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Alessi DR, Pfeffer SR. Leucine-Rich Repeat Kinases. Annu Rev Biochem 2024; 93:261-287. [PMID: 38621236 DOI: 10.1146/annurev-biochem-030122-051144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Activating mutations in leucine-rich repeat kinase 2 (LRRK2) represent the most common cause of monogenic Parkinson's disease. LRRK2 is a large multidomain protein kinase that phosphorylates a specific subset of the ∼65 human Rab GTPases, which are master regulators of the secretory and endocytic pathways. After phosphorylation by LRRK2, Rabs lose the capacity to bind cognate effector proteins and guanine nucleotide exchange factors. Moreover, the phosphorylated Rabs cannot interact with their cognate prenyl-binding retrieval proteins (also known as guanine nucleotide dissociation inhibitors) and, thus, they become trapped on membrane surfaces. Instead, they gain the capacity to bind phospho-Rab-specific effector proteins, such as RILPL1, with resulting pathological consequences. Rab proteins also act upstream of LRRK2 by controlling its activation and recruitment onto membranes. LRRK2 signaling is counteracted by the phosphoprotein phosphatase PPM1H, which selectively dephosphorylates phospho-Rab proteins. We present here our current understanding of the structure, biochemical properties, and cell biology of LRRK2 and its related paralog LRRK1 and discuss how this information guides the generation of LRRK2 inhibitors for the potential benefit of patients.
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Affiliation(s)
- Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, United Kingdom;
| | - Suzanne R Pfeffer
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
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2
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Tudorica DA, Basak B, Puerta Cordova AS, Khuu G, Rose K, Lazarou M, Holzbaur EL, Hurley JH. A RAB7A phosphoswitch coordinates Rubicon Homology protein regulation of Parkin-dependent mitophagy. J Cell Biol 2024; 223:e202309015. [PMID: 38728007 PMCID: PMC11090050 DOI: 10.1083/jcb.202309015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 01/12/2024] [Accepted: 04/05/2024] [Indexed: 05/15/2024] Open
Abstract
Activation of PINK1 and Parkin in response to mitochondrial damage initiates a response that includes phosphorylation of RAB7A at Ser72. Rubicon is a RAB7A binding negative regulator of autophagy. The structure of the Rubicon:RAB7A complex suggests that phosphorylation of RAB7A at Ser72 would block Rubicon binding. Indeed, in vitro phosphorylation of RAB7A by TBK1 abrogates Rubicon:RAB7A binding. Pacer, a positive regulator of autophagy, has an RH domain with a basic triad predicted to bind an introduced phosphate. Consistent with this, Pacer-RH binds to phosho-RAB7A but not to unphosphorylated RAB7A. In cells, mitochondrial depolarization reduces Rubicon:RAB7A colocalization whilst recruiting Pacer to phospho-RAB7A-positive puncta. Pacer knockout reduces Parkin mitophagy with little effect on bulk autophagy or Parkin-independent mitophagy. Rescue of Parkin-dependent mitophagy requires the intact pRAB7A phosphate-binding basic triad of Pacer. Together these structural and functional data support a model in which the TBK1-dependent phosphorylation of RAB7A serves as a switch, promoting mitophagy by relieving Rubicon inhibition and favoring Pacer activation.
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Affiliation(s)
- Dan A. Tudorica
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Bishal Basak
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Alexia S. Puerta Cordova
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Grace Khuu
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Kevin Rose
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael Lazarou
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
| | - Erika L.F. Holzbaur
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Department of Physiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - James H. Hurley
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Graduate Group in Biophysics, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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3
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Yuan Y, Li H, Sreeram K, Malankhanova T, Boddu R, Strader S, Chang A, Bryant N, Yacoubian TA, Standaert DG, Erb M, Moore DJ, Sanders LH, Lutz MW, Velmeshev D, West AB. Single molecule array measures of LRRK2 kinase activity in serum link Parkinson's disease severity to peripheral inflammation. Mol Neurodegener 2024; 19:47. [PMID: 38862989 PMCID: PMC11167795 DOI: 10.1186/s13024-024-00738-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/02/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND LRRK2-targeting therapeutics that inhibit LRRK2 kinase activity have advanced to clinical trials in idiopathic Parkinson's disease (iPD). LRRK2 phosphorylates Rab10 on endolysosomes in phagocytic cells to promote some types of immunological responses. The identification of factors that regulate LRRK2-mediated Rab10 phosphorylation in iPD, and whether phosphorylated-Rab10 levels change in different disease states, or with disease progression, may provide insights into the role of Rab10 phosphorylation in iPD and help guide therapeutic strategies targeting this pathway. METHODS Capitalizing on past work demonstrating LRRK2 and phosphorylated-Rab10 interact on vesicles that can shed into biofluids, we developed and validated a high-throughput single-molecule array assay to measure extracellular pT73-Rab10. Ratios of pT73-Rab10 to total Rab10 measured in biobanked serum samples were compared between informative groups of transgenic mice, rats, and a deeply phenotyped cohort of iPD cases and controls. Multivariable and weighted correlation network analyses were used to identify genetic, transcriptomic, clinical, and demographic variables that predict the extracellular pT73-Rab10 to total Rab10 ratio. RESULTS pT73-Rab10 is absent in serum from Lrrk2 knockout mice but elevated by LRRK2 and VPS35 mutations, as well as SNCA expression. Bone-marrow transplantation experiments in mice show that serum pT73-Rab10 levels derive primarily from circulating immune cells. The extracellular ratio of pT73-Rab10 to total Rab10 is dynamic, increasing with inflammation and rapidly decreasing with LRRK2 kinase inhibition. The ratio of pT73-Rab10 to total Rab10 is elevated in iPD patients with greater motor dysfunction, irrespective of disease duration, age, sex, or the usage of PD-related or anti-inflammatory medications. pT73-Rab10 to total Rab10 ratios are associated with neutrophil degranulation, antigenic responses, and suppressed platelet activation. CONCLUSIONS The extracellular serum ratio of pT73-Rab10 to total Rab10 is a novel pharmacodynamic biomarker for LRRK2-linked innate immune activation associated with disease severity in iPD. We propose that those iPD patients with higher serum pT73-Rab10 levels may benefit from LRRK2-targeting therapeutics that mitigate associated deleterious immunological responses.
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Affiliation(s)
- Yuan Yuan
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Huizhong Li
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Kashyap Sreeram
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Tuyana Malankhanova
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Ravindra Boddu
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Samuel Strader
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Allison Chang
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Nicole Bryant
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Talene A Yacoubian
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - David G Standaert
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Madalynn Erb
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Darren J Moore
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Laurie H Sanders
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA
- Department of Neurology, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
| | - Michael W Lutz
- Department of Neurology, Duke University, Durham, NC, USA
- Department of Pathology, Duke University, Durham, NC, USA
| | | | - Andrew B West
- Duke Center for Neurodegeneration and Neurotheraputics, Duke University, Durham, NC, USA.
- Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA.
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
- Department of Neurology, Duke University, Durham, NC, USA.
- Department of Neurobiology, Duke University, Durham, NC, USA.
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4
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Pena N, Richbourg T, Gonzalez-Hunt CP, Qi R, Wren P, Barlow C, Shanks NF, Carlisle HJ, Sanders LH. G2019S selective LRRK2 kinase inhibitor abrogates mitochondrial DNA damage. NPJ Parkinsons Dis 2024; 10:49. [PMID: 38429321 PMCID: PMC10907374 DOI: 10.1038/s41531-024-00660-y] [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: 01/05/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
Pathogenic mutations in LRRK2 cause Parkinson's disease (PD). The G2019S variant is the most common, which results in abnormally high kinase activity. Compounds that target LRRK2 kinase activity are currently being developed and tested in clinical trials. We recently found that G2019S LRRK2 causes mitochondrial DNA (mtDNA) damage and treatment with multiple classes of LRRK2 kinase inhibitors at concentrations associated with dephosphorylation of LRRK2 reversed mtDNA damage to healthy control levels. Because maintaining the normal function of LRRK2 in heterozygous G2019S LRRK2 carriers while specifically targeting the G2019S LRRK2 activity could have an advantageous safety profile, we explored the efficacy of a G2019S mutant selective LRRK2 inhibitor to reverse mtDNA damage in G2019S LRRK2 models and patient cells relative to non-selective LRRK2 inhibitors. Potency of LRRK2 kinase inhibition by EB-42168, a G2019S mutant LRRK2 kinase inhibitor, and MLi-2, a non-selective inhibitor, was determined by measuring phosphorylation of LRRK2 at Ser935 and/or Ser1292 using quantitative western immunoblot analysis. The Mito DNADX assay, which allows for the accurate real-time quantification of mtDNA damage in a 96-well platform, was performed in parallel. We confirmed that EB-42168 selectively inhibits LRRK2 phosphorylation on G2019S LRRK2 relative to wild-type LRRK2. On the other hand, MLi-2 was equipotent for wild-type and G2019S LRRK2. Acute treatment with EB-42168 inhibited LRRK2 phosphorylation and also restored mtDNA damage to healthy control levels. We further investigated the relationship between LRRK2 kinase activity, mtDNA damage and mitophagy. Levels of mtDNA damage caused by G2019S LRRK2 were fully re-established within 2 h of a LRRK2 inhibitor wash out and recovery experiment, indicating the mtDNA damage phenotype is highly dynamic. G2019S LRRK2 mitophagy defects were not alleviated with LRRK2 kinase inhibition, suggesting that mitophagy is not mechanistically regulating LRRK2 kinase-mediated reversal of mtDNA damage in this acute timeframe. Abrogation of mtDNA damage with the mutant selective tool inhibitor EB-42168 demonstrates the potential of a precision medicine approach for LRRK2 G2019S PD. Levels of mtDNA damage may serve as a potential pharmacodynamic biomarker of altered kinase activity that could be useful for small molecule development and clinical trials.
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Affiliation(s)
- Nicholas Pena
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Tara Richbourg
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Claudia P Gonzalez-Hunt
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Rui Qi
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Paul Wren
- ESCAPE Bio, Inc., South San Francisco, CA, 94080, USA
| | | | | | | | - Laurie H Sanders
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA.
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5
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Naaldijk Y, Fernández B, Fasiczka R, Fdez E, Leghay C, Croitoru I, Kwok JB, Boulesnane Y, Vizeneux A, Mutez E, Calvez C, Destée A, Taymans JM, Aragon AV, Yarza AB, Padmanabhan S, Delgado M, Alcalay RN, Chatterton Z, Dzamko N, Halliday G, Ruiz-Martínez J, Chartier-Harlin MC, Hilfiker S. A potential patient stratification biomarker for Parkinson´s disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells. NPJ Parkinsons Dis 2024; 10:12. [PMID: 38191886 PMCID: PMC10774440 DOI: 10.1038/s41531-023-00624-8] [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: 04/19/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Parkinson´s disease (PD) is a common neurodegenerative movement disorder and leucine-rich repeat kinase 2 (LRRK2) is a promising therapeutic target for disease intervention. However, the ability to stratify patients who will benefit from such treatment modalities based on shared etiology is critical for the success of disease-modifying therapies. Ciliary and centrosomal alterations are commonly associated with pathogenic LRRK2 kinase activity and can be detected in many cell types. We previously found centrosomal deficits in immortalized lymphocytes from G2019S-LRRK2 PD patients. Here, to investigate whether such deficits may serve as a potential blood biomarker for PD which is susceptible to LRKK2 inhibitor treatment, we characterized patient-derived cells from distinct PD cohorts. We report centrosomal alterations in peripheral cells from a subset of early-stage idiopathic PD patients which is mitigated by LRRK2 kinase inhibition, supporting a role for aberrant LRRK2 activity in idiopathic PD. Centrosomal defects are detected in R1441G-LRRK2 and G2019S-LRRK2 PD patients and in non-manifesting LRRK2 mutation carriers, indicating that they accumulate prior to a clinical PD diagnosis. They are present in immortalized cells as well as in primary lymphocytes from peripheral blood. These findings indicate that analysis of centrosomal defects as a blood-based patient stratification biomarker may help nominate idiopathic PD patients who will benefit from LRRK2-related therapeutics.
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Affiliation(s)
- Yahaira Naaldijk
- Department. of Anesthesiology and Department. of Physiology, Pharmacology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Belén Fernández
- Institute of Parasitology and Biomedicine ´López-Neyra¨, Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Rachel Fasiczka
- Department. of Anesthesiology and Department. of Physiology, Pharmacology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA
| | - Elena Fdez
- Institute of Parasitology and Biomedicine ´López-Neyra¨, Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Coline Leghay
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Ioana Croitoru
- Biodonostia Health Research Institute (IIS Biodonostia), San Sebastain, Spain
| | - John B Kwok
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, NSW, Australia
| | - Yanisse Boulesnane
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Amelie Vizeneux
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Eugenie Mutez
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Camille Calvez
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Alain Destée
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | - Jean-Marc Taymans
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - LilNCog - Lille Neuroscience & Cognition, F-59000, Lille, France
| | | | - Alberto Bergareche Yarza
- Biodonostia Health Research Institute (IIS Biodonostia), San Sebastain, Spain
- Donostia University Hospital, San Sebastian, Spain
| | | | - Mario Delgado
- Institute of Parasitology and Biomedicine ´López-Neyra¨, Consejo Superior de Investigaciones Científicas (CSIC), 18016, Granada, Spain
| | - Roy N Alcalay
- Department. of Neurology, Colsumbia University Medical Center, New York, NY, USA
- Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
| | - Zac Chatterton
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, NSW, Australia
| | - Nicolas Dzamko
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, NSW, Australia
| | - Glenda Halliday
- School of Medical Sciences, Faculty of Medicine and Health and the Brain and Mind Centre, University of Sydney, Camperdown, NSW, Australia
| | - Javier Ruiz-Martínez
- Biodonostia Health Research Institute (IIS Biodonostia), San Sebastain, Spain
- Donostia University Hospital, San Sebastian, Spain
| | | | - Sabine Hilfiker
- Department. of Anesthesiology and Department. of Physiology, Pharmacology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, 07103, USA.
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6
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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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7
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Komori T, Kuwahara T. An Update on the Interplay between LRRK2, Rab GTPases and Parkinson's Disease. Biomolecules 2023; 13:1645. [PMID: 38002327 PMCID: PMC10669493 DOI: 10.3390/biom13111645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/10/2023] [Accepted: 11/11/2023] [Indexed: 11/26/2023] Open
Abstract
Over the last decades, research on the pathobiology of neurodegenerative diseases has greatly evolved, revealing potential targets and mechanisms linked to their pathogenesis. Parkinson's disease (PD) is no exception, and recent studies point to the involvement of endolysosomal defects in PD. The endolysosomal system, which tightly controls a flow of endocytosed vesicles targeted either for degradation or recycling, is regulated by a number of Rab GTPases. Their associations with leucine-rich repeat kinase 2 (LRRK2), a major causative and risk protein of PD, has also been one of the hot topics in the field. Understanding their interactions and functions is critical for unraveling their contribution to PD pathogenesis. In this review, we summarize recent studies on LRRK2 and Rab GTPases and attempt to provide more insight into the interaction of LRRK2 with each Rab and its relationship to PD.
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Affiliation(s)
| | - Tomoki Kuwahara
- Department of Neuropathology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-0033, Japan
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8
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Reimer JM, Dickey AM, Lin YX, Abrisch RG, Mathea S, Chatterjee D, Fay EJ, Knapp S, Daugherty MD, Reck-Peterson SL, Leschziner AE. Structure of LRRK1 and mechanisms of autoinhibition and activation. Nat Struct Mol Biol 2023; 30:1735-1745. [PMID: 37857821 PMCID: PMC10643122 DOI: 10.1038/s41594-023-01109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/24/2023] [Indexed: 10/21/2023]
Abstract
Leucine Rich Repeat Kinase 1 and 2 (LRRK1 and LRRK2) are homologs in the ROCO family of proteins in humans. Despite their shared domain architecture and involvement in intracellular trafficking, their disease associations are strikingly different: LRRK2 is involved in familial Parkinson's disease while LRRK1 is linked to bone diseases. Furthermore, Parkinson's disease-linked mutations in LRRK2 are typically autosomal dominant gain-of-function while those in LRRK1 are autosomal recessive loss-of-function. Here, to understand these differences, we solved cryo-EM structures of LRRK1 in its monomeric and dimeric forms. Both differ from the corresponding LRRK2 structures. Unlike LRRK2, which is sterically autoinhibited as a monomer, LRRK1 is sterically autoinhibited in a dimer-dependent manner. LRRK1 has an additional level of autoinhibition that prevents activation of the kinase and is absent in LRRK2. Finally, we place the structural signatures of LRRK1 and LRRK2 in the context of the evolution of the LRRK family of proteins.
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Affiliation(s)
- Janice M Reimer
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Andrea M Dickey
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yu Xuan Lin
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Robert G Abrisch
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Sebastian Mathea
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Deep Chatterjee
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Elizabeth J Fay
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Stefan Knapp
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
- Institute of Pharmaceutical Chemistry, Goethe-Universität, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-Universität, Frankfurt, Germany
| | - Matthew D Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Samara L Reck-Peterson
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Cell and Developmental Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Andres E Leschziner
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA, USA.
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9
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Antico O, Nirujogi RS, Muqit MM. Whole proteome copy number dataset in primary mouse cortical neurons. Data Brief 2023; 49:109336. [PMID: 37456110 PMCID: PMC10344827 DOI: 10.1016/j.dib.2023.109336] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023] Open
Abstract
The functional diversity of neurons is specified through their proteome resulting in elaborate and tightly regulated protein interaction networks and signalling that regulates neuronal processes. Dysregulation of these dynamic networks in development or in adulthood lead to neurodevelopmental or neurological disorders respectively. Over the past few decades, mass spectrometry has become a powerful tool for quantifying and resolving any proteome, including complex tissues such as the brain proteome, with technological advances leading to higher levels of resolution and throughput than traditional biochemical techniques. In this article, we provide a proteomic reference dataset that has been generated to identify proteins and quantify their level of expression in primary mouse cortical neurons. It represents a summary analysis of previously published data in (Antico et al., 2021). Mouse cortical neurons were isolated from E16.5 C57Bl/6J mice and cultured for 21 days in vitro (DIV). We employed the mitochondrial uncouplers AntimycinA/Oligomycin (AO) to induce mitochondrial depolarisation that is a well-established paradigm to assess mitophagic signalling. Total lysates from mouse primary cortical neurons were subjected to label-free quantitative proteomic analysis using both data dependent acquisition (DDA) and data independent acquisition (DIA) modes. DDA proteomic analysis identified a total dataset of 9367 proteins in mouse cortical neurons and absolute abundance of proteins was calculated as copy numbers per cell. DDA dataset was also processed to generate a reference spectral library to fit in and quantify MS spectra generated in DIA mode. Quantitative DIA analysis identified more than 6000 protein groups and statistical comparison of the two analysed groups (untreated and AO-treated) revealed that the neuronal proteome was largely unchanged post mitochondrial depolarisation for 5 hours. To our knowledge, these files represent the most comprehensive DDA and DIA reference datasets of fully functional maturated mouse primary cortical neurons and serve as a valuable resource for further investigating the role of specific proteins involved in neurobiology and neurological disorders such as Alzheimer's disease (AD), Parkinson's disease (PD) and Autism Spectrum Disorders (ASD).
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Affiliation(s)
- Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom, DD1 5EH
- 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, United Kingdom, DD1 5EH
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Miratul M.K. Muqit
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, United Kingdom, DD1 5EH
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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10
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Zittlau K, Nashier P, Cavarischia-Rega C, Macek B, Spät P, Nalpas N. Recent progress in quantitative phosphoproteomics. Expert Rev Proteomics 2023; 20:469-482. [PMID: 38116637 DOI: 10.1080/14789450.2023.2295872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 12/12/2023] [Indexed: 12/21/2023]
Abstract
INTRODUCTION Protein phosphorylation is a critical post-translational modification involved in the regulation of numerous cellular processes from signal transduction to modulation of enzyme activities. Knowledge of dynamic changes of phosphorylation levels during biological processes, under various treatments or between healthy and disease models is fundamental for understanding the role of each phosphorylation event. Thereby, LC-MS/MS based technologies in combination with quantitative proteomics strategies evolved as a powerful strategy to investigate the function of individual protein phosphorylation events. AREAS COVERED State-of-the-art labeling techniques including stable isotope and isobaric labeling provide precise and accurate quantification of phosphorylation events. Here, we review the strengths and limitations of recent quantification methods and provide examples based on current studies, how quantitative phosphoproteomics can be further optimized for enhanced analytic depth, dynamic range, site localization, and data integrity. Specifically, reducing the input material demands is key to a broader implementation of quantitative phosphoproteomics, not least for clinical samples. EXPERT OPINION Despite quantitative phosphoproteomics is one of the most thriving fields in the proteomics world, many challenges still have to be overcome to facilitate even deeper and more comprehensive analyses as required in the current research, especially at single cell levels and in clinical diagnostics.
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Affiliation(s)
- Katharina Zittlau
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Payal Nashier
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Claudia Cavarischia-Rega
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Boris Macek
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Philipp Spät
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
| | - Nicolas Nalpas
- Quantitative Proteomics, Interfaculty Institute of Cell Biology, University of Tuebingen, Tuebingen , Germany
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11
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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: 11] [Impact Index Per Article: 11.0] [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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12
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Zhang J, Li J, You P, Jiang H, Liu Y, Han D, Liu M, Yu H, Su B. Mice with the Rab10 T73V mutation exhibit anxiety-like behavior and alteration of neuronal functions in the striatum. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166641. [PMID: 36669576 DOI: 10.1016/j.bbadis.2023.166641] [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: 09/09/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/19/2023]
Abstract
Hyperphosphorylated Rab10 has been implicated in the pathogenesis of neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease. However, the neurophysiological function of the evolutionarily conserved Thr73 phosphorylation of Rab10 remains poorly understood. Here, we generated a novel mouse model expressing the non-phosphorylatable T73V mutation of Rab10 and performed a comprehensive series of neurological analyses, including behavioral tests, synaptic evaluations, neuronal and glial staining, assessments of neurite arborization and spine morphogenesis. The Rab10 T73V mutantmice exhibited a characteristic anxiety-like phenotype with other behavioral modules relatively unaffected. Moreover, Rab10 T73V mutant mice displayed striatum-specific synaptic dysfunction, as indicated by aberrantly increased expression levels of synaptic proteins and impaired frequencies of miniature inhibitory postsynaptic currents. The genetic deletion of Rab10 phosphorylation enhanced neurite arborization and accelerated spine maturation in striatal medium spiny neurons. Our findings emphasize the specific role of intrinsic phospho-Rab10 in the regulation of the striatal circuitry and its related behaviors.
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Affiliation(s)
- Jing Zhang
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Jie Li
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Pan You
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Haitian Jiang
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Yanjun Liu
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Daobin Han
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Meiqi Liu
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Hui Yu
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Bo Su
- Department of Cell Biology, Shandong Provincial Key Laboratory of Mental Disorders, School of Basic Medical Sciences, Shandong University, Jinan, China.
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13
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Insights into the cellular consequences of LRRK2-mediated Rab protein phosphorylation. Biochem Soc Trans 2023; 51:587-595. [PMID: 36929701 DOI: 10.1042/bst20201145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/18/2023]
Abstract
Point mutations in leucine-rich repeat kinase 2 (LRRK2) which cause Parkinson's disease increase its kinase activity, and a subset of Rab GTPases have been identified as endogenous LRRK2 kinase substrates. Their phosphorylation correlates with a loss-of-function for the membrane trafficking steps they are normally involved in, but it also allows them to bind to a novel set of effector proteins with dominant cellular consequences. In this brief review, we will summarize novel findings related to the LRRK2-mediated phosphorylation of Rab GTPases and its various cellular consequences in vitro and in the intact brain, and we will highlight major outstanding questions in the field.
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14
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Virdi GS, Choi ML, Evans JR, Yao Z, Athauda D, Strohbuecker S, Nirujogi RS, Wernick AI, Pelegrina-Hidalgo N, Leighton C, Saleeb RS, Kopach O, Alrashidi H, Melandri D, Perez-Lloret J, Angelova PR, Sylantyev S, Eaton S, Heales S, Rusakov DA, Alessi DR, Kunath T, Horrocks MH, Abramov AY, Patani R, Gandhi S. Protein aggregation and calcium dysregulation are hallmarks of familial Parkinson's disease in midbrain dopaminergic neurons. NPJ Parkinsons Dis 2022; 8:162. [PMID: 36424392 PMCID: PMC9691718 DOI: 10.1038/s41531-022-00423-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 10/27/2022] [Indexed: 11/27/2022] Open
Abstract
Mutations in the SNCA gene cause autosomal dominant Parkinson's disease (PD), with loss of dopaminergic neurons in the substantia nigra, and aggregation of α-synuclein. The sequence of molecular events that proceed from an SNCA mutation during development, to end-stage pathology is unknown. Utilising human-induced pluripotent stem cells (hiPSCs), we resolved the temporal sequence of SNCA-induced pathophysiological events in order to discover early, and likely causative, events. Our small molecule-based protocol generates highly enriched midbrain dopaminergic (mDA) neurons: molecular identity was confirmed using single-cell RNA sequencing and proteomics, and functional identity was established through dopamine synthesis, and measures of electrophysiological activity. At the earliest stage of differentiation, prior to maturation to mDA neurons, we demonstrate the formation of small β-sheet-rich oligomeric aggregates, in SNCA-mutant cultures. Aggregation persists and progresses, ultimately resulting in the accumulation of phosphorylated α-synuclein aggregates. Impaired intracellular calcium signalling, increased basal calcium, and impairments in mitochondrial calcium handling occurred early at day 34-41 post differentiation. Once midbrain identity fully developed, at day 48-62 post differentiation, SNCA-mutant neurons exhibited mitochondrial dysfunction, oxidative stress, lysosomal swelling and increased autophagy. Ultimately these multiple cellular stresses lead to abnormal excitability, altered neuronal activity, and cell death. Our differentiation paradigm generates an efficient model for studying disease mechanisms in PD and highlights that protein misfolding to generate intraneuronal oligomers is one of the earliest critical events driving disease in human neurons, rather than a late-stage hallmark of the disease.
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Affiliation(s)
- Gurvir S Virdi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Minee L Choi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - James R Evans
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Zhi Yao
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Dilan Athauda
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | - Raja S Nirujogi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Anna I Wernick
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
| | - Noelia Pelegrina-Hidalgo
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Craig Leighton
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Rebecca S Saleeb
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Olga Kopach
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Haya Alrashidi
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Daniela Melandri
- Department of Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | | | - Plamena R Angelova
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Sergiy Sylantyev
- Rowett Institute, University of Aberdeen, Ashgrove Rd West, Aberdeen, AB25 2ZD, UK
| | - Simon Eaton
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Simon Heales
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Dmitri A Rusakov
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Tilo Kunath
- Center for Regenerative Medicine, University of Edinburgh, Edinburgh, EH16 4UU, UK
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Andrey Y Abramov
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Disease, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
| | - Sonia Gandhi
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Queen Square, London, WC1N 3BG, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, 20815, USA.
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15
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Malik AU, Karapetsas A, Nirujogi RS, Chatterjee D, Phung TK, Wightman M, Gourlay R, Morrice N, Mathea S, Knapp S, Alessi DR. PKC isoforms activate LRRK1 kinase by phosphorylating conserved residues (Ser1064, Ser1074 and Thr1075) within the CORB GTPase domain. Biochem J 2022; 479:1941-1965. [PMID: 36040231 PMCID: PMC9555798 DOI: 10.1042/bcj20220308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022]
Abstract
Leucine-rich-repeat-kinase 1 (LRRK1) and its homolog LRRK2 are multidomain kinases possessing a ROC-CORA-CORB containing GTPase domain and phosphorylate distinct Rab proteins. LRRK1 loss of function mutations cause the bone disorder osteosclerotic metaphyseal dysplasia, whereas LRRK2 missense mutations that enhance kinase activity cause Parkinson's disease. Previous work suggested that LRRK1 but not LRRK2, is activated via a Protein Kinase C (PKC)-dependent mechanism. Here we demonstrate that phosphorylation and activation of LRRK1 in HEK293 cells is blocked by PKC inhibitors including LXS-196 (Darovasertib), a compound that has entered clinical trials. We show multiple PKC isoforms phosphorylate and activate recombinant LRRK1 in a manner reversed by phosphatase treatment. PKCα unexpectedly does not activate LRRK1 by phosphorylating the kinase domain, but instead phosphorylates a cluster of conserved residues (Ser1064, Ser1074 and Thr1075) located within a region of the CORB domain of the GTPase domain. These residues are positioned at the equivalent region of the LRRK2 DK helix reported to stabilize the kinase domain αC-helix in the active conformation. Thr1075 represents an optimal PKC site phosphorylation motif and its mutation to Ala, blocked PKC-mediated activation of LRRK1. A triple Glu mutation of Ser1064/Ser1074/Thr1075 to mimic phosphorylation, enhanced LRRK1 kinase activity ∼3-fold. From analysis of available structures, we postulate that phosphorylation of Ser1064, Ser1074 and Thr1075 activates LRRK1 by promoting interaction and stabilization of the αC-helix on the kinase domain. This study provides new fundamental insights into the mechanism controlling LRRK1 activity and reveals a novel unexpected activation mechanism.
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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
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - 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
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Deep Chatterjee
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences and Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Toan K. Phung
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
| | - Melanie Wightman
- 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
| | - Nick Morrice
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, U.K
| | - Sebastian Mathea
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences and Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences and Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - 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
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, U.S.A
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16
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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: 13] [Impact Index Per Article: 6.5] [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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17
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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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18
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LRRK2 Deficiency Aggravates Sleep Deprivation-Induced Cognitive Loss by Perturbing Synaptic Pruning in Mice. Brain Sci 2022; 12:brainsci12091200. [PMID: 36138936 PMCID: PMC9496729 DOI: 10.3390/brainsci12091200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations of the leucine-rich repeat kinase 2 (LRRK2) gene are associated with pronounced sleep disorders or cognitive dysfunction in neurodegenerative diseases. However, the effects of LRRK2 deficiency on sleep rhythms and sleep deprivation-related cognitive changes, and the relevant underlying mechanism, remain unrevealed. In this study, Lrrk2-/- and Lrrk2+/+ mice were subjected to normal sleep (S) or sleep deprivation (SD). Sleep recording, behavioral testing, Golgi-cox staining, immunofluorescence, and real-time PCR were employed to evaluate the impacts of LRRK2 deficiency on sleep behaviors and to investigate the underlying mechanisms. The results showed that after SD, LRRK2-deficient mice displayed lengthened NREM and shortened REM, and reported decreased dendritic spines, increased microglial activation, and synaptic endocytosis in the prefrontal cortex. Meanwhile, after SD, LRRK2 deficiency aggravated cognitive impairments, especially in the recall memory cued by fear conditioning test. Our findings evidence that LRRK2 modulates REM/NREM sleep and its deficiency may exacerbate sleep deprivation-related cognitive disorders by perturbing synaptic plasticity and microglial synaptic pruning in mice.
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19
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Bellucci A, Longhena F, Spillantini MG. The Role of Rab Proteins in Parkinson's Disease Synaptopathy. Biomedicines 2022; 10:biomedicines10081941. [PMID: 36009486 PMCID: PMC9406004 DOI: 10.3390/biomedicines10081941] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/31/2022] [Accepted: 08/08/2022] [Indexed: 12/29/2022] Open
Abstract
In patients affected by Parkinson's disease (PD), the most common neurodegenerative movement disorder, the brain is characterized by the loss of dopaminergic neurons in the nigrostriatal system, leading to dyshomeostasis of the basal ganglia network activity that is linked to motility dysfunction. PD mostly arises as an age-associated sporadic disease, but several genetic forms also exist. Compelling evidence supports that synaptic damage and dysfunction characterize the very early phases of either sporadic or genetic forms of PD and that this early PD synaptopathy drives retrograde terminal-to-cell body degeneration, culminating in neuronal loss. The Ras-associated binding protein (Rab) family of small GTPases, which is involved in the maintenance of neuronal vesicular trafficking, synaptic architecture and function in the central nervous system, has recently emerged among the major players in PD synaptopathy. In this manuscript, we provide an overview of the main findings supporting the involvement of Rabs in either sporadic or genetic PD pathophysiology, and we highlight how Rab alterations participate in the onset of early synaptic damage and dysfunction.
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Affiliation(s)
- Arianna Bellucci
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Correspondence: ; Tel.: +39-0303-717-380
| | - Francesca Longhena
- Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
- Department of Clinical Neurosciences, University of Cambridge, Clifford Albutt Building, Cambridge CB2 0AH, UK
| | - Maria Grazia Spillantini
- Department of Clinical Neurosciences, University of Cambridge, Clifford Albutt Building, Cambridge CB2 0AH, UK
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20
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Pathophysiological evaluation of the LRRK2 G2385R risk variant for Parkinson’s disease. NPJ Parkinsons Dis 2022; 8:97. [PMID: 35931783 PMCID: PMC9355991 DOI: 10.1038/s41531-022-00367-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/20/2022] [Indexed: 11/13/2022] Open
Abstract
Missense variants in leucine-rich repeat kinase 2 (LRRK2) lead to familial and sporadic Parkinson’s disease (PD). The pathological features of PD patients with LRRK2 variants differ. Here, we report an autopsy case harboring the LRRK2 G2385R, a risk variant for PD occurring mainly in Asian populations. The patient exhibited levodopa-responsive parkinsonism at the early stage and visual hallucinations at the advanced stage. The pathological study revealed diffuse Lewy bodies with neurofibrillary tangles, amyloid plaques, and mild signs of neuroinflammation. Biochemically, detergent-insoluble phospho-α-synuclein was accumulated in the frontal, temporal, entorhinal cortexes, and putamen, consistent with the pathological observations. Elevated phosphorylation of Rab10, a substrate of LRRK2, was also prominent in various brain regions. In conclusion, G2385R appears to increase LRRK2 kinase activity in the human brain, inducing a deleterious brain environment that causes Lewy body pathology.
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21
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Fernández B, Chittoor-Vinod VG, Kluss JH, Kelly K, Bryant N, Nguyen APT, Bukhari SA, Smith N, Lara Ordóñez AJ, Fdez E, Chartier-Harlin MC, Montine TJ, Wilson MA, Moore DJ, West AB, Cookson MR, Nichols RJ, Hilfiker S. Evaluation of Current Methods to Detect Cellular Leucine-Rich Repeat Kinase 2 (LRRK2) Kinase Activity. JOURNAL OF PARKINSON'S DISEASE 2022; 12:1423-1447. [PMID: 35599495 PMCID: PMC9398093 DOI: 10.3233/jpd-213128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Background: Coding variation in the Leucine rich repeat kinase 2 gene linked to Parkinson’s disease (PD) promotes enhanced activity of the encoded LRRK2 kinase, particularly with respect to autophosphorylation at S1292 and/or phosphorylation of the heterologous substrate RAB10. Objective: To determine the inter-laboratory reliability of measurements of cellular LRRK2 kinase activity in the context of wildtype or mutant LRRK2 expression using published protocols. Methods: Benchmark western blot assessments of phospho-LRRK2 and phospho-RAB10 were performed in parallel with in situ immunological approaches in HEK293T, mouse embryonic fibroblasts, and lymphoblastoid cell lines. Rat brain tissue, with or without adenovirus-mediated LRRK2 expression, and human brain tissues from subjects with or without PD, were also evaluated for LRRK2 kinase activity markers. Results: Western blots were able to detect extracted LRRK2 activity in cells and tissue with pS1292-LRRK2 or pT73-RAB10 antibodies. However, while LRRK2 kinase signal could be detected at the cellular level with over-expressed mutant LRRK2 in cell lines, we were unable to demonstrate specific detection of endogenous cellular LRRK2 activity in cell culture models or tissues that we evaluated. Conclusion: Further development of reliable methods that can be deployed in multiple laboratories to measure endogenous LRRK2 activities are likely required, especially at cellular resolution.
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Affiliation(s)
- Belén Fernández
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | - Jillian H. Kluss
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Kaela Kelly
- Duke Center for Neurodegeneration Research, Department of Pharmacology, Duke University, Durham, NC, USA
| | - Nicole Bryant
- Duke Center for Neurodegeneration Research, Department of Pharmacology, Duke University, Durham, NC, USA
| | - An Phu Tran Nguyen
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Syed A. Bukhari
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Nathan Smith
- Department of Biochemistry, Redox Biology Center, The University of Nebraska-Lincoln, NE, USA
| | - Antonio Jesús Lara Ordóñez
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Elena Fdez
- Institute of Parasitology and Biomedicine López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | | | | | - Mark A. Wilson
- Department of Biochemistry, Redox Biology Center, The University of Nebraska-Lincoln, NE, USA
| | - Darren J. Moore
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Andrew B. West
- Duke Center for Neurodegeneration Research, Department of Pharmacology, Duke University, Durham, NC, USA
| | - Mark R. Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | | | - Sabine Hilfiker
- Department of Anesthesiology and Department of Pharmacology, Physiology and Neuroscience, Rutgers New Jersey Medical School, Newark, NJ, USA
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22
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Ordóñez AJL, Fasiczka R, Fernández B, Naaldijk Y, Fdez E, Ramírez MB, Phan S, Boassa D, Hilfiker S. The LRRK2 signaling network converges on a centriolar phospho-Rab10/RILPL1 complex to cause deficits in centrosome cohesion and cell polarization. Biol Open 2022; 11:275880. [PMID: 35776681 PMCID: PMC9346292 DOI: 10.1242/bio.059468] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 06/28/2022] [Indexed: 11/22/2022] Open
Abstract
The Parkinson's-disease-associated LRRK2 kinase phosphorylates multiple Rab GTPases including Rab8 and Rab10, which enhances their binding to RILPL1 and RILPL2. The nascent interaction between phospho-Rab10 and RILPL1 blocks ciliogenesis in vitro and in the intact brain, and interferes with the cohesion of duplicated centrosomes in dividing cells. We show here that regulators of the LRRK2 signaling pathway including vps35 and PPM1H converge upon causing centrosomal deficits. The cohesion alterations do not require the presence of other LRRK2 kinase substrates including Rab12, Rab35 and Rab43 or the presence of RILPL2. Rather, they depend on the RILPL1-mediated centrosomal accumulation of phosphorylated Rab10. RILPL1 localizes to the subdistal appendage of the mother centriole, followed by recruitment of the LRRK2-phosphorylated Rab proteins to cause the centrosomal defects. The centrosomal alterations impair cell polarization as monitored by scratch wound assays which is reverted by LRRK2 kinase inhibition. These data reveal a common molecular pathway by which enhanced LRRK2 kinase activity impacts upon centrosome-related events to alter the normal biology of a cell. Summary: The Parkinson's disease LRRK2 signaling pathway converges upon the formation of a complex at the subdistal appendage of the mother centriole which causes centrosomal deficits and impairs appropriate cell polarization.
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Affiliation(s)
- Antonio Jesús Lara Ordóñez
- Institute of Parasitology and Biomedicine "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Rachel Fasiczka
- Department of Anesthesiology and Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Belén Fernández
- Institute of Parasitology and Biomedicine "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Yahaira Naaldijk
- Department of Anesthesiology and Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
| | - Elena Fdez
- Institute of Parasitology and Biomedicine "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Marian Blanca Ramírez
- Institute of Parasitology and Biomedicine "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Granada, Spain
| | - Sébastien Phan
- Department of Neurosciences and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Daniela Boassa
- Department of Neurosciences and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA
| | - Sabine Hilfiker
- Department of Anesthesiology and Department of Physiology, Pharmacology and Neuroscience, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ, USA
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23
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Wang S, Unnithan S, Bryant N, Chang A, Rosenthal LS, Pantelyat A, Dawson TM, Al‐Khalidi HR, West AB. Elevated Urinary Rab10 Phosphorylation in Idiopathic Parkinson Disease. Mov Disord 2022; 37:1454-1464. [PMID: 35521944 PMCID: PMC9308673 DOI: 10.1002/mds.29043] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Pathogenic leucine-rich repeat kinase 2 LRRK2 mutations may increase LRRK2 kinase activity and Rab substrate phosphorylation. Genetic association studies link variation in LRRK2 to idiopathic Parkinson disease (iPD) risk. OBJECTIVES Through measurements of the LRRK2 kinase substrate pT73-Rab10 in urinary extracellular vesicles, this study seeks to understand how LRRK2 kinase activity might change with iPD progression. METHODS Using an immunoblotting approach validated in LRRK2 transgenic mice, the ratio of pT73-Rab10 to total Rab10 protein was measured in extracellular vesicles from a cross-section of G2019S LRRK2 mutation carriers (N = 45 participants) as well as 485 urine samples from a novel longitudinal cohort of iPD and controls (N = 85 participants). Generalized estimating equations were used to conduct analyses with commonly used clinical scales. RESULTS Although the G2019S LRRK2 mutation did not increase pT73-Rab10 levels, the ratio of pT73-Rab10 to total Rab10 nominally increased over baseline in iPD urine vesicle samples with time, but did not increase in age-matched controls (1.34-fold vs. 1.05-fold, 95% confidence interval [CI], 0.004-0.56; P = 0.046; Welch's t test). Effect estimates adjusting for sex, age, disease duration, diagnosis, and baseline clinical scores identified increasing total Movement Disorder Society-Sponsored Revision of the Unified (MDS-UPDRS) scores (β = 0.77; CI, 0.52-1.01; P = 0.0001) with each fold increase of pT73-Rab10 to total Rab10. Lower Montreal Cognitive Assessment (MoCA) score in iPD is also associated with increased pT73-Rab10. CONCLUSIONS These results provide initial insights into peripheral LRRK2-dependent Rab phosphorylation, measured in biobanked urine, where higher levels of pT73-Rab10 are associated with worse disease progression. © 2022 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society.
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Affiliation(s)
- Shijie Wang
- Duke Center for Neurodegeneration and NeurotherapeuticsDuke UniversityDurhamNorth CarolinaUSA
| | - Shakthi Unnithan
- Department of Biostatistics and BioinformaticsDuke UniversityDurhamNorth CarolinaUSA
| | - Nicole Bryant
- Duke Center for Neurodegeneration and NeurotherapeuticsDuke UniversityDurhamNorth CarolinaUSA
| | - Allison Chang
- Duke Center for Neurodegeneration and NeurotherapeuticsDuke UniversityDurhamNorth CarolinaUSA
| | | | | | - Ted M. Dawson
- Department of NeurologyThe Johns Hopkins UniversityBaltimoreMarylandUSA
- Neurodegeneration and Stem Cell Programs, Institute for Cell EngineeringJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Solomon H. Snyder Department of NeuroscienceJohns Hopkins University School of MedicineBaltimoreMarylandUSA
- Department of Pharmacology and Molecular SciencesJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - Hussein R. Al‐Khalidi
- Department of Biostatistics and BioinformaticsDuke UniversityDurhamNorth CarolinaUSA
| | - Andrew B. West
- Duke Center for Neurodegeneration and NeurotherapeuticsDuke UniversityDurhamNorth CarolinaUSA
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24
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Trinh J, Schymanski EL, Smajic S, Kasten M, Sammler E, Grünewald A. Molecular mechanisms defining penetrance of LRRK2-associated Parkinson's disease. MED GENET-BERLIN 2022; 34:103-116. [PMID: 38835904 PMCID: PMC11006382 DOI: 10.1515/medgen-2022-2127] [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] [Indexed: 06/06/2024]
Abstract
Mutations in Leucine-rich repeat kinase 2 (LRRK2) are the most frequent cause of dominantly inherited Parkinson's disease (PD). LRRK2 mutations, among which p.G2019S is the most frequent, are inherited with reduced penetrance. Interestingly, the disease risk associated with LRRK2 G2019S can vary dramatically depending on the ethnic background of the carrier. While this would suggest a genetic component in the definition of LRRK2-PD penetrance, only few variants have been shown to modify the age at onset of patients harbouring LRRK2 mutations, and the exact cellular pathways controlling the transition from a healthy to a diseased state currently remain elusive. In light of this knowledge gap, recent studies also explored environmental and lifestyle factors as potential modifiers of LRRK2-PD. In this article, we (i) describe the clinical characteristics of LRRK2 mutation carriers, (ii) review known genes linked to LRRK2-PD onset and (iii) summarize the cellular functions of LRRK2 with particular emphasis on potential penetrance-related molecular mechanisms. This section covers LRRK2's involvement in Rab GTPase and immune signalling as well as in the regulation of mitochondrial homeostasis and dynamics. Additionally, we explored the literature with regard to (iv) lifestyle and (v) environmental factors that may influence the penetrance of LRRK2 mutations, with a view towards further exposomics studies. Finally, based on this comprehensive overview, we propose potential future in vivo, in vitro and in silico studies that could provide a better understanding of the processes triggering PD in individuals with LRRK2 mutations.
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Affiliation(s)
- Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Emma L. Schymanski
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Semra Smajic
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Meike Kasten
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
- Department of Psychiatry and Psychotherapy, University of Lübeck, Lübeck, Germany
| | - Esther Sammler
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
- Department of Neurology, School of Medicine, Dundee, Ninewells Hospital, Dundee, UK
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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25
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Runde AP, Mack R, S J PB, Zhang J. The role of TBK1 in cancer pathogenesis and anticancer immunity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:135. [PMID: 35395857 PMCID: PMC8994244 DOI: 10.1186/s13046-022-02352-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023]
Abstract
The TANK-binding kinase 1 (TBK1) is a serine/threonine kinase belonging to the non-canonical inhibitor of nuclear factor-κB (IκB) kinase (IKK) family. TBK1 can be activated by pathogen-associated molecular patterns (PAMPs), inflammatory cytokines, and oncogenic kinases, including activated K-RAS/N-RAS mutants. TBK1 primarily mediates IRF3/7 activation and NF-κB signaling to regulate inflammatory cytokine production and the activation of innate immunity. TBK1 is also involved in the regulation of several other cellular activities, including autophagy, mitochondrial metabolism, and cellular proliferation. Although TBK1 mutations have not been reported in human cancers, aberrant TBK1 activation has been implicated in the oncogenesis of several types of cancer, including leukemia and solid tumors with KRAS-activating mutations. As such, TBK1 has been proposed to be a feasible target for pharmacological treatment of these types of cancer. Studies suggest that TBK1 inhibition suppresses cancer development not only by directly suppressing the proliferation and survival of cancer cells but also by activating antitumor T-cell immunity. Several small molecule inhibitors of TBK1 have been identified and interrogated. However, to this point, only momelotinib (MMB)/CYT387 has been evaluated as a cancer therapy in clinical trials, while amlexanox (AMX) has been evaluated clinically for treatment of type II diabetes, nonalcoholic fatty liver disease, and obesity. In this review, we summarize advances in research into TBK1 signaling pathways and regulation, as well as recent studies on TBK1 in cancer pathogenesis. We also discuss the potential molecular mechanisms of targeting TBK1 for cancer treatment. We hope that our effort can help to stimulate the development of novel strategies for targeting TBK1 signaling in future approaches to cancer therapy.
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Affiliation(s)
- Austin P Runde
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Ryan Mack
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Peter Breslin S J
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.,Departments of Molecular/Cellular Physiology and Biology, Loyola University Medical Center and Loyola University Chicago, Chicago, IL, 60660, USA
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA. .,Departments of Pathology and Radiation Oncology, Loyola University Medical Center, Maywood, IL, 60153, USA.
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26
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Rab GTPases in Parkinson's disease: a primer. Essays Biochem 2021; 65:961-974. [PMID: 34414419 PMCID: PMC8709891 DOI: 10.1042/ebc20210016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/05/2021] [Accepted: 08/09/2021] [Indexed: 12/15/2022]
Abstract
Parkinson's disease is a prominent and debilitating movement disorder characterized by the death of vulnerable neurons which share a set of structural and physiological properties. Over the recent years, increasing evidence indicates that Rab GTPases can directly as well as indirectly contribute to the cellular alterations leading to PD. Rab GTPases are master regulators of intracellular membrane trafficking events, and alterations in certain membrane trafficking steps can be particularly disruptive to vulnerable neurons. Here, we describe current knowledge on the direct links between altered Rab protein function and PD pathomechanisms.
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Maset A, Albanesi M, di Soccio A, Canova M, dal Maschio M, Lodovichi C. Aberrant Patterns of Sensory-Evoked Activity in the Olfactory Bulb of LRRK2 Knockout Mice. Cells 2021; 10:3212. [PMID: 34831434 PMCID: PMC8622670 DOI: 10.3390/cells10113212] [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: 09/30/2021] [Revised: 11/10/2021] [Accepted: 11/12/2021] [Indexed: 12/13/2022] Open
Abstract
The LRRK2 gene is the major genetic determinant of familiar Parkinson's disease (PD). Leucine-rich repeat kinase 2 (LRRK2) is a multidomain protein involved in several intracellular signaling pathways. A wealth of evidence indicates that LRRK2 is enriched at the presynaptic compartment where it regulates vesicle trafficking and neurotransmitter release. However, whether the role of LRRK2 affects neuronal networks dynamic at systems level remains unknown. Addressing this question is critical to unravel the impact of LRRK2 on brain function. Here, combining behavioral tests, electrophysiological recordings, and functional imaging, we investigated neuronal network dynamics, in vivo, in the olfactory bulb of mice carrying a null mutation in LRRK2 gene (LRRK2 knockout, LRRK2 KO, mice). We found that LRRK2 KO mice exhibit olfactory behavioral deficits. At the circuit level, the lack of LRRK2 expression results in altered gamma rhythms and odorant-evoked activity with significant impairments, while the spontaneous activity exhibited limited alterations. Overall, our data in the olfactory bulb suggest that the multifaced role of LRRK2 has a strong impact at system level when the network is engaged in active sensory processing.
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Affiliation(s)
- Andrea Maset
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy; (A.M.); (M.A.); (A.d.S.)
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
| | - Marco Albanesi
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy; (A.M.); (M.A.); (A.d.S.)
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
| | - Antonio di Soccio
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy; (A.M.); (M.A.); (A.d.S.)
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
| | - Martina Canova
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
| | - Marco dal Maschio
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
- Department of Biomedical Sciences-UNIPD, Università degli Studi di Padova, Via U. Bassi 58B, 35121 Padova, Italy
| | - Claudia Lodovichi
- Veneto Institute of Molecular Medicine, Via Orus 2, 35129 Padova, Italy; (A.M.); (M.A.); (A.d.S.)
- Padova Neuroscience Center (PNC), Università degli Studi di Padova Via Orus 2, 35129 Padova, Italy; (M.C.); (M.d.M.)
- Institute of Neuroscience-CNR, Viale G. Colombo 3, 35121 Padova, Italy
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Antico O, Ordureau A, Stevens M, Singh F, Nirujogi RS, Gierlinski M, Barini E, Rickwood ML, Prescott A, Toth R, Ganley IG, Harper JW, Muqit MMK. Global ubiquitylation analysis of mitochondria in primary neurons identifies endogenous Parkin targets following activation of PINK1. SCIENCE ADVANCES 2021; 7:eabj0722. [PMID: 34767452 PMCID: PMC8589319 DOI: 10.1126/sciadv.abj0722] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 09/21/2021] [Indexed: 05/16/2023]
Abstract
How activation of PINK1 and Parkin leads to elimination of damaged mitochondria by mitophagy is largely based on cell lines with few studies in neurons. Here, we have undertaken proteomic analysis of mitochondria from mouse neurons to identify ubiquitylated substrates of endogenous Parkin. Comparative analysis with human iNeuron datasets revealed a subset of 49 PINK1 activation–dependent diGLY sites in 22 proteins conserved across mouse and human systems. We use reconstitution assays to demonstrate direct ubiquitylation by Parkin in vitro. We also identified a subset of cytoplasmic proteins recruited to mitochondria that undergo PINK1 and Parkin independent ubiquitylation, indicating the presence of alternate ubiquitin E3 ligase pathways that are activated by mitochondrial depolarization in neurons. Last, we have developed an online resource to search for ubiquitin sites and enzymes in mitochondria of neurons, MitoNUb. These findings will aid future studies to understand Parkin activation in neuronal subtypes.
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Affiliation(s)
- Odetta Antico
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alban Ordureau
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Michael Stevens
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Francois Singh
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - 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
| | - Marek Gierlinski
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Erica Barini
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Mollie L. Rickwood
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Alan Prescott
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ian G. Ganley
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - J. Wade Harper
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Miratul M. K. Muqit
- 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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Focus on the Small GTPase Rab1: A Key Player in the Pathogenesis of Parkinson's Disease. Int J Mol Sci 2021; 22:ijms222112087. [PMID: 34769517 PMCID: PMC8584362 DOI: 10.3390/ijms222112087] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/04/2021] [Accepted: 11/06/2021] [Indexed: 12/19/2022] Open
Abstract
Parkinson’s disease (PD) is the second most frequent neurodegenerative disease. It is characterized by the loss of dopaminergic neurons in the substantia nigra and the formation of large aggregates in the survival neurons called Lewy bodies, which mainly contain α-synuclein (α-syn). The cause of cell death is not known but could be due to mitochondrial dysfunction, protein homeostasis failure, and alterations in the secretory/endolysosomal/autophagic pathways. Survival nigral neurons overexpress the small GTPase Rab1. This protein is considered a housekeeping Rab that is necessary to support the secretory pathway, the maintenance of the Golgi complex structure, and the regulation of macroautophagy from yeast to humans. It is also involved in signaling, carcinogenesis, and infection for some pathogens. It has been shown that it is directly linked to the pathogenesis of PD and other neurodegenerative diseases. It has a protective effect against α–σψν toxicity and has recently been shown to be a substrate of LRRK2, which is the most common cause of familial PD and the risk of sporadic disease. In this review, we analyze the key aspects of Rab1 function in dopamine neurons and its implications in PD neurodegeneration/restauration. The results of the current and former research support the notion that this GTPase is a good candidate for therapeutic strategies.
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Khan SS, Sobu Y, Dhekne HS, Tonelli F, Berndsen K, Alessi DR, Pfeffer SR. Pathogenic LRRK2 control of primary cilia and Hedgehog signaling in neurons and astrocytes of mouse brain. eLife 2021; 10:67900. [PMID: 34658337 PMCID: PMC8550758 DOI: 10.7554/elife.67900] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022] Open
Abstract
Activating LRRK2 mutations cause Parkinson’s disease, and pathogenic LRRK2 kinase interferes with ciliogenesis. Previously, we showed that cholinergic interneurons of the dorsal striatum lose their cilia in R1441C LRRK2 mutant mice (Dhekne et al., 2018). Here, we show that cilia loss is seen as early as 10 weeks of age in these mice and also in two other mouse strains carrying the most common human G2019S LRRK2 mutation. Loss of the PPM1H phosphatase that is specific for LRRK2-phosphorylated Rab GTPases yields the same cilia loss phenotype seen in mice expressing pathogenic LRRK2 kinase, strongly supporting a connection between Rab GTPase phosphorylation and cilia loss. Moreover, astrocytes throughout the striatum show a ciliation defect in all LRRK2 and PPM1H mutant models examined. Hedgehog signaling requires cilia, and loss of cilia in LRRK2 mutant rodents correlates with dysregulation of Hedgehog signaling as monitored by in situ hybridization of Gli1 and Gdnf transcripts. Dopaminergic neurons of the substantia nigra secrete a Hedgehog signal that is sensed in the striatum to trigger neuroprotection; our data support a model in which LRRK2 and PPM1H mutant mice show altered responses to critical Hedgehog signals in the nigrostriatal pathway.
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Affiliation(s)
- Shahzad S Khan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
| | - Yuriko Sobu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
| | - Herschel S Dhekne
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States
| | - Francesca Tonelli
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Kerryn Berndsen
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Dario R Alessi
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States.,MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, United Kingdom
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, United States.,Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, United States
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31
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Fan Y, Nirujogi RS, Garrido A, Ruiz-Martínez J, Bergareche-Yarza A, Mondragón-Rezola E, Vinagre-Aragón A, Croitoru I, Gorostidi Pagola A, Paternain Markinez L, Alcalay R, Hickman RA, Düring J, Gomes S, Pratuseviciute N, Padmanabhan S, Valldeoriola F, Pérez Sisqués L, Malagelada C, Ximelis T, Molina Porcel L, Martí MJ, Tolosa E, Alessi DR, Sammler EM. R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils. Acta Neuropathol 2021; 142:475-494. [PMID: 34125248 PMCID: PMC8357670 DOI: 10.1007/s00401-021-02325-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/30/2022]
Abstract
Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1-2% of all cases of Parkinson's disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2-either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10Thr73) was measured by quantitative multiplexed immunoblotting for pRab10Thr73/total Rab10 as well as targeted mass-spectrometry for absolute pRab10Thr73 occupancy. We found a significant over fourfold increase in pRab10Thr73 phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10Thr73 phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10Thr73 phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors.
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Affiliation(s)
- Ying Fan
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Raja S Nirujogi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Alicia Garrido
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Javier Ruiz-Martínez
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | | | | | - Ana Vinagre-Aragón
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | - Ioana Croitoru
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | - Ana Gorostidi Pagola
- Group of Neurodegenerative Diseases, Biodonostia Research Institute, San Sebastian, Spain
| | | | - Roy Alcalay
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Richard A Hickman
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jonas Düring
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Sara Gomes
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Neringa Pratuseviciute
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | | | - Francesc Valldeoriola
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Leticia Pérez Sisqués
- Departament de Biomedicina, Facultat de Medicina I Ciències de La Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Cristina Malagelada
- Departament de Biomedicina, Facultat de Medicina I Ciències de La Salut, Institut de Neurociències, Universitat de Barcelona, Barcelona, Catalonia, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Teresa Ximelis
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
| | - Laura Molina Porcel
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), Barcelona, Spain
- Alzheimer's Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Institut D'Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Maria José Martí
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Eduardo Tolosa
- Parkinson's Disease and Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Hospital Clínic, IDIBAPS, Universitat de Barcelona, Barcelona, Spain
| | - Dario R Alessi
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK
| | - Esther M Sammler
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, DD1 5EH, UK.
- Molecular and Clinical Medicine, Ninewells Hospital and Medical School, University of Dundee, Dundee, DD1 9SY, UK.
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Proteome Landscape of Epithelial-to-Mesenchymal Transition (EMT) of Retinal Pigment Epithelium Shares Commonalities With Malignancy-Associated EMT. Mol Cell Proteomics 2021; 20:100131. [PMID: 34455105 PMCID: PMC8482521 DOI: 10.1016/j.mcpro.2021.100131] [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: 01/03/2021] [Revised: 07/09/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023] Open
Abstract
Stress and injury to the retinal pigment epithelium (RPE) often lead to dedifferentiation and epithelial-to-mesenchymal transition (EMT). These processes have been implicated in several retinal diseases, including proliferative vitreoretinopathy, diabetic retinopathy, and age-related macular degeneration. Despite the importance of RPE-EMT and the large body of data characterizing malignancy-related EMT, comprehensive proteomic studies to define the protein changes and pathways underlying RPE-EMT have not been reported. This study sought to investigate the temporal protein expression changes that occur in a human-induced pluripotent stem cell–based RPE-EMT model. We utilized multiplexed isobaric tandem mass tag labeling followed by high-resolution tandem MS for precise and in-depth quantification of the RPE-EMT proteome. We have identified and quantified 7937 protein groups in our tandem mass tag–based MS analysis. We observed a total of 532 proteins that are differentially regulated during RPE-EMT. Furthermore, we integrated our proteomic data with prior transcriptomic (RNA-Seq) data to provide additional insights into RPE-EMT mechanisms. To validate these results, we have performed a label-free single-shot data-independent acquisition MS study. Our integrated analysis indicates both the commonality and uniqueness of RPE-EMT compared with malignancy-associated EMT. Our comparative analysis also revealed that multiple age-related macular degeneration–associated risk factors are differentially regulated during RPE-EMT. Together, our integrated dataset provides a comprehensive RPE-EMT atlas and resource for understanding the molecular signaling events and associated biological pathways that underlie RPE-EMT onset. This resource has already facilitated the identification of chemical modulators that could inhibit RPE-EMT, and it will hopefully aid in ongoing efforts to develop EMT inhibition as an approach for the treatment of retinal disease. Proteomics data were integrated with prior transcriptomic (RNA-Seq) data on RPE-EMT. Dysregulated RPE-EMT proteome shares commonality with malignancy-associated EMT. Altered RPE-EMT proteome signatures correlated with known AMD-associated risk factors. Protein kinases and phosphatases crosstalk modulate RPE-EMT.
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Wojewska DN, Kortholt A. LRRK2 Targeting Strategies as Potential Treatment of Parkinson's Disease. Biomolecules 2021; 11:1101. [PMID: 34439767 PMCID: PMC8392603 DOI: 10.3390/biom11081101] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 07/14/2021] [Accepted: 07/20/2021] [Indexed: 02/06/2023] Open
Abstract
Parkinson's Disease (PD) affects millions of people worldwide with no cure to halt the progress of the disease. Leucine-rich repeat kinase 2 (LRRK2) is the most common genetic cause of PD and, as such, LRRK2 inhibitors are promising therapeutic agents. In the last decade, great progress in the LRRK2 field has been made. This review provides a comprehensive overview of the current state of the art, presenting recent developments and challenges in developing LRRK2 inhibitors, and discussing extensively the potential targeting strategies from the protein perspective. As currently there are three LRRK2-targeting agents in clinical trials, more developments are predicted in the upcoming years.
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Affiliation(s)
- Dominika Natalia Wojewska
- Faculty of Science and Engineering, University of Groningen, Nijenborg 7, 9747AG Groningen, The Netherlands;
| | - Arjan Kortholt
- Faculty of Science and Engineering, University of Groningen, Nijenborg 7, 9747AG Groningen, The Netherlands;
- YETEM-Innovative Technologies Application and Research Center, Suleyman Demirel University, 32260 Isparta, Turkey
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Dhekne HS, Yanatori I, Vides EG, Sobu Y, Diez F, Tonelli F, Pfeffer SR. LRRK2-phosphorylated Rab10 sequesters Myosin Va with RILPL2 during ciliogenesis blockade. Life Sci Alliance 2021; 4:4/5/e202101050. [PMID: 33727250 PMCID: PMC7994366 DOI: 10.26508/lsa.202101050] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 02/26/2021] [Accepted: 03/01/2021] [Indexed: 01/08/2023] Open
Abstract
Pathogenic LRRK2 phosphorylation of Rab10 GTPase dramatically redistributes Myosin Va and RILPL2 proteins to the mother centriole and sequesters Myosin Va at that location in a manner that likely interferes with its role in ciliogenesis. Activating mutations in LRRK2 kinase causes Parkinson’s disease. Pathogenic LRRK2 phosphorylates a subset of Rab GTPases and blocks ciliogenesis. Thus, defining novel phospho-Rab interacting partners is critical to our understanding of the molecular basis of LRRK2 pathogenesis. RILPL2 binds with strong preference to LRRK2-phosphorylated Rab8A and Rab10. RILPL2 is a binding partner of the motor protein and Rab effector, Myosin Va. We show here that the globular tail domain of Myosin Va also contains a high affinity binding site for LRRK2-phosphorylated Rab10. In the presence of pathogenic LRRK2, RILPL2 and MyoVa relocalize to the peri-centriolar region in a phosphoRab10-dependent manner. PhosphoRab10 retains Myosin Va over pericentriolar membranes as determined by fluorescence loss in photobleaching microscopy. Without pathogenic LRRK2, RILPL2 is not essential for ciliogenesis but RILPL2 over-expression blocks ciliogenesis in RPE cells independent of tau tubulin kinase recruitment to the mother centriole. These experiments show that LRRK2 generated-phosphoRab10 dramatically redistributes a significant fraction of Myosin Va and RILPL2 to the mother centriole in a manner that likely interferes with Myosin Va’s role in ciliogenesis.
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Affiliation(s)
- Herschel S Dhekne
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Izumi Yanatori
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Edmundo G Vides
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Yuriko Sobu
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
| | - Federico Diez
- Medical Research Council Lab of Protein Phosphorylation and Ubiquitylation, University of Dundee, Dundee, Scotland
| | - Francesca Tonelli
- Medical Research Council Lab of Protein Phosphorylation and Ubiquitylation, University of Dundee, Dundee, Scotland
| | - Suzanne R Pfeffer
- Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA
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