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Diaz-Torres S, Lee SSY, Ogonowski NS, Mackey DA, MacGregor S, Gharahkhani P, Renteria ME. Macular structural integrity estimates are associated with Parkinson's disease genetic risk. Acta Neuropathol Commun 2024; 12:130. [PMID: 39135092 PMCID: PMC11320880 DOI: 10.1186/s40478-024-01841-9] [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: 03/18/2024] [Accepted: 07/29/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND Optical coherence tomography (OCT) is a non-invasive technique to measure retinal layer thickness, providing insights into retinal ganglion cell integrity. Studies have shown reduced retinal nerve fibre layer (RNFL) and ganglion cell inner plexiform layer (GCIPL) thickness in Parkinson's disease (PD) patients. However, it is unclear if there is a common genetic overlap between the macula and peripapillary estimates with PD and if the genetic risk of PD is associated with changes in ganglion cell integrity estimates in young adults. METHOD Western Australian young adults underwent OCT imaging. Their pRNFL, GCIPL, and overall retinal thicknesses were recorded, as well as their longitudinal changes between ages 20 and 28. Polygenic risk scores (PRS) were estimated for each participant based on genome-wide summary data from the largest PD genome-wide association study conducted to date. We further evaluated whether PD PRS was associated with changes in thickness at a younger age. To evaluate the overlap between retinal integrity estimates and PD, we annotated and prioritised genes using mBAT-combo and performed colocalisation through the GWAS pairwise method and HyPrColoc. We used a multi-omic approach and single-cell expression data of the retina and brain through a Mendelian randomisation framework to evaluate the most likely causal genes. Genes prioritised were analysed for missense variants that could have a pathogenic effect using AlphaMissense. RESULTS We found a significant association between the Parkinson's disease polygenic risk score (PD PRS) and changes in retinal thickness in the macula of young adults assessed at 20 and 28 years of age. Gene-based analysis identified 27 genes common to PD and retinal integrity, with a notable region on chromosome 17. Expression analyses highlighted NSF, CRHR1, and KANSL1 as potential causal genes shared between PD and ganglion cell integrity measures. CRHR1 showed consistent results across multiple omics levels. INTERPRETATION Our findings suggest that retinal measurements, particularly in young adults, could be a potential marker for PD risk, indicating a genetic overlap between retinal structural integrity and PD. The study highlights specific genes and loci, mainly on chromosome 17, as potential shared etiological factors for PD and retinal changes. Our results highlight the importance of further longitudinal studies to validate retinal structural metrics as early indicators of PD predisposition.
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Affiliation(s)
- Santiago Diaz-Torres
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Samantha Sze-Yee Lee
- Centre for Ophthalmology and Visual Science (incorporating the Lions Eye Institute), The University of Western Australia, Perth, WA, Australia
| | - Natalia S Ogonowski
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science (incorporating the Lions Eye Institute), The University of Western Australia, Perth, WA, Australia
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Puya Gharahkhani
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
| | - Miguel E Renteria
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Australia.
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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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Ahmad N, Yang ML, Zeb A, Zhou JT, Zubair M, Abbas T, Jiang XH, Zhang YW, Zhang H, Shah W, Shi QH. A novel missense mutation of CCDC34 causes male infertility with oligoasthenoteratozoospermia in a consanguineous Pakistani family. Asian J Androl 2024:00129336-990000000-00197. [PMID: 38856307 DOI: 10.4103/aja202432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 03/24/2024] [Indexed: 06/11/2024] Open
Abstract
ABSTRACT Male infertility is a worldwide health issue, affecting 8%-12% of the global population. Oligoasthenoteratozoospermia (OAT) represents a severe type of male infertility, characterized by reduced sperm count and motility and an increased frequency of sperm with aberrant morphology. Using whole-exome sequencing, this study identified a novel missense mutation (c.848C>A, p.A283E) in the coiled-coil domain-containing 34 gene (CCDC34) in a consanguineous Pakistani family. This rare mutation was predicted to be deleterious and to affect the protein stability. Hematoxylin and eosin staining of spermatozoa from the patient with OAT revealed multiple morphological abnormalities of the flagella and transmission electron microscopy indicated axonemal ultrastructural defects with a lack of outer dynein arms. These findings indicated that CCDC34 plays a role in maintaining the axonemal ultrastructure and the assembly or stability of the outer dynein arms, thus expanding the phenotypic spectrum of CCDC34 missense mutations.
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Affiliation(s)
- Nisar Ahmad
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Division of Reproduction and Genetics, First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Biomedical Sciences and Health Laboratory of Anhui Province, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
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Kars ME, Wu Y, Stenson PD, Cooper DN, Burisch J, Peter I, Itan Y. The landscape of rare genetic variation associated with inflammatory bowel disease and Parkinson's disease comorbidity. Genome Med 2024; 16:66. [PMID: 38741190 PMCID: PMC11092054 DOI: 10.1186/s13073-024-01335-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/16/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Inflammatory bowel disease (IBD) and Parkinson's disease (PD) are chronic disorders that have been suggested to share common pathophysiological processes. LRRK2 has been implicated as playing a role in both diseases. Exploring the genetic basis of the IBD-PD comorbidity through studying high-impact rare genetic variants can facilitate the identification of the novel shared genetic factors underlying this comorbidity. METHODS We analyzed whole exomes from the BioMe BioBank and UK Biobank, and whole genomes from a cohort of 67 European patients diagnosed with both IBD and PD to examine the effects of LRRK2 missense variants on IBD, PD and their co-occurrence (IBD-PD). We performed optimized sequence kernel association test (SKAT-O) and network-based heterogeneity clustering (NHC) analyses using high-impact rare variants in the IBD-PD cohort to identify novel candidate genes, which we further prioritized by biological relatedness approaches. We conducted phenome-wide association studies (PheWAS) employing BioMe BioBank and UK Biobank whole exomes to estimate the genetic relevance of the 14 prioritized genes to IBD-PD. RESULTS The analysis of LRRK2 missense variants revealed significant associations of the G2019S and N2081D variants with IBD-PD in addition to several other variants as potential contributors to increased or decreased IBD-PD risk. SKAT-O identified two significant genes, LRRK2 and IL10RA, and NHC identified 6 significant gene clusters that are biologically relevant to IBD-PD. We observed prominent overlaps between the enriched pathways in the known IBD, PD, and candidate IBD-PD gene sets. Additionally, we detected significantly enriched pathways unique to the IBD-PD, including MAPK signaling, LPS/IL-1 mediated inhibition of RXR function, and NAD signaling. Fourteen final candidate IBD-PD genes were prioritized by biological relatedness methods. The biological importance scores estimated by protein-protein interaction networks and pathway and ontology enrichment analyses indicated the involvement of genes related to immunity, inflammation, and autophagy in IBD-PD. Additionally, PheWAS provided support for the associations of candidate genes with IBD and PD. CONCLUSIONS Our study confirms and uncovers new LRRK2 associations in IBD-PD. The identification of novel inflammation and autophagy-related genes supports and expands previous findings related to IBD-PD pathogenesis, and underscores the significance of therapeutic interventions for reducing systemic inflammation.
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Affiliation(s)
- Meltem Ece Kars
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yiming Wu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- College of Life Science, China West Normal University, Nan Chong, Si Chuan, 637009, China
| | - Peter D Stenson
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Johan Burisch
- Gastrounit, Medical Division, Copenhagen University Hospital - Amager and Hvidovre, Kettegård Alle 30, Hvidovre, Copenhagen, 2650, Denmark
- Copenhagen Center for Inflammatory Bowel Disease in Children, Adolescents and Adults, Copenhagen University Hospital - Amager and Hvidovre, Kettegård Alle 30, Hvidovre, Copenhagen, 2650, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, Copenhagen, 2200, Denmark
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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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. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.15.589570. [PMID: 38659797 PMCID: PMC11042295 DOI: 10.1101/2024.04.15.589570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
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 activation, antigenic responses, and the suppression of platelet activation. Conclusions The extracellular ratio of pT73-Rab10 to total Rab10 in serum 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 to mitigate associated deleterious immunological responses.
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Mahlknecht P, Poewe W. Pharmacotherapy for Disease Modification in Early Parkinson's Disease: How Early Should We Be? JOURNAL OF PARKINSON'S DISEASE 2024:JPD230354. [PMID: 38427503 DOI: 10.3233/jpd-230354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/03/2024]
Abstract
Slowing or halting progression continues to be a major unmet medical need in Parkinson's disease (PD). Numerous trials over the past decades have tested a broad range of interventions without ultimate success. There are many potential reasons for this failure and much debate has focused on the need to test 'disease-modifying' candidate drugs in the earliest stages of disease. While generally accepted as a rational approach, it is also associated with significant challenges around the selection of trial populations as well as trial outcomes and durations. From a health care perspective, intervening even earlier and before at-risk subjects have gone on to develop overt clinical disease is at the heart of preventive medicine. Recent attempts to develop a framework for a biological definition of PD are aiming to enable 'preclinical' and subtype-specific diagnostic approaches. The present review addresses past efforts towards disease-modification, including drug targets and reasons for failure, as well as novel targets that are currently being explored in disease-modification trials in early established PD. The new biological definitions of PD may offer new opportunities to intervene even earlier. We critically discuss the potential and challenges around planning 'disease-prevention' trials in subjects with biologically defined 'preclinical' or prodromal PD.
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Affiliation(s)
- Philipp Mahlknecht
- Department of Neurology, Innsbruck Medical University, Innsbruck, Austria
| | - Werner Poewe
- Department of Neurology, Innsbruck Medical University, Innsbruck, Austria
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Fang S, Lee PAH, Wang Z, Zhao B. The Impact of 90 Parkinson's Disease-Risk Single Nucleotide Polymorphisms on Urinary Bis(monoacylglycerol)phosphate Levels in the Prodromal and PD Cohorts. Int J Mol Sci 2024; 25:2286. [PMID: 38396963 PMCID: PMC10889274 DOI: 10.3390/ijms25042286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/01/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease (PD) is a common neurodegenerative disorder with a prolonged prodromal phase. Higher urinary bis(monoacylglycerol)phosphate (BMP) levels associate with LRRK2 (leucine-rich repeat kinase 2) and GBA1 (glucocerebrosidase) mutations, and are considered as potential noninvasive biomarkers for predicting those mutations and PD progression. However, their reliability has been questioned, with inadequately investigated genetics, cohorts, and population. In this study, multiple statistical hypothesis tests were employed on urinary BMP levels and sequences of 90 PD-risk single nucleotide polymorphisms (SNPs) from Parkinson's Progression Markers Institution (PPMI) participants. Those SNPs were categorized into four groups based on their impact on BMP levels in various cohorts. Variants rs34637584 G/A and rs34637584 A/A (LRRK2 G2019S) were identified as the most relevant on increasing urinary BMP levels in the PD cohort. Meanwhile, rs76763715 T/T (GBA1) was the primary factor elevating BMP levels in the prodromal cohort compared to its T/C and C/C variants (N370S) and the PD cohort. Proteomics analysis indicated the changed transport pathways may be the reasons for elevated BMP levels in prodromal patients. Our findings demonstrated that higher urinary BMP levels alone were not reliable biomarkers for PD progression or gene mutations but might serve as supplementary indicators for early diagnosis and treatment.
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Affiliation(s)
| | | | - Zejian Wang
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (S.F.); (P.A.H.L.)
| | - Bo Zhao
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai 200240, China; (S.F.); (P.A.H.L.)
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8
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Zhu H, Tonelli F, Turk M, Prescott A, Alessi DR, Sun J. Rab29-dependent asymmetrical activation of leucine-rich repeat kinase 2. Science 2023; 382:1404-1411. [PMID: 38127736 PMCID: PMC10786121 DOI: 10.1126/science.adi9926] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Gain-of-function mutations in LRRK2, which encodes the leucine-rich repeat kinase 2 (LRRK2), are the most common genetic cause of late-onset Parkinson's disease. LRRK2 is recruited to membrane organelles and activated by Rab29, a Rab guanosine triphosphatase encoded in the PARK16 locus. We present cryo-electron microscopy structures of Rab29-LRRK2 complexes in three oligomeric states, providing key snapshots during LRRK2 recruitment and activation. Rab29 induces an unexpected tetrameric assembly of LRRK2, formed by two kinase-active central protomers and two kinase-inactive peripheral protomers. The central protomers resemble the active-like state trapped by the type I kinase inhibitor DNL201, a compound that underwent a phase 1 clinical trial. Our work reveals the structural mechanism of LRRK2 spatial regulation and provides insights into LRRK2 inhibitor design for Parkinson's disease treatment.
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Affiliation(s)
- Hanwen Zhu
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Martin Turk
- Cryo-EM and Tomography Center, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Alan Prescott
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Ji Sun
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
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El Otmani H, Daghi M, Tahiri Jouti N, Lesage S. An overview of the worldwide distribution of LRRK2 mutations in Parkinson's disease. Neurodegener Dis Manag 2023; 13:335-350. [PMID: 38305913 DOI: 10.2217/nmt-2023-0025] [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: 02/03/2024] Open
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder with significant genetic influence. The LRRK2 gene is a major genetic contributor, particularly the Gly2019Ser mutation. This focused review investigates the global distribution of LRRK2 mutations, with emphasis on Gly2019Ser and other pathogenic variants. Prevalence rates of Gly2019Ser are highest in North Africa and the Ashkenazi-Jewish population, indicating a potential common ancestor and founder effect. Other LRRK2 mutations, including Asn1437His, Arg1441Gly/Cys/His, Tyr1699Cys and Ile2020Thr, exhibit varying global prevalences. Understanding these distributions enhances our knowledge of PD genetics and aids personalized medicine. Further research is crucial to unravel clinical implications and develop targeted therapies for LRRK2 mutation carriers.
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Affiliation(s)
- Hicham El Otmani
- Laboratory of Medical Genetics & Molecular Pathology. Faculty of Medicine and Pharmacy, Hassan II University, 20250, Casablanca, Morocco
- Laboratory of Cellular and Molecular Inflammatory, Degenerative & Oncologic Pathophysiology. Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, 20250, Morocco
- Department of Neurology. Ibn Rochd University Hospital, Casablanca, 20360, Morocco
| | - Mohamed Daghi
- Research Laboratory of Nervous System Diseases, Neurosensory Disorders & Disability. Faculty of Medicine & Pharmacy, Hassan II University, Casablanca, 20250, Morocco
| | - Nadia Tahiri Jouti
- Laboratory of Cellular and Molecular Inflammatory, Degenerative & Oncologic Pathophysiology. Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, 20250, Morocco
| | - Suzanne Lesage
- Sorbonne University, Institut du Cerveau-Paris Brain Institute, ICM, INSERM, CNRS, Assistance Publique-Hôpitaux de Paris, Paris, 75013, France
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Mohamed W. Leveraging genetic diversity to understand monogenic Parkinson's disease's landscape in AfrAbia. AMERICAN JOURNAL OF NEURODEGENERATIVE DISEASE 2023; 12:108-122. [PMID: 37736165 PMCID: PMC10509492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
Abstract
Parkinson's disease may be caused by a single highly deleterious and penetrant pathogenic variant in 5-10% of cases (monogenic). Research into these mutational disorders yields important pathophysiological insights. This article examines the phenotype, genotype, pathophysiology, and geographic and ethnic distribution of genetic forms of disease. Well established Parkinson's disease (PD) causal variants can follow an autosomal dominant (SNCA, LRRK2, and VPS35) and autosomal recessive pattern of inheritance (PRKN, PINK1, and DJ). Parkinson's disease is a worldwide condition, yet the AfrAbia population is understudied in this regard. No prevalence or incidence investigations have been conducted yet. Few studies on genetic risk factors for PD in AfrAbia communities have been reported which supported the notion that the prevalence and incidence rates of PD in AfrAbia are generally lower than those reported for European and North American populations. There have been only a handful of documented genetic studies of PD in AfrAbia and very limited cohort and case-control research studies on PD have been documented. In this article, we provide a summary of prior conducted research on monogenic PD in Africa and highlight data gaps and promising new research directions. We emphasize that monogenic Parkinson's disease is influenced by distinctions in ethnicity and geography, thereby reinforcing the need for global initiatives to aggregate large numbers of patients and identify novel candidate genes. The current article increases our knowledge of the genetics of Parkinson's disease (PD) and helps to further our knowledge on the genetic factors that contribute to PD, such as the lower penetrance and varying clinical expressivity of known genetic variants, particularly in AfrAbian PD patients.
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Affiliation(s)
- Wael Mohamed
- Basic Medical Science Department, Kulliyah of Medicine, International Islamic University Malaysia Kuantan, Pahang, Malaysia
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11
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Cabezudo D, Tsafaras G, Van Acker E, Van den Haute C, Baekelandt V. Mutant LRRK2 exacerbates immune response and neurodegeneration in a chronic model of experimental colitis. Acta Neuropathol 2023; 146:245-261. [PMID: 37289222 PMCID: PMC10328902 DOI: 10.1007/s00401-023-02595-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/25/2023] [Indexed: 06/09/2023]
Abstract
The link between the gut and the brain in Parkinson's disease (PD) pathogenesis is currently a subject of intense research. Indeed, gastrointestinal dysfunction is known as an early symptom in PD and inflammatory bowel disease (IBD) has recently been recognised as a risk factor for PD. The leucine-rich repeat kinase 2 (LRRK2) is a PD- and IBD-related protein with highest expression in immune cells. In this study, we provide evidence for a central role of LRRK2 in gut inflammation and PD. The presence of the gain-of-function G2019S mutation significantly increases the disease phenotype and inflammatory response in a mouse model of experimental colitis based on chronic dextran sulphate sodium (DSS) administration. Bone marrow transplantation of wild-type cells into G2019S knock-in mice fully rescued this exacerbated response, proving the key role of mutant LRRK2 in immune cells in this experimental colitis model. Furthermore, partial pharmacological inhibition of LRRK2 kinase activity also reduced the colitis phenotype and inflammation. Moreover, chronic experimental colitis also induced neuroinflammation and infiltration of peripheral immune cells into the brain of G2019S knock-in mice. Finally, combination of experimental colitis with overexpression of α-synuclein in the substantia nigra aggravated motor deficits and dopaminergic neurodegeneration in G2019S knock-in mice. Taken together, our results link LRRK2 with the immune response in colitis and provide evidence that gut inflammation can impact brain homeostasis and contribute to neurodegeneration in PD.
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Affiliation(s)
- Diego Cabezudo
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, box 1023, 3000, Leuven, Belgium
| | - George Tsafaras
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, box 1023, 3000, Leuven, Belgium
| | - Eva Van Acker
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, box 1023, 3000, Leuven, Belgium
| | - Chris Van den Haute
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, box 1023, 3000, Leuven, Belgium
- Leuven Viral Vector Core, Herestraat 49, box 1023, 3000, Leuven, Belgium
| | - Veerle Baekelandt
- Laboratory for Neurobiology and Gene Therapy, Department of Neurosciences, Leuven Brain Institute, KU Leuven, Herestraat 49, box 1023, 3000, Leuven, Belgium.
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12
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Borsche M, Pratuseviciute N, Schaake S, Hinrichs F, Morel G, Uter J, Lohmann K, Klein C, Alessi DR, Hagenah J, Sammler E. The New p.F1700L LRRK2 Variant Causes Parkinson's Disease by Extensively Increasing Kinase Activity. Mov Disord 2023; 38:1105-1107. [PMID: 36971062 PMCID: PMC10947214 DOI: 10.1002/mds.29385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/06/2023] [Indexed: 07/22/2023] Open
Affiliation(s)
- Max Borsche
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
- Department of NeurologyUniversity of LübeckLübeckGermany
| | - Neringa Pratuseviciute
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Susen Schaake
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Gabriel Morel
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Jan Uter
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
- Department of NeurologyUniversity of LübeckLübeckGermany
| | - Katja Lohmann
- Institute of NeurogeneticsUniversity of LübeckLübeckGermany
| | | | - Dario R. Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
| | - Johann Hagenah
- Department of Neurology, Westküstenklinikum HeideHeideGermany
| | - Esther Sammler
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeDundeeUnited Kingdom
- Molecular and Clinical Medicine, Ninewells Hospital and Medical SchoolUniversity of DundeeDundeeUnited Kingdom
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13
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Ito G, Utsunomiya-Tate N. Overview of the Impact of Pathogenic LRRK2 Mutations in Parkinson's Disease. Biomolecules 2023; 13:biom13050845. [PMID: 37238714 DOI: 10.3390/biom13050845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/25/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a large protein kinase that physiologically phosphorylates and regulates the function of several Rab proteins. LRRK2 is genetically implicated in the pathogenesis of both familial and sporadic Parkinson's disease (PD), although the underlying mechanism is not well understood. Several pathogenic mutations in the LRRK2 gene have been identified, and in most cases the clinical symptoms that PD patients with LRRK2 mutations develop are indistinguishable from those of typical PD. However, it has been shown that the pathological manifestations in the brains of PD patients with LRRK2 mutations are remarkably variable when compared to sporadic PD, ranging from typical PD pathology with Lewy bodies to nigral degeneration with deposition of other amyloidogenic proteins. The pathogenic mutations in LRRK2 are also known to affect the functions and structure of LRRK2, the differences in which may be partly attributable to the variations observed in patient pathology. In this review, in order to help researchers unfamiliar with the field to understand the mechanism of pathogenesis of LRRK2-associated PD, we summarize the clinical and pathological manifestations caused by pathogenic mutations in LRRK2, their impact on the molecular function and structure of LRRK2, and their historical background.
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Affiliation(s)
- Genta Ito
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
| | - Naoko Utsunomiya-Tate
- Department of Biomolecular Chemistry, Faculty of Pharma-Sciences, Teikyo University, Tokyo 173-8605, Japan
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14
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Strader S, West AB. The interplay between monocytes, α-synuclein and LRRK2 in Parkinson's disease. Biochem Soc Trans 2023; 51:747-758. [PMID: 37013975 PMCID: PMC11110874 DOI: 10.1042/bst20201091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/05/2023]
Abstract
The accumulation of aggregated α-synuclein in susceptible neurons in the brain, together with robust activation of nearby myeloid cells, are pathological hallmarks of Parkinson's disease (PD). While microglia represent the dominant type of myeloid cell in the brain, recent genetic and whole-transcriptomic studies have implicated another type of myeloid cell, bone-marrow derived monocytes, in disease risk and progression. Monocytes in circulation harbor high concentrations of the PD-linked enzyme leucine-rich repeat kinase 2 (LRRK2) and respond to both intracellular and extracellular aggregated α-synuclein with a variety of strong pro-inflammatory responses. This review highlights recent findings from studies that functionally characterize monocytes in PD patients, monocytes that infiltrate into cerebrospinal fluid, and emerging analyses of whole myeloid cell populations in the PD-affected brain that include monocyte populations. Central controversies discussed include the relative contribution of monocytes acting in the periphery from those that might engraft in the brain to modify disease risk and progression. We conclude that further investigation into monocyte pathways and responses in PD, especially the discovery of additional markers, transcriptomic signatures, and functional classifications, that better distinguish monocyte lineages and responses in the brain from other types of myeloid cells may reveal points for therapeutic intervention, as well as a better understanding of ongoing inflammation associated with PD.
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Affiliation(s)
- Samuel Strader
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome Court, Durham, 27710, North Carolina, U.S.A
| | - Andrew B. West
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome Court, Durham, 27710, North Carolina, U.S.A
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15
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Yahya V, Di Fonzo A, Monfrini E. Genetic Evidence for Endolysosomal Dysfunction in Parkinson’s Disease: A Critical Overview. Int J Mol Sci 2023; 24:ijms24076338. [PMID: 37047309 PMCID: PMC10094484 DOI: 10.3390/ijms24076338] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/23/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023] Open
Abstract
Parkinson’s disease (PD) is the second most common neurodegenerative disorder in the aging population, and no disease-modifying therapy has been approved to date. The pathogenesis of PD has been related to many dysfunctional cellular mechanisms, however, most of its monogenic forms are caused by pathogenic variants in genes involved in endolysosomal function (LRRK2, VPS35, VPS13C, and ATP13A2) and synaptic vesicle trafficking (SNCA, RAB39B, SYNJ1, and DNAJC6). Moreover, an extensive search for PD risk variants revealed strong risk variants in several lysosomal genes (e.g., GBA1, SMPD1, TMEM175, and SCARB2) highlighting the key role of lysosomal dysfunction in PD pathogenesis. Furthermore, large genetic studies revealed that PD status is associated with the overall “lysosomal genetic burden”, namely the cumulative effect of strong and weak risk variants affecting lysosomal genes. In this context, understanding the complex mechanisms of impaired vesicular trafficking and dysfunctional endolysosomes in dopaminergic neurons of PD patients is a fundamental step to identifying precise therapeutic targets and developing effective drugs to modify the neurodegenerative process in PD.
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Affiliation(s)
- Vidal Yahya
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, 20122 Milan, Italy;
| | - Alessio Di Fonzo
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, 20122 Milan, Italy;
| | - Edoardo Monfrini
- Dino Ferrari Center, Department of Pathophysiology and Transplantation, University of Milan, 20122 Milan, Italy;
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Neurology Unit, 20122 Milan, Italy;
- Correspondence:
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16
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West AB, Schwarzschild MA. LRRK2-Targeting Therapies March Through the Valley of Death. Mov Disord 2023; 38:361-365. [PMID: 36942368 PMCID: PMC11076002 DOI: 10.1002/mds.29343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 01/24/2023] [Indexed: 03/23/2023] Open
Affiliation(s)
- Andrew B. West
- Duke Center for Neurodegeneration Research, Department of Pharmacology and Cancer Biology, Duke University, 3 Genome court, Durham, NC, 27710, USA
| | - Michael A. Schwarzschild
- MassGeneral Institute for Neurodegenerative Disease, Massachusetts General Hospital, 114 16th Street, Charlestown, MA 02129 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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Niotis K, West AB, Saunders-Pullman R. Who to Enroll in Parkinson Disease Prevention Trials? The Case for Genetically At-Risk Cohorts. Neurology 2022; 99:10-18. [PMID: 35970585 DOI: 10.1212/wnl.0000000000200812] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 04/15/2022] [Indexed: 12/15/2022] Open
Abstract
Therapies that prevent the occurrence of Parkinson disease (PD) (primary prevention) or mitigate the progression of symptoms in those with early disease (secondary prevention) are a critical unmet need in disease management. Despite great promise, PD prevention trials have not yet demonstrated success. Initiation of treatment too late in the disease course and the heterogeneity of disease are obstacles that may have contributed to the failure. Genetically stratified groups offer many advantages to primary and secondary prevention trials. In addition to their ease of identification, they decrease disease heterogeneity on several levels. Particularly, they comprise a phenotypically and pathologically enriched group with defined clinical features, pathogenic mechanisms and associated proteins that may serve as specific trial endpoints, therapeutic targets and biomarkers for disease state, and pharmacodynamic and pharmacokinetic status. However, challenges arise from genetic variant heterogeneity, from reduced penetrance whereby many carriers will not develop PD, and in recruiting a population that will meet the desired outcome in the proposed study duration. In this review, we discussed the opportunities afforded by the enrollment of genetically stratified cohorts (i.e., leucine-rich repeat kinase 2 and glucocerebrosidase 1) into prevention trials with a primary focus on primary prevention trials. We also outlined challenges surrounding the enrollment of these cohorts and offered suggestions to leverage their many advantages.
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Affiliation(s)
- Kellyann Niotis
- From the Department of Neurology (K.N., R.S.-P.), Mount Sinai Beth Israel Medical Center; Department of Neurology (K.N., R.S.-P.), Icahn School of Medicine at Mount Sinai, New York; and Duke Center for Neurodegeneration Research (A.B.W.), Departments of Pharmacology and Cancer Biology, Neurology, and Neurobiology, Duke University, Durham, NC
| | - Andrew B West
- From the Department of Neurology (K.N., R.S.-P.), Mount Sinai Beth Israel Medical Center; Department of Neurology (K.N., R.S.-P.), Icahn School of Medicine at Mount Sinai, New York; and Duke Center for Neurodegeneration Research (A.B.W.), Departments of Pharmacology and Cancer Biology, Neurology, and Neurobiology, Duke University, Durham, NC
| | - Rachel Saunders-Pullman
- From the Department of Neurology (K.N., R.S.-P.), Mount Sinai Beth Israel Medical Center; Department of Neurology (K.N., R.S.-P.), Icahn School of Medicine at Mount Sinai, New York; and Duke Center for Neurodegeneration Research (A.B.W.), Departments of Pharmacology and Cancer Biology, Neurology, and Neurobiology, Duke University, Durham, NC.
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19
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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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20
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Predicting Parkinson disease related genes based on PyFeat and gradient boosted decision tree. Sci Rep 2022; 12:10004. [PMID: 35705654 PMCID: PMC9200794 DOI: 10.1038/s41598-022-14127-8] [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: 01/02/2022] [Accepted: 06/01/2022] [Indexed: 11/10/2022] Open
Abstract
Identifying genes related to Parkinson’s disease (PD) is an active research topic in biomedical analysis, which plays a critical role in diagnosis and treatment. Recently, many studies have proposed different techniques for predicting disease-related genes. However, a few of these techniques are designed or developed for PD gene prediction. Most of these PD techniques are developed to identify only protein genes and discard long noncoding (lncRNA) genes, which play an essential role in biological processes and the transformation and development of diseases. This paper proposes a novel prediction system to identify protein and lncRNA genes related to PD that can aid in an early diagnosis. First, we preprocessed the genes into DNA FASTA sequences from the University of California Santa Cruz (UCSC) genome browser and removed the redundancies. Second, we extracted some significant features of DNA FASTA sequences using the PyFeat method with the AdaBoost as feature selection. These selected features achieved promising results compared with extracted features from some state-of-the-art feature extraction techniques. Finally, the features were fed to the gradient-boosted decision tree (GBDT) to diagnose different tested cases. Seven performance metrics were used to evaluate the performance of the proposed system. The proposed system achieved an average accuracy of 78.6%, the area under the curve equals 84.5%, the area under precision-recall (AUPR) equals 85.3%, F1-score equals 78.3%, Matthews correlation coefficient (MCC) equals 0.575, sensitivity (SEN) equals 77.1%, and specificity (SPC) equals 80.2%. The experiments demonstrate promising results compared with other systems. The predicted top-rank protein and lncRNA genes are verified based on a literature review.
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21
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Monogenic Parkinson’s Disease: Genotype, Phenotype, Pathophysiology, and Genetic Testing. Genes (Basel) 2022; 13:genes13030471. [PMID: 35328025 PMCID: PMC8950888 DOI: 10.3390/genes13030471] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/24/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease may be caused by a single pathogenic variant (monogenic) in 5–10% of cases, but investigation of these disorders provides valuable pathophysiological insights. In this review, we discuss each genetic form with a focus on genotype, phenotype, pathophysiology, and the geographic and ethnic distribution. Well-established Parkinson’s disease genes include autosomal dominant forms (SNCA, LRRK2, and VPS35) and autosomal recessive forms (PRKN, PINK1 and DJ1). Furthermore, mutations in the GBA gene are a key risk factor for Parkinson’s disease, and there have been major developments for X-linked dystonia parkinsonism. Moreover, atypical or complex parkinsonism may be due to mutations in genes such as ATP13A2, DCTN1, DNAJC6, FBXO7, PLA2G6, and SYNJ1. Furthermore, numerous genes have recently been implicated in Parkinson’s disease, such as CHCHD2, LRP10, TMEM230, UQCRC1, and VPS13C. Additionally, we discuss the role of heterozygous mutations in autosomal recessive genes, the effect of having mutations in two Parkinson’s disease genes, the outcome of deep brain stimulation, and the role of genetic testing. We highlight that monogenic Parkinson’s disease is influenced by ethnicity and geographical differences, reinforcing the need for global efforts to pool large numbers of patients and identify novel candidate genes.
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22
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Senkevich K, Rudakou U, Gan-Or Z. New therapeutic approaches to Parkinson's disease targeting GBA, LRRK2 and Parkin. Neuropharmacology 2021; 202:108822. [PMID: 34626666 DOI: 10.1016/j.neuropharm.2021.108822] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/01/2021] [Accepted: 10/04/2021] [Indexed: 01/23/2023]
Abstract
Parkinson's disease (PD) is defined as a complex disorder with multifactorial pathogenesis, yet a more accurate definition could be that PD is not a single entity, but rather a mixture of different diseases with similar phenotypes. Attempts to classify subtypes of PD have been made based on clinical phenotypes or biomarkers. However, the most practical approach, at least for a portion of the patients, could be to classify patients based on genes involved in PD. GBA and LRRK2 mutations are the most common genetic causes or risk factors of PD, and PRKN is the most common cause of autosomal recessive form of PD. Patients carrying variants in GBA, LRRK2 or PRKN differ in some of their clinical characteristics, pathology and biochemical parameters. Thus, these three PD-associated genes are of special interest for drug development. Existing therapeutic approaches in PD are strictly symptomatic, as numerous clinical trials aimed at modifying PD progression or providing neuroprotection have failed over the last few decades. The lack of precision medicine approach in most of these trials could be one of the reasons why they were not successful. In the current review we discuss novel therapeutic approaches targeting GBA, LRRK2 and PRKN and discuss different aspects related to these genes and clinical trials.
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Affiliation(s)
- Konstantin Senkevich
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada; First Pavlov State Medical University of St. Petersburg, Saint-Petersburg, Russia
| | - Uladzislau Rudakou
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada; Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Ziv Gan-Or
- The Neuro (Montreal Neurological Institute-Hospital), McGill University, Montréal, QC, Canada; Department of Neurology and neurosurgery, McGill University, Montréal, QC, Canada; Department of Human Genetics, McGill University, Montréal, QC, Canada.
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Lake J, Reed X, Langston RG, Nalls MA, Gan-Or Z, Cookson MR, Singleton AB, Blauwendraat C, Leonard HL. Coding and Noncoding Variation in LRRK2 and Parkinson's Disease Risk. Mov Disord 2021; 37:95-105. [PMID: 34542912 PMCID: PMC9292230 DOI: 10.1002/mds.28787] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 01/31/2023] Open
Abstract
Background The leucine‐rich repeat kinase 2 (LRRK2) gene harbors both rare highly damaging missense variants (eg, p.G2019S) and common noncoding variants (eg, rs76904798) with lower effect sizes that are associated with Parkinson's disease (PD) risk. Objectives This study aimed to investigate in a large meta‐analysis whether the LRRK2 Genome‐Wide Association Study (GWAS) signal represented by rs76904798 is independently associated with PD risk from LRRK2 coding variation and whether complex linkage disequilibrium structures with p.G2019S and the 5′ noncoding haplotype account for the association of LRRK2 coding variants. Methods We performed a meta‐analysis using imputed genotypes from 17,838 patients, 13,404 proxy patients, and 173,639 healthy controls of European ancestry. We excluded carriers of p.G2019S and/or rs76904798 to clarify the role of LRRK2 coding variation in mediating disease risk and excluded carriers of relatively rare LRRK2 coding variants to assess the independence of rs76904798. We also investigated the co‐inheritance of LRRK2 coding variants with p.G2019S, rs76904798, and p.N2081D. Results LRRK2 rs76904798 remained significantly associated with PD after excluding the carriers of relatively rare LRRK2 coding variants. LRRK2 p.R1514Q and p.N2081D were frequently co‐inherited with rs76904798, and the allele distribution of p.S1647T significantly changed among patients after removing rs76904798 carriers. Conclusions These data suggest that the LRRK2 coding variants previously related to PD (p.N551K, p.R1398H, p.M1646T, and p.N2081D) do not drive the 5′ noncoding GWAS signal. These data, however, do not preclude the independent association of the haplotype p.N551K‐p.R1398H and p.M1646T with altered disease risk. © 2021 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson Movement Disorder Society. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Julie Lake
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Xylena Reed
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Rebekah G Langston
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA
| | - Ziv Gan-Or
- Montreal Neurological Institute, McGill University, Montréal, Quebec, Canada.,Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, Quebec, Canada
| | - Mark R Cookson
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA
| | - Cornelis Blauwendraat
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA
| | - Hampton L Leonard
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland, USA.,Center for Alzheimer's and Related Dementias, National Institutes of Health, Bethesda, Maryland, USA.,Data Tecnica International, Glen Echo, Maryland, USA.,German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
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