| | - Hong Fang
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Feng Qian
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Shashi Amur
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - Wenjun Bao
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | | | - Vincent Bertholet
- Eppendorf Array Technologies, rue du Séminaire 20a, 5000 Namur, Belgium
| | - Xiaoxi Megan Cao
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Tzu-Ming Chu
- SAS Institute Inc., SAS Campus Drive, Cary, NC 27513, USA
| | - Patrick J Collins
- Agilent Technologies Inc., 5301 Stevens Creek Boulevard, Santa Clara, CA 95051, USA
| | - Xiao-hui Fan
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Felix W Frueh
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | - James C Fuscoe
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Xu Guo
- Affymetrix Inc., 3420 Central Expressway, Santa Clara, CA 95051, USA
| | - Jing Han
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Damir Herman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Huixiao Hong
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ernest S Kawasaki
- National Cancer Institute Advanced Technology Center, 8717 Grovemont Circle, Gaithersburg, MD 20877, USA
| | - Quan-Zhen Li
- University of Texas Southwestern Medical Center, 6000 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Yuling Luo
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Yunqing Ma
- Panomics Inc., 6519 Dumbarton Circle, Fremont, CA 94555, USA
| | - Nan Mei
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Ron L Peterson
- Novartis Institutes for Biomedical Research, 250 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Raj K Puri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 8800 Rockville Pike, Bethesda, MD 20892, USA
| | - Richard Shippy
- GE Healthcare, 7700 S River Parkway, Tempe, AZ 85284, USA
| | - Zhenqiang Su
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
| | | | - Hongmei Sun
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Brett Thorn
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Yaron Turpaz
- Pharmaceutical Informatics Institute, Zhejiang University, Hangzhou 310027, China
| | - Charles Wang
- UCLA David Geffen School of Medicine, Transcriptional Genomics Core, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, CA 90048, USA
| | - Sue Jane Wang
- Center for Drug Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA
| | | | - James C Willey
- Ohio Medical University, 3000 Arlington Avenue, Toledo, OH 43614, USA
| | - Jie Wu
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Qian Xie
- Z-Tech Corporation, an ICF International Company at NCTR/FDA, 3900 NCTR Road, Jefferson, AR 72079, USA
| | - Liang Zhang
- CapitalBio Corporation, 18 Life Science Parkway, Changping District, Beijing 102206, China
| | - Lu Zhang
- Solexa Inc., 25861 Industrial Boulevard, Hayward, CA 94545, USA
| | - Sheng Zhong
- University of Illinois at Urbana-Champaign, Department of Bioengineering, 1304 W. Springfield Avenue, Urbana, IL 61801, USA
| | | | - Weida Tong
- National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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50
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Thirumalai V, Cline HT. Endogenous dopamine suppresses initiation of swimming in prefeeding zebrafish larvae. J Neurophysiol 2008; 100:1635-48. [PMID: 18562547 DOI: 10.1152/jn.90568.2008] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Dopamine is a key neuromodulator of locomotory circuits, yet the role that dopamine plays during development of these circuits is less well understood. Here, we describe a suppressive effect of dopamine on swim circuits in larval zebrafish. Zebrafish larvae exhibit marked changes in swimming behavior between 3 days postfertilization (dpf) and 5dpf. We found that swim episodes were fewer and of longer durations at 3 than at 5dpf. At 3dpf, application of dopamine as well as bupropion, a dopamine reuptake blocker, abolished spontaneous fictive swim episodes. Blocking D2 receptors increased frequency of occurrence of episodes and activation of adenylyl cyclase, a downstream target inhibited by D2-receptor signaling, blocked the inhibitory effect of dopamine. Dopamine had no effect on motor neuron firing properties, input impedance, resting membrane potential, or the amplitude of spike afterhyperpolarization. Application of dopamine either to the isolated spinal cord or locally within the cord does not decrease episode frequency, whereas dopamine application to the brain silences episodes, suggesting a supraspinal locus of dopaminergic action. Treating larvae with 10 microM MPTP reduced catecholaminergic innervation in the brain and increased episode frequency. These data indicate that dopamine inhibits the initiation of fictive swimming episodes at 3dpf. We found that at 5dpf, exogenously applied dopamine inhibits swim episodes, yet the dopamine reuptake blocker or the D2-receptor antagonist have no effect on episode frequency. These results led us to propose that endogenous dopamine release transiently suppresses swim circuits in developing zebrafish.
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