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Toft M. New gene involved in the pathogenesis of Parkinson's disease. Lancet Neurol 2024; 23:550-552. [PMID: 38614109 DOI: 10.1016/s1474-4422(24)00166-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/15/2024]
Affiliation(s)
- Mathias Toft
- Department of Neurology, Oslo University Hospital, N-0424 Oslo, Norway; Institute of Clinical Medicine, University of Oslo, Oslo, Norway.
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2
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Gustavsson EK, Follett J, Trinh J, Barodia SK, Real R, Liu Z, Grant-Peters M, Fox JD, Appel-Cresswell S, Stoessl AJ, Rajput A, Rajput AH, Auer R, Tilney R, Sturm M, Haack TB, Lesage S, Tesson C, Brice A, Vilariño-Güell C, Ryten M, Goldberg MS, West AB, Hu MT, Morris HR, Sharma M, Gan-Or Z, Samanci B, Lis P, Tocino T, Amouri R, Sassi SB, Hentati F, Tonelli F, Alessi DR, Farrer MJ. A pathogenic variant in RAB32 causes autosomal dominant Parkinson's disease and activates LRRK2 kinase. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.01.17.24300927. [PMID: 38293014 PMCID: PMC10827257 DOI: 10.1101/2024.01.17.24300927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Background Parkinson's disease (PD) is a progressive neurodegenerative disorder. Mendelian forms have revealed multiple genes, with a notable emphasis on membrane trafficking; RAB GTPases play an important role in PD as a subset are both regulators and substrates of LRRK2 protein kinase. To explore the role of RAB GTPases in PD, we undertook a comprehensive examination of their genetic variability in familial PD. Methods Affected probands from 130 multi-incident PD families underwent whole-exome sequencing and genotyping, Potential pathogenic variants in 61 RAB GTPases were genotyped in relatives to assess disease segregation. These variants were also genotyped in a larger case-control series, totaling 3,078 individuals (2,734 with PD). The single most significant finding was subsequently validated within genetic data (6,043 with PD). Clinical and pathologic findings were summarized for gene-identified patients, and haplotypes were constructed. In parallel, wild-type and mutant RAB GTPase structural variation, protein interactions, and resultant enzyme activities were assessed. Findings We found RAB32 c.213C>G (Ser71Arg) to co-segregate with autosomal dominant parkinsonism in three multi-incident families. RAB32 Ser71Arg was also significantly associated with PD in case-control samples: genotyping and database searches identified thirteen more patients with the same variant that was absent in unaffected controls. Notably, RAB32 Ser71Arg heterozygotes share a common haplotype. At autopsy, one patient had sparse neurofibrillary tangle pathology in the midbrain and thalamus, without Lewy body pathology. In transfected cells the RAB32 Arg71 was twice as potent as Ser71 wild type to activate LRRK2 kinase. Interpretation Our study provides unequivocal evidence to implicate RAB32 Ser71Arg in PD. Functional analysis demonstrates LRRK2 kinase activation. We provide a mechanistic explanation to expand and unify the etiopathogenesis of monogenic PD. Funding National Institutes of Health, the Canada Excellence Research Chairs program, Aligning Science Across Parkinson's, the Michael J. Fox Foundation for Parkinson's Research, and the UK Medical Research Council.
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Affiliation(s)
- Emil K. Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Jordan Follett
- McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, Florida, USA
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Ratzeburger Allee 160, Lübeck 23538, Germany
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sandeep K. Barodia
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Zhiyong Liu
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa Grant-Peters
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Jesse D. Fox
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Silke Appel-Cresswell
- Pacific Parkinson’s Research Centre, Djavad Mowafaghian Centre for Brain Health, Division of Neurology, University of British Columbia, Vancouver, BC, Canada
| | - A. Jon Stoessl
- Pacific Parkinson’s Research Centre, Djavad Mowafaghian Centre for Brain Health, Division of Neurology, University of British Columbia, Vancouver, BC, Canada
| | - Alex Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Ali H. Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Roland Auer
- Department of Pathology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Russel Tilney
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Germany
| | - Tobias B. Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Germany
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Christelle Tesson
- Sorbonne Université, Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau–Paris Brain Institute–ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neurologie, Centre d’Investigation Clinique Neurosciences, DMU Neuroscience, Paris, France
| | - Carles Vilariño-Güell
- Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z3, Canada
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Matthew S. Goldberg
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew B. West
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome Court, Durham 27710, North Carolina, USA
| | - Michele T. Hu
- Division of Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, UK
| | - Huw R. Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- UCL Movement Disorders Centre, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Germany
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), Montreal, Quebec, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Bedia Samanci
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | | | - Rim Amouri
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis 1007, Tunisia
| | - Samia Ben Sassi
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis 1007, Tunisia
| | - Faycel Hentati
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis 1007, Tunisia
| | | | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Matthew J. Farrer
- McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, Florida, USA
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
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3
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Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J. Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science 2023; 382:1404-1411. [PMID: 38127736 PMCID: PMC10786121 DOI: 10.1126/science.adi9926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Gain-of-function mutations in LRRK2, which encodes the leucine-rich repeat kinase 2 (LRRK2), are the most common genetic cause of late-onset Parkinson's disease. LRRK2 is recruited to membrane organelles and activated by Rab29, a Rab guanosine triphosphatase encoded in the PARK16 locus. We present cryo-electron microscopy structures of Rab29-LRRK2 complexes in three oligomeric states, providing key snapshots during LRRK2 recruitment and activation. Rab29 induces an unexpected tetrameric assembly of LRRK2, formed by two kinase-active central protomers and two kinase-inactive peripheral protomers. The central protomers resemble the active-like state trapped by the type I kinase inhibitor DNL201, a compound that underwent a phase 1 clinical trial. Our work reveals the structural mechanism of LRRK2 spatial regulation and provides insights into LRRK2 inhibitor design for Parkinson's disease treatment.
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Affiliation(s)
- Hanwen Zhu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Martin Turk
- Cryo-EM and Tomography Center, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alan Prescott
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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4
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Pal P, Taylor M, Lam PY, Tonelli F, Hecht CA, Lis P, Nirujogi RS, Phung TK, Yeshaw WM, Jaimon E, Fasimoye R, Dickie EA, Wightman M, Macartney T, Pfeffer SR, Alessi DR. Parkinson's VPS35[D620N] mutation induces LRRK2-mediated lysosomal association of RILPL1 and TMEM55B. SCIENCE ADVANCES 2023; 9:eadj1205. [PMID: 38091401 PMCID: PMC10848721 DOI: 10.1126/sciadv.adj1205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/13/2023] [Indexed: 12/18/2023]
Abstract
We demonstrate that the Parkinson's VPS35[D620N] mutation alters the expression of ~220 lysosomal proteins and stimulates recruitment and phosphorylation of Rab proteins at the lysosome. This recruits the phospho-Rab effector protein RILPL1 to the lysosome where it binds to the lysosomal integral membrane protein TMEM55B. We identify highly conserved regions of RILPL1 and TMEM55B that interact and design mutations that block binding. In mouse fibroblasts, brain, and lung, we demonstrate that the VPS35[D620N] mutation reduces RILPL1 levels, in a manner reversed by LRRK2 inhibition and proteasome inhibitors. Knockout of RILPL1 enhances phosphorylation of Rab substrates, and knockout of TMEM55B increases RILPL1 levels. The lysosomotropic agent LLOMe also induced LRRK2 kinase-mediated association of RILPL1 to the lysosome, but to a lower extent than the D620N mutation. Our study uncovers a pathway through which dysfunctional lysosomes resulting from the VPS35[D620N] mutation recruit and activate LRRK2 on the lysosomal surface, driving assembly of the RILPL1-TMEM55B complex.
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Affiliation(s)
- Prosenjit Pal
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Matthew Taylor
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Pui Yiu Lam
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Chloe A. Hecht
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Raja S. Nirujogi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Toan K. Phung
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Wondwossen M. Yeshaw
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Ebsy Jaimon
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Rotimi Fasimoye
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Emily A. Dickie
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Suzanne R. Pfeffer
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305-5307, USA
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Andersen MS, Leikfoss IS, Brorson IS, Cappelletti C, Bettencourt C, Toft M, Pihlstrøm L. Epigenome-wide association study of peripheral immune cell populations in Parkinson's disease. NPJ Parkinsons Dis 2023; 9:149. [PMID: 37903812 PMCID: PMC10616224 DOI: 10.1038/s41531-023-00594-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Understanding the contribution of immune mechanisms to Parkinson's disease pathogenesis is an important challenge, potentially of major therapeutic implications. To further elucidate the involvement of peripheral immune cells, we studied epigenome-wide DNA methylation in isolated populations of CD14+ monocytes, CD19+ B cells, CD4+ T cells, and CD8+ T cells from Parkinson's disease patients and healthy control participants. We included 25 patients with a maximum five years of disease duration and 25 controls, and isolated four immune cell populations from each fresh blood sample. Epigenome-wide DNA methylation profiles were generated from 186 samples using the Illumina MethylationEpic array and association with disease status was tested using linear regression models. We identified six differentially methylated CpGs in CD14+ monocytes and one in CD8 + T cells. Four differentially methylated regions were identified in monocytes, including a region upstream of RAB32, a gene that has been linked to LRRK2. Methylation upstream of RAB32 correlated negatively with mRNA expression, and RAB32 expression was upregulated in Parkinson's disease both in our samples and in summary statistics from a previous study. Our epigenome-wide association study of early Parkinson's disease provides evidence for methylation changes across different peripheral immune cell types, highlighting monocytes and the RAB32 locus. The findings were predominantly cell-type-specific, demonstrating the value of isolating purified cell populations for genomic studies.
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Affiliation(s)
- Maren Stolp Andersen
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | | | | | - Conceicao Bettencourt
- Department of Neurodegenerative Disease and Queen Square Brain Bank for Neurological Disorders, Queen Square Institute of Neurology, University College London, London, UK
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway.
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6
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Dhekne HS, Tonelli F, Yeshaw WM, Chiang CY, Limouse C, Jaimon E, Purlyte E, Alessi DR, Pfeffer SR. Genome-wide screen reveals Rab12 GTPase as a critical activator of Parkinson's disease-linked LRRK2 kinase. eLife 2023; 12:e87098. [PMID: 37874635 PMCID: PMC10708890 DOI: 10.7554/elife.87098] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/22/2023] [Indexed: 10/25/2023] Open
Abstract
Activating mutations in the leucine-rich repeat kinase 2 (LRRK2) cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases, particularly Rab10 and Rab8A, and we showed previously that these phosphoRabs play an important role in LRRK2 membrane recruitment and activation (Vides et al., 2022). To learn more about LRRK2 pathway regulation, we carried out an unbiased, CRISPR-based genome-wide screen to identify modifiers of cellular phosphoRab10 levels. A flow cytometry assay was developed to detect changes in phosphoRab10 levels in pools of mouse NIH-3T3 cells harboring unique CRISPR guide sequences. Multiple negative and positive regulators were identified; surprisingly, knockout of the Rab12 gene was especially effective in decreasing phosphoRab10 levels in multiple cell types and knockout mouse tissues. Rab-driven increases in phosphoRab10 were specific for Rab12, LRRK2-dependent and PPM1H phosphatase-reversible, and did not require Rab12 phosphorylation; they were seen with wild type and pathogenic G2019S and R1441C LRRK2. As expected for a protein that regulates LRRK2 activity, Rab12 also influenced primary cilia formation. AlphaFold modeling revealed a novel Rab12 binding site in the LRRK2 Armadillo domain, and we show that residues predicted to be essential for Rab12 interaction at this site influence phosphoRab10 and phosphoRab12 levels in a manner distinct from Rab29 activation of LRRK2. Our data show that Rab12 binding to a new site in the LRRK2 Armadillo domain activates LRRK2 kinase for Rab phosphorylation and could serve as a new therapeutic target for a novel class of LRRK2 inhibitors that do not target the kinase domain.
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Affiliation(s)
- Herschel S Dhekne
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
| | - Francesca Tonelli
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Wondwossen M Yeshaw
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
| | - Claire Y Chiang
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
| | - Charles Limouse
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
| | - Ebsy Jaimon
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Dario R Alessi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of MedicineStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkStanfordUnited States
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7
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Lian H, Park D, Chen M, Schueder F, Lara-Tejero M, Liu J, Galán JE. Parkinson's disease kinase LRRK2 coordinates a cell-intrinsic itaconate-dependent defence pathway against intracellular Salmonella. Nat Microbiol 2023; 8:1880-1895. [PMID: 37640963 PMCID: PMC10962312 DOI: 10.1038/s41564-023-01459-y] [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: 01/13/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
Cell-intrinsic defences constitute the first line of defence against intracellular pathogens. The guanosine triphosphatase RAB32 orchestrates one such defence response against the bacterial pathogen Salmonella, through delivery of antimicrobial itaconate. Here we show that the Parkinson's disease-associated leucine-rich repeat kinase 2 (LRRK2) orchestrates this defence response by scaffolding a complex between RAB32 and aconitate decarboxylase 1, which synthesizes itaconate from mitochondrial precursors. Itaconate delivery to Salmonella-containing vacuoles was impaired and Salmonella replication increased in LRRK2-deficient cells. Loss of LRRK2 also restored virulence of a Salmonella mutant defective in neutralizing this RAB32-dependent host defence pathway in mice. Cryo-electron tomography revealed tether formation between Salmonella-containing vacuoles and host mitochondria upon Salmonella infection, which was significantly impaired in LRRK2-deficient cells. This positions LRRK2 centrally within a host defence mechanism, which may have favoured selection of a common familial Parkinson's disease mutant allele in the human population.
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Affiliation(s)
- Huan Lian
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Medical Research Institute, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, China
| | - Donghyun Park
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Science Institute, Yale University School of Medicine, New Haven, CT, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, CA, USA
| | - Meixin Chen
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Institute of Infectious Diseases, Shenzhen Bay Laboratory, Shenzhen, China
| | - Florian Schueder
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA
| | - Maria Lara-Tejero
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA
- Microbial Science Institute, Yale University School of Medicine, New Haven, CT, USA
| | - Jorge E Galán
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, USA.
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8
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Ito G, Utsunomiya-Tate N. Overview of the Impact of Pathogenic LRRK2 Mutations in Parkinson's Disease. Biomolecules 2023; 13:biom13050845. [PMID: 37238714 DOI: 10.3390/biom13050845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large protein kinase that physiologically phosphorylates and regulates the function of several Rab proteins. LRRK2 is genetically implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD), although the underlying mechanism is not well understood. Several pathogenic mutations in the LRRK2 gene have been identified, and in most cases the clinical symptoms that PD patients with LRRK2 mutations develop are indistinguishable from those of typical PD. However, it has been shown that the pathological manifestations in the brains of PD patients with LRRK2 mutations are remarkably variable when compared to sporadic PD, ranging from typical PD pathology with Lewy bodies to nigral degeneration with deposition of other amyloidogenic proteins. The pathogenic mutations in LRRK2 are also known to affect the functions and structure of LRRK2, the differences in which may be partly attributable to the variations observed in patient pathology. In this review, in order to help researchers unfamiliar with the field to understand the mechanism of pathogenesis of LRRK2-associated PD, we summarize the clinical and pathological manifestations caused by pathogenic mutations in LRRK2, their impact on the molecular function and structure of LRRK2, and their historical background.
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Affiliation(s)
- Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
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9
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Hu J, Zhang D, Tian K, Ren C, Li H, Lin C, Huang X, Liu J, Mao W, Zhang J. Small-molecule LRRK2 inhibitors for PD therapy: Current achievements and future perspectives. Eur J Med Chem 2023; 256:115475. [PMID: 37201428 DOI: 10.1016/j.ejmech.2023.115475] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/08/2023] [Accepted: 05/08/2023] [Indexed: 05/20/2023]
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multifunctional protein that orchestrates a diverse array of cellular processes, including vesicle transport, autophagy, lysosome degradation, neurotransmission, and mitochondrial activity. Hyperactivation of LRRK2 triggers vesicle transport dysfunction, neuroinflammation, accumulation of α-synuclein, mitochondrial dysfunction, and the loss of cilia, ultimately leading to Parkinson's disease (PD). Therefore, targeting LRRK2 protein is a promising therapeutic strategy for PD. The clinical translation of LRRK2 inhibitors was historically impeded by issues surrounding tissue specificity. Recent studies have identified LRRK2 inhibitors that have no effect on peripheral tissues. Currently, there are four small-molecule LRRK2 inhibitors undergoing clinical trials. This review provides a summary of the structure and biological functions of LRRK2, along with an overview of the binding modes and structure-activity relationships (SARs) of small-molecule inhibitors targeting LRRK2. It offers valuable references for developing novel drugs targeting LRRK2.
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Affiliation(s)
- Jiarui Hu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Keyue Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Changyu Ren
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Heng Li
- Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Congcong Lin
- Department of Medicinal Chemistry and Natural Medicine Chemistry, College of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xiaoli Huang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Jie Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wuyu Mao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China; Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Gerontology and Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, China.
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10
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Is Glial Dysfunction the Key Pathogenesis of LRRK2-Linked Parkinson's Disease? Biomolecules 2023; 13:biom13010178. [PMID: 36671564 PMCID: PMC9856048 DOI: 10.3390/biom13010178] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Leucine rich-repeat kinase 2 (LRRK2) is the most well-known etiologic gene for familial Parkinson's disease (PD). Its gene product is a large kinase with multiple functional domains that phosphorylates a subset of Rab small GTPases. However, studies of autopsy cases with LRRK2 mutations indicate a varied pathology, and the molecular functions of LRRK2 and its relationship to PD pathogenesis are largely unknown. Recently, non-autonomous neurodegeneration associated with glial cell dysfunction has attracted attention as a possible mechanism of dopaminergic neurodegeneration. Molecular studies of LRRK2 in astrocytes and microglia have also suggested that LRRK2 is involved in the regulation of lysosomal and other organelle dynamics and inflammation. In this review, we describe the proposed functions of LRRK2 in glial cells and discuss its involvement in the pathomechanisms of PD.
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11
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Wei Y, Awan MUN, Bai L, Bai J. The function of Golgi apparatus in LRRK2-associated Parkinson's disease. Front Mol Neurosci 2023; 16:1097633. [PMID: 36896008 PMCID: PMC9989030 DOI: 10.3389/fnmol.2023.1097633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/25/2023] Open
Abstract
Parkinson's disease (PD) is a chronic neurodegenerative disease associated with the intracellular organelles. Leucine-rich repeat kinase 2 (LRRK2) is a large multi-structural domain protein, and mutation in LRRK2 is associated with PD. LRRK2 regulates intracellular vesicle transport and function of organelles, including Golgi and lysosome. LRRK2 phosphorylates a group of Rab GTPases, including Rab29, Rab8, and Rab10. Rab29 acts in a common pathway with LRRK2. Rab29 has been shown to recruit LRRK2 to the Golgi complex (GC) to stimulate LRRK2 activity and alter the Golgi apparatus (GA). Interaction between LRRK2 and Vacuolar protein sorting protein 52 (VPS52), a subunit of the Golgi-associated retrograde protein (GARP) complex, mediates the function of intracellular soma trans-Golgi network (TGN) transport. VPS52 also interacts with Rab29. Knockdown of VPS52 leads to the loss of LRRK2/Rab29 transported to the TGN. Rab29, LRRK2, and VPS52 work together to regulate functions of the GA, which is associated with PD. We highlight recent advances in the roles of LRRK2, Rabs, VPS52, and other molecules, such as Cyclin-dependent kinase 5 (CDK5) and protein kinase C (PKC) in the GA, and discuss their possible association with the pathological mechanisms of PD.
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Affiliation(s)
- Yonghang Wei
- Laboratory of Molecular Neurobiology, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Maher Un Nisa Awan
- Laboratory of Molecular Neurobiology, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Liping Bai
- Laboratory of Molecular Neurobiology, Medical School, Kunming University of Science and Technology, Kunming, China
| | - Jie Bai
- Laboratory of Molecular Neurobiology, Medical School, Kunming University of Science and Technology, Kunming, China
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12
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Vides EG, Adhikari A, Chiang CY, Lis P, Purlyte E, Limouse C, Shumate JL, Spínola-Lasso E, Dhekne HS, Alessi DR, Pfeffer SR. A feed-forward pathway drives LRRK2 kinase membrane recruitment and activation. eLife 2022; 11:e79771. [PMID: 36149401 PMCID: PMC9576273 DOI: 10.7554/elife.79771] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/22/2022] [Indexed: 12/30/2022] Open
Abstract
Activating mutations in the leucine-rich repeat kinase 2 (LRRK2) cause Parkinson's disease, and previously we showed that activated LRRK2 phosphorylates a subset of Rab GTPases (Steger et al., 2017). Moreover, Golgi-associated Rab29 can recruit LRRK2 to the surface of the Golgi and activate it there for both auto- and Rab substrate phosphorylation. Here, we define the precise Rab29 binding region of the LRRK2 Armadillo domain between residues 360-450 and show that this domain, termed 'site #1,' can also bind additional LRRK2 substrates, Rab8A and Rab10. Moreover, we identify a distinct, N-terminal, higher-affinity interaction interface between LRRK2 phosphorylated Rab8 and Rab10 termed 'site #2' that can retain LRRK2 on membranes in cells to catalyze multiple, subsequent phosphorylation events. Kinase inhibitor washout experiments demonstrate that rapid recovery of kinase activity in cells depends on the ability of LRRK2 to associate with phosphorylated Rab proteins, and phosphorylated Rab8A stimulates LRRK2 phosphorylation of Rab10 in vitro. Reconstitution of purified LRRK2 recruitment onto planar lipid bilayers decorated with Rab10 protein demonstrates cooperative association of only active LRRK2 with phospho-Rab10-containing membrane surfaces. These experiments reveal a feed-forward pathway that provides spatial control and membrane activation of LRRK2 kinase activity.
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Affiliation(s)
- Edmundo G Vides
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Ayan Adhikari
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Claire Y Chiang
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Pawel Lis
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Charles Limouse
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Justin L Shumate
- Department of Biochemistry, Stanford UniversityStanfordUnited States
| | - Elena Spínola-Lasso
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
- Instituto Universitario de Investigaciones Biomédicas y Sanitarias (IUIBS), Departamento de Bioquímica y Biología Molecular, Universidad de Las Palmas de Gran CanariaGran CanariaSpain
| | - Herschel S Dhekne
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Dario R Alessi
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of DundeeDundeeUnited Kingdom
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford UniversityStanfordUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
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13
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Pfeffer SR. LRRK2
phosphorylation of Rab
GTPases
in Parkinson’s disease. FEBS Lett 2022; 597:811-818. [PMID: 36114007 DOI: 10.1002/1873-3468.14492] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/03/2022] [Accepted: 09/09/2022] [Indexed: 11/08/2022]
Abstract
Rab GTPases comprise a large family of conserved GTPases that are critical regulators of the secretory and endocytic pathways. The human genome encodes ~ 65 Rabs that localize to discrete membrane compartments and, when in their GTP-bound state, bind to effector proteins to carry out diverse functions. Activating mutations in LRRK2 kinase cause Parkinson's disease, and subsets of Rab GTPases are important LRRK2 substrates. LRRK2 phosphorylates a conserved threonine residue that is essential for Rab interaction with guanine nucleotide exchange factors, effectors, and GDI that recycles Rabs between membrane compartments. This brief review will highlight new findings related to LRRK2-mediated phosphorylation of Rab GTPases and its consequences. Remarkably, Rab phosphorylation flips a switch on Rab effector selection with dominant consequences for cell pathophysiology.
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Affiliation(s)
- Suzanne R. Pfeffer
- Department of Biochemistry Stanford University School of Medicine 279 Campus Drive Stanford CA 94305‐5307 USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network Chevy Chase MD USA
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14
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Kalogeropulou AF, Purlyte E, Tonelli F, Lange SM, Wightman M, Prescott AR, Padmanabhan S, Sammler E, Alessi DR. Impact of 100 LRRK2 variants linked to Parkinson's disease on kinase activity and microtubule binding. Biochem J 2022; 479:1759-1783. [PMID: 35950872 PMCID: PMC9472821 DOI: 10.1042/bcj20220161] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Mutations enhancing the kinase activity of leucine-rich repeat kinase-2 (LRRK2) cause Parkinson's disease (PD) and therapies that reduce LRRK2 kinase activity are being tested in clinical trials. Numerous rare variants of unknown clinical significance have been reported, but how the vast majority impact on LRRK2 function is unknown. Here, we investigate 100 LRRK2 variants linked to PD, including previously described pathogenic mutations. We identify 23 LRRK2 variants that robustly stimulate kinase activity, including variants within the N-terminal non-catalytic regions (ARM (E334K, A419V), ANK (R767H), LRR (R1067Q, R1325Q)), as well as variants predicted to destabilize the ROC:CORB interface (ROC (A1442P, V1447M), CORA (R1628P) CORB (S1761R, L1795F)) and COR:COR dimer interface (CORB (R1728H/L)). Most activating variants decrease LRRK2 biomarker site phosphorylation (pSer935/pSer955/pSer973), consistent with the notion that the active kinase conformation blocks their phosphorylation. We conclude that the impact of variants on kinase activity is best evaluated by deploying a cellular assay of LRRK2-dependent Rab10 substrate phosphorylation, compared with a biochemical kinase assay, as only a minority of activating variants (CORB (Y1699C, R1728H/L, S1761R) and kinase (G2019S, I2020T, T2031S)), enhance in vitro kinase activity of immunoprecipitated LRRK2. Twelve variants including several that activate LRRK2 and have been linked to PD, suppress microtubule association in the presence of a Type I kinase inhibitor (ARM (M712V), LRR (R1320S), ROC (A1442P, K1468E, S1508R), CORA (A1589S), CORB (Y1699C, R1728H/L) and WD40 (R2143M, S2350I, G2385R)). Our findings will stimulate work to better understand the mechanisms by which variants impact biology and provide rationale for variant carrier inclusion or exclusion in ongoing and future LRRK2 inhibitor clinical trials.
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Affiliation(s)
- Alexia F. Kalogeropulou
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Sven M. Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
| | - Alan R. Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | | | - Esther Sammler
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee DD1 9SY, U.K
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
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15
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Coku I, Mutez E, Eddarkaoui S, Carrier S, Marchand A, Deldycke C, Goveas L, Baille G, Tir M, Magnez R, Thuru X, Vermeersch G, Vandenberghe W, Buée L, Defebvre L, Sablonnière B, Chartier-Harlin MC, Taymans JM, Huin V. Functional Analyses of Two Novel LRRK2 Pathogenic Variants in Familial Parkinson's Disease. Mov Disord 2022; 37:1761-1767. [PMID: 35708213 PMCID: PMC9543145 DOI: 10.1002/mds.29124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 04/20/2022] [Accepted: 05/13/2022] [Indexed: 11/29/2022] Open
Abstract
Background Pathogenic variants in the LRRK2 gene are a common monogenic cause of Parkinson's disease. However, only seven variants have been confirmed to be pathogenic. Objectives We identified two novel LRRK2 variants (H230R and A1440P) and performed functional testing. Methods We transiently expressed wild‐type, the two new variants, or two known pathogenic mutants (G2019S and R1441G) in HEK‐293 T cells, with or without LRRK2 kinase inhibitor treatment. We characterized the phosphorylation and kinase activity of the mutants by western blotting. Thermal shift assays were performed to determine the folding and stability of the LRRK2 proteins. Results The two variants were found in two large families and segregate with the disease. They display altered LRRK2 phosphorylation and kinase activity. Conclusions We identified two novel LRRK2 variants which segregate with the disease. The results of functional testing lead us to propose these two variants as novel causative mutations for familial Parkinson's disease. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society
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Affiliation(s)
- Ilda Coku
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Eugénie Mutez
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France.,University of Lille, Inserm, CHU Lille, Expert Center for Parkinson's Disease, Lille, France
| | - Sabiha Eddarkaoui
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Sébastien Carrier
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Antoine Marchand
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Claire Deldycke
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Liesel Goveas
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Guillaume Baille
- University of Lille, Inserm, CHU Lille, Expert Center for Parkinson's Disease, Lille, France
| | - Mélissa Tir
- Department of Neurology and Expert Center for Parkinson's Disease, Amiens University Hospital, CHU Amiens-Picardie, Amiens, France
| | - Romain Magnez
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | - Xavier Thuru
- University of Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277-CANTHER-Cancer Heterogeneity Plasticity and Resistance to Therapies, Lille, France
| | | | - Wim Vandenberghe
- Department of Neurology, University Hospitals Leuven, Leuven, Belgium.,Laboratory for Parkinson Research, Department of Neurosciences, KU Leuven, Leuven, Belgium
| | - Luc Buée
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Luc Defebvre
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France.,University of Lille, Inserm, CHU Lille, Expert Center for Parkinson's Disease, Lille, France
| | - Bernard Sablonnière
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France.,University of Lille, Inserm, CHU Lille, Department of Toxicology and Genopathies, UF Neurobiology, Lille, France
| | | | - Jean-Marc Taymans
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France
| | - Vincent Huin
- University of Lille, Inserm, CHU Lille, U1172-LilNCog (JPARC)-Lille Neuroscience & Cognition, Lille, France.,University of Lille, Inserm, CHU Lille, Department of Toxicology and Genopathies, UF Neurobiology, Lille, France
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16
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Stormo AE, Shavarebi F, FitzGibbon M, Earley EM, Ahrendt H, Lum LS, Verschueren E, Swaney DL, Skibinski G, Ravisankar A, van Haren J, Davis EJ, Johnson JR, Von Dollen J, Balen C, Porath J, Crosio C, Mirescu C, Iaccarino C, Dauer WT, Nichols RJ, Wittmann T, Cox TC, Finkbeiner S, Krogan NJ, Oakes SA, Hiniker A. The E3 ligase TRIM1 ubiquitinates LRRK2 and controls its localization, degradation, and toxicity. J Cell Biol 2022; 221:e202010065. [PMID: 35266954 PMCID: PMC8919618 DOI: 10.1083/jcb.202010065] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 10/26/2021] [Accepted: 01/04/2022] [Indexed: 11/22/2022] Open
Abstract
Missense mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common cause of familial Parkinson's disease (PD); however, pathways regulating LRRK2 subcellular localization, function, and turnover are not fully defined. We performed quantitative mass spectrometry-based interactome studies to identify 48 novel LRRK2 interactors, including the microtubule-associated E3 ubiquitin ligase TRIM1 (tripartite motif family 1). TRIM1 recruits LRRK2 to the microtubule cytoskeleton for ubiquitination and proteasomal degradation by binding LRRK2911-919, a nine amino acid segment within a flexible interdomain region (LRRK2853-981), which we designate the "regulatory loop" (RL). Phosphorylation of LRRK2 Ser910/Ser935 within LRRK2 RL influences LRRK2's association with cytoplasmic 14-3-3 versus microtubule-bound TRIM1. Association with TRIM1 modulates LRRK2's interaction with Rab29 and prevents upregulation of LRRK2 kinase activity by Rab29 in an E3-ligase-dependent manner. Finally, TRIM1 rescues neurite outgrowth deficits caused by PD-driving mutant LRRK2 G2019S. Our data suggest that TRIM1 is a critical regulator of LRRK2, controlling its degradation, localization, binding partners, kinase activity, and cytotoxicity.
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Affiliation(s)
- Adrienne E.D. Stormo
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Farbod Shavarebi
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Molly FitzGibbon
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Elizabeth M. Earley
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Hannah Ahrendt
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Lotus S. Lum
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Erik Verschueren
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Danielle L. Swaney
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Gaia Skibinski
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Abinaya Ravisankar
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Jeffrey van Haren
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
- Department of Cell Biology, Erasmus MC, Rotterdam, The Netherlands
| | - Emily J. Davis
- Departments of Pathology, University of California San Francisco, San Francisco, CA
| | - Jeffrey R. Johnson
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - John Von Dollen
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
| | - Carson Balen
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Jacob Porath
- Department of Pathology, University of California San Diego, San Diego, CA
| | - Claudia Crosio
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | | | - Ciro Iaccarino
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - William T. Dauer
- Departments of Neurology and Neurotherapeutics, University of Texas Southwestern Medical Center, Dallas, TX
- Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX
| | | | - Torsten Wittmann
- Departments of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA
| | - Timothy C. Cox
- Department of Oral and Craniofacial Sciences, School of Medicine, University of Missouri Kansas City, Kansas City, MO
- School of Dentistry and Department of Pediatrics, School of Medicine, University of Missouri Kansas City, Kansas City, MO
| | - Steve Finkbeiner
- Departments of Neurology, University of California San Francisco, San Francisco, CA
- Departments of Physiology, University of California San Francisco, San Francisco, CA
- Taube/Koret Center for Neurodegenerative Disease Research, J. David Gladstone Institutes, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Nevan J. Krogan
- Departments of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA
- Center for Systems and Therapeutics, J. David Gladstone Institutes, San Francisco, CA
| | - Scott A. Oakes
- Departments of Pathology, University of California San Francisco, San Francisco, CA
- Department of Pathology, University of Chicago, Chicago, IL
| | - Annie Hiniker
- Department of Pathology, University of California San Diego, San Diego, CA
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17
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Hidalgo F, Nocka LM, Shah NH, Gorday K, Latorraca NR, Bandaru P, Templeton S, Lee D, Karandur D, Pelton JG, Marqusee S, Wemmer D, Kuriyan J. A saturation-mutagenesis analysis of the interplay between stability and activation in Ras. eLife 2022; 11:e76595. [PMID: 35272765 PMCID: PMC8916776 DOI: 10.7554/elife.76595] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 01/25/2022] [Indexed: 12/31/2022] Open
Abstract
Cancer mutations in Ras occur predominantly at three hotspots: Gly 12, Gly 13, and Gln 61. Previously, we reported that deep mutagenesis of H-Ras using a bacterial assay identified many other activating mutations (Bandaru et al., 2017). We now show that the results of saturation mutagenesis of H-Ras in mammalian Ba/F3 cells correlate well with the results of bacterial experiments in which H-Ras or K-Ras are co-expressed with a GTPase-activating protein (GAP). The prominent cancer hotspots are not dominant in the Ba/F3 data. We used the bacterial system to mutagenize Ras constructs of different stabilities and discovered a feature that distinguishes the cancer hotspots. While mutations at the cancer hotspots activate Ras regardless of construct stability, mutations at lower-frequency sites (e.g. at Val 14 or Asp 119) can be activating or deleterious, depending on the stability of the Ras construct. We characterized the dynamics of three non-hotspot activating Ras mutants by using NMR to monitor hydrogen-deuterium exchange (HDX). These mutations result in global increases in HDX rates, consistent with destabilization of Ras. An explanation for these observations is that mutations that destabilize Ras increase nucleotide dissociation rates, enabling activation by spontaneous nucleotide exchange. A further stability decrease can lead to insufficient levels of folded Ras - and subsequent loss of function. In contrast, the cancer hotspot mutations are mechanism-based activators of Ras that interfere directly with the action of GAPs. Our results demonstrate the importance of GAP surveillance and protein stability in determining the sensitivity of Ras to mutational activation.
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Affiliation(s)
- Frank Hidalgo
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Laura M Nocka
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - Neel H Shah
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, Columbia UniversityNew YorkUnited States
| | - Kent Gorday
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
| | - Naomi R Latorraca
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Pradeep Bandaru
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Sage Templeton
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - David Lee
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Deepti Karandur
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jeffrey G Pelton
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
| | - Susan Marqusee
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - David Wemmer
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | - John Kuriyan
- California Institute for Quantitative Biosciences (QB3), University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Department of Chemistry, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
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18
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Helton LG, Rideout HJ, Herberg FW, Kennedy EJ. Leucine rich repeat kinase 2 (
LRRK2
) peptide modulators: Recent advances and future directions. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Leah G. Helton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
| | - Hardy J. Rideout
- Center for Clinical, Experimental Surgery, and Translational Research Biomedical Research Foundation of the Academy of Athens Athens Greece
| | - Friedrich W. Herberg
- Department of Biochemistry Institute for Biology, University of Kassel Kassel Germany
| | - Eileen J. Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy University of Georgia Athens Georgia USA
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19
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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: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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20
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Conformation and dynamics of the kinase domain drive subcellular location and activation of LRRK2. Proc Natl Acad Sci U S A 2021; 118:2100844118. [PMID: 34088839 PMCID: PMC8201809 DOI: 10.1073/pnas.2100844118] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
To explore how pathogenic mutations of the multidomain leucine-rich repeat kinase 2 (LRRK2) hijack its finely tuned activation process and drive Parkinson's disease (PD), we used a multitiered approach. Most mutations mimic Rab-mediated activation by "unleashing" kinase activity, and many, like the kinase inhibitor MLi-2, trap LRRK2 onto microtubules. Here we mimic activation by simply deleting the inhibitory N-terminal domains and then characterize conformational changes induced by MLi-2 and PD mutations. After confirming that LRRK2RCKW retains full kinase activity, we used hydrogen-deuterium exchange mass spectrometry to capture breathing dynamics in the presence and absence of MLi-2. Solvent-accessible regions throughout the entire protein are reduced by MLi-2 binding. With molecular dynamics simulations, we created a dynamic portrait of LRRK2RCKW and demonstrate the consequences of kinase domain mutations. Although all domains contribute to regulating kinase activity, the kinase domain, driven by the DYGψ motif, is the allosteric hub that drives LRRK2 regulation.
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21
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Myasnikov A, Zhu H, Hixson P, Xie B, Yu K, Pitre A, Peng J, Sun J. Structural analysis of the full-length human LRRK2. Cell 2021; 184:3519-3527.e10. [PMID: 34107286 DOI: 10.1016/j.cell.2021.05.004] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/23/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022]
Abstract
Mutations in leucine-rich repeat kinase 2 (LRRK2) are commonly implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD). LRRK2 regulates critical cellular processes at membranous organelles and forms microtubule-based pathogenic filaments, yet the molecular basis underlying these biological roles of LRRK2 remains largely enigmatic. Here, we determined high-resolution structures of full-length human LRRK2, revealing its architecture and key interdomain scaffolding elements for rationalizing disease-causing mutations. The kinase domain of LRRK2 is captured in an inactive state, a conformation also adopted by the most common PD-associated mutation, LRRK2G2019S. This conformation serves as a framework for structure-guided design of conformational specific inhibitors. We further determined the structure of COR-mediated LRRK2 dimers and found that single-point mutations at the dimer interface abolished pathogenic filamentation in cells. Overall, our study provides mechanistic insights into physiological and pathological roles of LRRK2 and establishes a structural template for future therapeutic intervention in PD.
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Affiliation(s)
- Alexander Myasnikov
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Cryo-EM and Tomography Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Hanwen Zhu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Patricia Hixson
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Boer Xie
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Kaiwen Yu
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Aaron Pitre
- Cell & Tissue Imaging Center, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.
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22
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Vieira N, Rito T, Correia-Neves M, Sousa N. Sorting Out Sorting Nexins Functions in the Nervous System in Health and Disease. Mol Neurobiol 2021; 58:4070-4106. [PMID: 33931804 PMCID: PMC8280035 DOI: 10.1007/s12035-021-02388-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/05/2021] [Indexed: 12/18/2022]
Abstract
Endocytosis is a fundamental process that controls protein/lipid composition of the plasma membrane, thereby shaping cellular metabolism, sensing, adhesion, signaling, and nutrient uptake. Endocytosis is essential for the cell to adapt to its surrounding environment, and a tight regulation of the endocytic mechanisms is required to maintain cell function and survival. This is particularly significant in the central nervous system (CNS), where composition of neuronal cell surface is crucial for synaptic functioning. In fact, distinct pathologies of the CNS are tightly linked to abnormal endolysosomal function, and several genome wide association analysis (GWAS) and biochemical studies have identified intracellular trafficking regulators as genetic risk factors for such pathologies. The sorting nexins (SNXs) are a family of proteins involved in protein trafficking regulation and signaling. SNXs dysregulation occurs in patients with Alzheimer’s disease (AD), Down’s syndrome (DS), schizophrenia, ataxia and epilepsy, among others, establishing clear roles for this protein family in pathology. Interestingly, restoration of SNXs levels has been shown to trigger synaptic plasticity recovery in a DS mouse model. This review encompasses an historical and evolutionary overview of SNXs protein family, focusing on its organization, phyla conservation, and evolution throughout the development of the nervous system during speciation. We will also survey SNXs molecular interactions and highlight how defects on SNXs underlie distinct pathologies of the CNS. Ultimately, we discuss possible strategies of intervention, surveying how our knowledge about the fundamental processes regulated by SNXs can be applied to the identification of novel therapeutic avenues for SNXs-related disorders.
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Affiliation(s)
- Neide Vieira
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
| | - Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Nuno Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus Gualtar, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
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23
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Malik AU, Karapetsas A, Nirujogi RS, Mathea S, Chatterjee D, Pal P, Lis P, Taylor M, Purlyte E, Gourlay R, Dorward M, Weidlich S, Toth R, Polinski NK, Knapp S, Tonelli F, Alessi DR. Deciphering the LRRK code: LRRK1 and LRRK2 phosphorylate distinct Rab proteins and are regulated by diverse mechanisms. Biochem J 2021; 478:553-578. [PMID: 33459343 PMCID: PMC7886321 DOI: 10.1042/bcj20200937] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/08/2021] [Accepted: 01/18/2021] [Indexed: 01/05/2023]
Abstract
Autosomal dominant mutations in LRRK2 that enhance kinase activity cause Parkinson's disease. LRRK2 phosphorylates a subset of Rab GTPases including Rab8A and Rab10 within its effector binding motif. Here, we explore whether LRRK1, a less studied homolog of LRRK2 that regulates growth factor receptor trafficking and osteoclast biology might also phosphorylate Rab proteins. Using mass spectrometry, we found that in LRRK1 knock-out cells, phosphorylation of Rab7A at Ser72 was most impacted. This residue lies at the equivalent site targeted by LRRK2 on Rab8A and Rab10. Accordingly, recombinant LRRK1 efficiently phosphorylated Rab7A at Ser72, but not Rab8A or Rab10. Employing a novel phospho-specific antibody, we found that phorbol ester stimulation of mouse embryonic fibroblasts markedly enhanced phosphorylation of Rab7A at Ser72 via LRRK1. We identify two LRRK1 mutations (K746G and I1412T), equivalent to the LRRK2 R1441G and I2020T Parkinson's mutations, that enhance LRRK1 mediated phosphorylation of Rab7A. We demonstrate that two regulators of LRRK2 namely Rab29 and VPS35[D620N], do not influence LRRK1. Widely used LRRK2 inhibitors do not inhibit LRRK1, but we identify a promiscuous inhibitor termed GZD-824 that inhibits both LRRK1 and LRRK2. The PPM1H Rab phosphatase when overexpressed dephosphorylates Rab7A. Finally, the interaction of Rab7A with its effector RILP is not affected by LRRK1 phosphorylation and we observe that maximal stimulation of the TBK1 or PINK1 pathway does not elevate Rab7A phosphorylation. Altogether, these findings reinforce the idea that the LRRK enzymes have evolved as major regulators of Rab biology with distinct substrate specificity.
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Affiliation(s)
- Asad U. Malik
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Athanasios Karapetsas
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Raja S. Nirujogi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Sebastian Mathea
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Deep Chatterjee
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Prosenjit Pal
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Pawel Lis
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Matthew Taylor
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Elena Purlyte
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Robert Gourlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Mark Dorward
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Simone Weidlich
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Nicole K. Polinski
- Michael J Fox Foundation for Parkinson's Research, Grand Central Station, PO Box 4777, New York, NY 10163, U.S.A
| | - Stefan Knapp
- Structural Genomics Consortium, Institute for Pharmaceutical Chemistry and Buchmann Institute for Molecular Life Sciences, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Francesca Tonelli
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Dario R. Alessi
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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24
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Savitskiy S, Wachtel R, Pourjafar-Dehkordi D, Kang HS, Trauschke V, Lamb DC, Sattler M, Zacharias M, Itzen A. Proteolysis of Rab32 by Salmonella GtgE induces an inactive GTPase conformation. iScience 2020; 24:101940. [PMID: 33426511 PMCID: PMC7779776 DOI: 10.1016/j.isci.2020.101940] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/18/2020] [Accepted: 12/10/2020] [Indexed: 12/26/2022] Open
Abstract
Rab GTPases are central regulators of intracellular vesicular trafficking. They are frequently targeted by bacterial pathogens through post-translational modifications. Salmonella typhimurium secretes the cysteine protease GtgE during infection, leading to a regioselective proteolytic cleavage of the regulatory switch I loop in the small GTPases of the Rab32 subfamily. Here, using a combination of biochemical methods, molecular dynamics simulations, NMR spectroscopy, and single-pair Förster resonance energy transfer, we demonstrate that the cleavage of Rab32 causes a local increase of conformational flexibility in both switch regions. Cleaved Rab32 maintains its ability to interact with the GDP dissociation inhibitor (GDI). Interestingly, the Rab32 cleavage enables GDI binding also with an active GTP-bound Rab32 in vitro. Furthermore, the Rab32 proteolysis provokes disturbance in the interaction with its downstream effector VARP. Thus, the proteolysis of Rab32 is not a globally degradative mechanism but affects various biochemical and structural properties of the GTPase in a diverse manner.
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Affiliation(s)
- Sergey Savitskiy
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Rudolf Wachtel
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Danial Pourjafar-Dehkordi
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Hyun-Seo Kang
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Vanessa Trauschke
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Don C Lamb
- Department of Chemistry, Center for Nanoscience (CeNS), NanoSystems Initiative Munich (NIM) and Center for Integrated Protein Science Munich (CIPSM), Ludwig Maximilians-Universität München, Munich Germany
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany.,Chemistry Department, Biomolecular NMR and Center for Integrated Protein Science Munich, Technical University of Munich, 85748 Garching, Germany
| | - Martin Zacharias
- Physics Department T38, Technical University of Munich, James-Franck-Strasse 1, 85748 Garching, Germany
| | - Aymelt Itzen
- Department of Biochemistry and Signaltransduction, University Medical Centre Hamburg-Eppendorf (UKE), Martinistrasse 52, 20246 Hamburg, Germany.,Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany.,Centre for Structural Systems Biology (CSSB), University Medical Centre Hamburg-Eppendorf (UKE), Hamburg, Germany
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25
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Kalogeropulou AF, Freemantle JB, Lis P, Vides EG, Polinski NK, Alessi DR. Endogenous Rab29 does not impact basal or stimulated LRRK2 pathway activity. Biochem J 2020; 477:4397-4423. [PMID: 33135724 PMCID: PMC7702304 DOI: 10.1042/bcj20200458] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023]
Abstract
Mutations that enhance LRRK2 protein kinase activity cause inherited Parkinson's disease. LRRK2 phosphorylates a group of Rab GTPase proteins, including Rab10 and Rab12, within the effector-binding switch-II motif. Previous work has indicated that the PARK16 locus, which harbors the gene encoding for Rab29, is involved in Parkinson's, and that Rab29 operates in a common pathway with LRRK2. Co-expression of Rab29 and LRRK2 stimulates LRRK2 activity by recruiting LRRK2 to the surface of the trans Golgi network. Here, we report that knock-out of Rab29 does not influence endogenous LRRK2 activity, based on the assessment of Rab10 and Rab12 phosphorylation, in wild-type LRRK2, LRRK2[R1441C] or VPS35[D620N] knock-in mouse tissues and primary cell lines, including brain extracts and embryonic fibroblasts. We find that in brain extracts, Rab12 phosphorylation is more robustly impacted by LRRK2 inhibitors and pathogenic mutations than Rab10 phosphorylation. Transgenic overexpression of Rab29 in a mouse model was also insufficient to stimulate basal LRRK2 activity. We observed that stimulation of Rab10 and Rab12 phosphorylation induced by agents that stress the endolysosomal system (nigericin, monensin, chloroquine and LLOMe) is suppressed by LRRK2 inhibitors but not blocked in Rab29 deficient cells. From the agents tested, nigericin induced the greatest increase in Rab10 and Rab12 phosphorylation (5 to 9-fold). Our findings indicate that basal, pathogenic, as well as nigericin and monensin stimulated LRRK2 pathway activity is not controlled by Rab29. Further work is required to establish how LRRK2 activity is regulated, and whether other Rab proteins can control LRRK2 by targeting it to diverse membranes.
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Affiliation(s)
- Alexia F. Kalogeropulou
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Jordana B. Freemantle
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Pawel Lis
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
| | - Edmundo G. Vides
- Department of Biochemistry, Stanford University School of Medicine, Stanford 94305-5307, U.S.A
| | - Nicole K. Polinski
- Michael J Fox Foundation for Parkinson's Research, Grand Central Station, PO Box 4777, New York, NY 10163, U.S.A
| | - Dario R. Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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26
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Yu J, He X, Wei A, Liu T, Zhang Q, Pan Y, Hao Z, Yang L, Yuan Y, Zhang Z, Zhang C, Hao C, Liu Z, Li W. HPS1 Regulates the Maturation of Large Dense Core Vesicles and Lysozyme Secretion in Paneth Cells. Front Immunol 2020; 11:560110. [PMID: 33224134 PMCID: PMC7674556 DOI: 10.3389/fimmu.2020.560110] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/12/2020] [Indexed: 12/12/2022] Open
Abstract
HPS1, a BLOC-3 subunit that acts as a guanine nucleotide exchange factor of Rab32/38, may play a role in the removal of VAMP7 during the maturation of large dense core vesicles of Paneth cells. Loss of HPS1 impairs lysozyme secretion and alters the composition of intestinal microbiota, which may explain the susceptibility of HPS-associated inflammatory bowel disease. Hermansky-Pudlak syndrome (HPS) is characterized by oculocutaneous albinism, bleeding tendency, and other chronic organ lesions due to defects in tissue-specific lysosome-related organelles (LROs). For some HPS subtypes, such as HPS-1, it is common to have symptoms of HPS-associated inflammatory bowel disease (IBD). However, its underlying mechanism is largely unknown. HPS1 is a subunit of the BLOC-3 complex which functions in the biogenesis of LROs. Large dense core vesicles (LDCVs) in Paneth cells of the intestine are a type of LROs. We here first report the abnormal LDCV morphology (increased number and enlarged size) in HPS1-deficient pale ear (ep) mice. Similar to its role in melanosome maturation, HPS1 plays an important function in the removal of VAMP7 from LDCVs to promote the maturation of LDCVs. The immature LDCVs in ep mice are defective in regulated secretion of lysozyme, a key anti-microbial peptide in the intestine. We observed changes in the composition of intestinal microbiota in both HPS-1 patients and ep mice. These findings provide insights into the underlying mechanism of HPS-associated IBD development, which may be implicated in possible therapeutic intervention of this devastating condition.
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Affiliation(s)
- Jiaying Yu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China.,University of Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xin He
- University of Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Aihua Wei
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Teng Liu
- Department of Dermatology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qin Zhang
- Institute for Immunology, Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Ying Pan
- Institute for Immunology, Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Zhenhua Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Lin Yang
- University of Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yefeng Yuan
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Zhao Zhang
- University of Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chang Zhang
- University of Chinese Academy of Sciences, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Zhihua Liu
- Institute for Immunology, Tsinghua-Peking Center for Life Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Genetics and Birth Defects Control Center, National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, China
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27
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Padmanabhan S, Fiske BK, Baptista MA. The Michael J. Fox Foundation's Strategies for Accelerating Translation of LRRK2 into Therapies for Parkinson Disease. Cells 2020; 9:E1878. [PMID: 32796584 PMCID: PMC7466022 DOI: 10.3390/cells9081878] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/01/2020] [Accepted: 08/07/2020] [Indexed: 12/16/2022] Open
Abstract
Since 2005, The Michael J. Fox Foundation for Parkinson's Research (MJFF) has invested significant funding and non-funding effort to accelerate research and drug development activity around the Parkinson disease (PD)-associated protein LRRK2. MJFF has spearheaded multiple public/private pre-competitive collaborations that have contributed to our understanding of LRRK2 function; de-risked potential safety questions around the therapeutic use of LRRK2 kinase inhibitors; and generated critical research tools, biosamples, and data for the field. Several LRRK2-targeted therapies are now in human testing due to the hard work of so many in the PD community. In this perspective, we present a holistic description and model of how our Foundation's support targeted important barriers to LRRK2 research and helped move the field into clinical trials.
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Affiliation(s)
- Shalini Padmanabhan
- The Michael J. Fox Foundation for Parkinson’s Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
| | | | - Marco A.S. Baptista
- The Michael J. Fox Foundation for Parkinson’s Research, Grand Central Station, P.O. Box 4777, New York, NY 10120, USA
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28
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Abstract
Parkinson's disease (PD) is a leading cause of neurodegeneration that is defined by the selective loss of dopaminergic neurons and the accumulation of protein aggregates called Lewy bodies (LBs). The unequivocal identification of Mendelian inherited mutations in 13 genes in PD has provided transforming insights into the pathogenesis of this disease. The mechanistic analysis of several PD genes, including α-synuclein (α-syn), leucine-rich repeat kinase 2 (LRRK2), PTEN-induced kinase 1 (PINK1), and Parkin, has revealed central roles for protein aggregation, mitochondrial damage, and defects in endolysosomal trafficking in PD neurodegeneration. In this review, we outline recent advances in our understanding of these gene pathways with a focus on the emergent role of Rab (Ras analog in brain) GTPases and vesicular trafficking as a common mechanism that underpins how mutations in PD genes lead to neuronal loss. These advances have led to previously distinct genes such as vacuolar protein-sorting-associated protein 35 (VPS35) and LRRK2 being implicated in a common signaling pathway. A greater understanding of these common nodes of vesicular trafficking will be crucial for linking other PD genes and improving patient stratification in clinical trials underway against α-syn and LRRK2 targets.
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Affiliation(s)
- Pawan Kishor Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom;
| | - Miratul M K Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom;
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29
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Gloeckner CJ, Porras P. Guilt-by-Association - Functional Insights Gained From Studying the LRRK2 Interactome. Front Neurosci 2020; 14:485. [PMID: 32508578 PMCID: PMC7251075 DOI: 10.3389/fnins.2020.00485] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
The Parkinson's disease-associated Leucine-rich repeat kinase 2 (LRRK2) is a complex multi-domain protein belonging to the Roco protein family, a unique group of G-proteins. Variants of this gene are associated with an increased risk of Parkinson's disease. Besides its well-characterized enzymatic activities, conferred by its GTPase and kinase domains, and a central dimerization domain, it contains four predicted repeat domains, which are, based on their structure, commonly involved in protein-protein interactions (PPIs). In the past decades, tremendous progress has been made in determining comprehensive interactome maps for the human proteome. Knowledge of PPIs has been instrumental in assigning functions to proteins involved in human disease and helped to understand the connectivity between different disease pathways and also significantly contributed to the functional understanding of LRRK2. In addition to an increased kinase activity observed for proteins containing PD-associated variants, various studies helped to establish LRRK2 as a large scaffold protein in the interface between cytoskeletal dynamics and the vesicular transport. This review first discusses a number of specific LRRK2-associated PPIs for which a functional consequence can at least be speculated upon, and then considers the representation of LRRK2 protein interactions in public repositories, providing an outlook on open research questions and challenges in this field.
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Affiliation(s)
- Christian Johannes Gloeckner
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Center for Ophthalmology, Institute for Ophthalmic Research, Core Facility for Medical Bioanalytics, University of Tübingen, Tübingen, Germany
- Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
| | - Pablo Porras
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cherry Hinton, United Kingdom
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30
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Waschbüsch D, Purlyte E, Pal P, McGrath E, Alessi DR, Khan AR. Structural Basis for Rab8a Recruitment of RILPL2 via LRRK2 Phosphorylation of Switch 2. Structure 2020; 28:406-417.e6. [PMID: 32017888 PMCID: PMC7139218 DOI: 10.1016/j.str.2020.01.005] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/27/2019] [Accepted: 01/13/2020] [Indexed: 12/18/2022]
Abstract
Rab8a is associated with the dynamic regulation of membrane protrusions in polarized cells. Rab8a is one of several Rab GTPases that are substrates of leucine-rich repeat kinase 2 (LRRK2), a serine/threonine kinase that is linked to Parkinson's disease. Rab8a is phosphorylated at T72 (pT72) in its switch 2 helix and recruits the phospho-specific effector RILPL2, which subsequently regulates ciliogenesis. Here, we report the crystal structure of phospho-Rab8a (pRab8a) in complex with the RH2 (RILP homology) domain of RILPL2. The complex is a heterotetramer with RILPL2 forming a central α-helical dimer that bridges two pRab8a molecules. The N termini of the α helices cross over, forming an X-shaped cap (X-cap) that orients Arg residues from RILPL2 toward pT72. X-cap residues critical for pRab8a binding are conserved in JIP3 and JIP4, which also interact with LRRK2-phosphorylated Rab10. We propose a general mode of recognition for phosphorylated Rab GTPases by this family of phospho-specific effectors.
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Affiliation(s)
- Dieter Waschbüsch
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Elena Purlyte
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Prosenjit Pal
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emma McGrath
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Amir R Khan
- School of Biochemistry and Immunology, Trinity College, Dublin 2, Ireland; Division of Newborn Medicine, Boston Children's Hospital, Boston, USA.
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31
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Kuwahara T, Iwatsubo T. The Emerging Functions of LRRK2 and Rab GTPases in the Endolysosomal System. Front Neurosci 2020; 14:227. [PMID: 32256311 PMCID: PMC7095371 DOI: 10.3389/fnins.2020.00227] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/02/2020] [Indexed: 12/25/2022] Open
Abstract
The leucine-rich repeat kinase 2 (LRRK2), the most common causative gene for autosomal-dominant familial Parkinson’s disease, encodes a large protein kinase harboring multiple characteristic domains. LRRK2 phosphorylates a set of Rab GTPases in cells, which is enhanced by the Parkinson-associated LRRK2 mutations. Accumulating evidence suggests that LRRK2 regulates intracellular vesicle trafficking and organelle maintenance including Golgi, endosomes and lysosomes. Furthermore, genetic knockout or inhibition of LRRK2 cause lysosomal abnormalities in rodents and primates, and cells from Parkinson’s patients with LRRK2 mutations also exhibit altered lysosome morphology. Cell biological studies on LRRK2 in a diverse cellular context further strengthen the potential connection between LRRK2 and regulation of the endolysosomal system, part of which is mediated by Rab phosphorylation by LRRK2. We will focus on the latest advances on the role of LRRK2 and Rab in relation to the endolysosomal system, and discuss the possible link to the pathomechanism of Parkinson’s disease.
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Affiliation(s)
- Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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32
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Cunningham LA, Moore DJ. Endosomal sorting pathways in the pathogenesis of Parkinson's disease. PROGRESS IN BRAIN RESEARCH 2020; 252:271-306. [PMID: 32247367 PMCID: PMC7206894 DOI: 10.1016/bs.pbr.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The identification of Parkinson's disease (PD)-associated genes has created a powerful platform to begin to understand and nominate pathophysiological disease mechanisms. Herein, we discuss the genetic and experimental evidence supporting endolysosomal dysfunction as a major pathway implicated in PD. Well-studied familial PD-linked gene products, including LRRK2, VPS35, and α-synuclein, demonstrate how disruption of different aspects of endolysosomal sorting pathways by disease-causing mutations may manifest into PD-like phenotypes in many disease models. Newly-identified PD-linked genes, including auxilin, synaptojanin-1 and Rab39b, as well as putative risk genes for idiopathic PD (endophilinA1, Rab29, GAK), further support endosomal sorting deficits as being central to PD. LRRK2 may represent a nexus by regulating many distinct features of endosomal sorting, potentially via phosphorylation of key endocytosis machinery (i.e., auxilin, synaptojanin-1, endoA1) and Rab GTPases (i.e., Rab29, Rab8A, Rab10) that function within these pathways. In turn, LRRK2 kinase activity is critically regulated by Rab29 at the Golgi complex and retromer-associated VPS35 at endosomes. Taken together, the known functions of PD-associated gene products, the impact of disease-linked mutations, and the emerging functional interactions between these proteins points to endosomal sorting pathways as a key point of convergence in the pathogenesis of PD.
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Affiliation(s)
- Lindsey A Cunningham
- Van Andel Institute Graduate School, Grand Rapids, MI, United States; Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States
| | - Darren J Moore
- Center for Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, United States.
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33
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Nassari S, Del Olmo T, Jean S. Rabs in Signaling and Embryonic Development. Int J Mol Sci 2020; 21:E1064. [PMID: 32033485 PMCID: PMC7037298 DOI: 10.3390/ijms21031064] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 02/06/2023] Open
Abstract
Rab GTPases play key roles in various cellular processes. They are essential, among other roles, to membrane trafficking and intracellular signaling events. Both trafficking and signaling events are crucial for proper embryonic development. Indeed, embryogenesis is a complex process in which cells respond to various signals and undergo dramatic changes in their shape, position, and function. Over the last few decades, cellular studies have highlighted the novel signaling roles played by Rab GTPases, while numerous studies have shed light on the important requirements of Rab proteins at various steps of embryonic development. In this review, we aimed to generate an overview of Rab contributions during animal embryogenesis. We first briefly summarize the involvement of Rabs in signaling events. We then extensively highlight the contribution of Rabs in shaping metazoan development and conclude with new approaches that will allow investigation of Rab functions in vivo.
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Affiliation(s)
| | | | - Steve Jean
- Faculté de Médecine et des Sciences de la Santé, Department of Immunology and Cell Biology, Université de Sherbrooke, 3201 Rue Jean Mignault, Sherbrooke, QC J1E 4K8, Canada; (S.N.); (T.D.O.)
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34
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Bao J, Li X, Li Y, Huang C, Meng X, Li J. MicroRNA-141-5p Acts as a Tumor Suppressor via Targeting RAB32 in Chronic Myeloid Leukemia. Front Pharmacol 2020; 10:1545. [PMID: 32038235 PMCID: PMC6987442 DOI: 10.3389/fphar.2019.01545] [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: 08/14/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
MicroRNA-141-5p (miR-141-5p), an important member of the miR-200 family, has been reported to be involved in cellular proliferation, migration, invasion, and drug resistance in different kinds of human malignant tumors. However, the role and function of miR-141-5p in chronic myeloid leukemia (CML) are unclear. In this current study, we found that the level of miR-141-5p was significantly decreased in peripheral blood cells from CML patients compared with normal blood cells and human leukemic cell line (K562 cells) compared with normal CD34+ cells, but was remarkably elevated in patients after treatment with nilotinib or imatinib. Suppression of miR-141-5p promoted K562 cell proliferation and migration in vitro. As expected, overexpression of miR-141-5p weakened K562 cell proliferation, migration, and promoted cell apoptosis. A xenograft model in nude mice showed that overexpression of miR-141-5p markedly suppressed tumor growth in vivo. Mechanistic studies suggested that RAB32 was the potential target of miR-141-5p, and silencing of RAB32 suppressed the proliferation and migration of K562 cells and promoted cell apoptosis. Taken together, our study demonstrates that miR-141-5p plays an important role in the activation of K562 cells in vitro and may act as a tumor suppressor via targeting RAB32 in the development of CML.
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Affiliation(s)
- Jing Bao
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China.,Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xiaofeng Li
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China
| | - Yuhuan Li
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China
| | - Cheng Huang
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China
| | - Xiaoming Meng
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China
| | - Jun Li
- Anhui Province Key Laboratory of Major Autoimmune Diseases, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China.,The Key Laboratory of Anti-inflammatory and Immune Medicines, Ministry of Education, Hefei, China
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