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Teng L, Sun Y, Chen J, Wang C, Urbach JM, Kobe B, Ye N, Zeng Q. Exon shuffling and alternative splicing of ROCO genes in brown algae enables a diverse repertoire of candidate immune receptors. FRONTIERS IN PLANT SCIENCE 2024; 15:1445022. [PMID: 39246816 PMCID: PMC11378527 DOI: 10.3389/fpls.2024.1445022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/01/2024] [Indexed: 09/10/2024]
Abstract
The ROCO family is a family of GTPases characterized by a central ROC-COR tandem domain. Interest in the structure and function of ROCO proteins has increased with the identification of their important roles in human disease. Nevertheless, the functions of most ROCO proteins are still unknown. In the present study, we characterized the structure, evolution, and expression of ROCOs in four species of brown algae. Brown algae have a larger number of ROCO proteins than other organisms reported to date. Phylogenetic analyses showed that ROCOs have an ancient origin, likely originated in prokaryotes. ROCOs in brown algae clustered into four groups and showed no strong relationship with red algae or green algae. Brown algal ROCOs retain the ancestral LRR-ROC-COR domain arrangement, which is found in prokaryotes, plants and some basal metazoans. Remarkably, individual LRR motifs in ROCO genes are each encoded by separate exons and exhibit intense exon shuffling and diversifying selection. Furthermore, the tandem LRR exons exhibit alternative splicing to generate multiple transcripts. Both exon shuffling and alternative splicing of LRR repeats may be important mechanisms for generating diverse ligand-binding specificities as immune receptors. Besides their potential immune role, expression analysis shows that many ROCO genes are responsive to other stress conditions, suggesting they could participate in multiple signal pathways, not limited to the immune response. Our results substantially enhance our understanding of the structure and function of this mysterious gene family.
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Affiliation(s)
- Linhong Teng
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Yuhuan Sun
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Jiayi Chen
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Chenghui Wang
- College of Life Sciences, Dezhou University, Dezhou, China
| | - Jonathan M Urbach
- Ragon Institute of Mass General Brigham, MIT, and Harvard, Cambridge, MA, United States
| | - Bostjan Kobe
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience and Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, QLD, Australia
| | - Naihao Ye
- National Key Laboratory of Mariculture Biobreeding and Sustainable Production, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
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Holmes G, Ferguson SR, Lewis PA, Echeverri K. LRRK2 kinase activity is necessary for development and regeneration in Nematostella vectensis. Neural Dev 2024; 19:16. [PMID: 39118162 PMCID: PMC11308222 DOI: 10.1186/s13064-024-00193-3] [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: 10/31/2023] [Accepted: 07/23/2024] [Indexed: 08/10/2024] Open
Abstract
BACKGROUND The starlet sea anemone, Nematostella vectensis, is an emerging model organism with a high regenerative capacity, which was recently found to possess an orthologue to the human Leucine Rich Repeat Kinase 2 (LRRK2) gene. Mutations in this gene are the most common cause of inherited Parkinson's Disease (PD), highlighting the importance of understanding its function. Despite two decades of research, however, the function of LRRK2 is not well established. METHODS To investigate the function of LRRKs in Nematostella vectensis, we applied small molecule inhibitors targeting the kinase activity of LRRK2 to examine its function in development, homeostasis and regeneration in Nematostella vectensis. RESULTS In vivo analyses inhibiting the kinase function of this enzyme demonstrated a role of nvLRRK2 in development and regeneration of N. vectensis. These findings implicate a developmental role of LRRK2 in Nematostella, adding to the expanding knowledge of its physiological function. CONCLUSIONS Our work introduces a new model organism with which to study LRRK biology. We report that LRRK kinase activity is necessary for the development and regeneration of Nematostella. Given the short generation time, genetic trackability and in vivo imaging capabilities, this work introduces Nematostella vectensis as a new model in which to study genes linked to neurodegenerative diseases such as Parkinson's.
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Affiliation(s)
- Grace Holmes
- Royal Veterinary College, University of London, Camden, London, NW1 0TU, UK
| | - Sophie R Ferguson
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, 02543, USA
| | - Patrick Alfryn Lewis
- Royal Veterinary College, University of London, Camden, London, NW1 0TU, UK.
- UCL Queen Square Institute of Neurology, University of London, London, WC1N 3BG, UK.
| | - Karen Echeverri
- Marine Biological Laboratory, Eugene Bell Center for Regenerative Biology and Tissue Engineering, Woods Hole, MA, 02543, USA.
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Alessi DR, Pfeffer SR. Leucine-Rich Repeat Kinases. Annu Rev Biochem 2024; 93:261-287. [PMID: 38621236 DOI: 10.1146/annurev-biochem-030122-051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65 human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.
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Affiliation(s)
- Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom;
| | - Suzanne R Pfeffer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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Kang J, Huang G, Ma L, Tong Y, Shahapal A, Chen P, Shen J. Cell-autonomous role of leucine-rich repeat kinase in the protection of dopaminergic neuron survival. eLife 2024; 12:RP92673. [PMID: 38856715 PMCID: PMC11164531 DOI: 10.7554/elife.92673] [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] [Indexed: 06/11/2024] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease (PD). However, whether LRRK2 mutations cause PD and degeneration of dopaminergic (DA) neurons via a toxic gain-of-function or a loss-of-function mechanism is unresolved and has pivotal implications for LRRK2-based PD therapies. In this study, we investigate whether Lrrk2 and its functional homolog Lrrk1 play a cell-intrinsic role in DA neuron survival through the development of DA neuron-specific Lrrk conditional double knockout (cDKO) mice. Unlike Lrrk germline DKO mice, DA neuron-restricted Lrrk cDKO mice exhibit normal mortality but develop age-dependent loss of DA neurons, as shown by the progressive reduction of DA neurons in the substantia nigra pars compacta (SNpc) at the ages of 20 and 24 months. Moreover, DA neurodegeneration is accompanied with increases in apoptosis and elevated microgliosis in the SNpc as well as decreases in DA terminals in the striatum, and is preceded by impaired motor coordination. Taken together, these findings provide the unequivocal evidence for the cell-intrinsic requirement of LRRK in DA neurons and raise the possibility that LRRK2 mutations may impair its protection of DA neurons, leading to DA neurodegeneration in PD.
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Affiliation(s)
- Jongkyun Kang
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Guodong Huang
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Long Ma
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Youren Tong
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Anu Shahapal
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Phoenix Chen
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
| | - Jie Shen
- Department of Neurology, Brigham and Women’s HospitalBostonUnited States
- Program in Neuroscience, Harvard Medical SchoolBostonUnited States
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Kang J, Huang G, Ma L, Tong Y, Shahapal A, Chen P, Shen J. Cell autonomous role of leucine-rich repeat kinase in protection of dopaminergic neuron survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.06.561293. [PMID: 37873418 PMCID: PMC10592668 DOI: 10.1101/2023.10.06.561293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common genetic cause of Parkinson's disease (PD), which is the leading neurodegenerative movement disorder characterized by the progressive loss of dopaminergic (DA) neurons in the substantia nigra pars compacta (SNpc). However, whether LRRK2 mutations cause PD and degeneration of DA neurons via a toxic gain-of-function or a loss-of-function mechanism is unresolved and has pivotal implications for LRRK2-based PD therapies. In this study, we investigate whether LRRK2 and its functional homologue LRRK1 play an essential, intrinsic role in DA neuron survival through the development of DA neuron-specific LRRK conditional double knockout (cDKO) mice. We first generated and characterized floxed LRRK1 and LRRK2 mice and then confirmed that germline deletions of the floxed LRRK1 and LRRK2 alleles result in null mutations, as evidenced by the absence of LRRK1 and LRRK2 mRNA and protein in the respective homozygous deleted mutant mice. We further examined the specificity of Cre-mediated recombination driven by the dopamine transporter-Cre (DAT-Cre) knockin (KI) allele using a GFP reporter line and confirmed that DAT-Cre-mediated recombination is restricted to DA neurons in the SNpc. Crossing these validated floxed LRRK1 and LRRK2 mice with DAT-Cre KI mice, we then generated DA neuron-restricted LRRK cDKO mice and further showed that levels of LRRK1 and LRRK2 are reduced in dissected ventral midbrains of LRRK cDKO mice. While DA neuron-restricted LRRK cDKO mice of both sexes exhibit normal mortality and body weight, they develop age-dependent loss of DA neurons in the SNpc, as demonstrated by the progressive reduction of DA neurons in the SNpc of LRRK cDKO mice at the ages of 20 and 24 months but the unaffected number of DA neurons at the age of 15 months. Moreover, DA neurodegeneration is accompanied with increases of apoptosis and elevated microgliosis in the SNpc as well as decreases of DA terminals in the striatum, and is preceded by impaired motor coordination. Taken together, these findings provide the unequivocal evidence for the importance of LRRK in DA neurons and raise the possibility that LRRK2 mutations may impair its protection of DA neurons, leading to DA neurodegeneration in PD.
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Affiliation(s)
- Jongkyun Kang
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Guodong Huang
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Long Ma
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Youren Tong
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Anu Shahapal
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Phoenix Chen
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
| | - Jie Shen
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, United States of America
- Program in Neuroscience, Harvard Medical School, Boston, MA 02115, United States of America
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Holmes G, Ferguson SR, Lewis PA, Echeverri K. LRRK2 kinase activity is necessary for development and regeneration in Nematostella vectensis. RESEARCH SQUARE 2023:rs.3.rs-3525606. [PMID: 37986927 PMCID: PMC10659525 DOI: 10.21203/rs.3.rs-3525606/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Background The starlet sea anemone, Nematostella vectensis, is an emerging model organism with a high regenerative capacity, which was recently found to possess an orthologue to the human LRRK2 gene (nvLRRK2). The leucine rich repeat kinase 2 (LRRK2) gene, when mutated, is the most common cause of inherited Parkinson's Disease (PD). Its protein product (LRRK2) has implications in a variety of cellular processes, however, the full function of LRRK2 is not well established. Current research is focusing on understanding the function of LRRK2, including both its physiological role as well as its pathobiological underpinnings. Methods We used bioinformatics to determine the cross-species conservation of LRRK2, then applied drugs targeting the kinase activity of LRRK2 to examine its function in development, homeostasis and regeneration in Nematostella vectensis. Results An in-silico characterization and phylogenetic analysis of nvLRRK2 comparing it to human LRRK2 highlighted key conserved motifs and residues. In vivo analyses inhibiting the kinase function of this enzyme demonstrated a role of nvLRRK2 in development and regeneration of N. vectensis. These findings implicate a developmental role of LRRK2 in Nematostella, adding to the expanding knowledge of its physiological function. Conclusions Our work introduces a new model organism with which to study LRRK biology. We show a necessity for LRRK2 in development and regeneration. Given the short generation time, genetic trackability and in vivo imaging capabilities, this work introduces Nematostella vectensis as a new model in which to study genes linked to neurodegenerative diseases such as Parkinson's.
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Reimer JM, Dickey AM, Lin YX, Abrisch RG, Mathea S, Chatterjee D, Fay EJ, Knapp S, Daugherty MD, Reck-Peterson SL, Leschziner AE. Structure of LRRK1 and mechanisms of autoinhibition and activation. Nat Struct Mol Biol 2023; 30:1735-1745. [PMID: 37857821 PMCID: PMC10643122 DOI: 10.1038/s41594-023-01109-1] [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: 02/21/2023] [Accepted: 08/24/2023] [Indexed: 10/21/2023]
Abstract
Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, their disease associations are strikingly different: LRRK2 is involved in familial Parkinson's disease while LRRK1 is linked to bone diseases. Furthermore, Parkinson's disease-linked mutations in LRRK2 are typically autosomal dominant gain-of-function while those in LRRK1 are autosomal recessive loss-of-function. Here, to understand these differences, we solved cryo-EM structures of LRRK1 in its monomeric and dimeric forms. Both differ from the corresponding LRRK2 structures. Unlike LRRK2, which is sterically autoinhibited as a monomer, LRRK1 is sterically autoinhibited in a dimer-dependent manner. LRRK1 has an additional level of autoinhibition that prevents activation of the kinase and is absent in LRRK2. Finally, we place the structural signatures of LRRK1 and LRRK2 in the context of the evolution of the LRRK family of proteins.
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Affiliation(s)
- Janice M Reimer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Andrea M Dickey
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yu Xuan Lin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Robert G Abrisch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sebastian Mathea
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Deep Chatterjee
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Elizabeth J Fay
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stefan Knapp
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Matthew D Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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Nechushtai L, Frenkel D, Pinkas-Kramarski R. Autophagy in Parkinson's Disease. Biomolecules 2023; 13:1435. [PMID: 37892117 PMCID: PMC10604695 DOI: 10.3390/biom13101435] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 09/14/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Parkinson's disease (PD) is a devastating disease associated with accumulation of α-synuclein (α-Syn) within dopaminergic neurons, leading to neuronal death. PD is characterized by both motor and non-motor clinical symptoms. Several studies indicate that autophagy, an important intracellular degradation pathway, may be involved in different neurodegenerative diseases including PD. The autophagic process mediates the degradation of protein aggregates, damaged and unneeded proteins, and organelles, allowing their clearance, and thereby maintaining cell homeostasis. Impaired autophagy may cause the accumulation of abnormal proteins. Incomplete or impaired autophagy may explain the neurotoxic accumulation of protein aggregates in several neurodegenerative diseases including PD. Indeed, studies have suggested the contribution of impaired autophagy to α-Syn accumulation, the death of dopaminergic neurons, and neuroinflammation. In this review, we summarize the recent literature on the involvement of autophagy in PD pathogenesis.
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Affiliation(s)
| | | | - Ronit Pinkas-Kramarski
- Department of Neurobiology, School of Neurobiology, Biochemistry and Biophysics, Tel-Aviv University, Ramat-Aviv, Tel Aviv 69978, Israel; (L.N.); (D.F.)
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Zhu C, Herbst S, Lewis PA. Leucine-rich repeat kinase 2 at a glance. J Cell Sci 2023; 136:jcs259724. [PMID: 37698513 PMCID: PMC10508695 DOI: 10.1242/jcs.259724] [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] [Indexed: 09/13/2023] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multidomain scaffolding protein with dual guanosine triphosphatase (GTPase) and kinase enzymatic activities, providing this protein with the capacity to regulate a multitude of signalling pathways and act as a key mediator of diverse cellular processes. Much of the interest in LRRK2 derives from mutations in the LRRK2 gene being the most common genetic cause of Parkinson's disease, and from the association of the LRRK2 locus with a number of other human diseases, including inflammatory bowel disease. Therefore, the LRRK2 research field has focused on the link between LRRK2 and pathology, with the aim of uncovering the underlying mechanisms and, ultimately, finding novel therapies and treatments to combat them. From the biochemical and cellular functions of LRRK2, to its relevance to distinct disease mechanisms, this Cell Science at a Glance article and the accompanying poster deliver a snapshot of our current understanding of LRRK2 function, dysfunction and links to disease.
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Affiliation(s)
- Christiane Zhu
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Susanne Herbst
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Patrick A. Lewis
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Marín I. Emergence of the Synucleins. BIOLOGY 2023; 12:1053. [PMID: 37626939 PMCID: PMC10451939 DOI: 10.3390/biology12081053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/21/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023]
Abstract
This study establishes the origin and evolutionary history of the synuclein genes. A combination of phylogenetic analyses of the synucleins from twenty-two model species, characterization of local synteny similarities among humans, sharks and lampreys, and statistical comparisons among lamprey and human chromosomes, provides conclusive evidence for the current diversity of synuclein genes arising from the whole-genome duplications (WGDs) that occurred in vertebrates. An ancestral synuclein gene was duplicated in a first WGD, predating the diversification of all living vertebrates. The two resulting genes are still present in agnathan vertebrates. The second WGD, specific to the gnathostome lineage, led to the emergence of the three classical synuclein genes, SNCA, SNCB and SNCG, which are present in all jawed vertebrate lineages. Additional WGDs have added new genes in both agnathans and gnathostomes, while some gene losses have occurred in particular species. The emergence of synucleins through WGDs prevented these genes from experiencing dosage effects, thus avoiding the potential detrimental effects associated with individual duplications of genes that encode proteins prone to aggregation. Additional insights into the structural and functional features of synucleins are gained through the analysis of the highly divergent synuclein proteins present in chondrichthyans and agnathans.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas (IBV-CSIC), 46010 Valencia, Spain
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11
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Khatoon F, Haque S, Hashem A, Mahmoud A, Tashkandi H, Mathkor D, Harakeh S, Alghamdi B, Kumar V. Network-based approach for targeting human kinases commonly associated with amyotrophic lateral sclerosis and cancer. Front Mol Neurosci 2022; 15:1023286. [PMID: 36590916 PMCID: PMC9802580 DOI: 10.3389/fnmol.2022.1023286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/09/2022] [Indexed: 12/23/2022] Open
Abstract
Background Amyotrophic Lateral Sclerosis (ALS) is a rare progressive and chronic motor neuron degenerative disease for which at present no cure is available. In recent years, multiple genes encode kinases and other causative agents for ALS have been identified. Kinases are enzymes that show pleiotropic nature and regulate different signal transduction processes and pathways. The dysregulation of kinase activity results in dramatic changes in processes and causes many other human diseases including cancers. Methods In this study, we have adopted a network-based system biology approach to investigate the kinase-based molecular interplay between ALS and other human disorders. A list of 62 ALS-associated-kinases was first identified and then we identified the disease associated with them by scanning multiple disease-gene interaction databases to understand the link between the ALS-associated kinases and other disorders. Results An interaction network with 36 kinases and 381 different disorders associated with them was prepared, which represents the complexity and the comorbidity associated with the kinases. Further, we have identified 5 miRNAs targeting the majority of the kinases in the disease-causing network. The gene ontology and pathways enrichment analysis of those miRNAs were performed to understand their biological and molecular functions along with to identify the important pathways. We also identified 3 drug molecules that can perturb the disease-causing network by drug repurposing. Conclusion This network-based study presented hereby contributes to a better knowledge of the molecular underpinning of comorbidities associated with the kinases associated with the ALS disease and provides the potential therapeutic targets to disrupt the highly complex disease-causing network.
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Affiliation(s)
- Fatima Khatoon
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, Uttar Pradesh, India
| | - Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Anwar Hashem
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Vaccines and Immunotherapy Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ahmad Mahmoud
- College of Applied Medical Sciences, Taibah University, Medina, Saudi Arabia
| | - Hanaa Tashkandi
- Department of General Surgery, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Darin Mathkor
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
| | - Steve Harakeh
- King Fahd Medical Research Center, and Yousef Abdullatif Jameel Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Badra Alghamdi
- Department of Physiology, Neuroscience Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Vijay Kumar
- Amity Institute of Neuropsychology and Neurosciences, Amity University, Noida, Uttar Pradesh, India,*Correspondence: Vijay Kumar,
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Rahman MU, Bilal M, Shah JA, Kaushik A, Teissedre PL, Kujawska M. CRISPR-Cas9-Based Technology and Its Relevance to Gene Editing in Parkinson's Disease. Pharmaceutics 2022; 14:1252. [PMID: 35745824 PMCID: PMC9229276 DOI: 10.3390/pharmaceutics14061252] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 06/07/2022] [Accepted: 06/09/2022] [Indexed: 12/12/2022] Open
Abstract
Parkinson's disease (PD) and other chronic and debilitating neurodegenerative diseases (NDs) impose a substantial medical, emotional, and financial burden on individuals and society. The origin of PD is unknown due to a complex combination of hereditary and environmental risk factors. However, over the last several decades, a significant amount of available data from clinical and experimental studies has implicated neuroinflammation, oxidative stress, dysregulated protein degradation, and mitochondrial dysfunction as the primary causes of PD neurodegeneration. The new gene-editing techniques hold great promise for research and therapy of NDs, such as PD, for which there are currently no effective disease-modifying treatments. As a result, gene therapy may offer new treatment options, transforming our ability to treat this disease. We present a detailed overview of novel gene-editing delivery vehicles, which is essential for their successful implementation in both cutting-edge research and prospective therapeutics. Moreover, we review the most recent advancements in CRISPR-based applications and gene therapies for a better understanding of treating PD. We explore the benefits and drawbacks of using them for a range of gene-editing applications in the brain, emphasizing some fascinating possibilities.
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Affiliation(s)
- Mujeeb ur Rahman
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
| | - Muhammad Bilal
- College of Biotechnology, Tianjin University of Science and Technology, Tianjin 300457, China;
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
- Fergana Medical Institute of Public Health Uzbekistan, Fergana 150110, Uzbekistan
| | - Ajeet Kaushik
- NanoBioTech Laboratory, Health System Engineering, Department of Environmental Engineering, Florida Polytechnic University, Lakeland, FL 33805, USA;
- School of Engineering, University of Petroleum and Energy Studies (UPES), Dehradun 248007, Uttarakhand, India
| | - Pierre-Louis Teissedre
- Institut des Sciences de la Vigne et du Vin, Université de Bordeaux, EA 4577, Œnologie, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France;
- Institut des Sciences de la Vigne et du Vin, INRA, USC 1366 INRA, IPB, 210 Chemin de Leysotte, F-33140 Villenave d’Ornon, France
| | - Małgorzata Kujawska
- Department of Toxicology, Faculty of Pharmacy, Poznan University of Medical Sciences, Dojazd 30, 60-631 Poznan, Poland;
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13
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Chandler R, Cogo S, Lewis P, Kevei E. Modelling the functional genomics of Parkinson's disease in Caenorhabditis elegans: LRRK2 and beyond. Biosci Rep 2021; 41:BSR20203672. [PMID: 34397087 PMCID: PMC8415217 DOI: 10.1042/bsr20203672] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 08/03/2021] [Accepted: 08/13/2021] [Indexed: 12/12/2022] Open
Abstract
For decades, Parkinson's disease (PD) cases have been genetically categorised into familial, when caused by mutations in single genes with a clear inheritance pattern in affected families, or idiopathic, in the absence of an evident monogenic determinant. Recently, genome-wide association studies (GWAS) have revealed how common genetic variability can explain up to 36% of PD heritability and that PD manifestation is often determined by multiple variants at different genetic loci. Thus, one of the current challenges in PD research stands in modelling the complex genetic architecture of this condition and translating this into functional studies. Caenorhabditis elegans provide a profound advantage as a reductionist, economical model for PD research, with a short lifecycle, straightforward genome engineering and high conservation of PD relevant neural, cellular and molecular pathways. Functional models of PD genes utilising C. elegans show many phenotypes recapitulating pathologies observed in PD. When contrasted with mammalian in vivo and in vitro models, these are frequently validated, suggesting relevance of C. elegans in the development of novel PD functional models. This review will discuss how the nematode C. elegans PD models have contributed to the uncovering of molecular and cellular mechanisms of disease, with a focus on the genes most commonly found as causative in familial PD and risk factors in idiopathic PD. Specifically, we will examine the current knowledge on a central player in both familial and idiopathic PD, Leucine-rich repeat kinase 2 (LRRK2) and how it connects to multiple PD associated GWAS candidates and Mendelian disease-causing genes.
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Affiliation(s)
| | - Susanna Cogo
- School of Biological Sciences, University of Reading, Reading, RG6 6AH, U.K
- Department of Biology, University of Padova, Padova, Via Ugo Bassi 58/B, 35121, Italy
| | - Patrick A. Lewis
- Royal Veterinary College, University of London, London, NW1 0TU, U.K
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, University College London, London, WC1N 3BG, U.K
| | - Eva Kevei
- School of Biological Sciences, University of Reading, Reading, RG6 6AH, U.K
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14
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Mehmood A, Ali W, Din ZU, Song S, Sohail M, Shah W, Guo J, Guo RY, Ilahi I, Shah S, Al-Shaebi F, Zeb L, Asiamah EA, Al-Dhamin Z, Bilal H, Li B. Clustered regularly interspaced short palindromic repeats as an advanced treatment for Parkinson's disease. Brain Behav 2021; 11:e2280. [PMID: 34291612 PMCID: PMC8413717 DOI: 10.1002/brb3.2280] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/26/2021] [Accepted: 06/27/2021] [Indexed: 12/04/2022] Open
Abstract
Recently, genome-editing technology like clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 has improved the translational gap in the treatments mediated through gene therapy. The advantages of the CRISPR system, such as, work in the living cells and tissues, candidate this technique for the employing in experiments and the therapy of central nervous system diseases. Parkinson's disease (PD) is a widespread, disabling, neurodegenerative disease induced by dopaminergic neuron loss and linked to progressive motor impairment. Pathophysiological basis knowledge of PD has modified the PD classification model and expresses in the sporadic and familial types. Analyses of the earliest genetic linkage have shown in PD the inclusion of synuclein alpha (SNCA) genomic duplication and SNCA mutations in the familial types of PD pathogenesis. This review analyzes the structure, development, and function in genome editing regulated through the CRISPR/Cas9. Also, it explains the genes associated with PD pathogenesis and the appropriate modifications to favor PD. This study follows the direction by understanding the PD linking analyses in which the CRISPR technique is applied. Finally, this study explains the limitations and future trends of CRISPR service in relation to the genome-editing process in PD patients' induced pluripotent stem cells.
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Affiliation(s)
- Arshad Mehmood
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, P. R. China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, 050000, P. R. China
| | - Wajid Ali
- Key Laboratory of Functional Inorganic Materials Chemistry, School of Chemistry and Materials Science, Heilongjiang University, Harbin, 150080, China
| | - Zaheer Ud Din
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, Liaoning, 116044, China
| | - Shuang Song
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, P. R. China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, 050000, P. R. China
| | - Muhammad Sohail
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| | - Wahid Shah
- Department of Physiology, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Jiangyuan Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, P. R. China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, 050000, P. R. China
| | - Ruo-Yi Guo
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, P. R. China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, 050000, P. R. China
| | - Ikram Ilahi
- Department of Zoology, University of Malakand, Chakdara, Khyber Pakhtunkhwa, 18800, Pakistan
| | - Suleman Shah
- Department of Genetics, Hebei Medical University, Hebei Key Lab of Laboratory Animal, Shijiazhuang, Hebei, 050017, China
| | - Fadhl Al-Shaebi
- Department of Immunology, Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Hebei Medical University, Shijiazhuang, 050017, China
| | - Liaqat Zeb
- School of Bioengineering, Dalian University of Technology, Dalian, Liaoning, 116024, P. R. China
| | - Ernest Amponsah Asiamah
- Hebei Research Center for Stem Cell Medical Translational Engineering, Shijiazhuang, Hebei, 050017, China
| | - Zaid Al-Dhamin
- Department of Traditional and Western Medical Hepatology, Third Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050051, China
| | - Hazrat Bilal
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmacy, Guangxi Normal University, Guilin, Guangxi, 541004, China
| | - Bin Li
- Department of Neurology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050000, P. R. China.,Key Laboratory of Neurology of Hebei Province, Shijiazhuang, Hebei, 050000, P. R. China
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15
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Allosteric modulation of the GTPase activity of a bacterial LRRK2 homolog by conformation-specific Nanobodies. Biochem J 2020; 477:1203-1218. [PMID: 32167135 PMCID: PMC7135905 DOI: 10.1042/bcj20190843] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 03/09/2020] [Accepted: 03/13/2020] [Indexed: 01/02/2023]
Abstract
Mutations in the Parkinson's disease (PD)-associated protein leucine-rich repeat kinase 2 (LRRK2) commonly lead to a reduction of GTPase activity and increase in kinase activity. Therefore, strategies for drug development have mainly been focusing on the design of LRRK2 kinase inhibitors. We recently showed that the central RocCOR domains (Roc: Ras of complex proteins; COR: C-terminal of Roc) of a bacterial LRRK2 homolog cycle between a dimeric and monomeric form concomitant with GTP binding and hydrolysis. PD-associated mutations can slow down GTP hydrolysis by stabilizing the protein in its dimeric form. Here, we report the identification of two Nanobodies (NbRoco1 and NbRoco2) that bind the bacterial Roco protein (CtRoco) in a conformation-specific way, with a preference for the GTP-bound state. NbRoco1 considerably increases the GTP turnover rate of CtRoco and reverts the decrease in GTPase activity caused by a PD-analogous mutation. We show that NbRoco1 exerts its effect by allosterically interfering with the CtRoco dimer–monomer cycle through the destabilization of the dimeric form. Hence, we provide the first proof of principle that allosteric modulation of the RocCOR dimer–monomer cycle can alter its GTPase activity, which might present a potential novel strategy to overcome the effect of LRRK2 PD mutations.
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16
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Deshpande P, Flinkman D, Hong Y, Goltseva E, Siino V, Sun L, Peltonen S, Elo LL, Kaasinen V, James P, Coffey ET. Protein synthesis is suppressed in sporadic and familial Parkinson's disease by LRRK2. FASEB J 2020; 34:14217-14233. [PMID: 32926469 DOI: 10.1096/fj.202001046r] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 07/12/2020] [Accepted: 07/29/2020] [Indexed: 12/21/2022]
Abstract
Gain of function LRRK2-G2019S is the most frequent mutation found in familial and sporadic Parkinson's disease. It is expected therefore that understanding the cellular function of LRRK2 will provide insight on the pathological mechanism not only of inherited Parkinson's, but also of sporadic Parkinson's, the more common form. Here, we show that constitutive LRRK2 activity controls nascent protein synthesis in rodent neurons. Specifically, pharmacological inhibition of LRRK2, Lrrk2 knockdown or Lrrk2 knockout, all lead to increased translation. In the rotenone model for sporadic Parkinson's, LRRK2 activity increases, dopaminergic neuron translation decreases, and the neurites atrophy. All are prevented by LRRK2 inhibitors. Moreover, in striatum and substantia nigra of rotenone treated rats, phosphorylation changes are observed on eIF2α-S52(↑), eIF2s2-S2(↓), and eEF2-T57(↑) in directions that signify protein synthesis arrest. Significantly, translation is reduced by 40% in fibroblasts from Parkinson's patients (G2019S and sporadic cases alike) and this is reversed upon LRRK2 inhibitor treatment. In cells from multiple system atrophy patients, translation is unchanged suggesting that repression of translation is specific to Parkinson's disease. These findings indicate that repression of translation is a proximal function of LRRK2 in Parkinson's pathology.
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Affiliation(s)
| | - Dani Flinkman
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Immunotechnology, Lund University, Lund, Sweden
| | - Ye Hong
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Elena Goltseva
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Lund, Sweden
| | - Lihua Sun
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Sirkku Peltonen
- Department of Dermatology, University of Turku and Turku University Hospital, Turku, Finland
| | - Laura L Elo
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
| | - Valtteri Kaasinen
- Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Peter James
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland.,Department of Immunotechnology, Lund University, Lund, Sweden
| | - Eleanor T Coffey
- Turku Bioscience, University of Turku and Åbo Akademi University, Turku, Finland
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17
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Kuhlmann N, Milnerwood AJ. A Critical LRRK at the Synapse? The Neurobiological Function and Pathophysiological Dysfunction of LRRK2. Front Mol Neurosci 2020; 13:153. [PMID: 32973447 PMCID: PMC7482583 DOI: 10.3389/fnmol.2020.00153] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 12/25/2022] Open
Abstract
Since the discovery of LRRK2 mutations causal to Parkinson's disease (PD) in the early 2000s, the LRRK2 protein has been implicated in a plethora of cellular processes in which pathogenesis could occur, yet its physiological function remains elusive. The development of genetic models of LRRK2 PD has helped identify the etiological and pathophysiological underpinnings of the disease, and may identify early points of intervention. An important role for LRRK2 in synaptic function has emerged in recent years, which links LRRK2 to other genetic forms of PD, most notably those caused by mutations in the synaptic protein α-synuclein. This point of convergence may provide useful clues as to what drives dysfunction in the basal ganglia circuitry and eventual death of substantia nigra (SN) neurons. Here, we discuss the evolution and current state of the literature placing LRRK2 at the synapse, through the lens of knock-out, overexpression, and knock-in animal models. We hope that a deeper understanding of LRRK2 neurobiology, at the synapse and beyond, will aid the eventual development of neuroprotective interventions for PD, and the advancement of useful treatments in the interim.
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Affiliation(s)
- Naila Kuhlmann
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Austen J Milnerwood
- Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology & Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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18
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Safari F, Hatam G, Behbahani AB, Rezaei V, Barekati-Mowahed M, Petramfar P, Khademi F. CRISPR System: A High-throughput Toolbox for Research and Treatment of Parkinson's Disease. Cell Mol Neurobiol 2020; 40:477-493. [PMID: 31773362 DOI: 10.1007/s10571-019-00761-w] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 11/14/2019] [Indexed: 12/13/2022]
Abstract
In recent years, the innovation of gene-editing tools such as the CRISPR/Cas9 system improves the translational gap of treatments mediated by gene therapy. The privileges of CRISPR/Cas9 such as working in living cells and organs candidate this technology for using in research and treatment of the central nervous system (CNS) disorders. Parkinson's disease (PD) is a common, debilitating, neurodegenerative disorder which occurs due to loss of dopaminergic neurons and is associated with progressive motor dysfunction. Knowledge about the pathophysiological basis of PD has altered the classification system of PD, which manifests in familial and sporadic forms. The first genetic linkage studies in PD demonstrated the involvement of Synuclein alpha (SNCA) mutations and SNCA genomic duplications in the pathogenesis of PD familial forms. Subsequent studies have also insinuated mutations in leucine repeat kinase-2 (LRRK2), Parkin, PTEN-induced putative kinase 1 (PINK1), as well as DJ-1 causing familial forms of PD. This review will attempt to discuss the structure, function, and development in genome editing mediated by CRISP/Cas9 system. Further, it describes the genes involved in the pathogenesis of PD and the pertinent alterations to them. We will pursue this line by delineating the PD linkage studies in which CRISPR system was employed. Finally, we will discuss the pros and cons of CRISPR employment vis-à-vis the process of genome editing in PD patients' iPSCs.
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Affiliation(s)
- Fatemeh Safari
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Gholamreza Hatam
- Basic Sciences in Infectious Diseases Research Center, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Behzad Behbahani
- Diagnostic Laboratory Sciences and Technology Research Center, School of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Vahid Rezaei
- Department of Medical Nanotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mazyar Barekati-Mowahed
- Department of Physiology & Biophysics, School of Medicine, Case Western Reserve University, Ohio, USA
| | - Peyman Petramfar
- Clinical Neurology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Farzaneh Khademi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran.
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19
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Berwick DC, Heaton GR, Azeggagh S, Harvey K. LRRK2 Biology from structure to dysfunction: research progresses, but the themes remain the same. Mol Neurodegener 2019; 14:49. [PMID: 31864390 PMCID: PMC6925518 DOI: 10.1186/s13024-019-0344-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 11/07/2019] [Indexed: 12/12/2022] Open
Abstract
Since the discovery of leucine-rich repeat kinase 2 (LRRK2) as a protein that is likely central to the aetiology of Parkinson’s disease, a considerable amount of work has gone into uncovering its basic cellular function. This effort has led to the implication of LRRK2 in a bewildering range of cell biological processes and pathways, and probable roles in a number of seemingly unrelated medical conditions. In this review we summarise current knowledge of the basic biochemistry and cellular function of LRRK2. Topics covered include the identification of phosphorylation substrates of LRRK2 kinase activity, in particular Rab proteins, and advances in understanding the activation of LRRK2 kinase activity via dimerisation and association with membranes, especially via interaction with Rab29. We also discuss biochemical studies that shed light on the complex LRRK2 GTPase activity, evidence of roles for LRRK2 in a range of cell signalling pathways that are likely cell type specific, and studies linking LRRK2 to the cell biology of organelles. The latter includes the involvement of LRRK2 in autophagy, endocytosis, and processes at the trans-Golgi network, the endoplasmic reticulum and also key microtubule-based cellular structures. We further propose a mechanism linking LRRK2 dimerisation, GTPase function and membrane recruitment with LRRK2 kinase activation by Rab29. Together these data paint a picture of a research field that in many ways is moving forward with great momentum, but in other ways has not changed fundamentally. Many key advances have been made, but very often they seem to lead back to the same places.
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Affiliation(s)
- Daniel C Berwick
- School of Health, Life and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK.
| | - George R Heaton
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK
| | - Sonia Azeggagh
- School of Health, Life and Chemical Sciences, The Open University, Walton Hall, Milton Keynes, MK7 6AA, UK
| | - Kirsten Harvey
- Department of Pharmacology, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, UK.
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20
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Zaldivar-Diez J, Li L, Garcia AM, Zhao WN, Medina-Menendez C, Haggarty SJ, Gil C, Morales AV, Martinez A. Benzothiazole-Based LRRK2 Inhibitors as Wnt Enhancers and Promoters of Oligodendrocytic Fate. J Med Chem 2019; 63:2638-2655. [DOI: 10.1021/acs.jmedchem.9b01752] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Josefa Zaldivar-Diez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Lingling Li
- Instituto Cajal, CSIC, Av. Doctor Arce, 37, 28002 Madrid, Spain
| | - Ana M. Garcia
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Wen-Ning Zhao
- Chemical Neurobiology Lab, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | | | - Stephen. J. Haggarty
- Chemical Neurobiology Lab, Center for Genomic Medicine, Departments of Neurology and Psychiatry, Massachusetts General Hospital, Harvard Medical School, 185 Cambridge Street, Boston, Massachusetts 02114, United States
| | - Carmen Gil
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
| | - Aixa V. Morales
- Instituto Cajal, CSIC, Av. Doctor Arce, 37, 28002 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
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21
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Lewis PA. Leucine rich repeat kinase 2: a paradigm for pleiotropy. J Physiol 2019; 597:3511-3521. [PMID: 31124140 DOI: 10.1113/jp276163] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 05/09/2019] [Indexed: 12/11/2022] Open
Abstract
The LRRK2 gene, coding for leucine rich repeat kinase 2 (LRRK2), is a key player in the genetics of Parkinson's disease. Despite extensive efforts, LRRK2 has proved remarkably evasive with regard to attempts to understand both the role it plays in disease and its normal physiological function. At least part of why LRRK2 has been so difficult to define is that it appears to be many things to many cellular functions and diseases - a pleiotropic actor at both the genetic and the molecular level. Gaining greater insight into the mechanisms and pathways allowing LRRK2 to act in this manner will have implications for our understanding of the role of genes in the aetiology of complex disease, the molecular underpinnings of signal transduction pathways in the cell, and drug discovery in the genome era.
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Affiliation(s)
- Patrick A Lewis
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AP, UK.,Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
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22
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Structure and nucleotide-induced conformational dynamics of the Chlorobium tepidum Roco protein. Biochem J 2019; 476:51-66. [PMID: 30538153 DOI: 10.1042/bcj20180803] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The LRR (leucine-rich repeat)-Roc (Ras of complex proteins)-COR (C-terminal of Roc) domains are central to the action of nearly all Roco proteins, including the Parkinson's disease-associated protein LRRK2 (leucine-rich repeat kinase 2). We previously demonstrated that the Roco protein from Chlorobium tepidum (CtRoco) undergoes a dimer-monomer cycle during the GTPase reaction, with the protein being mainly dimeric in the nucleotide-free and GDP (guanosine-5'-diphosphate)-bound states and monomeric in the GTP (guanosine-5'-triphosphate)-bound state. Here, we report a crystal structure of CtRoco in the nucleotide-free state showing for the first time the arrangement of the LRR-Roc-COR. This structure reveals a compact dimeric arrangement and shows an unanticipated intimate interaction between the Roc GTPase domains in the dimer interface, involving residues from the P-loop, the switch II loop, the G4 region and a loop which we named the 'Roc dimerization loop'. Hydrogen-deuterium exchange coupled to mass spectrometry (HDX-MS) is subsequently used to highlight structural alterations induced by individual steps along the GTPase cycle. The structure and HDX-MS data propose a pathway linking nucleotide binding to monomerization and relaying the conformational changes via the Roc switch II to the LRR and COR domains. Together, this work provides important new insights in the regulation of the Roco proteins.
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23
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Breger LS, Fuzzati Armentero MT. Genetically engineered animal models of Parkinson's disease: From worm to rodent. Eur J Neurosci 2018; 49:533-560. [PMID: 30552719 DOI: 10.1111/ejn.14300] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/13/2018] [Accepted: 11/16/2018] [Indexed: 12/26/2022]
Abstract
Parkinson's disease (PD) is a progressive neurological disorder characterised by aberrant accumulation of insoluble proteins, including alpha-synuclein, and a loss of dopaminergic neurons in the substantia nigra. The extended neurodegeneration leads to a drop of striatal dopamine levels responsible for disabling motor and non-motor impairments. Although the causes of the disease remain unclear, it is well accepted among the scientific community that the disorder may also have a genetic component. For that reason, the number of genetically engineered animal models has greatly increased over the past two decades, ranging from invertebrates to more complex organisms such as mice and rats. This trend is growing as new genetic variants associated with the disease are discovered. The EU Joint Programme - Neurodegenerative Disease Research (JPND) has promoted the creation of an online database aiming at summarising the different features of experimental models of Parkinson's disease. This review discusses available genetic models of PD and the extent to which they adequately mirror the human pathology and reflects on future development and uses of genetically engineered experimental models for the study of PD.
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Affiliation(s)
- Ludivine S Breger
- Institut des Maladies Neurodégénératives, CNRS UMR 5293, Centre Broca Nouvelle Aquitaine, Université de Bordeaux, Bordeaux cedex, France
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Bae EJ, Kim DK, Kim C, Mante M, Adame A, Rockenstein E, Ulusoy A, Klinkenberg M, Jeong GR, Bae JR, Lee C, Lee HJ, Lee BD, Di Monte DA, Masliah E, Lee SJ. LRRK2 kinase regulates α-synuclein propagation via RAB35 phosphorylation. Nat Commun 2018; 9:3465. [PMID: 30150626 PMCID: PMC6110743 DOI: 10.1038/s41467-018-05958-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 07/17/2018] [Indexed: 01/08/2023] Open
Abstract
Propagation of α-synuclein aggregates has been suggested as a contributing factor in Parkinson's disease (PD) progression. However, the molecular mechanisms underlying α-synuclein aggregation are not fully understood. Here, we demonstrate in cell culture, nematode, and rodent models of PD that leucine-rich repeat kinase 2 (LRRK2), a PD-linked kinase, modulates α-synuclein propagation in a kinase activity-dependent manner. The PD-linked G2019S mutation in LRRK2, which increases kinase activity, enhances propagation efficiency. Furthermore, we show that the role of LRRK2 in α-synuclein propagation is mediated by RAB35 phosphorylation. Constitutive activation of RAB35 overrides the reduced α-synuclein propagation phenotype in lrk-1 mutant C. elegans. Finally, in a mouse model of synucleinopathy, administration of an LRRK2 kinase inhibitor reduced α-synuclein aggregation via enhanced interaction of α-synuclein with the lysosomal degradation pathway. These results suggest that LRRK2-mediated RAB35 phosphorylation is a potential therapeutic target for modifying disease progression.
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Affiliation(s)
- Eun-Jin Bae
- Departments of Biomedical Sciences and Medicine, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Dong-Kyu Kim
- Departments of Biomedical Sciences and Medicine, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea
| | - Changyoun Kim
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.,Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Michael Mante
- Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Anthony Adame
- Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Edward Rockenstein
- Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ayse Ulusoy
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127, Bonn, Germany
| | - Michael Klinkenberg
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127, Bonn, Germany
| | - Ga Ram Jeong
- Department of Neuroscience, Graduate School, Kyung Hee University, Seoul, 02447, Korea
| | - Jae Ryul Bae
- Department of Neuroscience, Graduate School, Kyung Hee University, Seoul, 02447, Korea
| | - Cheolsoon Lee
- Department of Anatomy, School of Medicine, Konkuk University, Seoul, 05029, Korea
| | - He-Jin Lee
- Department of Anatomy, School of Medicine, Konkuk University, Seoul, 05029, Korea
| | - Byung-Dae Lee
- Department of Physiology, School of Medicine, Kyung Hee University, Seoul, 02447, Korea
| | - Donato A Di Monte
- German Center for Neurodegenerative Diseases (DZNE), Sigmund-Freud-Strasse 27, 53127, Bonn, Germany
| | - Eliezer Masliah
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.,Department Neurosciences, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA.,Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Seung-Jae Lee
- Departments of Biomedical Sciences and Medicine, Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, 03080, Korea.
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Nagarajan N, Chellam J, Kannan RR. Exploring the functional impact of mutational drift in LRRK2 gene and identification of specific inhibitors for the treatment of Parkinson disease. J Cell Biochem 2018; 119:4878-4889. [PMID: 29369408 DOI: 10.1002/jcb.26703] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Abstract
Parkinson's disease (PD) is a disorder of the central nervous system that is caused due to the death of the dopaminergic neurons in the region of the brain called substantia nigra. Mutations in LRRK2 genes are associated with disease condition and it's been reported as crucial factor for drug resistance. Identification of deleterious mutations and studying the structural and functional impact of such mutations may lead to the identification of potential selective inhibitors. In this study, we analyzed 52 PD associated mutations, among that 20 were identified as highly deleterious. The deleterious mutations G2019S and I2020T in the kinase domain were playing a key role in causing resistance to drug levedopa. Molecular docking analyses have been performed to understand the binding affinity of levodapa with LRRK2 in wild and mutant condition. Molecular docking results show that levedopa binds differentially and obtained less number of hydrogen bonds in compared with wild type LRRK2. In addition, molecular dynamics simulations were performed to study the efficacy of docked complexes and it was observed that the efficacy of the mutant complexes (G2019S-Levodopa and I2020T-Levodopa) affected in the presence of mutation. Finally, through virtual screening approach specific inhibitors SCHEMBL6473053 and SCHEMBL1278779 have been identified that could potentially inhibit LLRK2 mutants G2019S and I2020T respectively. Over all this computational investigation correlates the impact of genotypic modulation in structure and function of drug target which enhanced in the identification of precision medicine to treat PD.
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Affiliation(s)
- Nagasundaram Nagarajan
- Molecular and Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama University, Chennai, Tamil Nadu, India
| | - Jaynthy Chellam
- Department of Bioinformatics, Sathyabama University, Chennai, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Molecular and Nanomedicine Research Unit, Centre for Nanoscience and Nanotechnology, Sathyabama University, Chennai, Tamil Nadu, India
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The unconventional G-protein cycle of LRRK2 and Roco proteins. Biochem Soc Trans 2017; 44:1611-1616. [PMID: 27913669 DOI: 10.1042/bst20160224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 09/09/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
Abstract
Mutations in the human leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of hereditary Parkinson's disease (PD). LRRK2 belongs to the Roco family of proteins, which are characterized by the presence of a Ras of complex proteins domain (Roc), a C-terminal of Roc domain (COR) and a kinase domain. Despite intensive research, much remains unknown about activity and the effect of PD-associated mutations. Recent biochemical and structural studies suggest that LRRK2 and Roco proteins are noncanonical G-proteins that do not depend on guanine nucleotide exchange factors or GTPase-activating proteins for activation. In this review, we will discuss the unusual G-protein cycle of LRRK2 in the context of the complex intramolecular LRRK2 activation mechanism.
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Abstract
Leucine-rich repeat kinase 2 (LRRK2) has been implicated in a wide range of cellular processes, including the catabolic pathways collectively described as autophagy. In this chapter, the evidence linking LRRK2 to autophagy will be examined, along with how regulation of autophagy and lysosomal pathways may provide a nexus between the physiological function of this protein and the different diseases with which it has been associated. Data from cellular and animal models for LRRK2 function and dysfunction support a role in the regulation and control of autophagic pathways in the cell, although the extant results do not provide a clear indication as to whether LRRK2 is a positive or negative regulator of these pathways, and there are conflicting data as to the impact of mutations in LRRK2 causative for Parkinson's disease. Given that LRRK2 is a priority drug target for Parkinson's, the evidence suggesting that knockout or inhibition of LRRK2 can result in deregulation of autophagy may have important implications and is discussed in the context of our wider understanding of LRRK2.
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Affiliation(s)
- Claudia Manzoni
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK
| | - Patrick A Lewis
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK.
- Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London, UK.
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Roosen DA, Cookson MR. LRRK2 at the interface of autophagosomes, endosomes and lysosomes. Mol Neurodegener 2016; 11:73. [PMID: 27927216 PMCID: PMC5142374 DOI: 10.1186/s13024-016-0140-1] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/03/2016] [Indexed: 02/07/2023] Open
Abstract
Over the past 20 years, substantial progress has been made in identifying the underlying genetics of Parkinson's disease (PD). Of the known genes, LRRK2 is a major genetic contributor to PD. However, the exact function of LRRK2 remains to be elucidated. In this review, we discuss how familial forms of PD have led us to hypothesize that alterations in endomembrane trafficking play a role in the pathobiology of PD. We will discuss the major observations that have been made to elucidate the role of LRRK2 in particular, including LRRK2 animal models and high-throughput proteomics approaches. Taken together, these studies strongly support a role of LRRK2 in vesicular dynamics. We also propose that targeting these pathways may not only be beneficial for developing therapeutics for LRRK2-driven PD, but also for other familial and sporadic cases.
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Affiliation(s)
- Dorien A. Roosen
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bldg. 35, 35 Convent Drive, Bethesda, MD 20892-3707 USA
- School of Pharmacy, University of Reading, Whiteknights, Reading, RG6 6AP UK
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bldg. 35, 35 Convent Drive, Bethesda, MD 20892-3707 USA
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Langston RG, Rudenko IN, Cookson MR. The function of orthologues of the human Parkinson's disease gene LRRK2 across species: implications for disease modelling in preclinical research. Biochem J 2016; 473:221-32. [PMID: 26811536 PMCID: PMC5165698 DOI: 10.1042/bj20150985] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In the period since LRRK2 (leucine-rich repeat kinase 2) was identified as a causal gene for late-onset autosomal dominant parkinsonism, a great deal of work has been aimed at understanding whether the LRRK2 protein might be a druggable target for Parkinson's disease (PD). As part of this effort, animal models have been developed to explore both the normal and the pathophysiological roles of LRRK2. However, LRRK2 is part of a wider family of proteins whose functions in different organisms remain poorly understood. In this review, we compare the information available on biochemical properties of LRRK2 homologues and orthologues from different species from invertebrates (e.g. Caenorhabditis elegans and Drosophila melanogaster) to mammals. We particularly discuss the mammalian LRRK2 homologue, LRRK1, and those species where there is only a single LRRK homologue, discussing examples where each of the LRRK family of proteins has distinct properties as well as those cases where there appear to be functional redundancy. We conclude that uncovering the function of LRRK2 orthologues will help to elucidate the key properties of human LRRK2 as well as to improve understanding of the suitability of different animal models for investigation of LRRK2-related PD.
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Affiliation(s)
- Rebekah G. Langston
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
| | - Iakov N. Rudenko
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
| | - Mark R. Cookson
- Cell Biology and Gene Expression Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD, 20892
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Abstract
Meprins are astacin metalloproteases with a characteristic, easily recognizable structure, given that they are the only proteases with both MAM and MATH domains plus a transmembrane region. So far assumed to be vertebrate-specific, it is shown here, using a combination of evolutionary and genomic analyses, that meprins originated before the urochordates/vertebrates split. In particular, three genes encoding structurally typical meprin proteins are arranged in tandem in the genome of the urochordate Ciona intestinalis. Phylogenetic analyses showed that the protease and MATH domains present in the meprin-like proteins encoded by the Ciona genes are very similar in sequence to the domains found in vertebrate meprins, which supports them having a common origin. While many vertebrates have the two canonical meprin-encoding genes orthologous to human MEP1A and MEP1B (which respectively encode for the proteins known as meprin α and meprin β), a single gene has been found so far in the genome of the chondrichthyan fish Callorhinchus milii, and additional meprin-encoding genes are present in some species. Particularly, a group of bony fish species have genes encoding highly divergent meprins, here named meprin-F. Genes encoding meprin-F proteins, derived from MEP1B genes, are abundant in some species, as the Amazon molly, Poecilia formosa, which has 7 of them. Finally, it is confirmed that the MATH domains of meprins are very similar to the ones in TRAF ubiquitin ligases, which suggests that meprins originated when protease and TRAF E3-encoding sequences were combined.
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Affiliation(s)
- Ignacio Marín
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, (IBV-CSIC), Valencia, Spain
- * E-mail:
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Boddu R, Hull TD, Bolisetty S, Hu X, Moehle MS, Daher JPL, Kamal AI, Joseph R, George JF, Agarwal A, Curtis LM, West AB. Leucine-rich repeat kinase 2 deficiency is protective in rhabdomyolysis-induced kidney injury. Hum Mol Genet 2015; 24:4078-93. [PMID: 25904107 DOI: 10.1093/hmg/ddv147] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/20/2015] [Indexed: 12/16/2022] Open
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2) gene are the most common known genetic cause of Parkinson's disease, and LRRK2 is also linked to Crohn's and Hansen's disease. LRRK2 is expressed in many organs in mammals but is particularly abundant in the kidney. We find that LRRK2 protein is predominantly localized to collecting duct cells in the rat kidney, with much lower expression in other kidney cells. While genetic knockout (KO) of LRRK2 expression is well-tolerated in mice and rats, a unique age-dependent pathology develops in the kidney. The cortex and medulla of LRRK2 KO rat kidneys become darkly pigmented in early adulthood, yet aged animals display no overt signs of kidney failure. Accompanying the dark pigment we find substantial macrophage infiltration in LRRK2 KO kidneys, suggesting the presence of chronic inflammation that may predispose to kidney disease. Unexpectedly, the dark kidneys of the LRRK2 KO rats are highly resistant to rhabdomyolysis-induced acute kidney injury compared with wild-type rats. Biochemical profiling of the LRRK2 KO kidneys using immunohistochemistry, proteomic and lipidomic analyses show a massive accumulation of hemoglobin and lipofuscin in renal tubules that account for the pigmentation. The proximal tubules demonstrate a corresponding up-regulation of the cytoprotective protein heme oxygenase-1 (HO-1) which is capable of mitigating acute kidney injury. The unusual kidney pathology of LRRK2 KO rats highlights several novel physiological roles for LRRK2 and provides indirect evidence for HO-1 expression as a protective mechanism in acute kidney injury in LRRK2 deficiency.
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Affiliation(s)
| | | | | | - Xianzhen Hu
- Department of Neurology, University of Alabama at Birmingham, Birmingham 35294, USA and
| | - Mark S Moehle
- Department of Neurology, University of Alabama at Birmingham, Birmingham 35294, USA and
| | - João Paulo Lima Daher
- Department of Neurology, University of Alabama at Birmingham, Birmingham 35294, USA and
| | | | | | | | - Anupam Agarwal
- Department of Medicine, Birmingham Veterans Administration Medical Center, Birmingham, Birmingham 35294, USA
| | - Lisa M Curtis
- Department of Medicine, Birmingham Veterans Administration Medical Center, Birmingham, Birmingham 35294, USA
| | - Andrew B West
- Department of Neurology, University of Alabama at Birmingham, Birmingham 35294, USA and
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Abstract
Interactions between genetic and environmental factors are thought to contribute to the pathogenesis of the majority of Parkinson's disease (PD) cases. However, our understanding of these interactions is at an early stage. Mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of hereditary PD. Penetrance of LRRK2 mutations is incomplete and variable, suggesting that other environmental or genetic factors may contribute to the development of the disorder. Recently, using animal models, several attempts have been made to understand if LRRK2 may mediate sensitivity to environmental neurotoxicants. Here, we critically review the most current data on how LRRK2 mutations influence neurotoxicity in PD models.
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Affiliation(s)
- Jang-Won Lee
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Jason R Cannon
- School of Health Sciences, Purdue University, West Lafayette, IN 47907, USA
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Daniel G, Moore DJ. Modeling LRRK2 Pathobiology in Parkinson's Disease: From Yeast to Rodents. Curr Top Behav Neurosci 2015; 22:331-368. [PMID: 24850078 DOI: 10.1007/7854_2014_311] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mutations in the leucine-rich repeat kinase 2 (LRRK2, PARK8) gene represent the most common cause of familial Parkinson's disease (PD) with autosomal dominant inheritance, whereas common variation at the LRRK2 genomic locus influences the risk of developing idiopathic PD. LRRK2 is a member of the ROCO protein family and contains multiple domains, including Ras-of-Complex (ROC) GTPase, kinase, and protein-protein interaction domains. In the last decade, the biochemical characterization of LRRK2 and the development of animal model s have provided important insight into the pathobiology of LRRK2. In this review, we comprehensively describe the different models employed to understand LRRK2-associated PD, including yeast, invertebrates, transgenic and viral-based rodents, and patient-derived induced pluripotent stem cells. We discuss how these models have contributed to understanding LRRK2 pathobiology and the advantages and limitations of each model for exploring aspects of LRRK2-associated PD.
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Affiliation(s)
- Guillaume Daniel
- School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland
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Li JQ, Tan L, Yu JT. The role of the LRRK2 gene in Parkinsonism. Mol Neurodegener 2014; 9:47. [PMID: 25391693 PMCID: PMC4246469 DOI: 10.1186/1750-1326-9-47] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 10/21/2014] [Indexed: 12/13/2022] Open
Abstract
Parkinson’s disease (PD), like many common age-related conditions, has been recognized to have a substantial genetic component. Multiple lines of evidence suggest that Leucine-rich repeat kinase 2 (LRRK2) is a crucial factor to understanding the etiology of PD. LRRK2 is a large, widely expressed, multi-domain and multifunctional protein. LRRK2 mutations are the major cause to inherited and sporadic PD. In this review, we discuss the pathology and clinical features which show diversity and variability of LRRK2-associated PD. In addition, we do a thorough literature review and provide theoretical data for gene counseling. Further, we present the evidence linking LRRK2 to various possible pathogenic mechanism of PD such as α-synuclein, tau, inflammatory response, oxidative stress, mitochondrial dysfunction, synaptic dysfunction as well as autophagy-lysosomal system. Based on the above work, we investigate activities both within GTPase and outside enzymatic regions in order to obtain a potential therapeutic approach to solve the LRRK2 problem.
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Affiliation(s)
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, No, 5 Donghai Middle Road, Qingdao 266071, PR China.
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Reyniers L, Del Giudice MG, Civiero L, Belluzzi E, Lobbestael E, Beilina A, Arrigoni G, Derua R, Waelkens E, Li Y, Crosio C, Iaccarino C, Cookson MR, Baekelandt V, Greggio E, Taymans JM. Differential protein-protein interactions of LRRK1 and LRRK2 indicate roles in distinct cellular signaling pathways. J Neurochem 2014; 131:239-50. [PMID: 24947832 PMCID: PMC4272680 DOI: 10.1111/jnc.12798] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Revised: 05/30/2014] [Accepted: 06/17/2014] [Indexed: 02/07/2023]
Abstract
Genetic studies show that LRRK2, and not its closest paralogue LRRK1, is linked to Parkinson's disease. To gain insight into the molecular and cellular basis of this discrepancy, we searched for LRRK1- and LRRK2-specific cellular processes by identifying their distinct interacting proteins. A protein microarray-based interaction screen was performed with recombinant 3xFlag-LRRK1 and 3xFlag-LRRK2 and, in parallel, co-immunoprecipitation followed by mass spectrometry was performed from SH-SY5Y neuroblastoma cell lines stably expressing 3xFlag-LRRK1 or 3xFlag-LRRK2. We identified a set of LRRK1- and LRRK2-specific as well as common interactors. One of our most prominent findings was that both screens pointed to epidermal growth factor receptor (EGF-R) as a LRRK1-specific interactor, while 14-3-3 proteins were LRRK2-specific. This is consistent with phosphosite mapping of LRRK1, revealing phosphosites outside of 14-3-3 consensus binding motifs. To assess the functional relevance of these interactions, SH-SY5Y-LRRK1 and -LRRK2 cell lines were treated with LRRK2 kinase inhibitors that disrupt 14-3-3 binding, or with EGF, an EGF-R agonist. Redistribution of LRRK2, not LRRK1, from diffuse cytoplasmic to filamentous aggregates was observed after inhibitor treatment. Similarly, EGF induced translocation of LRRK1, but not of LRRK2, to endosomes. Our study confirms that LRRK1 and LRRK2 can carry out distinct functions by interacting with different cellular proteins. LRRK1 and LRRK2 (leucine-rich repeat kinase) interaction partners were identified by two different protein-protein interaction screens. These confirmed epidermal growth factor receptor (EGR-R) as a LRRK1-specific interactor, while 14-3-3 proteins were LRRK2-specific. Functional analysis of these interactions and the pathways they mediate shows that LRRK1 and LRRK2 signaling do not intersect, reflective of the differential role of both LRRKs in Parkinson's disease.
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Affiliation(s)
- Lauran Reyniers
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | | | - Laura Civiero
- Department of Biology, University of Padova, Padova, Italy
| | - Elisa Belluzzi
- Department of Biology, University of Padova, Padova, Italy
| | - Evy Lobbestael
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Alexandra Beilina
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA
| | - Giorgio Arrigoni
- Department of Biomedical Sciences, University of Padova, Padova, Italy.,Proteomics Center of Padova University, Padova, Italy
| | - Rita Derua
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of protein phosphorylation and proteomics, Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, Laboratory of protein phosphorylation and proteomics, Leuven, Belgium
| | - Yan Li
- Protein/Peptide Sequencing Facility, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland, USA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, Maryland, USA
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
| | - Jean-Marc Taymans
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven, Leuven, Belgium
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Boon JY, Dusonchet J, Trengrove C, Wolozin B. Interaction of LRRK2 with kinase and GTPase signaling cascades. Front Mol Neurosci 2014; 7:64. [PMID: 25071441 PMCID: PMC4087324 DOI: 10.3389/fnmol.2014.00064] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 06/19/2014] [Indexed: 02/04/2023] Open
Abstract
LRRK2 is a protein that interacts with a plethora of signaling molecules, but the complexity of LRRK2 function presents a challenge for understanding the role of LRRK2 in the pathophysiology of Parkinson's disease (PD). Studies of LRRK2 using over-expression in transgenic mice have been disappointing, however, studies using invertebrate systems have yielded a much clearer picture, with clear effects of LRRK2 expression, knockdown or deletion in Caenorhabditis elegans and Drosophila on modulation of survival of dopaminergic neurons. Recent studies have begun to focus attention on particular signaling cascades that are a target of LRRK2 function. LRRK2 interacts with members of the mitogen activated protein kinase (MAPK) pathway and might regulate the pathway action by acting as a scaffold that directs the location of MAPK pathway activity, without strongly affecting the amount of MAPK pathway activity. Binding to GTPases, GTPase-activating proteins and GTPase exchange factors are another strong theme in LRRK2 biology, with LRRK2 binding to rac1, cdc42, rab5, rab7L1, endoA, RGS2, ArfGAP1, and ArhGEF7. All of these molecules appear to feed into a function output for LRRK2 that modulates cytoskeletal outgrowth and vesicular dynamics, including autophagy. These functions likely impact modulation of α-synuclein aggregation and associated toxicity eliciting the disease processes that we term PD.
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Affiliation(s)
- Joon Y Boon
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA
| | - Julien Dusonchet
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA
| | - Chelsea Trengrove
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA
| | - Benjamin Wolozin
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA ; Neurology, Boston University School of Medicine Boston, MA, USA
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Cardona F, Tormos-Pérez M, Pérez-Tur J. Structural and functional in silico analysis of LRRK2 missense substitutions. Mol Biol Rep 2014; 41:2529-42. [PMID: 24488318 DOI: 10.1007/s11033-014-3111-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/10/2014] [Indexed: 11/27/2022]
Abstract
The LRRK2 gene (Leucine-Rich Repeat Kinase 2, PARK8) is mutated in a significant number of cases of autosomal dominant Parkinson's disease (PD) and in some sporadic cases of late-onset PD. LRRK2 is a large, complex protein that comprises several interaction domains: armadillo, ankyrin, leucine-rich repeats and WD40 domains; two catalytic domains: ROC-GTPase and serine/threonine kinase; and a COR domain (unknown function). Pathogenic mutations are scattered all over the domains of LRRK2, although the prevalence of mutations in some domains is higher (ROC-GTPase, COR and kinase). In this work, we model the structure of each domain to predict and explore the effects of described missense mutations and polymorphisms. The results allow us to postulate the possible effects of pathogenic mutations in the function of the protein, and hypothesize the importance of some polymorphisms that have not been linked directly to PD, but act as risk factors for the disease. In our analysis, we also study the effects of PD-related mutations in the kinase domain structure and in the phosphorylation of the activation loop to determine effects on kinase activity.
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Affiliation(s)
- Fernando Cardona
- Unitat de Genètica Molecular, Institut de Biomedicina de València, Consejo Superior de Investigaciones Científicas (IBV-CSIC), Jaume Roig 11, 46010, Valencia, Spain,
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Taymans JM, Gao F, Baekelandt V. Metabolic labeling of leucine rich repeat kinases 1 and 2 with radioactive phosphate. J Vis Exp 2013:e50523. [PMID: 24084685 DOI: 10.3791/50523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Leucine rich repeat kinases 1 and 2 (LRRK1 and LRRK2) are paralogs which share a similar domain organization, including a serine-threonine kinase domain, a Ras of complex proteins domain (ROC), a C-terminal of ROC domain (COR), and leucine-rich and ankyrin-like repeats at the N-terminus. The precise cellular roles of LRRK1 and LRRK2 have yet to be elucidated, however LRRK1 has been implicated in tyrosine kinase receptor signaling, while LRRK2 is implicated in the pathogenesis of Parkinson's disease. In this report, we present a protocol to label the LRRK1 and LRRK2 proteins in cells with (32)P orthophosphate, thereby providing a means to measure the overall phosphorylation levels of these 2 proteins in cells. In brief, affinity tagged LRRK proteins are expressed in HEK293T cells which are exposed to medium containing (32)P-orthophosphate. The (32)P-orthophosphate is assimilated by the cells after only a few hours of incubation and all molecules in the cell containing phosphates are thereby radioactively labeled. Via the affinity tag (3xflag) the LRRK proteins are isolated from other cellular components by immunoprecipitation. Immunoprecipitates are then separated via SDS-PAGE, blotted to PVDF membranes and analysis of the incorporated phosphates is performed by autoradiography ((32)P signal) and western detection (protein signal) of the proteins on the blots. The protocol can readily be adapted to monitor phosphorylation of any other protein that can be expressed in cells and isolated by immunoprecipitation.
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Affiliation(s)
- Jean-Marc Taymans
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, KU Leuven and Leuven Institute for Neuroscience and Disease (LIND)
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Expression analysis of Lrrk1, Lrrk2 and Lrrk2 splice variants in mice. PLoS One 2013; 8:e63778. [PMID: 23675505 PMCID: PMC3651128 DOI: 10.1371/journal.pone.0063778] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/05/2013] [Indexed: 11/19/2022] Open
Abstract
Missense mutations in the leucine-rich repeat kinase 2 gene (LRRK2) are linked to autosomal dominant forms of Parkinson's disease (PD). In order to get insights into the physiological role of Lrrk2, we examined the distribution of Lrrk2 mRNA and different splice variants in the developing murine embryo and the adult brain of Mus musculus. To analyse if the Lrrk2-paralog, Lrrk1, may have redundant functions in PD-development, we also compared Lrrk1 and Lrrk2 expression in the same tissues. Using radioactive in situ hybridization, we found ubiquitous expression of both genes at low level from embryonic stage E9.5 onward, which progressively increased up until birth. The developing central nervous system (CNS) displayed no prominent Lrrk2 mRNA signals at these time-points. However, in the entire postnatal brain Lrrk2 became detectable, showing strongest level in the striatum and the cortex of adult mice; Lrrk1 was only detectable in the mitral cell layer of the olfactory bulb. Thus, due to the non-overlapping expression patterns, a redundant function of Lrrk2 and Lrrk1 in the pathogenesis of PD seems to be unlikely. Quantification of Lrrk2 mRNA and protein level in several brain regions by real-time PCR and Western blot verified the striatum and cortex as hotspots of postnatal Lrrk2 expression. Strong expression of Lrrk2 is mainly found in neurons, specifically in the dopamine receptor 1 (DRD1a) and 2 (DRD2)-positive subpopulations of the striatal medium spiny neurons. Finally, we identified 2 new splice-variants of Lrrk2 in RNA-samples from various adult brain regions and organs: a variant with a skipped exon 5 and a truncated variant terminating in an alternative exon 42a. In order to identify the origin of these two splice variants, we also analysed primary neural cultures independently and found cell-specific expression patterns for these variants in microglia and astrocytes.
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Pérez M, Berlanga R, Sanz I, Aramburu MJ. BioUSeR: a semantic-based tool for retrieving Life Science web resources driven by text-rich user requirements. J Biomed Semantics 2013; 4:12. [PMID: 23635042 PMCID: PMC3698192 DOI: 10.1186/2041-1480-4-12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Accepted: 04/18/2013] [Indexed: 12/05/2022] Open
Abstract
Background Open metadata registries are a fundamental tool for researchers in the Life Sciences trying to locate resources. While most current registries assume that resources are annotated with well-structured metadata, evidence shows that most of the resource annotations simply consists of informal free text. This reality must be taken into account in order to develop effective techniques for resource discovery in Life Sciences. Results BioUSeR is a semantic-based tool aimed at retrieving Life Sciences resources described in free text. The retrieval process is driven by the user requirements, which consist of a target task and a set of facets of interest, both expressed in free text. BioUSeR is able to effectively exploit the available textual descriptions to find relevant resources by using semantic-aware techniques. Conclusions BioUSeR overcomes the limitations of the current registries thanks to: (i) rich specification of user information needs, (ii) use of semantics to manage textual descriptions, (iii) retrieval and ranking of resources based on user requirements.
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Affiliation(s)
- María Pérez
- Department of Computer Science and Engineering, Universitat Jaume I, Castellón, Spain.
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41
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Dzamko N, Halliday GM. Unlocking the secrets of LRRK2 function with selective kinase inhibitors. FUTURE NEUROLOGY 2013. [DOI: 10.2217/fnl.13.9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LRRK2 is currently considered to be a potential therapeutic target for the treatment of Parkinson’s disease. A number of pathological mutations, the majority of which lie in the dual catalytic domains of LRRK2, segregate with Parkinson’s disease in an autosomal-dominant fashion. The most common mutation, G2019S, results in an increase in the kinase activity of LRRK2 and much work has, therefore, gone into the development of potent and specific inhibitors of LRRK2 kinase activity. A number of LRRK2 kinase inhibitors have now been employed in the search for the physiological function of LRRK2 and the targets of LRRK2 kinase activity.
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Affiliation(s)
- Nicolas Dzamko
- The School of Medical Sciences, University of New South Wales, Randwick, Australia
- Neuroscience Research Australia, Randwick, Australia.
| | - Glenda M Halliday
- Neuroscience Research Australia, Randwick, Australia
- The School of Medical Sciences, University of New South Wales, Randwick, Australia
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Human leucine-rich repeat kinase 1 and 2: intersecting or unrelated functions? Biochem Soc Trans 2013; 40:1095-101. [PMID: 22988872 DOI: 10.1042/bst20120123] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mutations in LRRK2 (leucine-rich repeat kinase 2) are associated with both familial and sporadic PD (Parkinson's disease). LRRK1 (leucine-rich repeat kinase 1) shares a similar domain structure with LRRK2, but it is not linked to PD. LRRK proteins belong to a gene family known as ROCO, which codes for large proteins with several domains. All ROCO proteins have a ROC (Ras of complex proteins) GTPase domain followed by a domain of unknown function [COR (C-terminal of ROC)]. LRRK2, LRRK1 and other ROCO proteins also possess a kinase domain. To date, the function of LRRK1 and both the physiological and the pathological roles of LRRK2 are only beginning to unfold. The comparative analysis of these two proteins is a strategy to single out the specific properties of LRRKs to understand their cellular physiology. This comparison is the starting point to unravel the pathways that may lead to PD and eventually to develop therapeutic strategies for its treatment. In the present review, we discuss recently published results on LRRK2 and its paralogue LRRK1 concerning their evolutionary significance, biochemical properties and potential functional roles.
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Abstract
In 2004 it was first shown that mutations in LRRK2 can cause Parkinson's disease. This initial discovery was quickly followed by the observation that a single particular mutation is a relatively common cause of Parkinson's disease across varied populations. Further genetic investigation has revealed a variety of genetic ties to Parkinson's disease across this gene. These include common alleles with quite broad effects on risk, likely through both alterations at the protein sequence level, and in the context of expression. A great deal of functional characterization of LRRK2 and disease-causing mutations in this protein has occurred over the last 9 years, and considerable progress has been made. Particular attention has been paid to the kinase activity of LRRK2 as a therapeutic target, and while it is no means certain that this is viable target it is likely that this hypothesis will be tested in clinical trials sooner rather than later. We believe that the future goals for LRRK2 research are, while challenging, relatively clear and that the next 10 years of research promises to be perhaps more exciting than the last.
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Affiliation(s)
- Coro Paisán-Ruiz
- Department of Neurology, Psychiatry, and Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, NY, USA
- Friedman Brain and Mindich Child Health and Development Institutes, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, NY, USA
| | - Patrick A. Lewis
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London, UK
- School of Pharmacy, University of Reading, Whiteknights, Reading, UK
| | - Andrew B. Singleton
- Laboratory of Neurogenetics, National Institute on Aging Intramural Research Program, Bethesda, MD, USA
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Civiero L, Vancraenenbroeck R, Belluzzi E, Beilina A, Lobbestael E, Reyniers L, Gao F, Micetic I, De Maeyer M, Bubacco L, Baekelandt V, Cookson MR, Greggio E, Taymans JM. Biochemical characterization of highly purified leucine-rich repeat kinases 1 and 2 demonstrates formation of homodimers. PLoS One 2012; 7:e43472. [PMID: 22952686 PMCID: PMC3430690 DOI: 10.1371/journal.pone.0043472] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 07/20/2012] [Indexed: 02/06/2023] Open
Abstract
Leucine-rich repeat kinase 1 and 2 (LRRK1 and LRRK2) are large multidomain proteins containing kinase, GTPase and multiple protein-protein interaction domains, but only mutations in LRRK2 are linked to familial Parkinson's disease (PD). Independent studies suggest that LRRK2 exists in the cell as a complex compatible with the size of a dimer. However, whether this complex is truly a homodimer or a heterologous complex formed by monomeric LRRK2 with other proteins has not been definitively proven due to the limitations in obtaining highly pure proteins suitable for structural characterization. Here, we used stable expression of LRRK1 and LRRK2 in HEK293T cell lines to produce recombinant LRRK1 and LRRK2 proteins of greater than 90% purity. Both purified LRRKs are folded, with a predominantly alpha-helical secondary structure and are capable of binding GTP with similar affinity. Furthermore, recombinant LRRK2 exhibits robust autophosphorylation activity, phosphorylation of model peptides in vitro and ATP binding. In contrast, LRRK1 does not display significant autophosphorylation activity and fails to phosphorylate LRRK2 model substrates, although it does bind ATP. Using these biochemically validated proteins, we show that LRRK1 and LRRK2 are capable of forming homodimers as shown by single-particle transmission electron microscopy and immunogold labeling. These LRRK dimers display an elongated conformation with a mean particle size of 145 Å and 175 Å respectively, which is disrupted by addition of 6M guanidinium chloride. Immunogold staining revealed double-labeled particles also in the pathological LRRK2 mutant G2019S and artificial mutants disrupting GTPase and kinase activities, suggesting that point mutations do not hinder the dimeric conformation. Overall, our findings indicate for the first time that purified and active LRRK1 and LRRK2 can form dimers in their full-length conformation.
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Affiliation(s)
- Laura Civiero
- Department of Biology, University of Padova, Padova, Italy
| | - Renée Vancraenenbroeck
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
- Laboratory for Biomolecular Modelling, Katholieke Universiteit Leuven, Heverlee, Belgium
| | - Elisa Belluzzi
- Department of Biology, University of Padova, Padova, Italy
| | - Alexandra Beilina
- Cell Biology and Gene Expression Unit, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Evy Lobbestael
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lauran Reyniers
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Fangye Gao
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ivan Micetic
- Department of Biology, University of Padova, Padova, Italy
| | - Marc De Maeyer
- Laboratory for Biomolecular Modelling, Katholieke Universiteit Leuven, Heverlee, Belgium
| | - Luigi Bubacco
- Department of Biology, University of Padova, Padova, Italy
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mark R. Cookson
- Cell Biology and Gene Expression Unit, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, Maryland, United States of America
| | - Elisa Greggio
- Department of Biology, University of Padova, Padova, Italy
- * E-mail: (EG); (JMT)
| | - Jean-Marc Taymans
- Laboratory for Neurobiology and Gene Therapy, Katholieke Universiteit Leuven, Leuven, Belgium
- * E-mail: (EG); (JMT)
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Li J, Yuan S, Qi L, Huang S, Huang G, Yang M, Xu L, Li Y, Zhang R, Yu Y, Chen S, Xu A. Functional Conservation and Innovation of Amphioxus RIP1-Mediated Signaling in Cell Fate Determination. THE JOURNAL OF IMMUNOLOGY 2011; 187:3962-71. [DOI: 10.4049/jimmunol.1100816] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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46
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Liu Z, Hamamichi S, Lee BD, Yang D, Ray A, Caldwell GA, Caldwell KA, Dawson TM, Smith WW, Dawson VL. Inhibitors of LRRK2 kinase attenuate neurodegeneration and Parkinson-like phenotypes in Caenorhabditis elegans and Drosophila Parkinson's disease models. Hum Mol Genet 2011; 20:3933-42. [PMID: 21768216 DOI: 10.1093/hmg/ddr312] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) have been identified as a genetic cause of familial Parkinson's disease (PD) and have also been found in the more common sporadic form of PD, thus positioning LRRK2 as important in the pathogenesis of PD. Biochemical studies of the disease-causing mutants of LRRK2 implicates an enhancement of kinase activity as the basis of neuronal toxicity and thus possibly the pathogenesis of PD due to LRRK2 mutations. Previously, a chemical library screen identified inhibitors of LRRK2 kinase activity. Here, two of these inhibitors, GW5074 and sorafenib, are shown to protect against G2019S LRRK2-induced neurodegeneration in vivo in Caenorhabditis elegans and in Drosophila. These findings indicate that increased kinase activity of LRRK2 is neurotoxic and that inhibition of LRRK2 activity can have a disease-modifying effect. This suggests that inhibition of LRRK2 holds promise as a treatment for PD.
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Affiliation(s)
- Zhaohui Liu
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, USA
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Abstract
Parkinson disease is a common and usually sporadic neurodegenerative disorder. However, a subset of cases are inherited and, of these, mutations in the gene encoding leucine-rich repeat kinase 2 (LRRK2) are the most frequent genetic cause of disease. Here, we will discuss recent progress in understanding how LRRK2 mutations lead to disease and how this might have therapeutic implications. The effect of mutations on LRRK2 enzyme function provides clues as to which functions of the protein are important to disease. Recent work has focused on the kinase and GTP-binding domains of LRRK2, and it is assumed that these will be therapeutically important, although there is a substantial amount of work to be done to address this hypothesis.
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Kicka S, Shen Z, Annesley SJ, Fisher PR, Lee S, Briggs S, Firtel RA. The LRRK2-related Roco kinase Roco2 is regulated by Rab1A and controls the actin cytoskeleton. Mol Biol Cell 2011; 22:2198-211. [PMID: 21551065 PMCID: PMC3128523 DOI: 10.1091/mbc.e10-12-0937] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We identify a new pathway that is required for proper pseudopod formation. We show that Roco2, a leucine-rich repeat kinase 2 (LRRK2)-related Roco kinase, is activated in response to chemoattractant stimulation and helps mediate cell polarization and chemotaxis by regulating cortical F-actin polymerization and pseudopod extension in a pathway that requires Rab1A. We found that Roco2 binds the small GTPase Rab1A as well as the F-actin cross-linking protein filamin (actin-binding protein 120, abp120) in vivo. We show that active Rab1A (Rab1A-GTP) is required for and regulates Roco2 kinase activity in vivo and that filamin lies downstream from Roco2 and controls pseudopod extension during chemotaxis and random cell motility. Therefore our study uncovered a new signaling pathway that involves Rab1A and controls the actin cytoskeleton and pseudopod extension, and thereby, cell polarity and motility. These findings also may have implications in the regulation of other Roco kinases, including possibly LRRK2, in metazoans.
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Affiliation(s)
- Sebastian Kicka
- Section of Cell and Developmental Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093-0380, USA
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Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder principally affecting the dopaminergic neurons of the substantia nigra. The pathogenic mechanisms are unknown and there are currently no cure or disease-modifying therapies. Recent genetic linkage studies have begun to identify single-gene mutations responsible for rare heritable forms of PD and define genetic risk factors contributing to disease prevalence in sporadic cases. These findings provide an opportunity to gain insight into the molecular mechanisms of this disorder through the creation and analysis of appropriate genetic models. One model system that has proven surprisingly tractable for these studies is the fruit fly, Drosophila melanogaster. Analysis of a number of Drosophila models of PD has revealed some profound and sometimes surprising insights into PD pathogenesis. Moreover, these models can be used to investigate potential therapeutic strategies that may be effective in vivo, and tests have highlighted the efficacy of a number of neuroprotective compounds. Here, I review the methodologies employed in developing the various Drosophila models, and the recent advances that these models in particular have contributed to our understanding of the mechanisms that underlie PD pathogenesis and possible treatment strategies.
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Affiliation(s)
- Alexander J Whitworth
- MRC Centre for Developmental and Biomedical Genetics, Department of Biomedical Sciences, University of Sheffield, Sheffield, UK
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Taymans JM, Cookson MR. Mechanisms in dominant parkinsonism: The toxic triangle of LRRK2, alpha-synuclein, and tau. Bioessays 2010; 32:227-235. [PMID: 20127702 DOI: 10.1002/bies.200900163] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Parkinson's disease (PD) is generally sporadic but a number of genetic diseases have parkinsonism as a clinical feature. Two dominant genes, alpha-synuclein (SNCA) and leucine-rich repeat kinase 2 (LRRK2), are important for understanding inherited and sporadic PD. SNCA is a major component of pathologic inclusions termed Lewy bodies found in PD. LRRK2 is found in a significant proportion of PD cases. These two proteins may be linked as most LRRK2 PD cases have SNCA-positive Lewy bodies. Mutations in both proteins are associated with toxic effects in model systems although mechanisms are unclear. LRRK2 is an intracellular signaling protein possessing both GTPase and kinase activities that may contribute to pathogenicity. A third protein, tau, is implicated as a risk factor for PD. We discuss the potential relationship between these genes and suggest a model for PD pathogenesis where LRRK2 is upstream of pathogenic effects through SNCA, tau, or both proteins.
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Affiliation(s)
- Jean-Marc Taymans
- Cell Biology and Gene Expression Unit, Laboratory of Neurogenetics, NIA, National Institutes of Health, Bethesda, MD, USA.,Laboratory for Neurobiology and Gene Therapy, Division of Molecular Medicine, Department of Molecular and Cellular Medicine, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mark R Cookson
- Cell Biology and Gene Expression Unit, Laboratory of Neurogenetics, NIA, National Institutes of Health, Bethesda, MD, USA
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