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Menozzi E, Schapira AHV. The Gut Microbiota in Parkinson Disease: Interactions with Drugs and Potential for Therapeutic Applications. CNS Drugs 2024; 38:315-331. [PMID: 38570412 PMCID: PMC11026199 DOI: 10.1007/s40263-024-01073-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2024] [Indexed: 04/05/2024]
Abstract
The concept of a 'microbiota-gut-brain axis' has recently emerged as an important player in the pathophysiology of Parkinson disease (PD), not least because of the reciprocal interaction between gut bacteria and medications. The gut microbiota can influence levodopa kinetics, and conversely, drugs administered for PD can influence gut microbiota composition. Through a two-step enzymatic pathway, gut microbes can decarboxylate levodopa to dopamine in the small intestine and then dehydroxylate it to m-tyramine, thus reducing availability. Inhibition of bacterial decarboxylation pathways could therefore represent a strategy to increase levodopa absorption. Other bacterial perturbations common in PD, such as small intestinal bacterial overgrowth and Helicobacter pylori infection, can also modulate levodopa metabolism, and eradication therapies may improve levodopa absorption. Interventions targeting the gut microbiota offer a novel opportunity to manage disabling motor complications and dopa-unresponsive symptoms. Mediterranean diet-induced changes in gut microbiota composition might improve a range of non-motor symptoms. Prebiotics can increase levels of short-chain fatty acid-producing bacteria and decrease pro-inflammatory species, with positive effects on clinical symptoms and levodopa kinetics. Different formulations of probiotics showed beneficial outcomes on constipation, with some of them improving dopamine levels; however, the most effective dosage and duration and long-term effects of these treatments remain unknown. Data from faecal microbiota transplantation studies are preliminary, but show encouraging trends towards improvement in both motor and non-motor outcomes.This article summarises the most up-to-date knowledge in pharmacomicrobiomics in PD, and discusses how the manipulation of gut microbiota represents a potential new therapeutic avenue for PD.
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Affiliation(s)
- Elisa Menozzi
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, NW3 2PF, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, NW3 2PF, UK.
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Bhore N, Bogacki EC, O'Callaghan B, Plun-Favreau H, Lewis PA, Herbst S. Common genetic risk for Parkinson's disease and dysfunction of the endo-lysosomal system. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220517. [PMID: 38368938 PMCID: PMC10874702 DOI: 10.1098/rstb.2022.0517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 10/18/2023] [Indexed: 02/20/2024] Open
Abstract
Parkinson's disease is a progressive neurological disorder, characterized by prominent movement dysfunction. The past two decades have seen a rapid expansion of our understanding of the genetic basis of Parkinson's, initially through the identification of monogenic forms and, more recently, through genome-wide association studies identifying common risk variants. Intriguingly, a number of cellular pathways have emerged from these analysis as playing central roles in the aetiopathogenesis of Parkinson's. In this review, the impact of data deriving from genome-wide analyses for Parkinson's upon our functional understanding of the disease will be examined, with a particular focus on examples of endo-lysosomal and mitochondrial dysfunction. The challenges of moving from a genetic to a functional understanding of common risk variants for Parkinson's will be discussed, with a final consideration of the current state of the genetic architecture of the disorder. This article is part of a discussion meeting issue 'Understanding the endo-lysosomal network in neurodegeneration'.
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Affiliation(s)
- Noopur Bhore
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University of London, London WC1N 3BG, UK
| | - Erin C. Bogacki
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Benjamin O'Callaghan
- Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University of London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Helene Plun-Favreau
- Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University of London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Patrick A. Lewis
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University of London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Susanne Herbst
- Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Neurodegenerative Diseases, UCL Queen Square Institute of Neurology, University of London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Gonzalez-Latapi P, Bustos B, Dong S, Lubbe S, Simuni T, Krainc D. Alterations in Blood Methylome as Potential Epigenetic Biomarker in Sporadic Parkinson's Disease. Ann Neurol 2024. [PMID: 38563317 DOI: 10.1002/ana.26923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 02/03/2024] [Accepted: 02/19/2024] [Indexed: 04/04/2024]
Abstract
OBJECTIVE To characterize DNA methylation (DNAm) differences between sporadic Parkinson's disease (PD) and healthy control (HC) individuals enrolled in the Parkinson's Progression Markers Initiative (PPMI). METHODS Using whole blood, we characterized longitudinal differences in DNAm between sporadic PD patients (n = 196) and HCs (n = 86) enrolled in PPMI. RNA sequencing (RNAseq) was used to conduct gene expression analyses for genes mapped to differentially methylated cytosine-guanine sites (CpGs). RESULTS At the time of patient enrollment, 5,178 CpGs were differentially methylated (2,683 hypermethylated and 2,495 hypomethylated) in PD compared to HC. Of these, 579 CpGs underwent significant methylation changes over 3 years. Several differentially methylated CpGs were found near the cytochrome P450 family 2 subfamily E member 1 (CYP2E1) gene. Additionally, multiple hypermethylated CpGs were associated with the N-myc downregulated gene family member 4 (NDRG4) gene. RNA-Seq analyses showed 75 differentially expressed genes in PD patients compared to controls. An integrative analysis of both differentially methylated sites and differentially expressed genes revealed 20 genes that exhibited hypomethylation concomitant with overexpression. Additionally, 1 gene, cathepsin H (CTSH), displayed hypermethylation that was associated with its decreased expression. INTERPRETATION We provide initial evidence of alterations in DNAm in blood of PD patients that may serve as potential epigenetic biomarker of disease. To evaluate the significance of these changes throughout the progression of PD, additional profiling at longer intervals and during the prodromal stages of disease will be necessary. ANN NEUROL 2024.
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Affiliation(s)
- Paulina Gonzalez-Latapi
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Bernabe Bustos
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Siyuan Dong
- Biostatistics Collaboration Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Steven Lubbe
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Tanya Simuni
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Furderer ML, Berhe B, Chen TC, Wincovitch S, Jiang X, Tayebi N, Sidransky E, Han TU. A Comparative Biochemical and Pathological Evaluation of Brain Samples from Knock-In Murine Models of Gaucher Disease. Int J Mol Sci 2024; 25:1827. [PMID: 38339105 PMCID: PMC10855869 DOI: 10.3390/ijms25031827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Gaucher disease (GD) is a lysosomal storage disorder stemming from biallelic mutations in GBA1, characterized by glucocerebrosidase dysfunction and glucocerebroside and glucosylsphingosine accumulation. Since phenotypes of murine models of GD often differ from those in patients, the careful characterization of Gba1 mutant mice is necessary to establish their ability to model GD. We performed side-by-side comparative biochemical and pathologic analyses of four murine Gba1 models with genotypes L444P/L444P (p.L483P/p.L483P), L444P/null, D409H/D409H (p.D448H/p.D448H) and D409H/null, along with matched wildtype mice, all with the same genetic background and cage conditions. All mutant mice exhibited significantly lower glucocerebrosidase activity (p < 0.0001) and higher glucosylsphingosine levels than wildtype, with the lowest glucocerebrosidase and the highest glucosylsphingosine levels in mice carrying a null allele. Although glucocerebrosidase activity in L444P and D409H mice was similar, D409H mice showed more lipid accumulation. No Gaucher or storage-like cells were detected in any of the Gba1 mutant mice. Quantification of neuroinflammation, dopaminergic neuronal loss, alpha-synuclein levels and motor behavior revealed no significant findings, even in aged animals. Thus, while the models may have utility for testing the effect of different therapies on enzymatic activity, they did not recapitulate the pathological phenotype of patients with GD, and better models are needed.
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Affiliation(s)
- Makaila L. Furderer
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Bahafta Berhe
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tiffany C. Chen
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Stephen Wincovitch
- Advanced Imaging & Analysis Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Xuntian Jiang
- Washington University Metabolomics Facility, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Nahid Tayebi
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Ellen Sidransky
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Tae-Un Han
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; (M.L.F.); (B.B.); (T.C.C.); (N.T.)
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Chu Y, Hirst WD, Federoff HJ, Harms AS, Stoessl AJ, Kordower JH. Nigrostriatal tau pathology in parkinsonism and Parkinson's disease. Brain 2024; 147:444-457. [PMID: 38006313 PMCID: PMC10834249 DOI: 10.1093/brain/awad388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/11/2023] [Accepted: 11/02/2023] [Indexed: 11/27/2023] Open
Abstract
While Parkinson's disease remains clinically defined by cardinal motor symptoms resulting from nigrostriatal degeneration, it is now appreciated that the disease commonly consists of multiple pathologies, but it is unclear where these co-pathologies occur early in disease and whether they are responsible for the nigrostriatal degeneration. For the past number of years, we have been studying a well-characterized cohort of subjects with motor impairment that we have termed mild motor deficits. Motor deficits were determined on a modified and validated Unified Parkinson's Disease Rating Scale III but were insufficient in degree to diagnose Parkinson's disease. However, in our past studies, cases in this cohort had a selection bias, as both a clinical syndrome in between no motor deficits and Parkinson's disease, plus nigral Lewy pathology as defined post-mortem, were required for inclusion. Therefore, in the current study, we only based inclusion on the presence of a clinical phenotype with mild motor impairment insufficient to diagnose Parkinson's disease. Then, we divided this group further based upon whether or not subjects had a synucleinopathy in the nigrostriatal system. Here we demonstrate that loss of nigral dopaminergic neurons, loss of putamenal dopaminergic innervation and loss of the tyrosine hydroxylase-phenotype in the substantia nigra and putamen occur equally in mild motor deficit groups with and without nigral alpha-synuclein aggregates. Indeed, the common feature of these two groups is that both have similar degrees of AT8 positive phosphorylated tau, a pathology not seen in the nigrostriatal system of age-matched controls. These findings were confirmed with early (tau Ser208 phosphorylation) and late (tau Ser396/Ser404 phosphorylation) tau markers. This suggests that the initiation of nigrostriatal dopaminergic neurodegeneration occurs independently of alpha-synuclein aggregation and can be tau mediated.
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Affiliation(s)
- Yaping Chu
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
| | - Warren D Hirst
- Neurodegenerative Diseases Research Unit, Biogen, Cambridge, MA 02142, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Howard J Federoff
- Neurology, School of Medicine, Georgetown University Medical Center, Washington, DC 20007, USA
| | - Ashley S Harms
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - A Jon Stoessl
- Pacific Parkinson’s Research Centre and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Jeffrey H Kordower
- ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ 85281, USA
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Hicks AR, Reynolds RH, O’Callaghan B, García-Ruiz S, Gil-Martínez AL, Botía J, Plun-Favreau H, Ryten M. The non-specific lethal complex regulates genes and pathways genetically linked to Parkinson's disease. Brain 2023; 146:4974-4987. [PMID: 37522749 PMCID: PMC10689904 DOI: 10.1093/brain/awad246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023] Open
Abstract
Genetic variants conferring risks for Parkinson's disease have been highlighted through genome-wide association studies, yet exploration of their specific disease mechanisms is lacking. Two Parkinson's disease candidate genes, KAT8 and KANSL1, identified through genome-wide studies and a PINK1-mitophagy screen, encode part of the histone acetylating non-specific lethal complex. This complex localizes to the nucleus, where it plays a role in transcriptional activation, and to mitochondria, where it has been suggested to have a role in mitochondrial transcription. In this study, we sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinson's disease in human brain. Correlation in the expression of non-specific lethal genes and Parkinson's disease-associated genes was investigated in primary gene co-expression networks using publicly-available transcriptomic data from multiple brain regions (provided by the Genotype-Tissue Expression Consortium and UK Brain Expression Consortium), whilst secondary networks were used to examine cell type specificity. Reverse engineering of gene regulatory networks generated regulons of the complex, which were tested for heritability using stratified linkage disequilibrium score regression. Prioritized gene targets were then validated in vitro using a QuantiGene multiplex assay and publicly-available chromatin immunoprecipitation-sequencing data. Significant clustering of non-specific lethal genes was revealed alongside Parkinson's disease-associated genes in frontal cortex primary co-expression modules, amongst other brain regions. Both primary and secondary co-expression modules containing these genes were enriched for mainly neuronal cell types. Regulons of the complex contained Parkinson's disease-associated genes and were enriched for biological pathways genetically linked to disease. When examined in a neuroblastoma cell line, 41% of prioritized gene targets showed significant changes in mRNA expression following KANSL1 or KAT8 perturbation. KANSL1 and H4K8 chromatin immunoprecipitation-sequencing data demonstrated non-specific lethal complex activity at many of these genes. In conclusion, genes encoding the non-specific lethal complex are highly correlated with and regulate genes associated with Parkinson's disease. Overall, these findings reveal a potentially wider role for this protein complex in regulating genes and pathways implicated in Parkinson's disease.
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Affiliation(s)
- Amy R Hicks
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Regina H Reynolds
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
| | - Benjamin O’Callaghan
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sonia García-Ruiz
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
| | - Ana Luisa Gil-Martínez
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
- Department of Information and Communication Engineering, University of Murcia, Murcia 30100, Spain
| | - Juan Botía
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Department of Information and Communication Engineering, University of Murcia, Murcia 30100, Spain
| | - Hélène Plun-Favreau
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Mina Ryten
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London WC1N 3BG, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
- NIHR GOSH Biomedical Research Centre, Great Ormond Street Institute of Child Health, Bloomsbury, London WC1N 1EH, UK
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Chocarro J, Rico AJ, Ariznabarreta G, Roda E, Honrubia A, Collantes M, Peñuelas I, Vázquez A, Rodríguez-Pérez AI, Labandeira-García JL, Vila M, Lanciego JL. Neuromelanin accumulation drives endogenous synucleinopathy in non-human primates. Brain 2023; 146:5000-5014. [PMID: 37769648 PMCID: PMC10689915 DOI: 10.1093/brain/awad331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 08/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023] Open
Abstract
Although neuromelanin is a dark pigment characteristic of dopaminergic neurons in the human substantia nigra pars compacta, its potential role in the pathogenesis of Parkinson's disease (PD) has often been neglected since most commonly used laboratory animals lack neuromelanin. Here we took advantage of adeno-associated viral vectors encoding the human tyrosinase gene for triggering a time-dependent neuromelanin accumulation within substantia nigra pars compacta dopaminergic neurons in macaques up to similar levels of pigmentation as observed in elderly humans. Furthermore, neuromelanin accumulation induced an endogenous synucleinopathy mimicking intracellular inclusions typically observed in PD together with a progressive degeneration of neuromelanin-expressing dopaminergic neurons. Moreover, Lewy body-like intracellular inclusions were observed in cortical areas of the frontal lobe receiving dopaminergic innervation, supporting a circuit-specific anterograde spread of endogenous synucleinopathy by permissive trans-synaptic templating. In summary, the conducted strategy resulted in the development and characterization of a new macaque model of PD matching the known neuropathology of this disorder with unprecedented accuracy. Most importantly, evidence is provided showing that intracellular aggregation of endogenous α-synuclein is triggered by neuromelanin accumulation, therefore any therapeutic approach intended to decrease neuromelanin levels may provide appealing choices for the successful implementation of novel PD therapeutics.
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Affiliation(s)
- Julia Chocarro
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Alberto J Rico
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Goiaz Ariznabarreta
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Elvira Roda
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Adriana Honrubia
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - María Collantes
- Translational Molecular Imaging Unit, Department of Nuclear Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Iván Peñuelas
- Translational Molecular Imaging Unit, Department of Nuclear Medicine, Clínica Universidad de Navarra, 31008 Pamplona, Spain
| | - Alfonso Vázquez
- Department of Neurosurgery, Hospital Universitario de Navarra, Servicio Navarro de Salud, 31008 Pamplona, Spain
| | - Ana I Rodríguez-Pérez
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Research Center for Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - José L Labandeira-García
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Research Center for Molecular Medicine and Chronic Diseases (CIMUS), University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Miquel Vila
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Vall d’Hebron Research Institute, Neurodegenerative Diseses Research Group, 08035 Barcelona, Spain
- Autonomous University of Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - José L Lanciego
- CNS Gene Therapy Program, Center for Applied Medical Research (CIMA), University of Navarra, 31008 Pamplona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (Ciberned-ISCIII), 28031 Madrid, Spain
- Aligning Science Across Parkinsons’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Toffoli M, Schapira AHV, Proukakis C. Sex Distribution of GBA1 Variants Carriers with Dementia with Lewy Bodies and Parkinson's Disease. Mov Disord 2023; 38:2137-2139. [PMID: 37736925 DOI: 10.1002/mds.29609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 09/05/2023] [Indexed: 09/23/2023] Open
Affiliation(s)
- Marco Toffoli
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Christos Proukakis
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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Zhu C, Herbst S, Lewis PA. Leucine-rich repeat kinase 2 at a glance. J Cell Sci 2023; 136:jcs259724. [PMID: 37698513 PMCID: PMC10508695 DOI: 10.1242/jcs.259724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2023] Open
Abstract
Leucine-rich repeat kinase 2 (LRRK2) is a multidomain scaffolding protein with dual guanosine triphosphatase (GTPase) and kinase enzymatic activities, providing this protein with the capacity to regulate a multitude of signalling pathways and act as a key mediator of diverse cellular processes. Much of the interest in LRRK2 derives from mutations in the LRRK2 gene being the most common genetic cause of Parkinson's disease, and from the association of the LRRK2 locus with a number of other human diseases, including inflammatory bowel disease. Therefore, the LRRK2 research field has focused on the link between LRRK2 and pathology, with the aim of uncovering the underlying mechanisms and, ultimately, finding novel therapies and treatments to combat them. From the biochemical and cellular functions of LRRK2, to its relevance to distinct disease mechanisms, this Cell Science at a Glance article and the accompanying poster deliver a snapshot of our current understanding of LRRK2 function, dysfunction and links to disease.
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Affiliation(s)
- Christiane Zhu
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
| | - Susanne Herbst
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Patrick A. Lewis
- Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London NW1 0TU, UK
- Department of Neurodegenerative diseases, UCL Queen Square Institute of Neurology, University College London, London WC1N 3BG, UK
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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10
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Boktor JC, Sharon G, Verhagen Metman LA, Hall DA, Engen PA, Zreloff Z, Hakim DJ, Bostick JW, Ousey J, Lange D, Humphrey G, Ackermann G, Carlin M, Knight R, Keshavarzian A, Mazmanian SK. Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome. Mov Disord 2023; 38:399-409. [PMID: 36691982 DOI: 10.1002/mds.29300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD). OBJECTIVES The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression. METHODS Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features. RESULTS We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling. CONCLUSIONS A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Gil Sharon
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Leo A Verhagen Metman
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Deborah A Hall
- Department of Neurology Sciences, Rush University Medical Center, Chicago, Illinois, USA
| | - Phillip A Engen
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
| | - Zoe Zreloff
- The BioCollective, LLC, Denver, Colorado, USA
| | - Daniel J Hakim
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
| | - James Ousey
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | | | - Gregory Humphrey
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
| | | | - Rob Knight
- Center for Microbiome Innovation, Jacobs School of Engineering, University of California San Diego, La Jolla, California, USA
- Department of Pediatrics, School of Medicine, University of California, San Diego, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Ali Keshavarzian
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical Center, Chicago, Illinois, USA
- Departments of Internal Medicine, Anatomy & Cell Biology, Rush University Medical Center, Chicago, Illinois, USA
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, Maryland, USA
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11
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Wu S, Hernandez Villegas NC, Sirkis DW, Thomas-Wright I, Wade-Martins R, Schekman R. Unconventional secretion of α-synuclein mediated by palmitoylated DNAJC5 oligomers. eLife 2023; 12:e85837. [PMID: 36626307 PMCID: PMC9876576 DOI: 10.7554/elife.85837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 01/11/2023] Open
Abstract
Alpha-synuclein (α-syn), a major component of Lewy bodies found in Parkinson's disease (PD) patients, has been found exported outside of cells and may mediate its toxicity via cell-to-cell transmission. Here, we reconstituted soluble, monomeric α-syn secretion by the expression of DnaJ homolog subfamily C member 5 (DNAJC5) in HEK293T cells. DNAJC5 undergoes palmitoylation and anchors on the membrane. Palmitoylation is essential for DNAJC5-induced α-syn secretion, and the secretion is not limited by substrate size or unfolding. Cytosolic α-syn is actively translocated and sequestered in an endosomal membrane compartment in a DNAJC5-dependent manner. Reduction of α-syn secretion caused by a palmitoylation-deficient mutation in DNAJC5 can be reversed by a membrane-targeting peptide fusion-induced oligomerization of DNAJC5. The secretion of endogenous α-syn mediated by DNAJC5 is also found in a human neuroblastoma cell line, SH-SY5Y, differentiated into neurons in the presence of retinoic acid, and in human-induced pluripotent stem cell-derived midbrain dopamine neurons. We propose that DNAJC5 forms a palmitoylated oligomer to accommodate and export α-syn.
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Affiliation(s)
- Shenjie Wu
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | | | - Daniel W Sirkis
- Memory and Aging Center, Department of Neurology, University of California, San FranciscoSan FranciscoUnited States
| | - Iona Thomas-Wright
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Richard Wade-Martins
- Oxford Parkinson’s Disease Centre, Department of Physiology, Anatomy and Genetics and Kavli Institute for Nanoscience Discovery, University of OxfordOxfordUnited Kingdom
| | - Randy Schekman
- Department of Molecular and Cell Biology, Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
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12
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Amos C, Xu P, De Camilli P. Erythroid Differentiation Dependent Interaction of VPS13A with XK at the Plasma Membrane of K562 Cells. Contact (Thousand Oaks) 2023; 6:25152564231215133. [PMID: 38144430 PMCID: PMC10748539 DOI: 10.1177/25152564231215133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/31/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023]
Abstract
Mutations of the bridge-like lipid transport protein VPS13A and the lipid scramblase XK result in Chorea Acanthocytosis (ChAc) and McLeod syndrome (MLS), respectively, two similar conditions involving neurodegeneration and deformed erythrocytes (acanthocytes). VPS13A binds XK, suggesting a model in which VPS13A forms a lipid transport bridge between the endoplasmic reticulum (ER) and the plasma membrane (PM), where XK resides. However, studies of VPS13A in HeLa and COS7 cells showed that this protein localizes primarily at contacts of the ER with mitochondria. Overexpression of XK in these cells redistributed VPS13A to the biosynthetic XK pool in the ER but not to PM-localized XK. Colocalization of VPS13A with XK at the PM was only observed if overexpressed XK harbored mutations that disengaged its VPS13A-binding site from an intramolecular interaction. As the acanthocytosis phenotype of ChAc and MLS suggests a role of the two proteins in cells of the erythroid lineage, we explored their localization in K562 cells, which differentiate into erythroblasts upon hemin addition. When tagged VPS13A was overexpressed in hemin-treated K562 cells, robust formation of ER-PM contacts positive for VPS13A was observed and their formation was abolished in XK KO cells. ER-PM contacts positive for VPS13A were seldom observed in undifferentiated K562 cells, despite the presence of XK in these cells at concentrations similar to those observed after differentiation. These findings reveal that the interaction of VPS13A with XK at ER-PM contacts requires a permissive state which depends upon cell type and/or functional state of the cell.
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Affiliation(s)
- Chase Amos
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Peng Xu
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Pietro De Camilli
- Departments of Neuroscience and of Cell Biology, Howard Hughes Medical Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale University School of Medicine, New Haven, CT, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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13
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Abdel-Haq R, Schlachetzki JCM, Boktor JC, Cantu-Jungles TM, Thron T, Zhang M, Bostick JW, Khazaei T, Chilakala S, Morais LH, Humphrey G, Keshavarzian A, Katz JE, Thomson M, Knight R, Gradinaru V, Hamaker BR, Glass CK, Mazmanian SK. A prebiotic diet modulates microglial states and motor deficits in α-synuclein overexpressing mice. eLife 2022; 11:e81453. [PMID: 36346385 PMCID: PMC9668333 DOI: 10.7554/elife.81453] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Parkinson's disease (PD) is a movement disorder characterized by neuroinflammation, α-synuclein pathology, and neurodegeneration. Most cases of PD are non-hereditary, suggesting a strong role for environmental factors, and it has been speculated that disease may originate in peripheral tissues such as the gastrointestinal (GI) tract before affecting the brain. The gut microbiome is altered in PD and may impact motor and GI symptoms as indicated by animal studies, although mechanisms of gut-brain interactions remain incompletely defined. Intestinal bacteria ferment dietary fibers into short-chain fatty acids, with fecal levels of these molecules differing between PD and healthy controls and in mouse models. Among other effects, dietary microbial metabolites can modulate activation of microglia, brain-resident immune cells implicated in PD. We therefore investigated whether a fiber-rich diet influences microglial function in α-synuclein overexpressing (ASO) mice, a preclinical model with PD-like symptoms and pathology. Feeding a prebiotic high-fiber diet attenuates motor deficits and reduces α-synuclein aggregation in the substantia nigra of mice. Concomitantly, the gut microbiome of ASO mice adopts a profile correlated with health upon prebiotic treatment, which also reduces microglial activation. Single-cell RNA-seq analysis of microglia from the substantia nigra and striatum uncovers increased pro-inflammatory signaling and reduced homeostatic responses in ASO mice compared to wild-type counterparts on standard diets. However, prebiotic feeding reverses pathogenic microglial states in ASO mice and promotes expansion of protective disease-associated macrophage (DAM) subsets of microglia. Notably, depletion of microglia using a CSF1R inhibitor eliminates the beneficial effects of prebiotics by restoring motor deficits to ASO mice despite feeding a prebiotic diet. These studies uncover a novel microglia-dependent interaction between diet and motor symptoms in mice, findings that may have implications for neuroinflammation and PD.
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Affiliation(s)
- Reem Abdel-Haq
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Johannes CM Schlachetzki
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Joseph C Boktor
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Thaisa M Cantu-Jungles
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Taren Thron
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Mengying Zhang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - John W Bostick
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Tahmineh Khazaei
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Sujatha Chilakala
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Livia H Morais
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Greg Humphrey
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
| | - Ali Keshavarzian
- Department of Internal Medicine, Division of Gastroenterology, Rush University Medical CenterChicagoUnited States
- Rush Center for Integrated Microbiome and Chronobiology Research, Rush University Medical CenterChicagoUnited States
| | - Jonathan E Katz
- Lawrence J Ellison Institute for Transformative Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Matthew Thomson
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Rob Knight
- Department of Pediatrics, University of California, San DiegoSan DiegoUnited States
- Department of Computer Science and Engineering, University of California, San DiegoSan DiegoUnited States
- Department of Bioengineering, University of California, San DiegoSan DiegoUnited States
- Center for Microbiome Innovation, University of California San DiegoSan DiegoUnited States
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Bruce R Hamaker
- Department of Food Science, Whistler Center for Carbohydrate Research, Purdue University West LafayetteWest LafayetteUnited States
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Sarkis K Mazmanian
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
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14
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Li H, Busquets O, Verma Y, Syed KM, Kutnowski N, Pangilinan GR, Gilbert LA, Bateup HS, Rio DC, Hockemeyer D, Soldner F. Highly efficient generation of isogenic pluripotent stem cell models using prime editing. eLife 2022; 11:e79208. [PMID: 36069759 PMCID: PMC9584603 DOI: 10.7554/elife.79208] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/06/2022] [Indexed: 11/19/2022] Open
Abstract
The recent development of prime editing (PE) genome engineering technologies has the potential to significantly simplify the generation of human pluripotent stem cell (hPSC)-based disease models. PE is a multicomponent editing system that uses a Cas9-nickase fused to a reverse transcriptase (nCas9-RT) and an extended PE guide RNA (pegRNA). Once reverse transcribed, the pegRNA extension functions as a repair template to introduce precise designer mutations at the target site. Here, we systematically compared the editing efficiencies of PE to conventional gene editing methods in hPSCs. This analysis revealed that PE is overall more efficient and precise than homology-directed repair of site-specific nuclease-induced double-strand breaks. Specifically, PE is more effective in generating heterozygous editing events to create autosomal dominant disease-associated mutations. By stably integrating the nCas9-RT into hPSCs we achieved editing efficiencies equal to those reported for cancer cells, suggesting that the expression of the PE components, rather than cell-intrinsic features, limit PE in hPSCs. To improve the efficiency of PE in hPSCs, we optimized the delivery modalities for the PE components. Delivery of the nCas9-RT as mRNA combined with synthetically generated, chemically-modified pegRNAs and nicking guide RNAs improved editing efficiencies up to 13-fold compared with transfecting the PE components as plasmids or ribonucleoprotein particles. Finally, we demonstrated that this mRNA-based delivery approach can be used repeatedly to yield editing efficiencies exceeding 60% and to correct or introduce familial mutations causing Parkinson's disease in hPSCs.
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Affiliation(s)
- Hanqin Li
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Oriol Busquets
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineThe BronxUnited States
| | - Yogendra Verma
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Khaja Mohieddin Syed
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Nitzan Kutnowski
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
| | - Gabriella R Pangilinan
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Luke A Gilbert
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- Helen Diller Family Comprehensive Cancer Center, University of California, San FranciscoSan FranciscoUnited States
- Department of Urology, University of California, San FranciscoSan FranciscoUnited States
- Arc InstitutePalo AltoUnited States
| | - Helen S Bateup
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
- Helen Wills Neuroscience Institute, University of California, BerkeleyBerkeleyUnited States
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, BerkeleyBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
| | - Frank Soldner
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research NetworkChevy ChaseUnited States
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of MedicineThe BronxUnited States
- Department of Genetics, Albert Einstein College of MedicineThe BronxUnited States
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of MedicineThe BronxUnited States
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15
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Smith LJ, Lee CY, Menozzi E, Schapira AHV. Genetic variations in GBA1 and LRRK2 genes: Biochemical and clinical consequences in Parkinson disease. Front Neurol 2022; 13:971252. [PMID: 36034282 PMCID: PMC9416236 DOI: 10.3389/fneur.2022.971252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/25/2022] [Indexed: 11/24/2022] Open
Abstract
Variants in the GBA1 and LRRK2 genes are the most common genetic risk factors associated with Parkinson disease (PD). Both genes are associated with lysosomal and autophagic pathways, with the GBA1 gene encoding for the lysosomal enzyme, glucocerebrosidase (GCase) and the LRRK2 gene encoding for the leucine-rich repeat kinase 2 enzyme. GBA1-associated PD is characterized by earlier age at onset and more severe non-motor symptoms compared to sporadic PD. Mutations in the GBA1 gene can be stratified into severe, mild and risk variants depending on the clinical presentation of disease. Both a loss- and gain- of function hypothesis has been proposed for GBA1 variants and the functional consequences associated with each variant is often linked to mutation severity. On the other hand, LRRK2-associated PD is similar to sporadic PD, but with a more benign disease course. Mutations in the LRRK2 gene occur in several structural domains and affect phosphorylation of GTPases. Biochemical studies suggest a possible convergence of GBA1 and LRRK2 pathways, with double mutant carriers showing a milder phenotype compared to GBA1-associated PD. This review compares GBA1 and LRRK2-associated PD, and highlights possible genotype-phenotype associations for GBA1 and LRRK2 separately, based on biochemical consequences of single variants.
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Affiliation(s)
- Laura J. Smith
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Chiao-Yin Lee
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Elisa Menozzi
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Anthony H. V. Schapira
- Department of Clinical and Movement Neurosciences, Queen Square Institute of Neurology, University College London (UCL), London, United Kingdom
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
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16
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Gustavsson EK, Zhang D, Reynolds RH, Garcia-Ruiz S, Ryten M. ggtranscript: an R package for the visualization and interpretation of transcript isoforms using ggplot2. Bioinformatics 2022; 38:3844-3846. [PMID: 35751589 PMCID: PMC9344834 DOI: 10.1093/bioinformatics/btac409] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/06/2022] [Accepted: 06/22/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we introduce ggtranscript, an R package that provides a fast and flexible method to visualize and compare transcripts. As a ggplot2 extension, ggtranscript inherits the functionality and familiarity of ggplot2 making it easy to use. AVAILABILITY AND IMPLEMENTATION ggtranscript is an R package available at https://github.com/dzhang32/ggtranscript (DOI: https://doi.org/10.5281/zenodo.6374061) via an open-source MIT licence. Further documentation is available at https://dzhang32.github.io/ggtranscript/.
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Affiliation(s)
| | | | - Regina H Reynolds
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Sonia Garcia-Ruiz
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London WC1N 1EH, UK
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17
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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. Sci Adv 2021; 7:eabj0722. [PMID: 34767452 PMCID: PMC8589319 DOI: 10.1126/sciadv.abj0722] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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