1
|
Zhang H, Nagai J, Hao L, Jiang X. Identification of Key Genes and Immunological Features Associated with Copper Metabolism in Parkinson's Disease by Bioinformatics Analysis. Mol Neurobiol 2024; 61:799-811. [PMID: 37659036 DOI: 10.1007/s12035-023-03565-8] [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: 05/19/2023] [Accepted: 08/07/2023] [Indexed: 09/05/2023]
Abstract
To explore diagnostic genes associated with cuproptosis in Parkinson's disease (PD) and to characterize immune cell infiltration by comprehensive bioinformatics analysis, three PD datasets were downloaded from the GEO database, two of which were merged and preprocessed as the internal training set and the remaining one as the external validation set. Based on the internal training set, differential analysis was performed to obtain differentially expressed genes (DEGs), and weighted gene co-expression network analysis (WGCNA) was conducted to obtain significant module genes. The genes obtained here were intersected to form the intersecting genes. The intersecting genes obtained from DEGs and WGCNA were intersected with cuproptosis-related genes (CRGs) to generate cuproptosis-related disease signature genes, and functional enrichment analysis was performed on Disease Ontology (DO), Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG). Subsequently, LASSO analysis of the cuproptosis-related disease signature genes was performed to identify key genes and construct a diagnostic and predictive model. Then, single sample gene set enrichment analysis (ssGSEA) was performed on the internal training set to further analyze the correlation between key genes and immune cells. Lastly, the results were validated using an external validation set. A total of 405 DEGs were obtained by differential analysis, and 6 gene modules were identified by WGCNA analysis. The genes in the most significant modules were intersected with the DEGs to obtain 21 intersecting genes. The functions of the intersecting genes were mainly enriched in neurotransmitter transport, GABA-ergic synapse, synaptic vesicle cycle, serotonergic synapse, phenylalanine metabolism, tyrosine metabolism, tryptophan metabolism, etc. Subsequently, the intersecting genes were intersected with CRGs, and LASSO regression analysis was performed to screen 3 key cuproptosis-related disease signature genes, namely, SLC18A2, SLC6A3, and SV2C. The calibration curve of the nomogram model constructed based on these 3 key genes to predict PD showed good agreement, with a C-index of 0.944 and an area under the ROC (AUC) of 0.944 (0.833-1.000). It was also validated by the external dataset that the model constructed with these 3 key genes had good diagnostic and predictive power for PD. The ssGSEA analysis revealed that neutrophils might be the potential core immune cells and that SLC18A2, SLC6A3, and SV2C were significantly negatively correlated with neutrophils, which was also verified in the validation set. PD diagnosis and prediction model based on CRGs (SLC18A2, SLC6A3, and SV2C) has good diagnostic and predictive performance and could be a useful tool in the diagnosis of PD.
Collapse
Affiliation(s)
- Haofuzi Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China
- Laboratory for Glia-Neuron Circuit Dynamics, RIKEN Center for Brain Science, Wako, 351-0198, Japan
| | - Jun Nagai
- Laboratory for Glia-Neuron Circuit Dynamics, RIKEN Center for Brain Science, Wako, 351-0198, Japan
| | - Lu Hao
- Department of Emergency, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
- Department of Nursing, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, China.
| |
Collapse
|
2
|
Yu Y, Chen D, Farmer SM, Xu S, Rios B, Solbach A, Ye X, Ye L, Zhang S. Endolysosomal trafficking controls yolk granule biogenesis in vitellogenic Drosophila oocytes. PLoS Genet 2024; 20:e1011152. [PMID: 38315726 PMCID: PMC10898735 DOI: 10.1371/journal.pgen.1011152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 02/27/2024] [Accepted: 01/22/2024] [Indexed: 02/07/2024] Open
Abstract
Endocytosis and endolysosomal trafficking are essential for almost all aspects of physiological functions of eukaryotic cells. As our understanding on these membrane trafficking events are mostly from studies in yeast and cultured mammalian cells, one challenge is to systematically evaluate the findings from these cell-based studies in multicellular organisms under physiological settings. One potentially valuable in vivo system to address this challenge is the vitellogenic oocyte in Drosophila, which undergoes extensive endocytosis by Yolkless (Yl), a low-density lipoprotein receptor (LDLR), to uptake extracellular lipoproteins into oocytes and package them into a specialized lysosome, the yolk granule, for storage and usage during later development. However, by now there is still a lack of sufficient understanding on the molecular and cellular processes that control yolk granule biogenesis. Here, by creating genome-tagging lines for Yl receptor and analyzing its distribution in vitellogenic oocytes, we observed a close association of different endosomal structures with distinct phosphoinositides and actin cytoskeleton dynamics. We further showed that Rab5 and Rab11, but surprisingly not Rab4 and Rab7, are essential for yolk granules biogenesis. Instead, we uncovered evidence for a potential role of Rab7 in actin regulation and observed a notable overlap of Rab4 and Rab7, two Rab GTPases that have long been proposed to have distinct spatial distribution and functional roles during endolysosomal trafficking. Through a small-scale RNA interference (RNAi) screen on a set of reported Rab5 effectors, we showed that yolk granule biogenesis largely follows the canonical endolysosomal trafficking and maturation processes. Further, the data suggest that the RAVE/V-ATPase complexes function upstream of or in parallel with Rab7, and are involved in earlier stages of endosomal trafficking events. Together, our study provides s novel insights into endolysosomal pathways and establishes vitellogenic oocyte in Drosophila as an excellent in vivo model for dissecting the highly complex membrane trafficking events in metazoan.
Collapse
Affiliation(s)
- Yue Yu
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Dongsheng Chen
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- The College of Life Sciences, Anhui Normal University, #1 Beijing East Road, Wuhu, Anhui, People’s Republic of China
| | - Stephen M. Farmer
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Program in Biochemistry and Cell Biology, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Shiyu Xu
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Beatriz Rios
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Amanda Solbach
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
| | - Xin Ye
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Lili Ye
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| | - Sheng Zhang
- The Brown Foundation Institute of Molecular Medicine, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
- Program in Neuroscience, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Programs in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences (MD Anderson UTHealth GSBS), Houston, Texas, United States of America
- Department of Neurobiology and Anatomy, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth), Houston, Texas, United States of America
| |
Collapse
|
3
|
Ciampelli C, Galleri G, Puggioni S, Fais M, Iannotta L, Galioto M, Becciu M, Greggio E, Bernardoni R, Crosio C, Iaccarino C. Inhibition of the Exocyst Complex Attenuates the LRRK2 Pathological Effects. Int J Mol Sci 2023; 24:12656. [PMID: 37628835 PMCID: PMC10454163 DOI: 10.3390/ijms241612656] [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: 06/09/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023] Open
Abstract
Pathological mutations in leucine-rich repeat kinase 2 (LRRK2) gene are the major genetic cause of Parkinson's disease (PD). Multiple lines of evidence link LRRK2 to the control of vesicle dynamics through phosphorylation of a subset of RAB proteins. However, the molecular mechanisms underlying these processes are not fully elucidated. We have previously demonstrated that LRRK2 increases the exocyst complex assembly by Sec8 interaction, one of the eight members of the exocyst complex, and that Sec8 over-expression mitigates the LRRK2 pathological effect in PC12 cells. Here, we extend this analysis using LRRK2 drosophila models and show that the LRRK2-dependent exocyst complex assembly increase is downstream of RAB phosphorylation. Moreover, exocyst complex inhibition rescues mutant LRRK2 pathogenic phenotype in cellular and drosophila models. Finally, prolonged exocyst inhibition leads to a significant reduction in the LRRK2 protein level, overall supporting the role of the exocyst complex in the LRRK2 pathway. Taken together, our study suggests that modulation of the exocyst complex may represent a novel therapeutic target for PD.
Collapse
Affiliation(s)
- Cristina Ciampelli
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Grazia Galleri
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Silvia Puggioni
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Milena Fais
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Lucia Iannotta
- Department of Biology, University of Padova, 35131 Padova, Italy; (L.I.); (E.G.)
| | - Manuela Galioto
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Marta Becciu
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Elisa Greggio
- Department of Biology, University of Padova, 35131 Padova, Italy; (L.I.); (E.G.)
| | - Roberto Bernardoni
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (C.C.); (G.G.); (S.P.); (M.F.); (M.G.); (M.B.); (C.C.)
| |
Collapse
|
4
|
Exploration of the Shared Molecular Mechanisms between COVID-19 and Neurodegenerative Diseases through Bioinformatic Analysis. Int J Mol Sci 2023; 24:ijms24054839. [PMID: 36902271 PMCID: PMC10002862 DOI: 10.3390/ijms24054839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/15/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The COVID-19 pandemic has caused millions of deaths and remains a major public health burden worldwide. Previous studies found that a large number of COVID-19 patients and survivors developed neurological symptoms and might be at high risk of neurodegenerative diseases, such as Alzheimer's disease (AD) and Parkinson's disease (PD). We aimed to explore the shared pathways between COVID-19, AD, and PD by using bioinformatic analysis to reveal potential mechanisms, which may explain the neurological symptoms and degeneration of brain that occur in COVID-19 patients, and to provide early intervention. In this study, gene expression datasets of the frontal cortex were employed to detect common differentially expressed genes (DEGs) of COVID-19, AD, and PD. A total of 52 common DEGs were then examined using functional annotation, protein-protein interaction (PPI) construction, candidate drug identification, and regulatory network analysis. We found that the involvement of the synaptic vesicle cycle and down-regulation of synapses were shared by these three diseases, suggesting that synaptic dysfunction might contribute to the onset and progress of neurodegenerative diseases caused by COVID-19. Five hub genes and one key module were obtained from the PPI network. Moreover, 5 drugs and 42 transcription factors (TFs) were also identified on the datasets. In conclusion, the results of our study provide new insights and directions for follow-up studies of the relationship between COVID-19 and neurodegenerative diseases. The hub genes and potential drugs we identified may provide promising treatment strategies to prevent COVID-19 patients from developing these disorders.
Collapse
|
5
|
Bustos BI, Billingsley K, Blauwendraat C, Gibbs JR, Gan-Or Z, Krainc D, Singleton AB, Lubbe SJ. Genome-wide contribution of common short-tandem repeats to Parkinson's disease genetic risk. Brain 2023; 146:65-74. [PMID: 36347471 DOI: 10.1093/brain/awac301] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 08/01/2022] [Accepted: 08/06/2022] [Indexed: 11/11/2022] Open
Abstract
Parkinson's disease is a complex neurodegenerative disorder with a strong genetic component, for which most known disease-associated variants are single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels). DNA repetitive elements account for >50% of the human genome; however, little is known of their contribution to Parkinson's disease aetiology. While select short tandem repeats (STRs) within candidate genes have been studied in Parkinson's disease, their genome-wide contribution remains unknown. Here we present the first genome-wide association study of STRs in Parkinson's disease. Through a meta-analysis of 16 imputed genome-wide association study cohorts from the International Parkinson's Disease Genomic Consortium (IPDGC), totalling 39 087 individuals (16 642 cases and 22 445 controls of European ancestry), we identified 34 genome-wide significant STR loci (P < 5.34 × 10-6), with the strongest signal located in KANSL1 [chr17:44 205 351:[T]11, P = 3 × 10-39, odds ratio = 1.31 (95% confidence interval = 1.26-1.36)]. Conditional-joint analyses suggested that four significant STRs mapping nearby NDUFAF2, TRIML2, MIRNA-129-1 and NCOR1 were independent from known risk SNPs. Including STRs in heritability estimates increased the variance explained by SNPs alone. Gene expression analysis of STRs (eSTRs) in RNA sequencing data from 13 brain regions identified significant associations of STRs influencing the expression of multiple genes, including known Parkinson's disease genes. Further functional annotation of candidate STRs revealed that significant eSTRs within NUDFAF2 and ZSWIM7 overlap with regulatory features and are associated with change in the expression levels of nearby genes. Here, we show that STRs at known and novel candidate loci contribute to Parkinson's disease risk and have functional effects in disease-relevant tissues and pathways, supporting previously reported disease-associated genes and giving further evidence for their functional prioritization. These data represent a valuable resource for researchers currently dissecting Parkinson's disease risk loci.
Collapse
Affiliation(s)
- Bernabe I Bustos
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada.,Department of Human Genetics, McGill University, Montréal, QC, Canada.,Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada
| | - Dimitri Krainc
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steven J Lubbe
- Ken and Ruth Davee Department of Neurology and Simpson Querrey Center for Neurogenetics, Northwestern University, Feinberg School of Medicine, Chicago, IL 60611, USA
| | | |
Collapse
|
6
|
Brown-Panton CA, Sabour S, Zoidl GSO, Zoidl C, Tabatabaei N, Zoidl GR. Gap junction Delta-2b ( gjd2b/Cx35.1) depletion causes hyperopia and visual-motor deficiencies in the zebrafish. Front Cell Dev Biol 2023; 11:1150273. [PMID: 36936688 PMCID: PMC10017553 DOI: 10.3389/fcell.2023.1150273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2023] [Indexed: 03/06/2023] Open
Abstract
The zebrafish is a powerful model to investigate the developmental roles of electrical synapses because many signaling pathways that regulate the development of the nervous system are highly conserved from fish to humans. Here, we provide evidence linking the mammalian connexin-36 (Cx36) ortholog gjd2b/Cx35.1, a major component of electrical synapses in the zebrafish, with a refractive error in the context of morphological, molecular, and behavioral changes of zebrafish larvae. Two abnormalities were identified. The optical coherence tomography analysis of the adult retina confirmed changes to the refractive properties caused by eye axial length reduction, leading to hyperopic shifts. The gjd2b/Cx35.1 depletion was also correlated with morphological changes to the head and body ratios in larvae. The differential expression of Wnt/ß-catenin signaling genes, connexins, and dopamine receptors suggested a contribution to the observed phenotypic differences. The alteration of visual-motor behavioral responses to abrupt light transitions was aggravated in larvae, providing evidence that cone photoreceptor cell activity was enhanced when gjd2b/Cx35.1 was depleted. The visual disturbances were reversed under low light conditions in gjd2b -/- /Cx35.1-/- larvae. Since qRT-PCR data demonstrated that two rhodopsin genes were downregulated, we speculated that rod photoreceptor cells in gjd2b/Cx35.1-/- larvae were less sensitive to bright light transitions, thus providing additional evidence that a cone-mediated process caused the VMR light-ON hyperactivity after losing Cx35.1 expression. Together, this study provides evidence for the role of gjd2b/Cx35.1 in the development of the visual system and visually guided behaviors.
Collapse
Affiliation(s)
- Cherie A. Brown-Panton
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
- *Correspondence: Cherie A. Brown-Panton, ; Georg R. Zoidl,
| | - Shiva Sabour
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Georg S. O. Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
| | - Christiane Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
| | - Nima Tabatabaei
- Center for Vision Research, York University, Toronto, ON, Canada
- Department of Mechanical Engineering, York University, Toronto, ON, Canada
| | - Georg R. Zoidl
- Department of Biology, York University, Toronto, ON, Canada
- Center for Vision Research, York University, Toronto, ON, Canada
- Department of Psychology, York University, Toronto, ON, Canada
- *Correspondence: Cherie A. Brown-Panton, ; Georg R. Zoidl,
| |
Collapse
|
7
|
Discovery of levodopa-induced dyskinesia-associated genes using genomic studies in patients and Drosophila behavioral analyses. Commun Biol 2022; 5:872. [PMID: 36008531 PMCID: PMC9411113 DOI: 10.1038/s42003-022-03830-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 08/11/2022] [Indexed: 11/11/2022] Open
Abstract
Although levodopa is the most effective medication for Parkinson’s disease, long-term levodopa treatment is largely compromised due to late motor complications, including levodopa-induced dyskinesia (LID). However, the genetic basis of LID pathogenesis has not been fully understood. Here, we discover genes pathogenic for LID using Drosophila genetics and behavioral analyses combined with genome-wide association studies on 578 patients clinically diagnosed with LID. Similar to the therapeutic effect of levodopa in patients, acute levodopa treatments restore the motor defect of Parkinson’s disease model flies, while prolonged treatments cause LID-related symptoms, such as increased yawing, freezing and abrupt acceleration of locomotion. These symptoms require dopamine 1-like receptor 1 and are induced by neuronal overexpression of the receptor. Among genes selected from our analyses in the patient genome, neuronal knockdown of adenylyl cyclase 2 suppresses the levodopa-induced phenotypes and the receptor overexpression-induced symptoms in Drosophila. Together, our study provides genetic insights for LID pathogenesis through the D1-like receptor-adenylyl cyclase 2 signaling axis. A combined research approach using GWAS on Parkinson's disease patients and a Drosophila model of L-DOPA-induced dyskinesia (LID) reveals that LID is linked to ADCY2 signaling.
Collapse
|
8
|
Farrow SL, Schierding W, Gokuladhas S, Golovina E, Fadason T, Cooper AA, O’Sullivan JM. Establishing gene regulatory networks from Parkinson's disease risk loci. Brain 2022; 145:2422-2435. [PMID: 35094046 PMCID: PMC9373962 DOI: 10.1093/brain/awac022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 12/02/2021] [Accepted: 12/20/2021] [Indexed: 11/25/2022] Open
Abstract
The latest meta-analysis of genome-wide association studies identified 90 independent variants across 78 genomic regions associated with Parkinson's disease, yet the mechanisms by which these variants influence the development of the disease remains largely elusive. To establish the functional gene regulatory networks associated with Parkinson's disease risk variants, we utilized an approach combining spatial (chromosomal conformation capture) and functional (expression quantitative trait loci) data. We identified 518 genes subject to regulation by 76 Parkinson's variants across 49 tissues, whicih encompass 36 peripheral and 13 CNS tissues. Notably, one-third of these genes were regulated via trans-acting mechanisms (distal; risk locus-gene separated by >1 Mb, or on different chromosomes). Of particular interest is the identification of a novel trans-expression quantitative trait loci-gene connection between rs10847864 and SYNJ1 in the adult brain cortex, highlighting a convergence between familial studies and Parkinson's disease genome-wide association studies loci for SYNJ1 (PARK20) for the first time. Furthermore, we identified 16 neurodevelopment-specific expression quantitative trait loci-gene regulatory connections within the foetal cortex, consistent with hypotheses suggesting a neurodevelopmental involvement in the pathogenesis of Parkinson's disease. Through utilizing Louvain clustering we extracted nine significant and highly intraconnected clusters within the entire gene regulatory network. The nine clusters are enriched for specific biological processes and pathways, some of which have not previously been associated with Parkinson's disease. Together, our results not only contribute to an overall understanding of the mechanisms and impact of specific combinations of Parkinson's disease variants, but also highlight the potential impact gene regulatory networks may have when elucidating aetiological subtypes of Parkinson's disease.
Collapse
Affiliation(s)
- Sophie L Farrow
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | | | - Evgeniia Golovina
- Liggins Institute, The University of Auckland, Auckland, New Zealand
| | - Tayaza Fadason
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Antony A Cooper
- Australian Parkinson’s Mission, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, UNSW Sydney, Sydney, New South Wales, Australia
| | - Justin M O’Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Australian Parkinson’s Mission, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Brain Research New Zealand, The University of Auckland, Auckland, New Zealand
- MRC Lifecourse Epidemiology Unit, University of Southampton, UK
| |
Collapse
|
9
|
Palmieri I, Poloni TE, Medici V, Zucca S, Davin A, Pansarasa O, Ceroni M, Tronconi L, Guaita A, Gagliardi S, Cereda C. Differential Neuropathology, Genetics, and Transcriptomics in Two Kindred Cases with Alzheimer’s Disease and Lewy Body Dementia. Biomedicines 2022; 10:biomedicines10071687. [PMID: 35884993 PMCID: PMC9313121 DOI: 10.3390/biomedicines10071687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/17/2022] Open
Abstract
Alzheimer’s disease (AD) and Lewy body dementia (LBD) are two different forms of dementia, but their pathology may involve the same cortical areas with overlapping cognitive manifestations. Nonetheless, the clinical phenotype is different due to the topography of the lesions driven by the different underlying molecular processes that arise apart from genetics, causing diverse neurodegeneration. Here, we define the commonalities and differences in the pathological processes of dementia in two kindred cases, a mother and a son, who developed classical AD and an aggressive form of AD/LBD, respectively, through a neuropathological, genetic (next-generation sequencing), and transcriptomic (RNA-seq) comparison of four different brain areas. A genetic analysis did not reveal any pathogenic variants in the principal AD/LBD-causative genes. RNA sequencing highlighted high transcriptional dysregulation within the substantia nigra in the AD/LBD case, while the AD case showed lower transcriptional dysregulation, with the parietal lobe being the most involved brain area. The hippocampus (the most degenerated area) and basal ganglia (lacking specific lesions) expressed the lowest level of dysregulation. Our data suggest that there is a link between transcriptional dysregulation and the amount of tissue damage accumulated across time, assessed through neuropathology. Moreover, we highlight that the molecular bases of AD and LBD follow very different pathways, which underlie their neuropathological signatures. Indeed, the transcriptome profiling through RNA sequencing may be an important tool in flanking the neuropathological analysis for a deeper understanding of AD and LBD pathogenesis.
Collapse
Affiliation(s)
- Ilaria Palmieri
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (I.P.); (M.C.); (S.G.); (C.C.)
| | - Tino Emanuele Poloni
- Department of Neurology-Neuropathology and Abbiategrasso Brain Bank, Golgi-Cenci Foundation, Abbiategrasso, 20081 Milan, Italy; (T.E.P.); (V.M.); (A.G.)
- Department of Rehabilitation, ASP Golgi-Redaelli, Abbiategrasso, 20081 Milan, Italy
| | - Valentina Medici
- Department of Neurology-Neuropathology and Abbiategrasso Brain Bank, Golgi-Cenci Foundation, Abbiategrasso, 20081 Milan, Italy; (T.E.P.); (V.M.); (A.G.)
| | | | - Annalisa Davin
- Laboratory of Neurobiology and Neurogenetics, Golgi Cenci Foundation, Abbiategrasso, 20081 Milan, Italy;
| | - Orietta Pansarasa
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (I.P.); (M.C.); (S.G.); (C.C.)
- Correspondence:
| | - Mauro Ceroni
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (I.P.); (M.C.); (S.G.); (C.C.)
- Department of Neurology-Neuropathology and Abbiategrasso Brain Bank, Golgi-Cenci Foundation, Abbiategrasso, 20081 Milan, Italy; (T.E.P.); (V.M.); (A.G.)
| | - Livio Tronconi
- U.O. Medicina Legale, IRCCS Mondino Foundation, 27100 Pavia, Italy;
- Unit of Legal Medicine and Forensic Sciences “A. Fornari”, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Antonio Guaita
- Department of Neurology-Neuropathology and Abbiategrasso Brain Bank, Golgi-Cenci Foundation, Abbiategrasso, 20081 Milan, Italy; (T.E.P.); (V.M.); (A.G.)
- Laboratory of Neurobiology and Neurogenetics, Golgi Cenci Foundation, Abbiategrasso, 20081 Milan, Italy;
| | - Stella Gagliardi
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (I.P.); (M.C.); (S.G.); (C.C.)
| | - Cristina Cereda
- IRCCS Mondino Foundation, 27100 Pavia, Italy; (I.P.); (M.C.); (S.G.); (C.C.)
- Department of Women, Mothers and Neonatal Care, Children’s Hospital “V. Buzzi”, 20100 Milan, Italy
| |
Collapse
|
10
|
Birdsall V, Kirwan K, Zhu M, Imoto Y, Wilson SM, Watanabe S, Waites CL. Axonal transport of Hrs is activity dependent and facilitates synaptic vesicle protein degradation. Life Sci Alliance 2022; 5:5/10/e202000745. [PMID: 35636965 PMCID: PMC9152131 DOI: 10.26508/lsa.202000745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 11/29/2022] Open
Abstract
This study describes an activity-dependent mechanism for transporting ESCRT-0 protein Hrs to synaptic vesicle (SV) pools, facilitating SV protein degradation in response to increased neuronal firing. Turnover of synaptic vesicle (SV) proteins is vital for the maintenance of healthy and functional synapses. SV protein turnover is driven by neuronal activity in an endosomal sorting complex required for transport (ESCRT)-dependent manner. Here, we characterize a critical step in this process: axonal transport of ESCRT-0 component Hrs, necessary for sorting proteins into the ESCRT pathway and recruiting downstream ESCRT machinery to catalyze multivesicular body (MVB) formation. We find that neuronal activity stimulates the formation of presynaptic endosomes and MVBs, as well as the motility of Hrs+ vesicles in axons and their delivery to SV pools. Hrs+ vesicles co-transport ESCRT-0 component STAM1 and comprise a subset of Rab5+ vesicles, likely representing pro-degradative early endosomes. Furthermore, we identify kinesin motor protein KIF13A as essential for the activity-dependent transport of Hrs to SV pools and the degradation of SV membrane proteins. Together, these data demonstrate a novel activity- and KIF13A-dependent mechanism for mobilizing axonal transport of ESCRT machinery to facilitate the degradation of SV membrane proteins.
Collapse
Affiliation(s)
- Veronica Birdsall
- Neurobiology and Behavior PhD Program, Columbia University, New York, NY, USA
| | - Konner Kirwan
- Neurobiology and Behavior PhD Program, Columbia University, New York, NY, USA
| | - Mei Zhu
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Scott M Wilson
- Department of Neurobiology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shigeki Watanabe
- Department of Cell Biology, Johns Hopkins University, Baltimore, MD, USA.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Clarissa L Waites
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA .,Department of Neuroscience, Columbia University, New York, NY, USA
| |
Collapse
|
11
|
Hatstat AK, Pupi MD, Reinhart MC, McCafferty DG. Small Molecule Improvement of Trafficking Defects in Models of Neurodegeneration. ACS Chem Neurosci 2021; 12:3972-3984. [PMID: 34652126 DOI: 10.1021/acschemneuro.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Disrupted cellular trafficking and transport processes are hallmarks of many neurodegenerative disorders (NDs). Recently, efforts have been made toward developing and implementing experimental platforms to identify small molecules that may help restore normative trafficking functions. There have been a number of successes in targeting endomembrane trafficking with the identification of compounds that restore cell viability through rescue of protein transport and trafficking. Here, we describe some of the experimental platforms implemented for small molecule screening efforts for rescue of trafficking defects in neurodegeneration. A survey of phenotypically active small molecules identified to date is provided, including a summary of medicinal chemistry efforts and insights into putative targets and mechanisms of action. In particular, emphasis is put on ligands that demonstrate activity in more than one model of neurodegeneration as retention of phenotypic activity across ND models suggests conservation of biological targets across NDs.
Collapse
Affiliation(s)
- A. Katherine Hatstat
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michael D. Pupi
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Michaela C. Reinhart
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Dewey G. McCafferty
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| |
Collapse
|
12
|
Bidesi NSR, Vang Andersen I, Windhorst AD, Shalgunov V, Herth MM. The role of neuroimaging in Parkinson's disease. J Neurochem 2021; 159:660-689. [PMID: 34532856 PMCID: PMC9291628 DOI: 10.1111/jnc.15516] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/09/2021] [Accepted: 09/10/2021] [Indexed: 11/29/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder that affects millions of people worldwide. Two hallmarks of PD are the accumulation of alpha-synuclein and the loss of dopaminergic neurons in the brain. There is no cure for PD, and all existing treatments focus on alleviating the symptoms. PD diagnosis is also based on the symptoms, such as abnormalities of movement, mood, and cognition observed in the patients. Molecular imaging methods such as magnetic resonance imaging (MRI), single-photon emission computed tomography (SPECT), and positron emission tomography (PET) can detect objective alterations in the neurochemical machinery of the brain and help diagnose and study neurodegenerative diseases. This review addresses the application of functional MRI, PET, and SPECT in PD patients. We provide an overview of the imaging targets, discuss the rationale behind target selection, the agents (tracers) with which the imaging can be performed, and the main findings regarding each target's state in PD. Molecular imaging has proven itself effective in supporting clinical diagnosis of PD and has helped reveal that PD is a heterogeneous disorder, which has important implications for the development of future therapies. However, the application of molecular imaging for early diagnosis of PD or for differentiation between PD and atypical parkinsonisms has remained challenging. The final section of the review is dedicated to new imaging targets with which one can detect the PD-related pathological changes upstream from dopaminergic degeneration. The foremost of those targets is alpha-synuclein. We discuss the progress of tracer development achieved so far and challenges on the path toward alpha-synuclein imaging in humans.
Collapse
Affiliation(s)
- Natasha S R Bidesi
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Vang Andersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Albert D Windhorst
- Radiology and Nuclear Medicine, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Vladimir Shalgunov
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Matthias M Herth
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Physiology, Nuclear Medicine and PET, Rigshospitalet, Copenhagen, Denmark
| |
Collapse
|
13
|
Xiong M, Roshanbin S, Rokka J, Schlein E, Ingelsson M, Sehlin D, Eriksson J, Syvänen S. In vivo imaging of synaptic density with [ 11C]UCB-J PET in two mouse models of neurodegenerative disease. Neuroimage 2021; 239:118302. [PMID: 34174391 DOI: 10.1016/j.neuroimage.2021.118302] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/15/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
The positron emission tomography (PET) radioligand [11C]UCB-J binds to synaptic vesicle protein 2A (SV2A) and is used to investigate synaptic density in the living brain. Clinical studies have indicated reduced [11C]UCB-J binding in Alzheimer's disease (AD) and Parkinson's disease (PD) brains compared to healthy controls. Still, it is unknown whether [11C]UCB-J PET can visualise synaptic loss in mouse models of these disorders. Such models are essential for understanding disease pathology and for evaluating the effects of novel disease-modifying drug candidates. In the present study, synaptic density in transgenic models of AD (ArcSwe) and PD (L61) was studied using [11C]UCB-J PET. Data were acquired during 60 min after injection, and time-activity curves (TACs) in different brain regions and the left ventricle of the heart were generated based on the dynamic PET images. The [11C]UCB-J brain concentrations were expressed as standardised uptake value (SUV) over time. The area under the SUV curve (AUC), the ratio of AUC in the brain to that in the heart (AUCbrain/blood), and the volume of distribution (VT) obtained by kinetic modelling using the heart TAC as input were compared between transgenic and age-matched wild type (WT) mice. The L61 mice displayed 11-13% lower AUCbrain/blood ratio and brain VT generated by kinetic modeling compared to the control WT mice. In general, also transgenic ArcSwe mice tended to show lower [11C]UCB-J brain exposure than age-matched WT controls, but variation within the different animal groups was high. Older WT mice (18-20 months) showed lower [11C]UCB-J brain exposure than younger WT mice (8-9 months). Together, these data imply that [11C]UCB-J PET reflects synaptic density in mouse models of neurodegeneration and that inter-subject variation is large. In addition, the study suggested that model-independent AUCbrain/blood ratio can be used to evaluate [11C]UCB-J binding as an alternative to full pharmacokinetic modelling.
Collapse
Affiliation(s)
- Mengfei Xiong
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Sahar Roshanbin
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Johanna Rokka
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Eva Schlein
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Martin Ingelsson
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Dag Sehlin
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden
| | - Jonas Eriksson
- Department of Medicinal Chemistry, Uppsala University, Uppsala SE-751 23, Sweden; PET Centre, Uppsala University Hospital, Uppsala SE-751 85, Sweden
| | - Stina Syvänen
- Molecular Geriatrics, Department of Public Health and Caring Sciences, Uppsala University, Uppsala SE-751 85, Sweden.
| |
Collapse
|
14
|
Binda KH, Lillethorup TP, Real CC, Bærentzen SL, Nielsen MN, Orlowski D, Brooks DJ, Chacur M, Landau AM. Exercise protects synaptic density in a rat model of Parkinson's disease. Exp Neurol 2021; 342:113741. [PMID: 33965411 DOI: 10.1016/j.expneurol.2021.113741] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/04/2021] [Indexed: 01/09/2023]
Abstract
BACKGROUND Parkinson's disease (PD) is characterized by Lewy body and neurite pathology associated with dopamine terminal dysfunction. Clinically, it is associated with motor slowing, rigidity, and tremor. Postural instability and pain are also features. Physical exercise benefits PD patients - possibly by promoting neuroplasticity including synaptic regeneration. OBJECTIVES In a parkinsonian rat model, we test the hypotheses that exercise: (a) increases synaptic density and reduces neuroinflammation and (b) lowers the nociceptive threshold by increasing μ-opioid receptor expression. METHODS Brain autoradiography was performed on rats unilaterally injected with either 6-hydroxydopamine (6-OHDA) or saline and subjected to treadmill exercise over 5 weeks. [3H]UCB-J was used to measure synaptic vesicle glycoprotein 2A (SV2A) density. Dopamine D2/3 receptor and μ-opioid receptor availability were assessed with [3H]Raclopride and [3H]DAMGO, respectively, while neuroinflammation was detected with the 18kDA translocator protein (TSPO) marker [3H]PK11195. The nociceptive threshold was determined prior to and throughout the exercise protocol. RESULTS We confirmed a dopaminegic deficit with increased striatal [3H]Raclopride D2/3 receptor availability and reduced nigral tyrosine hydroxylase immunoreactivity in the ipsilateral hemisphere of all 6-OHDA-injected rats. Sedentary rats lesioned with 6-OHDA showed significant reduction of ipsilateral striatal and substantia nigra [3H]UCB-J binding while [3H]PK11195 showed increased ipsilateral striatal neuroinflammation. Lesioned rats who exercised had higher levels of ipsilateral striatal [3H]UCB-J binding and lower levels of neuroinflammation compared to sedentary lesioned rats. Striatal 6-OHDA injections reduced thalamic μ-opioid receptor availability but subsequent exercise restored binding. Exercise also raised thalamic and hippocampal SV2A synaptic density in 6-OHDA lesioned rats, accompanied by a rise in nociceptive threshold. CONCLUSION These data suggest that treadmill exercise protects nigral and striatal synaptic integrity in a rat lesion model of PD - possibly by promoting compensatory mechanisms. Exercise was also associated with reduced neuroinflammation post lesioning and altered opioid transmission resulting in an increased nociceptive threshold.
Collapse
Affiliation(s)
- K H Binda
- Translational Neuropsychiatry Unit, Aarhus University, Universitetsbyen 13, Building 2b, Aarhus C 8000, Denmark; Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark; Laboratory of Functional Neuroanatomy of Pain, Departamento de Anatomia, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| | - T P Lillethorup
- Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark.
| | - C C Real
- Translational Neuropsychiatry Unit, Aarhus University, Universitetsbyen 13, Building 2b, Aarhus C 8000, Denmark; Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark; Laboratory of Nuclear Medicine (LIM 43), Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| | - S L Bærentzen
- Translational Neuropsychiatry Unit, Aarhus University, Universitetsbyen 13, Building 2b, Aarhus C 8000, Denmark; Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark.
| | - M N Nielsen
- Translational Neuropsychiatry Unit, Aarhus University, Universitetsbyen 13, Building 2b, Aarhus C 8000, Denmark.
| | - D Orlowski
- Center for Experimental Neuroscience (CENSE), Department of Clinical Medicine, Aarhus University and Department of Neurosurgery, Aarhus University Hospital, Aarhus N, 8200, Denmark.
| | - D J Brooks
- Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark; Institute for Translational and Clinical Research, Newcastle University, Newcastle upon Tyne NE4 5PL, UK.
| | - M Chacur
- Laboratory of Functional Neuroanatomy of Pain, Departamento de Anatomia, Universidade de Sao Paulo, Sao Paulo, SP, Brazil.
| | - A M Landau
- Translational Neuropsychiatry Unit, Aarhus University, Universitetsbyen 13, Building 2b, Aarhus C 8000, Denmark; Department of Nuclear Medicine and PET, Aarhus University and Hospital, Palle Juul-Jensens Boulevard 165, J109, Aarhus N 8200, Denmark.
| |
Collapse
|
15
|
Na + leak-current channel (NALCN) at the junction of motor and neuropsychiatric symptoms in Parkinson's disease. J Neural Transm (Vienna) 2021; 128:749-762. [PMID: 33961117 DOI: 10.1007/s00702-021-02348-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/30/2021] [Indexed: 12/27/2022]
Abstract
Parkinson's disease (PD) is a debilitating movement disorder often accompanied by neuropsychiatric symptoms that stem from the loss of dopaminergic function in the basal ganglia and altered neurotransmission more generally. Akinesia, postural instability, tremors and frozen gait constitute the major motor disturbances, whereas neuropsychiatric symptoms include altered circadian rhythms, disordered sleep, depression, psychosis and cognitive impairment. Evidence is emerging that the motor and neuropsychiatric symptoms may share etiologic factors. Calcium/ion channels (CACNA1C, NALCN), synaptic proteins (SYNJ1) and neuronal RNA-binding proteins (RBFOX1) are among the risk genes that are common to PD and various psychiatric disorders. The Na+ leak-current channel (NALCN) is the focus of this review because it has been implicated in dystonia, regulation of movement, cognitive impairment, sleep and circadian rhythms. It regulates the resting membrane potential in neurons, mediates pace-making activity, participates in synaptic vesicle recycling and is functionally co-localized to the endoplasmic reticulum (ER)-several of the major processes adversely affected in PD. Here, we summarize the literature on mechanisms and pathways that connect the motor and neuropsychiatric symptoms of PD with a focus on recurring relationships to the NALCN. It is hoped that the various connections outlined here will stimulate further discussion, suggest additional areas for exploration and ultimately inspire novel treatment strategies.
Collapse
|
16
|
Kurvits L, Lättekivi F, Reimann E, Kadastik-Eerme L, Kasterpalu KM, Kõks S, Taba P, Planken A. Transcriptomic profiles in Parkinson's disease. Exp Biol Med (Maywood) 2021; 246:584-595. [PMID: 33148011 PMCID: PMC7934142 DOI: 10.1177/1535370220967325] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/17/2020] [Indexed: 12/31/2022] Open
Abstract
Transcriptomics in Parkinson's disease offers insights into the pathogenesis of Parkinson's disease but obtaining brain tissue has limitations. In order to bypass this issue, we profile and compare differentially expressed genes and enriched pathways (KEGG) in two peripheral tissues (blood and skin) of 12 Parkinson's disease patients and 12 healthy controls using RNA-sequencing technique and validation with RT-qPCR. Furthermore, we compare our results to previous Parkinson's disease post mortem brain tissue and blood results using the robust rank aggregation method. The results show no overlapping differentially expressed genes or enriched pathways in blood vs. skin in our sample sets (25 vs. 1068 differentially expressed genes with an FDR ≤ 0.05; 1 vs. 9 pathways in blood and skin, respectively). A meta-analysis from previous transcriptomic sample sets using either microarrays or RNA-Seq yields a robust rank aggregation list of cortical gene expression changes with 43 differentially expressed genes; a list of substantia nigra changes with 2 differentially expressed genes and a list of blood changes with 1 differentially expressed gene being statistically significant at FDR ≤ 0.05. In cortex 1, KEGG pathway was enriched, four in substantia nigra and two in blood. None of the differentially expressed genes or pathways overlap between these tissues. When comparing our previously published skin transcription analysis, two differentially expressed genes between the cortex robust rank aggregation and skin overlap. In this study, for the first time a meta-analysis is applied on transcriptomic sample sets in Parkinson's disease. Simultaneously, it explores the notion that Parkinson's disease is not just a neuronal tissue disease by exploring peripheral tissues. The comparison of different Parkinson's disease tissues yields surprisingly few significant differentially expressed genes and pathways, suggesting that divergent gene expression profiles in distinct cell lineages, metabolic and possibly iatrogenic effects create too much transcriptomic noise for detecting significant signal. On the other hand, there are signs that point towards Parkinson's disease-specific changes in non-neuronal peripheral tissues in Parkinson's disease, indicating that Parkinson's disease might be a multisystem disorder.
Collapse
Affiliation(s)
- Lille Kurvits
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Department of Neurology, Charité – Universitätsmedizin Berlin, Berlin 10117, Germany
| | - Freddy Lättekivi
- Institute of Pathophysiology, University of Tartu, Tartu 50411, Estonia
| | - Ene Reimann
- Estonian Genome Center Science Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Liis Kadastik-Eerme
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | | | - Sulev Kõks
- Centre for Comparative Genomics, Murdoch University, Perth, WA 6150, Australia
- Perron Institute for Neurological and Translational Science, University of Western Australia, QE II Medical Centre, Nedlands, WA 6009, Australia
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
| | - Anu Planken
- Department of Neurology and Neurosurgery, University of Tartu, Tartu 50406, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu 50406, Estonia
- Oncology and Haematology Clinic, North-Estonian Medical Centre, Tallinn 13419, Estonia
| |
Collapse
|
17
|
Fais M, Sanna G, Galioto M, Nguyen TTD, Trần MUT, Sini P, Carta F, Turrini F, Xiong Y, Dawson TM, Dawson VL, Crosio C, Iaccarino C. LRRK2 Modulates the Exocyst Complex Assembly by Interacting with Sec8. Cells 2021; 10:203. [PMID: 33498474 PMCID: PMC7909581 DOI: 10.3390/cells10020203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 11/17/2022] Open
Abstract
Mutations in LRRK2 play a critical role in both familial and sporadic Parkinson's disease (PD). Up to date, the role of LRRK2 in PD onset and progression remains largely unknown. However, experimental evidence highlights a critical role of LRRK2 in the control of vesicle trafficking, likely by Rab phosphorylation, that in turn may regulate different aspects of neuronal physiology. Here we show that LRRK2 interacts with Sec8, one of eight subunits of the exocyst complex. The exocyst complex is an evolutionarily conserved multisubunit protein complex mainly involved in tethering secretory vesicles to the plasma membrane and implicated in the regulation of multiple biological processes modulated by vesicle trafficking. Interestingly, Rabs and exocyst complex belong to the same protein network. Our experimental evidence indicates that LRRK2 kinase activity or the presence of the LRRK2 kinase domain regulate the assembly of exocyst subunits and that the over-expression of Sec8 significantly rescues the LRRK2 G2019S mutant pathological effect. Our findings strongly suggest an interesting molecular mechanism by which LRRK2 could modulate vesicle trafficking and may have important implications to decode the complex role that LRRK2 plays in neuronal physiology.
Collapse
Affiliation(s)
- Milena Fais
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Giovanna Sanna
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Manuela Galioto
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Thi Thanh Duyen Nguyen
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Mai Uyên Thi Trần
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Paola Sini
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | | | - Franco Turrini
- Nurex Srl, 07100 Sassari, Italy; (F.C.); (F.T.)
- Department of Oncology, University of Turin, 10126 Turin, Italy
| | - Yulan Xiong
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (Y.X.); (T.M.D.); (V.L.D.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ted M. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (Y.X.); (T.M.D.); (V.L.D.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Valina L. Dawson
- Neuroregeneration and Stem Cell Programs, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; (Y.X.); (T.M.D.); (V.L.D.)
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (M.F.); (G.S.); (M.G.); (T.T.D.N.); (M.U.T.T.); (P.S.); (C.C.)
| |
Collapse
|
18
|
Systems biology reveals reprogramming of the S-nitroso-proteome in the cortical and striatal regions of mice during aging process. Sci Rep 2020; 10:13913. [PMID: 32807865 PMCID: PMC7431412 DOI: 10.1038/s41598-020-70383-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
Cell aging depends on the rate of cumulative oxidative and nitrosative damage to DNA and proteins. Accumulated data indicate the involvement of protein S-nitrosylation (SNO), the nitric oxide (NO)-mediated posttranslational modification (PTM) of cysteine thiols, in different brain disorders. However, the changes and involvement of SNO in aging including the development of the organism from juvenile to adult state is still unknown. In this study, using the state-of-the-art mass spectrometry technology to identify S-nitrosylated proteins combined with large-scale computational biology, we tested the S-nitroso-proteome in juvenile and adult mice in both cortical and striatal regions. We found reprogramming of the S-nitroso-proteome in adult mice of both cortex and striatum regions. Significant biological processes and protein–protein clusters associated with synaptic and neuronal terms were enriched in adult mice. Extensive quantitative analysis revealed a large set of potentially pathological proteins that were significantly upregulated in adult mice. Our approach, combined with large scale computational biology allowed us to perform a system-level characterization and identification of the key proteins and biological processes that can serve as drug targets for aging and brain disorders in future studies.
Collapse
|
19
|
Matuskey D, Tinaz S, Wilcox KC, Naganawa M, Toyonaga T, Dias M, Henry S, Pittman B, Ropchan J, Nabulsi N, Suridjan I, Comley RA, Huang Y, Finnema SJ, Carson RE. Synaptic Changes in Parkinson Disease Assessed with in vivo Imaging. Ann Neurol 2020; 87:329-338. [PMID: 31953875 PMCID: PMC7065227 DOI: 10.1002/ana.25682] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Parkinson disease is characterized by motor and nonmotor symptoms, reduced striatal dopamine signaling, and loss of dopamine neurons in the substantia nigra. It is now known that the pathological process in Parkinson disease may begin decades before the clinical diagnosis and include a variety of neuronal alterations in addition to the dopamine system. METHODS This study examined the density of all synapses with synaptic vesicle glycoprotein 2A (SV2A) in Parkinson disease subjects with mild bilateral disease (n = 12) and matched normal controls (n = 12) using in vivo high-resolution positron emission tomographic imaging as well as postmortem autoradiography in an independent sample with Parkinson disease (n = 15) and normal controls (n = 13) in the substantia nigra and putamen. RESULTS A group-by-brain region interaction effect (F10, 22 = 3.52, p = 0.007) was observed in the primary brain areas with in vivo SV2A binding. Post hoc analyses revealed that the Parkinson disease group exhibited lower SV2A in the substantia nigra (-45%; p < 0.001), red nucleus (-31%; p = 0.03), and locus coeruleus (-17%; p = 0.03). Exploratory analyses also revealed lower SV2A binding in clinically relevant cortical areas. Using autoradiography, we confirmed lower SV2A in the substantia nigra (-17%; p < 0.005) and nonsignificant findings in the putamen (-4%; p = 0.06). INTERPRETATION This work provides the first evidence of synaptic loss in brainstem nuclei involved in the pathogenesis of Parkinson disease in living patients. SV2A imaging holds promise for understanding synaptic changes central to the disease. Ann Neurol 2020;87:329-338.
Collapse
Affiliation(s)
- David Matuskey
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
- Department of PsychiatryYale UniversityNew HavenCT
- Department of NeurologyYale UniversityNew HavenCT
| | - Sule Tinaz
- Department of NeurologyYale UniversityNew HavenCT
| | - Kyle C. Wilcox
- Translational ImagingIntegrated Science and TechnologyAbbVieNorth ChicagoIL
| | - Mika Naganawa
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Takuya Toyonaga
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Mark Dias
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Shannan Henry
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | | | - Jim Ropchan
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Nabeel Nabulsi
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Ivonne Suridjan
- Translational ImagingIntegrated Science and TechnologyAbbVieNorth ChicagoIL
| | - Robert A. Comley
- Translational ImagingIntegrated Science and TechnologyAbbVieNorth ChicagoIL
| | - Yiyun Huang
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| | - Sjoerd J. Finnema
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
- Translational ImagingIntegrated Science and TechnologyAbbVieNorth ChicagoIL
| | - Richard E. Carson
- Positron Emission Tomography Research Center, Department of Radiology and Biomedical ImagingYale UniversityNew HavenCT
| |
Collapse
|
20
|
Area-Specific Synapse Structure in Branched Posterior Nucleus Axons Reveals a New Level of Complexity in Thalamocortical Networks. J Neurosci 2020; 40:2663-2679. [PMID: 32054677 PMCID: PMC7096142 DOI: 10.1523/jneurosci.2886-19.2020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 02/04/2020] [Accepted: 02/05/2020] [Indexed: 12/05/2022] Open
Abstract
Thalamocortical posterior nucleus (Po) axons innervating the vibrissal somatosensory (S1) and motor (MC) cortices are key links in the brain neuronal network that allows rodents to explore the environment whisking with their motile snout vibrissae. Thalamocortical posterior nucleus (Po) axons innervating the vibrissal somatosensory (S1) and motor (MC) cortices are key links in the brain neuronal network that allows rodents to explore the environment whisking with their motile snout vibrissae. Here, using fine-scale high-end 3D electron microscopy, we demonstrate in adult male C57BL/6 wild-type mice marked differences between MC versus S1 Po synapses in (1) bouton and active zone size, (2) neurotransmitter vesicle pool size, (3) distribution of mitochondria around synapses, and (4) proportion of synapses established on dendritic spines and dendritic shafts. These differences are as large, or even more pronounced, than those between Po and ventro-posterior thalamic nucleus synapses in S1. Moreover, using single-axon transfection labeling, we demonstrate that the above differences actually occur on the MC versus the S1 branches of individual Po cell axons that innervate both areas. Along with recently-discovered divergences in efficacy and plasticity, the synaptic structure differences reported here thus reveal a new subcellular level of complexity. This is a finding that upends current models of thalamocortical circuitry, and that might as well illuminate the functional logic of other branched projection axon systems. SIGNIFICANCE STATEMENT Many long-distance brain connections depend on neurons whose branched axons target separate regions. Using 3D electron microscopy and single-cell transfection, we investigated the mouse Posterior thalamic nucleus (Po) cell axons that simultaneously innervate motor and sensory areas of the cerebral cortex involved in whisker movement control. We demonstrate significant differences in the size of the boutons made in each area by individual Po axons, as well as in functionally-relevant parameters in the composition of their synapses. In addition, we found similarly large differences between the synapses of Po versus ventral posteromedial thalamic nucleus axons in the whisker sensory cortex. Area-specific synapse structure in individual axons implies a new, unsuspected level of complexity in long-distance brain connections.
Collapse
|
21
|
Bayne AN, Trempe JF. Mechanisms of PINK1, ubiquitin and Parkin interactions in mitochondrial quality control and beyond. Cell Mol Life Sci 2019; 76:4589-4611. [PMID: 31254044 PMCID: PMC11105328 DOI: 10.1007/s00018-019-03203-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/13/2019] [Accepted: 06/19/2019] [Indexed: 12/20/2022]
Abstract
Parkinson's disease (PD) is a degenerative movement disorder resulting from the loss of specific neuron types in the midbrain. Early environmental and pathophysiological studies implicated mitochondrial damage and protein aggregation as the main causes of PD. These findings are now vindicated by the characterization of more than 20 genes implicated in rare familial forms of the disease. In particular, two proteins encoded by the Parkin and PINK1 genes, whose mutations cause early-onset autosomal recessive PD, function together in a mitochondrial quality control pathway. In this review, we will describe recent development in our understanding of their mechanisms of action, structure, and function. We explain how PINK1 acts as a mitochondrial damage sensor via the regulated proteolysis of its N-terminus and the phosphorylation of ubiquitin tethered to outer mitochondrial membrane proteins. In turn, phospho-ubiquitin recruits and activates Parkin via conformational changes that increase its ubiquitin ligase activity. We then describe how the formation of polyubiquitin chains on mitochondria triggers the recruitment of the autophagy machinery or the formation of mitochondria-derived vesicles. Finally, we discuss the evidence for the involvement of these mechanisms in physiological processes such as immunity and inflammation, as well as the links to other PD genes.
Collapse
Affiliation(s)
- Andrew N Bayne
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada
| | - Jean-François Trempe
- Department of Pharmacology and Therapeutics and Centre for Structural Biology, McGill University, 3655 Prom Sir William Osler, Montreal, QC, H3G 1Y6, Canada.
| |
Collapse
|
22
|
Abstract
Defects in membrane trafficking are hallmarks of neurodegeneration. Rab GTPases are key regulators of membrane trafficking. Alterations of Rab GTPases, or the membrane compartments they regulate, are associated with virtually all neuronal activities in health and disease. The observation that many Rab GTPases are associated with neurodegeneration has proven a challenge in the quest for cause and effect. Neurodegeneration can be a direct consequence of a defect in membrane trafficking. Alternatively, changes in membrane trafficking may be secondary consequences or cellular responses. The secondary consequences and cellular responses, in turn, may protect, represent inconsequential correlates or function as drivers of pathology. Here, we attempt to disentangle the different roles of membrane trafficking in neurodegeneration by focusing on selected associations with Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and selected neuropathies. We provide an overview of current knowledge on Rab GTPase functions in neurons and review the associations of Rab GTPases with neurodegeneration with respect to the following classifications: primary cause, secondary cause driving pathology or secondary correlate. This analysis is devised to aid the interpretation of frequently observed membrane trafficking defects in neurodegeneration and facilitate the identification of true causes of pathology.
Collapse
|
23
|
Su M, Zhou J, Duan Z, Zhang J. Transcriptional analysis of renal dopamine-mediated Na + homeostasis response to environmental salinity stress in Scatophagus argus. BMC Genomics 2019; 20:418. [PMID: 31126236 PMCID: PMC6534869 DOI: 10.1186/s12864-019-5795-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 05/10/2019] [Indexed: 02/07/2023] Open
Abstract
Background To control the osmotic pressure in the body, physiological adjustments to salinity fluctuations require the fish to regulate body fluid homeostasis in relation to environmental change via osmoregulation. Previous studies related to osmoregulation were focused primarily on the gill; however, little is known about another organ involved in osmoregulation, the kidney. The salinity adaptation of marine fish involves complex physiological traits, metabolic pathways and molecular and gene networks in osmoregulatory organs. To further explore of the salinity adaptation of marine fish with regard to the role of the kidney, the euryhaline fish Scatophagus argus was employed in the present study. Renal expression profiles of S. argus at different salinity levels were characterized using RNA-sequencing, and an integrated approach of combining molecular tools with physiological and biochemical techniques was utilized to reveal renal osmoregulatory mechanisms in vivo and in vitro. Results S. argus renal transcriptomes from the hyposaline stress (0‰, freshwater [FW]), hypersaline stress (50‰, hypersaline water [HW]) and control groups (25‰) were compared to elucidate potential osmoregulatory mechanisms. In total, 19,012 and 36,253 differentially expressed genes (DEGs) were obtained from the FW and HW groups, respectively. Based on the functional classification of DEGs, the renal dopamine system-induced Na+ transport was demonstrated to play a fundamental role in osmoregulation. In addition, for the first time in fish, many candidate genes associated with the dopamine system were identified. Furthermore, changes in environmental salinity affected renal dopamine release/reuptake by regulating the expression of genes related to dopamine reuptake (dat and nkaα1), vesicular traffic-mediated dopamine release (pink1, lrrk2, ace and apn), DAT phosphorylation (CaMKIIα and pkcβ) and internalization (akt1). The associated transcriptional regulation ensured appropriate extracellular dopamine abundance in the S. argus kidney, and fluctuations in extracellular dopamine produced a direct influence on Na+/K+-ATPase (NKA) expression and activity, which is associated with Na+ homeostasis. Conclusions These transcriptomic data provided insight into the molecular basis of renal osmoregulation in S. argus. Significantly, the results of this study revealed the mechanism of renal dopamine system-induced Na+ transport is essential in fish osmoregulation. Electronic supplementary material The online version of this article (10.1186/s12864-019-5795-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Maoliang Su
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Jianan Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Zhengyu Duan
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, College of Fisheries and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Junbin Zhang
- Shenzhen Key Laboratory of Marine Bioresource & Eco-Environmental Science, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China. .,Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| |
Collapse
|
24
|
Seol W, Nam D, Son I. Rab GTPases as Physiological Substrates of LRRK2 Kinase. Exp Neurobiol 2019; 28:134-145. [PMID: 31138985 PMCID: PMC6526114 DOI: 10.5607/en.2019.28.2.134] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/14/2019] [Accepted: 02/21/2019] [Indexed: 12/11/2022] Open
Abstract
LRRK2 (Leucine-Rich Repeat Kinase 2) is a gene whose specific mutations cause Parkinson's disease (PD), the most common neurodegenerative movement disorder. LRRK2 harbors GTPase and kinase activities, two enzyme activities that play critical roles in the regulation of cellular signal transduction. Among the several LRRK2 pathogenic mutations, the most prevalent G2019S mutation increases its kinase activity when compared with the wild-type (WT), suggesting that LRRK2 kinase substrates are potential culprits of PD pathogenesis. Although there were several studies to identify LRRK2 kinase substrates, most of them mainly employed in vitro kinase assays. Therefore, it remains uncertain whether the identified substrates were real physiological substrates. However, efforts to determine physiological LRRK2 kinase substrates have recently identified several members of the Rab GTPase family as physiological LRRK2 kinase substrates. A conserved threonine or serine in the switch II domain of certain Rab GTPase family members (Rab3A/B/C/D, Rab5A/B, Rab8A/B, Rab10, Rab12, Rab29, Rab35 and Rab43) has been pinpointed to be phosphorylated by LRRK2 in cells using sophisticated phosphoproteomics technology in combination with LRRK2-specific kinase inhibitors. The Rab GTPases regulate vesicle trafficking, suggesting that LRRK2 may be a regulator of such vesicle trafficking, confirming previously suggested LRRK2 functions. However, how the consequence of the LRRK2-mediated Rab phosphorylation is related to PD pathogenesis is not clear. This review briefly summarizes the recent results about LRRK2-mediated Rab phosphorylation studies.
Collapse
Affiliation(s)
- Wongi Seol
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Daleum Nam
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| | - Ilhong Son
- InAm Neuroscience Research Center, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
- Department of Neurology, Sanbon Medical Center, College of Medicine, Wonkwang University, Gunpo 15865, Korea
| |
Collapse
|
25
|
Abstract
Parkinson’s disease (PD) is a neurodegenerative disease characterized by a progressive loss of dopaminergic neurons from the nigrostriatal pathway, formation of Lewy bodies, and microgliosis. During the past decades multiple cellular pathways have been associated with PD pathology (i.e., oxidative stress, endosomal-lysosomal dysfunction, endoplasmic reticulum stress, and immune response), yet disease-modifying treatments are not available. We have recently used genetic data from familial and sporadic cases in an unbiased approach to build a molecular landscape for PD, revealing lipids as central players in this disease. Here we extensively review the current knowledge concerning the involvement of various subclasses of fatty acyls, glycerolipids, glycerophospholipids, sphingolipids, sterols, and lipoproteins in PD pathogenesis. Our review corroborates a central role for most lipid classes, but the available information is fragmented, not always reproducible, and sometimes differs by sex, age or PD etiology of the patients. This hinders drawing firm conclusions about causal or associative effects of dietary lipids or defects in specific steps of lipid metabolism in PD. Future technological advances in lipidomics and additional systematic studies on lipid species from PD patient material may improve this situation and lead to a better appreciation of the significance of lipids for this devastating disease.
Collapse
|
26
|
Taguchi YH, Wang H. Exploring MicroRNA Biomarkers for Parkinson's Disease from mRNA Expression Profiles. Cells 2018; 7:E245. [PMID: 30563060 PMCID: PMC6315543 DOI: 10.3390/cells7120245] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a chronic, progressive neurodegenerative disease characterized by both motor and nonmotor features. The diagnose of PD is based on a review of patients' signs and symptoms, and neurological and physical examinations. So far, no tests have been devised that can conclusively diagnose PD. In this study, we explore both microRNA and gene biomarkers for PD. Microarray gene expression profiles for PD patients and healthy control are analyzed using a principal component analysis (PCA)-based unsupervised feature extraction (FE). 244 genes are selected to be potential gene biomarkers for PD. In addition, we implement these genes into Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, and find that the 15 microRNAs (miRNAs), hsa-miR-92a-3p, 16-5p, 615-3p, 877-3p, 100-5p, 320a, 877-5p, 23a-3p, 484, 23b-3p, 15a-5p, 324-3p, 19b-3p, 7b-5p and 505-3p, significantly target these 244 genes. These miRNAs are shown to be significantly related to PD. This reveals that both selected genes and miRNAs are potential biomarkers for PD.
Collapse
Affiliation(s)
- Y-H Taguchi
- Department of Physics, Chuo University, 1-13-27 Kasuga, Bunky-ku, Tokyo 112-8551, Japan.
| | - Hsiuying Wang
- Institute of Statistics, National Chiao Tung University, Hsinchu 30010, Taiwan.
| |
Collapse
|
27
|
Thalamic Proteome Changes and Behavioral Impairments in Thiamine-deficient Rats. Neuroscience 2018; 385:181-197. [DOI: 10.1016/j.neuroscience.2018.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 04/24/2018] [Accepted: 06/04/2018] [Indexed: 11/23/2022]
|
28
|
Sharma S, Young RJ, Chen J, Chen X, Oh EC, Schiller MR. Minimotifs dysfunction is pervasive in neurodegenerative disorders. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2018; 4:414-432. [PMID: 30225339 PMCID: PMC6139474 DOI: 10.1016/j.trci.2018.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Minimotifs are modular contiguous peptide sequences in proteins that are important for posttranslational modifications, binding to other molecules, and trafficking to specific subcellular compartments. Some molecular functions of proteins in cellular pathways can be predicted from minimotif consensus sequences identified through experimentation. While a role for minimotifs in regulating signal transduction and gene regulation during disease pathogenesis (such as infectious diseases and cancer) is established, the therapeutic use of minimotif mimetic drugs is limited. In this review, we discuss a general theme identifying a pervasive role of minimotifs in the pathomechanism of neurodegenerative diseases. Beyond their longstanding history in the genetics of familial neurodegeneration, minimotifs are also major players in neurotoxic protein aggregation, aberrant protein trafficking, and epigenetic regulation. Generalizing the importance of minimotifs in neurodegenerative diseases offers a new perspective for the future study of neurodegenerative mechanisms and the investigation of new therapeutics.
Collapse
Affiliation(s)
- Surbhi Sharma
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Richard J. Young
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
| | - Jingchun Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
| | - Xiangning Chen
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- Department of Psychology, Las Vegas, NV, USA
| | - Edwin C. Oh
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
| | - Martin R. Schiller
- Nevada Institute of Personalized Medicine, Las Vegas, NV, USA
- School of Life Sciences, Las Vegas, NV, USA
- School of Medicine, Las Vegas, NV, USA
| |
Collapse
|
29
|
|
30
|
Moradifard S, Hoseinbeyki M, Ganji SM, Minuchehr Z. Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. Sci Rep 2018; 8:4767. [PMID: 29555910 PMCID: PMC5859169 DOI: 10.1038/s41598-018-20959-0] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 01/24/2018] [Indexed: 12/11/2022] Open
Abstract
Understanding the molecular mechanisms underlying Alzheimer’s disease (AD) is necessary for the diagnosis and treatment of this neurodegenerative disorder. It is therefore important to detect the most important genes and miRNAs, which are associated with molecular events, and studying their interactions for recognition of AD mechanisms. Here we focus on the genes and miRNAs expression profile, which we have detected the miRNA target genes involved in AD. These are the most quintessential to find the most important miRNA, to target genes and their important pathways. A total of 179 differentially expressed miRNAs (DEmiRs) and 1404 differentially expressed genes (DEGs) were obtained from a comprehensive meta-analysis. Also, regions specific genes with their molecular function in AD have been demonstrated. We then focused on miRNAs which regulated most genes in AD, alongside we analyzed their pathways. The miRNA-30a-5p and miRNA-335 elicited a major function in AD after analyzing the regulatory network, we showed they were the most regulatory miRNAs in the AD. In conclusion, we demonstrated the most important genes, miRNAs, miRNA-mRNA interactions and their related pathways in AD using Bioinformatics methods. Accordingly, our defined genes and miRNAs could be used for future molecular studies in the context of AD.
Collapse
Affiliation(s)
- Shirin Moradifard
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Moslem Hoseinbeyki
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | | | - Zarrin Minuchehr
- National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran.
| |
Collapse
|
31
|
Wang Q, Li WX, Dai SX, Guo YC, Han FF, Zheng JJ, Li GH, Huang JF. Meta-Analysis of Parkinson's Disease and Alzheimer's Disease Revealed Commonly Impaired Pathways and Dysregulation of NRF2-Dependent Genes. J Alzheimers Dis 2018; 56:1525-1539. [PMID: 28222515 DOI: 10.3233/jad-161032] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Many lines of evidence suggest that Parkinson's disease (PD) and Alzheimer's disease (AD) have common characteristics, such as mitochondrial dysfunction and oxidative stress. As the underlying molecular mechanisms are unclear, we perform a meta-analysis with 9 microarray datasets of PD studies and 7 of AD studies to explore it. Functional enrichment analysis revealed that PD and AD both showed dysfunction in the synaptic vesicle cycle, GABAergic synapses, phagosomes, oxidative phosphorylation, and TCA cycle pathways, and AD had more enriched genes. Comparing the differentially expressed genes between AD and PD, we identified 54 common genes shared by more than six tissues. Among them, 31 downregulated genes contained the antioxidant response element (ARE) consensus sequence bound by NRF2. NRF2 is a transcription factor, which protects cells against oxidative stress through coordinated upregulation of ARE-driven genes. To our surprise, although NRF2 was upregulated, its target genes were all downregulated. Further exploration found that MAFF was upregulated in all tissues and significantly negatively correlated with the 31 NRF2-dependent genes in diseased conditions. Previous studies have demonstrated over-expressed small MAFs can form homodimers and act as transcriptional repressors. Therefore, MAFF might play an important role in dysfunction of NRF2 regulatory network in PD and AD.
Collapse
Affiliation(s)
- Qian Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Wen-Xing Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Institute of Health Sciences, Anhui University, Hefei, Anhui, China
| | - Shao-Xing Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Cheng Guo
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Fei-Fei Han
- Immuno-Metabolic Computational Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Jun-Juan Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Gong-Hua Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jing-Fei Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China.,KIZ-SU Joint Laboratory of Animal Models and Drug Development, College of Pharmaceutical Sciences, Soochow University, Kunming, Yunnan, China.,Collaborative Innovation Center for Natural Products and Biological Drugs of Yunnan, Kunming, Yunnan, China.,Chinese University of Hong Kong Joint Research Center for Bio-resources and Human Disease Mechanisms, Kunming, Yunnan, China
| |
Collapse
|
32
|
Liao EH, Gray L, Tsurudome K, El-Mounzer W, Elazzouzi F, Baim C, Farzin S, Calderon MR, Kauwe G, Haghighi AP. Kinesin Khc-73/KIF13B modulates retrograde BMP signaling by influencing endosomal dynamics at the Drosophila neuromuscular junction. PLoS Genet 2018; 14:e1007184. [PMID: 29373576 PMCID: PMC5802963 DOI: 10.1371/journal.pgen.1007184] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 02/07/2018] [Accepted: 01/03/2018] [Indexed: 11/18/2022] Open
Abstract
Retrograde signaling is essential for neuronal growth, function and survival; however, we know little about how signaling endosomes might be directed from synaptic terminals onto retrograde axonal pathways. We have identified Khc-73, a plus-end directed microtubule motor protein, as a regulator of sorting of endosomes in Drosophila larval motor neurons. The number of synaptic boutons and the amount of neurotransmitter release at the Khc-73 mutant larval neuromuscular junction (NMJ) are normal, but we find a significant decrease in the number of presynaptic release sites. This defect in Khc-73 mutant larvae can be genetically enhanced by a partial genetic loss of Bone Morphogenic Protein (BMP) signaling or suppressed by activation of BMP signaling in motoneurons. Consistently, activation of BMP signaling that normally enhances the accumulation of phosphorylated form of BMP transcription factor Mad in the nuclei, can be suppressed by genetic removal of Khc-73. Using a number of assays including live imaging in larval motor neurons, we show that loss of Khc-73 curbs the ability of retrograde-bound endosomes to leave the synaptic area and join the retrograde axonal pathway. Our findings identify Khc-73 as a regulator of endosomal traffic at the synapse and modulator of retrograde BMP signaling in motoneurons.
Collapse
Affiliation(s)
- Edward H. Liao
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Lindsay Gray
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - Kazuya Tsurudome
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | | | - Fatima Elazzouzi
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Christopher Baim
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Sarah Farzin
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Mario R. Calderon
- Buck Institute for Research on Aging, Novato, CA, United States of America
- Department of Physiology, McGill University, Montreal, QC, Canada
| | - Grant Kauwe
- Buck Institute for Research on Aging, Novato, CA, United States of America
| | - A. Pejmun Haghighi
- Buck Institute for Research on Aging, Novato, CA, United States of America
- Department of Physiology, McGill University, Montreal, QC, Canada
- * E-mail:
| |
Collapse
|
33
|
Joensuu M, Martínez-Mármol R, Padmanabhan P, Glass NR, Durisic N, Pelekanos M, Mollazade M, Balistreri G, Amor R, Cooper-White JJ, Goodhill GJ, Meunier FA. Visualizing endocytic recycling and trafficking in live neurons by subdiffractional tracking of internalized molecules. Nat Protoc 2017; 12:2590-2622. [PMID: 29189775 DOI: 10.1038/nprot.2017.116] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of endocytic pathway dynamics is restricted by the diffraction limit of light microscopy. Although super-resolution techniques can overcome this issue, highly crowded cellular environments, such as nerve terminals, can also dramatically limit the tracking of multiple endocytic vesicles such as synaptic vesicles (SVs), which in turn restricts the analytical dissection of their discrete diffusional and transport states. We recently introduced a pulse-chase technique for subdiffractional tracking of internalized molecules (sdTIM) that allows the visualization of fluorescently tagged molecules trapped in individual signaling endosomes and SVs in presynapses or axons with 30- to 50-nm localization precision. We originally developed this approach for tracking single molecules of botulinum neurotoxin type A, which undergoes activity-dependent internalization and retrograde transport in autophagosomes. This method was then adapted to localize the signaling endosomes containing cholera toxin subunit-B that undergo retrograde transport in axons and to track SVs in the crowded environment of hippocampal presynapses. We describe (i) the construction of a custom-made microfluidic device that enables control over neuronal orientation; (ii) the 3D printing of a perfusion system for sdTIM experiments performed on glass-bottom dishes; (iii) the dissection, culturing and transfection of hippocampal neurons in microfluidic devices; and (iv) guidance on how to perform the pulse-chase experiments and data analysis. In addition, we describe the use of single-molecule-tracking analytical tools to reveal the average and the heterogeneous single-molecule mobility behaviors. We also discuss alternative reagents and equipment that can, in principle, be used for sdTIM experiments and describe how to adapt sdTIM to image nanocluster formation and/or tubulation in early endosomes during sorting events. The procedures described in this protocol take ∼1 week.
Collapse
Affiliation(s)
- Merja Joensuu
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Ramon Martínez-Mármol
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Pranesh Padmanabhan
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Nick R Glass
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia
| | - Nela Durisic
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Matthew Pelekanos
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Mahdie Mollazade
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Giuseppe Balistreri
- Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| | - Justin J Cooper-White
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland, Australia.,Division of General Microbiology, Department of Biosciences, University of Helsinki, Helsinki, Finland.,School of Chemical Engineering, The University of Queensland, Brisbane, Queensland, Australia.,Materials Science and Engineering Division, CSIRO, Clayton, Victoria, Australia.,UQ Centre for Stem Cell Ageing and Regenerative Engineering, The University of Queensland, Brisbane, Queensland, Australia
| | - Geoffrey J Goodhill
- Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia.,School of Mathematics and Physics, The University of Queensland, Brisbane, Queensland, Australia
| | - Frédéric A Meunier
- Clem Jones Centre for Ageing Dementia Research, The University of Queensland, Brisbane, Queensland, Australia.,Queensland Brain Institute, The University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
34
|
Chuang YH, Paul KC, Bronstein JM, Bordelon Y, Horvath S, Ritz B. Parkinson's disease is associated with DNA methylation levels in human blood and saliva. Genome Med 2017; 9:76. [PMID: 28851441 PMCID: PMC5576382 DOI: 10.1186/s13073-017-0466-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/08/2017] [Indexed: 12/21/2022] Open
Abstract
Background Several articles suggest that DNA methylation levels in blood relate to Parkinson’s disease (PD) but there is a need for a large-scale study that involves suitable population based controls. The purposes of the study were: (1) to study whether PD status is associated with DNA methylation levels in blood/saliva; (2) to study whether observed associations relate to blood cell types; and (3) to characterize genome-wide significant markers (“CpGs”) and clusters of CpGs (co-methylation modules) in terms of biological pathways. Methods In a population-based case control study of PD, we studied blood samples from 335 PD cases and 237 controls and saliva samples from another 128 cases and 131 controls. DNA methylation data were generated from over 486,000 CpGs using the Illumina Infinium array. We identified modules of CpGs (clusters) using weighted correlation network analysis (WGCNA). Results Our cross-sectional analysis of blood identified 82 genome-wide significant CpGs (including cg02489202 in LARS2 p = 8.3 × 10–11 and cg04772575 in ABCB9 p = 4.3 × 10–10). Three out of six PD related co-methylation modules in blood were significantly enriched with immune system related genes. Our analysis of saliva identified five significant CpGs. PD-related CpGs are located near genes that relate to mitochondrial function, neuronal projection, cytoskeleton organization, systemic immune response, and iron handling. Conclusions This study demonstrates that: (1) PD status has a profound association with DNA methylation levels in blood and saliva; and (2) the most significant PD-related changes reflect changes in blood cell composition. Overall, this study highlights the role of the immune system in PD etiology but future research will need to address the causal structure of these relationships. Electronic supplementary material The online version of this article (doi:10.1186/s13073-017-0466-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yu-Hsuan Chuang
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, 650 Charles E. Young Drive, Box 951772, Los Angeles, CA, 90095-1772, USA
| | - Kimberly C Paul
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, 650 Charles E. Young Drive, Box 951772, Los Angeles, CA, 90095-1772, USA
| | - Jeff M Bronstein
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Yvette Bordelon
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA, 90095-7088, USA. .,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, 650 Charles E. Young Drive, Box 951772, Los Angeles, CA, 90095-1772, USA. .,Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA. .,Department of Environmental Health, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
| |
Collapse
|
35
|
Synaptic vesicle 2C and its synaptic-related function. Clin Chim Acta 2017; 472:112-117. [PMID: 28774501 DOI: 10.1016/j.cca.2017.07.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 07/27/2017] [Accepted: 07/30/2017] [Indexed: 11/22/2022]
Abstract
Synaptic vesicle 2 C (SV2C) is a novel isoform belonging to the synaptic vesicle 2 (SV2) protein superfamily; a family of proteins known to have roles in vesicle trafficking, exocytosis and neurotransmission. In humans, SV2C is expressed in evolutionarily older brain regions, and is a known receptor for botulinum neurotoxin/A (BoNT/A), controlling glucose-evoked granule recruitment and regulating dopamine release, thus serving as a potential target molecule in the treatment of psychosis. In addition, recent researches have shown that SV2C regulates hypertension and accelerates venous thromboembolism (VTE) and coagulation pathways and may play roles in several non-nervous system diseases. In terms of regulation, SV2C is positively regulated by both alendronate and statins. As SV2C may provide a potential novel therapeutic target for psychosis and other diseases, this article reviews the progress made thus far in understanding the structure, distribution, function and regulation of SV2C.
Collapse
|
36
|
Activity-Dependent Degradation of Synaptic Vesicle Proteins Requires Rab35 and the ESCRT Pathway. J Neurosci 2017; 36:8668-86. [PMID: 27535913 DOI: 10.1523/jneurosci.0725-16.2016] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 06/29/2016] [Indexed: 02/06/2023] Open
Abstract
UNLABELLED Synaptic vesicle (SV) pools must maintain a functional repertoire of proteins to efficiently release neurotransmitter. The accumulation of old or damaged proteins on SV membranes is linked to synaptic dysfunction and neurodegeneration. However, despite the importance of SV protein turnover for neuronal health, the molecular mechanisms underlying this process are largely unknown. Here, we have used dissociated rat hippocampal neurons to investigate the pathway for SV protein degradation. We find that neuronal activity drives the degradation of a subset of SV proteins and that the endosomal sorting complex required for transport (ESCRT) machinery and SV-associated GTPase Rab35 are key elements of this use-dependent degradative pathway. Specifically, neuronal activity induces Rab35 activation and binding to the ESCRT-0 protein Hrs, which we have identified as a novel Rab35 effector. These actions recruit the downstream ESCRT machinery to SV pools, thereby initiating SV protein degradation via the ESCRT pathway. Our findings show that the Rab35/ESCRT pathway facilitates the activity-dependent removal of specific proteins from SV pools, thereby maintaining presynaptic protein homeostasis. SIGNIFICANCE STATEMENT Synaptic transmission is mediated by the release of chemical neurotransmitters from synaptic vesicles (SVs). This tightly regulated process requires a functional pool of SVs, necessitating cellular mechanisms for removing old or damaged proteins that could impair SV cycling. Here, we show that a subset of SV proteins is degraded in an activity-dependent manner and that key steps in this degradative pathway are the activation of the small GTPase Rab35 and the subsequent recruitment of the endosomal sorting complex required for transport (ESCRT) machinery to SV pools. Further, we demonstrate that ESCRT-0 component Hrs is an effector of Rab35, thus providing novel mechanistic insight into the coupling of neuronal activity with SV protein degradation and the maintenance of functional SV pools.
Collapse
|
37
|
Martí Y, Matthaeus F, Lau T, Schloss P. Methyl-4-phenylpyridinium (MPP+) differentially affects monoamine release and re-uptake in murine embryonic stem cell-derived dopaminergic and serotonergic neurons. Mol Cell Neurosci 2017; 83:37-45. [PMID: 28673772 DOI: 10.1016/j.mcn.2017.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 06/06/2017] [Accepted: 06/26/2017] [Indexed: 11/19/2022] Open
Abstract
1-Methyl-4-phenyl-1,2,5,6-tetrahydropyridine (MPTP) is known to selectively damage dopaminergic (DA) cells in the substantia nigra and to produce symptoms which are alike to those observed in Parkinson's disease (PD). Based on the similarity between MPTP-induced neurotoxicity and PD-related neuropathology, application of MPTP or its metabolite methyl-4-phenylpyridinium (MPP+) was successfully established in experimental rodent models to study PD-related neurodegenerative events. MPP+ is taken up by the dopamine transporter (DAT) into DA neurons where it exerts its neurotoxic action on mitochondria by affecting complex I of the respiratory chain. MPP+ is also a high affinity substrate for the serotonin transporter (SERT), however little is known about possible toxic effects of MPP+ on serotonergic (5-HT) neurons. In order to compare cell type-specific effects of MPP+ treatment, we have differentiated mouse embryonic stem (ES) cells into DA and 5-HT neurons and studied the impact of MPP+ treatment on both types of monoaminergic neurons in vitro. MPP+ treatment impacts on mitochondrial membrane potential in DA as well as 5-HT ES cell-derived neurons. Although mitochondria metabolisms are similarly affected, synaptic vesicle cycling is only impaired in DA ES cell-derived neurons. Most importantly we show that MPP+ induces DAT externalization in DA neurons, but internalization of SERT in 5-HT neurons. This diverse MPP+-induced transporter trafficking is reflected by elevated substrate uptake in DA neurons, and diminished substrate uptake in 5-HT neurons. In summary, our experimental data point toward differential effects of MPP+ intoxication on neurotransmitter release and re-uptake in different types of monoaminergic neurons.
Collapse
Affiliation(s)
- Yasmina Martí
- Biochemical Laboratory, Dept. Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany; Hector Institute for Translational Brain Research, Central Institute for Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Friederike Matthaeus
- Biochemical Laboratory, Dept. Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany
| | - Thorsten Lau
- Hector Institute for Translational Brain Research, Central Institute for Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany.
| | - Patrick Schloss
- Biochemical Laboratory, Dept. Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Germany
| |
Collapse
|
38
|
Maulik M, Mitra S, Bult-Ito A, Taylor BE, Vayndorf EM. Behavioral Phenotyping and Pathological Indicators of Parkinson's Disease in C. elegans Models. Front Genet 2017; 8:77. [PMID: 28659967 PMCID: PMC5468440 DOI: 10.3389/fgene.2017.00077] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/22/2017] [Indexed: 12/14/2022] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with symptoms that progressively worsen with age. Pathologically, PD is characterized by the aggregation of α-synuclein in cells of the substantia nigra in the brain and loss of dopaminergic neurons. This pathology is associated with impaired movement and reduced cognitive function. The etiology of PD can be attributed to a combination of environmental and genetic factors. A popular animal model, the nematode roundworm Caenorhabditis elegans, has been frequently used to study the role of genetic and environmental factors in the molecular pathology and behavioral phenotypes associated with PD. The current review summarizes cellular markers and behavioral phenotypes in transgenic and toxin-induced PD models of C. elegans.
Collapse
Affiliation(s)
- Malabika Maulik
- Department of Chemistry and Biochemistry, University of Alaska FairbanksFairbanks, AK, United States
| | - Swarup Mitra
- Department of Chemistry and Biochemistry, University of Alaska FairbanksFairbanks, AK, United States
| | - Abel Bult-Ito
- Department of Biology and Wildlife, University of Alaska FairbanksFairbanks, AK, United States
| | - Barbara E Taylor
- Department of Biological Sciences, California State University, Long BeachLong Beach, CA, United States
| | - Elena M Vayndorf
- Institute of Arctic Biology, University of Alaska FairbanksFairbanks, AK, United States
| |
Collapse
|
39
|
Rassu M, Del Giudice MG, Sanna S, Taymans JM, Morari M, Brugnoli A, Frassineti M, Masala A, Esposito S, Galioto M, Valle C, Carri MT, Biosa A, Greggio E, Crosio C, Iaccarino C. Role of LRRK2 in the regulation of dopamine receptor trafficking. PLoS One 2017; 12:e0179082. [PMID: 28582422 PMCID: PMC5459500 DOI: 10.1371/journal.pone.0179082] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 05/23/2017] [Indexed: 11/18/2022] Open
Abstract
Mutations in LRRK2 play a critical role in both familial and sporadic Parkinson’s disease (PD). Up to date, the role of LRRK2 in PD onset and progression remains largely unknown. However, experimental evidence highlights a critical role of LRRK2 in the control of vesicle trafficking that in turn may regulate different aspects of neuronal physiology. We have analyzed the role of LRRK2 in regulating dopamine receptor D1 (DRD1) and D2 (DRD2) trafficking. DRD1 and DRD2 are the most abundant dopamine receptors in the brain. They differ in structural, pharmacological and biochemical properties, as well as in localization and internalization mechanisms. Our results indicate that disease-associated mutant G2019S LRRK2 impairs DRD1 internalization, leading to an alteration in signal transduction. Moreover, the mutant forms of LRRK2 affect receptor turnover by decreasing the rate of DRD2 trafficking from the Golgi complex to the cell membrane. Collectively, our findings are consistent with the conclusion that LRRK2 influences the motility of neuronal vesicles and the neuronal receptor trafficking. These findings have important implications for the complex role that LRRK2 plays in neuronal physiology and the possible pathological mechanisms that may lead to neuronal death in PD.
Collapse
Affiliation(s)
- Mauro Rassu
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Simona Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Jean Marc Taymans
- UMR-S1172, Jean-Pierre Aubert Research Center (Inserm – Université de Lille – CHRU de Lille), Lille, France
| | - Michele Morari
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy and National Institute for Neuroscience, Ferrara, Italy
| | - Alberto Brugnoli
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy and National Institute for Neuroscience, Ferrara, Italy
| | - Martina Frassineti
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy and National Institute for Neuroscience, Ferrara, Italy
| | - Alessandra Masala
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Sonia Esposito
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Manuela Galioto
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Cristiana Valle
- Fondazione Santa Lucia, IRCCS, Rome, Italy
- Institute of Cell Biology and Neurobiology, IBCN, CNR, Rome, Italy
| | - Maria Teresa Carri
- Fondazione Santa Lucia, IRCCS, Rome, Italy
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Alice Biosa
- Department of Biology, University of Padova, Padova, Italy
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- * E-mail:
| |
Collapse
|
40
|
Son MY, Sim H, Son YS, Jung KB, Lee MO, Oh JH, Chung SK, Jung CR, Kim J. Distinctive genomic signature of neural and intestinal organoids from familial Parkinson's disease patient-derived induced pluripotent stem cells. Neuropathol Appl Neurobiol 2017; 43:584-603. [PMID: 28235153 DOI: 10.1111/nan.12396] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 01/22/2017] [Accepted: 02/19/2017] [Indexed: 02/06/2023]
Abstract
AIMS The leucine-rich repeat kinase 2 (LRRK2) G2019S mutation is the most common genetic cause of Parkinson's disease (PD). There is compelling evidence that PD is not only a brain disease but also a gastrointestinal disorder; nonetheless, its pathogenesis remains unclear. We aimed to develop human neural and intestinal tissue models of PD patients harbouring an LRRK2 mutation to understand the link between LRRK2 and PD pathology by investigating the gene expression signature. METHODS We generated PD patient-specific induced pluripotent stem cells (iPSCs) carrying an LRRK2 G2019S mutation (LK2GS) and then differentiated into three-dimensional (3D) human neuroectodermal spheres (hNESs) and human intestinal organoids (hIOs). To unravel the gene and signalling networks associated with LK2GS, we analysed differentially expressed genes in the microarray data by functional clustering, gene ontology (GO) and pathway analyses. RESULTS The expression profiles of LK2GS were distinct from those of wild-type controls in hNESs and hIOs. The most represented GO biological process in hNESs and hIOs was synaptic transmission, specifically synaptic vesicle trafficking, some defects of which are known to be related to PD. The results were further validated in four independent PD-specific hNESs and hIOs by microarray and qRT-PCR analysis. CONCLUSION We provide the first evidence that LK2GS also causes significant changes in gene expression in the intestinal cells. These hNES and hIO models from the same genetic background of PD patients could be invaluable resources for understanding PD pathophysiology and for advancing the complexity of in vitro models with 3D expandable organoids.
Collapse
Affiliation(s)
- M-Y Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - H Sim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - Y S Son
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - K B Jung
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - M-O Lee
- Immunotherapy Convergence Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea
| | - J-H Oh
- Korea Institute of Toxicology, Daejeon, 34114, Republic of Korea.,Department of human and environmental toxicology, University of Science & Technology, Daejeon, 34113, Republic of Korea
| | - S-K Chung
- Medical Research Division, Korea Institute of Oriental Medicine, Yuseong-gu, Daejeon, 34054, Republic of Korea
| | - C-R Jung
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| | - J Kim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.,Department of functional genomics, University of Science & Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea
| |
Collapse
|
41
|
Gopi M, Arambakkam Janardhanam V. Asiaticoside: Attenuation of rotenone induced oxidative burden in a rat model of hemiparkinsonism by maintaining the phosphoinositide-mediated synaptic integrity. Pharmacol Biochem Behav 2017; 155:1-15. [PMID: 28238857 DOI: 10.1016/j.pbb.2017.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 02/14/2017] [Accepted: 02/20/2017] [Indexed: 02/06/2023]
Abstract
Asiaticoside (AS), a triterpenoid saponin isolated from the Indian medicinal herb Centella asiatica is known to exert a neuroprotective effect by attenuating the neurobehavioral, neurochemical and pathological changes in animal models. However, its potential neuroprotection in rotenone-induced hemiparkinsonism which implicates phospholipid-mediated neurotransmission remains unclear. Therefore, we have investigated the neuroprotective effects of AS in rat model of ROT-infused hemiparkinsonism with respect to phosphoinositides-assisted cytodynamics and synaptic function. Adult male Sprague-Dawley rats (250-300g) were distributed randomly into 6 groups, with 6 rats in each group: Sham control, Vehicle control (DMSO-0.1%), ROT-infused group (6μg/μl/kg), AS-treated group (50mg/kg/day), Drug (AS) control and Levodopa (l-DOPA)-treated group (6mg/kg/day). At the end of the experimental period, the rats were sacrificed after performing behavioral analyses and the striatum regions were dissected out. Phosphoinositides (PI) are involved in intrinsic membrane signals that regulate intracellular membrane trafficking vesicle and endocytosis. We have assessed mRNA and protein expressions of genes involved in PI-mediated signaling and also in synaptic function (PI3K, PDK 1, PEBP, Stx 1A and TH) in addition to the levels of neurotransmitters and the enzymatic antioxidant profile. AS caused an improved working memory and motor co-ordination in the ROT group. It alters the levels of neurotransmitters (p<0.01), the expression of mRNA and protein assessed which were significantly affected (P<0.001) by rotenone, thus exhibiting its intervention in the progression of neurodegeneration. We demonstrate that AS can mediate distinct function in PI-assisted vesicle endocytosis, cytoprotective signaling and in the synaptic function thereby mitigating the ROT-infused hemiparkinsonism, however, its specific regulatory role remains to be unraveled.
Collapse
Affiliation(s)
- Margabandhu Gopi
- Department of Biochemistry, University of Madras, Guindy Campus, Chennai 600 025, Tamilnadu, India.
| | | |
Collapse
|
42
|
Murdoch JD, Rostosky CM, Gowrisankaran S, Arora AS, Soukup SF, Vidal R, Capece V, Freytag S, Fischer A, Verstreken P, Bonn S, Raimundo N, Milosevic I. Endophilin-A Deficiency Induces the Foxo3a-Fbxo32 Network in the Brain and Causes Dysregulation of Autophagy and the Ubiquitin-Proteasome System. Cell Rep 2016; 17:1071-1086. [PMID: 27720640 PMCID: PMC5080600 DOI: 10.1016/j.celrep.2016.09.058] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Revised: 06/24/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022] Open
Abstract
Endophilin-A, a well-characterized endocytic adaptor essential for synaptic vesicle recycling, has recently been linked to neurodegeneration. We report here that endophilin-A deficiency results in impaired movement, age-dependent ataxia, and neurodegeneration in mice. Transcriptional analysis of endophilin-A mutant mice, complemented by proteomics, highlighted ataxia- and protein-homeostasis-related genes and revealed upregulation of the E3-ubiquitin ligase FBXO32/atrogin-1 and its transcription factor FOXO3A. FBXO32 overexpression triggers apoptosis in cultured cells and neurons but, remarkably, coexpression of endophilin-A rescues it. FBXO32 interacts with all three endophilin-A proteins. Similarly to endophilin-A, FBXO32 tubulates membranes and localizes on clathrin-coated structures. Additionally, FBXO32 and endophilin-A are necessary for autophagosome formation, and both colocalize transiently with autophagosomes. Our results point to a role for endophilin-A proteins in autophagy and protein degradation, processes that are impaired in their absence, potentially contributing to neurodegeneration and ataxia. Endophilin-A is needed for autophagosome formation in mammalian neurons and brain Absence of endophilin-A upregulates the E3-ubiquitin ligase FBXO32 FBXO32-endophilin-A interaction maintains neuronal health and protein homeostasis Endophilin-A KO mice show age-dependent ataxia, motor impairments, and neurodegeneration
Collapse
Affiliation(s)
- John D Murdoch
- European Neuroscience Institute (ENI), 37077 Göttingen, Germany; Institute of Cellular Biochemistry, University Medical Center Göttingen (UMG), 37073 Göttingen, Germany
| | | | | | | | - Sandra-Fausia Soukup
- VIB Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), 3000 Leuven, Belgium
| | - Ramon Vidal
- Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Vincenzo Capece
- Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Siona Freytag
- European Neuroscience Institute (ENI), 37077 Göttingen, Germany
| | - Andre Fischer
- Epigenetics and Systems Medicine in Neurodegenerative Diseases, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany; Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, 37077 Göttingen, Germany
| | - Patrik Verstreken
- VIB Center for Brain & Disease Research, 3000 Leuven, Belgium; KU Leuven Department of Human Genetics, Leuven Institute for Neurodegenerative Disease (LIND), 3000 Leuven, Belgium
| | - Stefan Bonn
- Computational Systems Biology, German Center for Neurodegenerative Diseases (DZNE), 37077 Göttingen, Germany
| | - Nuno Raimundo
- Institute of Cellular Biochemistry, University Medical Center Göttingen (UMG), 37073 Göttingen, Germany.
| | - Ira Milosevic
- European Neuroscience Institute (ENI), 37077 Göttingen, Germany.
| |
Collapse
|
43
|
Proteome Analysis of Potential Synaptic Vesicle Cycle Biomarkers in the Cerebrospinal Fluid of Patients with Sporadic Creutzfeldt-Jakob Disease. Mol Neurobiol 2016; 54:5177-5191. [PMID: 27562179 DOI: 10.1007/s12035-016-0029-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 08/01/2016] [Indexed: 01/01/2023]
Abstract
Sporadic Creutzfeldt-Jakob disease (sCJD) is the most frequent fatal human prion disease with a rapid progression and unknown mechanism. The synaptic vesicle (SV) cycle pathway has been a hot research field associated with many neurodegenerative diseases that affect synaptic function and thus may affect pathogenesis of the disorder. Here, we used the iTRAQ-based proteomic method and a KEGG pathway enrichment analysis to meticulously analyze all pathways involved in sCJD disease. In total, 1670 proteins were validated in pooled cerebrospinal fluid (CSF) from 20 patients with sCJD compared with that from 13 patients without CJD. The demographic analysis demonstrated that 557 proteins were upregulated and 595 proteins were downregulated with a 1.5-fold change, and 690 proteins involved in 39 pathways changed significantly (p ≤ 0.05) according to the enrichment analysis. The SV cycle pathway and proteins involved were further evaluated, and 14 proteins were confirmed to participate in the SV cycle pathway due to increased expression. Six key proteins, such as AP2A1, SYT1, SNAP25, STXBP1, CLTB, and Rab3a, showed the same trend by western blot as detected by iTRAQ. This is the first study to use high-throughput proteomics to accurately identify and quantify proteins in the SV cycle pathway of a neurodegenerative disease. These results will help define the mechanism and provide new insight into the pathogenetic factors involved in the SV cycle pathway in patients with sCJD. We hope that promising biomarkers can be identified in the CSF of patients with sCJD and other neurodegenerative disorders to help predict disease progression.
Collapse
|
44
|
Exogenous Alpha-Synuclein Alters Pre- and Post-Synaptic Activity by Fragmenting Lipid Rafts. EBioMedicine 2016; 7:191-204. [PMID: 27322472 PMCID: PMC4909369 DOI: 10.1016/j.ebiom.2016.03.038] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 02/24/2016] [Accepted: 03/24/2016] [Indexed: 12/28/2022] Open
Abstract
Alpha-synuclein (αSyn) interferes with multiple steps of synaptic activity at pre-and post-synaptic terminals, however the mechanism/s by which αSyn alters neurotransmitter release and synaptic potentiation is unclear. By atomic force microscopy we show that human αSyn, when incubated with reconstituted membrane bilayer, induces lipid rafts' fragmentation. As a consequence, ion channels and receptors are displaced from lipid rafts with consequent changes in their activity. The enhanced calcium entry leads to acute mobilization of synaptic vesicles, and exhaustion of neurotransmission at later stages. At the post-synaptic terminal, an acute increase in glutamatergic transmission, with increased density of PSD-95 puncta, is followed by disruption of the interaction between N-methyl-d-aspartate receptor (NMDAR) and PSD-95 with ensuing decrease of long term potentiation. While cholesterol loading prevents the acute effect of αSyn at the presynapse; inhibition of casein kinase 2, which appears activated by reduction of cholesterol, restores the correct localization and clustering of NMDARs. Extracellular αSyn disrupts lipid raft platforms with consequent mislocalization of several pre- and post-synaptic proteins. αSyn-driven changes in raft-partitioning of proteins blunt neurotransmission and LTP. Cholesterol loading and inhibition of CK2 restore αSyn-induced alterations of the post-synaptic density assembly.
Alpha-synuclein (αSyn), a cytosolic protein that can be released from neurons, becomes pathogenic when expressed at high levels, as in Parkinson's disease, due to multiplication of αSyn gene. We show that the mechanism responsible for the defects in synaptic vesicles mobilization and post-synaptic activity induced by extracellular αSyn is the fragmentation of lipid rafts, cholesterol-rich microdomains of the plasma membrane. Moreover restoration of lipid raft platforms and raft-partitioning of surface proteins prevents the alteration of synaptic transmission caused by exposure of neurons to αSyn.
Collapse
|
45
|
Feligioni M, Mango D, Piccinin S, Imbriani P, Iannuzzi F, Caruso A, De Angelis F, Blandini F, Mercuri NB, Pisani A, Nisticò R. Subtle alterations of excitatory transmission are linked to presynaptic changes in the hippocampus of PINK1-deficient mice. Synapse 2016; 70:223-30. [PMID: 26850695 DOI: 10.1002/syn.21894] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 02/01/2016] [Accepted: 02/02/2016] [Indexed: 12/13/2022]
Abstract
Homozygous or heterozygous mutations in the PTEN-induced kinase 1 (PINK1) gene have been linked to early-onset Parkinson's disease (PD). Several neurophysiological studies have demonstrated alterations in striatal synaptic plasticity along with impaired dopamine release in PINK1-deficient mice. Using electrophysiological methods, here we show that PINK1 loss of function causes a progressive increase of spontaneous glutamate-mediated synaptic events in the hippocampus, without influencing long-term potentiation. Moreover, fluorescence analysis reveals increased neurotrasmitter release although our biochemical results failed to detect which presynaptic proteins might be engaged. This study provides a novel role for PINK1 beyond the physiology of nigrostriatal dopaminergic circuit. Specifically, PINK1 might contribute to preserve synaptic function and glutamatergic homeostasis in the hippocampus, a brain region underlying cognition. The subtle changes in excitatory transmission here observed might be a pathogenic precursor to excitotoxic neurodegeneration and cognitive decline often observed in PD. Using electrophysiological and fluorescence techniques, we demonstrate that lack of PINK1 causes increased excitatory transmission and neurotransmitter release in the hippocampus, which might lead to the cognitive decline often observed in Parkinson's disease.
Collapse
Affiliation(s)
- Marco Feligioni
- EBRI-European Brain Research Institute, Rome, Italy.,Casa Cura Policlinico, Milan, Italy
| | - Dalila Mango
- EBRI-European Brain Research Institute, Rome, Italy
| | | | | | | | | | | | - Fabio Blandini
- IRCSS "C. Mondino", National Neurological Institute, Pavia, Italy
| | - Nicola B Mercuri
- University of Rome "Tor Vergata", Rome, Italy.,IRCSS Santa Lucia Foundation, Rome, Italy
| | | | - Robert Nisticò
- EBRI-European Brain Research Institute, Rome, Italy.,University of Rome "Tor Vergata", Rome, Italy
| |
Collapse
|
46
|
Rice ME, Patel JC. Somatodendritic dopamine release: recent mechanistic insights. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0185. [PMID: 26009764 DOI: 10.1098/rstb.2014.0185] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Dopamine (DA) is a key transmitter in motor, reward and cogitative pathways, with DA dysfunction implicated in disorders including Parkinson's disease and addiction. Located in midbrain, DA neurons of the substantia nigra pars compacta project via the medial forebrain bundle to the dorsal striatum (caudate putamen), and DA neurons in the adjacent ventral tegmental area project to the ventral striatum (nucleus accumbens) and prefrontal cortex. In addition to classical vesicular release from axons, midbrain DA neurons exhibit DA release from their cell bodies and dendrites. Somatodendritic DA release leads to activation of D2 DA autoreceptors on DA neurons that inhibit their firing via G-protein-coupled inwardly rectifying K(+) channels. This helps determine patterns of DA signalling at distant axonal release sites. Somatodendritically released DA also acts via volume transmission to extrasynaptic receptors that modulate local transmitter release and neuronal activity in the midbrain. Thus, somatodendritic release is a pivotal intrinsic feature of DA neurons that must be well defined in order to fully understand the physiology and pathophysiology of DA pathways. Here, we review recent mechanistic aspects of somatodendritic DA release, with particular emphasis on the Ca(2+) dependence of release and the potential role of exocytotic proteins.
Collapse
Affiliation(s)
- Margaret E Rice
- Department of Neurosurgery, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA Department of Neuroscience and Physiology, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| | - Jyoti C Patel
- Department of Neurosurgery, New York University School of Medicine, 550 First Avenue, New York, NY 10016, USA
| |
Collapse
|
47
|
Endocytic pathways and endosomal trafficking: a primer. Wien Med Wochenschr 2016; 166:196-204. [PMID: 26861668 DOI: 10.1007/s10354-016-0432-7] [Citation(s) in RCA: 149] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 01/05/2016] [Indexed: 01/05/2023]
Abstract
This brief overview of endocytic trafficking is written in honor of Renate Fuchs, who retires this year. In the mid-1980s, Renate pioneered studies on the ion-conducting properties of the recently discovered early and late endosomes and the mechanisms governing endosomal acidification. As described in this review, after uptake through one of many mechanistically distinct endocytic pathways, internalized proteins merge into a common early/sorting endosome. From there they again diverge along distinct sorting pathways, back to the cell surface, on to the trans-Golgi network or across polarized cells. Other transmembrane receptors are packaged into intraluminal vesicles of late endosomes/multivesicular bodies that eventually fuse with and deliver their content to lysosomes for degradation. Endosomal acidification, in part, determines sorting along this pathway. We describe other sorting machinery and mechanisms, as well as the rab proteins and phosphatidylinositol lipids that serve to dynamically define membrane compartments along the endocytic pathway.
Collapse
|
48
|
Swaney DL, Rodríguez-Mias RA, Villén J. Phosphorylation of ubiquitin at Ser65 affects its polymerization, targets, and proteome-wide turnover. EMBO Rep 2015; 16:1131-44. [PMID: 26142280 DOI: 10.15252/embr.201540298] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 06/15/2015] [Indexed: 12/21/2022] Open
Abstract
Ubiquitylation is an essential post-translational modification that regulates numerous cellular processes, most notably protein degradation. Ubiquitin can itself be phosphorylated at nearly every serine, threonine, and tyrosine residue. However, the effect of this modification on ubiquitin function is largely unknown. Here, we characterized the effects of phosphorylation of yeast ubiquitin at serine 65 in vivo and in vitro. We find this post-translational modification to be regulated under oxidative stress, occurring concomitantly with the restructuring of the ubiquitin landscape into a highly polymeric state. Phosphomimetic mutation of S65 recapitulates the oxidative stress phenotype, causing a dramatic accumulation of ubiquitylated proteins and a proteome-wide reduction of protein turnover rates. Importantly, this mutation impacts ubiquitin chain disassembly, chain linkage distribution, ubiquitin interactions, and substrate targeting. These results demonstrate that phosphorylation is an additional mode of ubiquitin regulation with broad implications in cellular physiology.
Collapse
Affiliation(s)
- Danielle L Swaney
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| |
Collapse
|
49
|
Triplett JC, Zhang Z, Sultana R, Cai J, Klein JB, Büeler H, Butterfield DA. Quantitative expression proteomics and phosphoproteomics profile of brain from PINK1 knockout mice: insights into mechanisms of familial Parkinson's disease. J Neurochem 2015; 133:750-65. [PMID: 25626353 DOI: 10.1111/jnc.13039] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 01/12/2015] [Indexed: 12/27/2022]
Abstract
Parkinson's disease (PD) is an age-related, neurodegenerative motor disorder characterized by progressive degeneration of dopaminergic neurons in the substantia nigra pars compacta and presence of α-synuclein-containing protein aggregates. Mutations in the mitochondrial Ser/Thr kinase PTEN-induced kinase 1 (PINK1) are associated with an autosomal recessive familial form of early-onset PD. Recent studies have suggested that PINK1 plays important neuroprotective roles against mitochondrial dysfunction by phosphorylating and recruiting Parkin, a cytosolic E3 ubiquitin ligase, to facilitate elimination of damaged mitochondria via autophagy-lysosomal pathways. Loss of PINK1 in cells and animals leads to various mitochondrial impairments and oxidative stress, culminating in dopaminergic neuronal death in humans. Using a 2-D polyacrylamide gel electrophoresis proteomics approach, the differences in expressed brain proteome and phosphoproteome between 6-month-old PINK1-deficient mice and wild-type mice were identified. The observed changes in the brain proteome and phosphoproteome of mice lacking PINK1 suggest that defects in signaling networks, energy metabolism, cellular proteostasis, and neuronal structure and plasticity are involved in the pathogenesis of familial PD. Mutations in PINK1 are associated with an early-onset form of Parkinson's disease (PD). This study examines changes in the proteome and phosphoproteome of the PINK1 knockout mouse brain. Alterations were noted in several key proteins associated with: increased oxidative stress, aberrant cellular signaling, altered neuronal structure, decreased synaptic plasticity, reduced neurotransmission, diminished proteostasis networks, and altered metabolism. 14-3-3ε, 14-3-3 protein epsilon; 3-PGDH, phosphoglycerate dehydrogenase; ALDOA, aldolase A; APT1, acyl-protein thioesterase 1; CaM, calmodulin; CBR3, carbonyl reductase [NADPH] 3; ENO2, gamma-enolase; HPRT, hypoxanthine-guanine phosphoribosyltransferase; HSP70, heat-shock-related 70 kDa protein 2; IDHc, cytoplasmic isocitrate dehydrogenase [NADP+]; MAPK1, mitogen-activated protein kinase 1; MEK1, MAP kinase kinase 1; MDHc, cytoplasmic malate dehydrogenase; NFM, neurofilament medium polypeptide; NSF, N-ethylmaleimide-sensitive fusion protein; PHB, prohibitin; PINK1, PTEN-induced putative kinase 1; PPIaseA, peptidyl-prolyl cis-trans isomerase A; PSA2, proteasome subunit alpha type-2; TK, transketolase; VDAC-2, voltage-dependent anion-selective channel protein 2.
Collapse
Affiliation(s)
- Judy C Triplett
- Department of Chemistry, University of Kentucky, Lexington, Kentucky, USA
| | | | | | | | | | | | | |
Collapse
|
50
|
Vanhauwaert R, Verstreken P. Flies with Parkinson's disease. Exp Neurol 2015; 274:42-51. [PMID: 25708988 DOI: 10.1016/j.expneurol.2015.02.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 02/11/2015] [Indexed: 12/21/2022]
Abstract
Parkinson's disease is an incurable neurodegenerative disease. Most cases of the disease are of sporadic origin, but about 10% of the cases are familial. The genes thus far identified in Parkinson's disease are well conserved. Drosophila is ideally suited to study the molecular neuronal cell biology of these genes and the pathogenic mutations in Parkinson's disease. Flies reproduce quickly, and their elaborate genetic tools in combination with their small size allow researchers to analyze identified cells and neurons in large numbers of animals. Furthermore, fruit flies recapitulate many of the cellular and molecular defects also seen in patients, and these defects often result in clear locomotor and behavioral phenotypes, facilitating genetic modifier screens. Hence, Drosophila has played a prominent role in Parkinson's disease research and has provided invaluable insight into the molecular mechanisms of this disease.
Collapse
Affiliation(s)
- Roeland Vanhauwaert
- VIB Center for the Biology of Disease, KU Leuven, Herestraat 49,3000 Leuven, Belgium; Laboratory of Neuronal Communication, Leuven Institute for Neurodegenerative Disease (LIND), Center for Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Patrik Verstreken
- VIB Center for the Biology of Disease, KU Leuven, Herestraat 49,3000 Leuven, Belgium; Laboratory of Neuronal Communication, Leuven Institute for Neurodegenerative Disease (LIND), Center for Human Genetics, KU Leuven, Herestraat 49, 3000 Leuven, Belgium.
| |
Collapse
|