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Arena G, Landoulsi Z, Grossmann D, Payne T, Vitali A, Delcambre S, Baron A, Antony P, Boussaad I, Bobbili DR, Sreelatha AAK, Pavelka L, J Diederich N, Klein C, Seibler P, Glaab E, Foltynie T, Bandmann O, Sharma M, Krüger R, May P, Grünewald A. Polygenic Risk Scores Validated in Patient-Derived Cells Stratify for Mitochondrial Subtypes of Parkinson's Disease. Ann Neurol 2024. [PMID: 38767023 DOI: 10.1002/ana.26949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/22/2024]
Abstract
OBJECTIVE The aim of our study is to better understand the genetic architecture and pathological mechanisms underlying neurodegeneration in idiopathic Parkinson's disease (iPD). We hypothesized that a fraction of iPD patients may harbor a combination of common variants in nuclear-encoded mitochondrial genes ultimately resulting in neurodegeneration. METHODS We used mitochondria-specific polygenic risk scores (mitoPRSs) and created pathway-specific mitoPRSs using genotype data from different iPD case-control datasets worldwide, including the Luxembourg Parkinson's Study (412 iPD patients and 576 healthy controls) and COURAGE-PD cohorts (7,270 iPD cases and 6,819 healthy controls). Cellular models from individuals stratified according to the most significant mitoPRS were subsequently used to characterize different aspects of mitochondrial function. RESULTS Common variants in genes regulating Oxidative Phosphorylation (OXPHOS-PRS) were significantly associated with a higher PD risk in independent cohorts (Luxembourg Parkinson's Study odds ratio, OR = 1.31[1.14-1.50], p-value = 5.4e-04; COURAGE-PD OR = 1.23[1.18-1.27], p-value = 1.5e-29). Functional analyses in fibroblasts and induced pluripotent stem cells-derived neuronal progenitors revealed significant differences in mitochondrial respiration between iPD patients with high or low OXPHOS-PRS (p-values < 0.05). Clinically, iPD patients with high OXPHOS-PRS have a significantly earlier age at disease onset compared to low-risk patients (false discovery rate [FDR]-adj p-value = 0.015), similar to prototypic monogenic forms of PD. Finally, iPD patients with high OXPHOS-PRS responded more effectively to treatment with mitochondrially active ursodeoxycholic acid. INTERPRETATION OXPHOS-PRS may provide a precision medicine tool to stratify iPD patients into a pathogenic subgroup genetically defined by specific mitochondrial impairment, making these individuals eligible for future intelligent clinical trial designs. ANN NEUROL 2024.
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Affiliation(s)
- Giuseppe Arena
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dajana Grossmann
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology, University Medical Center Rostock, University of Rostock, Rostock, Germany
| | - Thomas Payne
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Armelle Vitali
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Sylvie Delcambre
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Alexandre Baron
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Paul Antony
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ibrahim Boussaad
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ashwin Ashok Kumar Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Lukas Pavelka
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier du Luxembourg, Luxembourg, Luxembourg
| | - Nico J Diederich
- Department of Neurosciences, Centre Hospitalier de Luxembourg, Strassen, Luxembourg
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Enrico Glaab
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Thomas Foltynie
- Department of Clinical and Movement Neurosciences, Institute of Neurology, University College London, London, UK
| | - Oliver Bandmann
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier du Luxembourg, Luxembourg, Luxembourg
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anne Grünewald
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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2
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Chopra A, Lang AE, Höglinger G, Outeiro TF. Towards a biological diagnosis of PD. Parkinsonism Relat Disord 2024; 122:106078. [PMID: 38472075 DOI: 10.1016/j.parkreldis.2024.106078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024]
Abstract
Since the original description by James Parkinson, Parkinson's disease (PD) has intrigued us for over 200 years. PD is a progressive condition that is incurable so far, and affects millions of people worldwide. Over the years, our knowledge has expanded tremendously, and a range of criteria have been put forward and used to try to define PD. However, owing to the complexity of the problem, it is still not consensual how to diagnose and classify a disease that manifests with diverse features, and that responds differently to existing therapies and to those under development. We are now living a time when 'biological' information is becoming abundant, precise, and accessible enabling us to attempt to incorporate different sources of information to classify different forms of PD. These refinements are essential for basic science, as they will enable us to develop improved models for studying PD, and to implement new findings into clinical practice, as this will be the path towards effective personalized medicine.
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Affiliation(s)
- Avika Chopra
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany
| | - Anthony E Lang
- Edmond J Safra Program in Parkinson's Disease, Krembil Brain Institute, University Health Network and the Department of Medicine, University of Toronto, Canada
| | - Günter Höglinger
- Department of Neurology, LMU University Hospital, Ludwig-Maximilians-Universität (LMU) München, Munich, Germany; German Center for Neurodegenerative Diseases (DZNE), Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center Göttingen, Göttingen, Germany; Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; German Center for Neurodegenerative Diseases (DZNE), Göttingen, Germany.
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3
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Fiorini MR, Dilliott AA, Thomas RA, Farhan SMK. Transcriptomics of Human Brain Tissue in Parkinson's Disease: a Comparison of Bulk and Single-cell RNA Sequencing. Mol Neurobiol 2024:10.1007/s12035-024-04124-5. [PMID: 38578357 DOI: 10.1007/s12035-024-04124-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/12/2024] [Indexed: 04/06/2024]
Abstract
Parkinson's disease (PD) is a chronic and progressive neurodegenerative disease leading to motor dysfunction and, in some cases, dementia. Transcriptome analysis is one promising approach for characterizing PD and other neurodegenerative disorders by informing how specific disease events influence gene expression and contribute to pathogenesis. With the emergence of single-cell and single-nucleus RNA sequencing (scnRNA-seq) technologies, the transcriptional landscape of neurodegenerative diseases can now be described at the cellular level. As the application of scnRNA-seq is becoming routine, it calls to question how results at a single-cell resolution compare to those obtained from RNA sequencing of whole tissues (bulk RNA-seq), whether the findings are compatible, and how the assays are complimentary for unraveling the elusive transcriptional changes that drive neurodegenerative disease. Herein, we review the studies that have leveraged RNA-seq technologies to investigate PD. Through the integration of bulk and scnRNA-seq findings from human, post-mortem brain tissue, we use the PD literature as a case study to evaluate the compatibility of the results generated from each assay and demonstrate the complementarity of the sequencing technologies. Finally, through the lens of the PD transcriptomic literature, we evaluate the current feasibility of bulk and scnRNA-seq technologies to illustrate the necessity of both technologies for achieving a comprehensive insight into the mechanism by which gene expression promotes neurodegenerative disease. We conclude that the continued application of both assays will provide the greatest insight into neurodegenerative disease pathology, providing both cell-specific and whole-tissue level information.
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Affiliation(s)
- Michael R Fiorini
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Allison A Dilliott
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada
| | - Rhalena A Thomas
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
| | - Sali M K Farhan
- The Montreal Neurological Institute-Hospital, Montreal, QC, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, McGill University, Montreal, QC, Canada.
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4
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Kulcsarova K, Skorvanek M, Postuma RB, Berg D. Defining Parkinson's Disease: Past and Future. JOURNAL OF PARKINSON'S DISEASE 2024:JPD230411. [PMID: 38489197 DOI: 10.3233/jpd-230411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/17/2024]
Abstract
Parkinson's disease (PD) is the second most common still relentlessly progressive neurodegenerative disorder with a long period in which the pathophysiological process is already spreading but cardinal motor symptoms are not present. This review outlines the major developments and milestones in our understanding of PD that have shaped the way we define this disorder. Past criteria and definitions of PD have been based on clinical motor manifestations enabling diagnosis of the disease only in later symptomatic stages. Nevertheless, with advancing knowledge of disease pathophysiology and aim of early disease detection, a major shift of the diagnostic paradigm is being advocated towards a biological definition similar to other neurodegenerative disorders including Alzheimer's disease and Huntington's disease, with the ultimate goal of an earlier, disease course modifying therapy. We summarize the major pillars of this possible approach including in vivo detection of neuronal α-synuclein aggregation, neurodegeneration and genetics and outline their possible application in different contexts of use in the frame of biological PD definition.
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Affiliation(s)
- Kristina Kulcsarova
- Department of Neurology, P. J. Safarik University, Kosice, Slovak Republic
- Department of Neurology, L. Pasteur University Hospital, Kosice, Slovak Republic
- Department of Clinical Neurosciences, University Scientific Park MEDIPARK, P. J. Safarik University, Kosice, Slovak Republic
| | - Matej Skorvanek
- Department of Neurology, P. J. Safarik University, Kosice, Slovak Republic
- Department of Neurology, L. Pasteur University Hospital, Kosice, Slovak Republic
| | - Ronald B Postuma
- Department of Neurology, Montreal Neurological Institute, Montreal, Quebec, Canada
| | - Daniela Berg
- Department of Neurology, Kiel University and University Medical Center Schleswig-Holstein, Kiel, Germany
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5
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Pavelka L, Rawal R, Ghosh S, Pauly C, Pauly L, Hanff AM, Kolber PL, Jónsdóttir SR, Mcintyre D, Azaiz K, Thiry E, Vilasboas L, Soboleva E, Giraitis M, Tsurkalenko O, Sapienza S, Diederich N, Klucken J, Glaab E, Aguayo GA, Jubal ER, Perquin M, Vaillant M, May P, Gantenbein M, Satagopam VP, Krüger R. Luxembourg Parkinson's study -comprehensive baseline analysis of Parkinson's disease and atypical parkinsonism. Front Neurol 2023; 14:1330321. [PMID: 38174101 PMCID: PMC10763250 DOI: 10.3389/fneur.2023.1330321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Background Deep phenotyping of Parkinson's disease (PD) is essential to investigate this fastest-growing neurodegenerative disorder. Since 2015, over 800 individuals with PD and atypical parkinsonism along with more than 800 control subjects have been recruited in the frame of the observational, monocentric, nation-wide, longitudinal-prospective Luxembourg Parkinson's study. Objective To profile the baseline dataset and to explore risk factors, comorbidities and clinical profiles associated with PD, atypical parkinsonism and controls. Methods Epidemiological and clinical characteristics of all 1,648 participants divided in disease and control groups were investigated. Then, a cross-sectional group comparison was performed between the three largest groups: PD, progressive supranuclear palsy (PSP) and controls. Subsequently, multiple linear and logistic regression models were fitted adjusting for confounders. Results The mean (SD) age at onset (AAO) of PD was 62.3 (11.8) years with 15% early onset (AAO < 50 years), mean disease duration 4.90 (5.16) years, male sex 66.5% and mean MDS-UPDRS III 35.2 (16.3). For PSP, the respective values were: 67.6 (8.2) years, all PSP with AAO > 50 years, 2.80 (2.62) years, 62.7% and 53.3 (19.5). The highest frequency of hyposmia was detected in PD followed by PSP and controls (72.9%; 53.2%; 14.7%), challenging the use of hyposmia as discriminating feature in PD vs. PSP. Alcohol abstinence was significantly higher in PD than controls (17.6 vs. 12.9%, p = 0.003). Conclusion Luxembourg Parkinson's study constitutes a valuable resource to strengthen the understanding of complex traits in the aforementioned neurodegenerative disorders. It corroborated several previously observed clinical profiles, and provided insight on frequency of hyposmia in PSP and dietary habits, such as alcohol abstinence in PD.Clinical trial registration: clinicaltrials.gov, NCT05266872.
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Affiliation(s)
- Lukas Pavelka
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rajesh Rawal
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Soumyabrata Ghosh
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Claire Pauly
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Laure Pauly
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anne-Marie Hanff
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Faculty of Science, Technology and Medicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
- Department of Epidemiology, CAPHRI School for Public Health and Primary Care, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Pierre Luc Kolber
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Department of Neurosciences, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
| | - Sonja R. Jónsdóttir
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Deborah Mcintyre
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
| | - Kheira Azaiz
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Elodie Thiry
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Liliana Vilasboas
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Ekaterina Soboleva
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Marijus Giraitis
- Department of Precision Health, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Olena Tsurkalenko
- Department of Precision Health, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Stefano Sapienza
- Department of Precision Health, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Nico Diederich
- Department of Neurosciences, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
| | - Jochen Klucken
- Department of Precision Health, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Enrico Glaab
- Biomedical Data Science Group, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Gloria A. Aguayo
- Deep Digital Phenotyping Research Unit, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Eduardo Rosales Jubal
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Magali Perquin
- Department of Precision Health, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Michel Vaillant
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Patrick May
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Manon Gantenbein
- Translational Medicine Operations Hub, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
| | - Venkata P. Satagopam
- Bioinformatics Core, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Rejko Krüger
- Transversal Translational Medicine, Luxembourg Institute of Health (LIH), Strassen, Luxembourg
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Strassen, Luxembourg
- Translational Neuroscience, Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Esch-sur-Alzette, Luxembourg
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6
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Abstract
The multifaceted microbiota characterizing our gut plays a crucial role in maintaining immune, metabolic and tissue homeostasis of the intestine as well as of distal organs, including the central nervous system. Microbial dysbiosis is reported in several inflammatory intestinal diseases characterized by the impairment of the gut epithelial and vascular barriers, defined as leaky gut, and it is reported as a potential danger condition associated with the development of metabolic, inflammatory and neurodegenerative diseases. Recently, we pointed out the strict connection between the gut and the brain via a novel vascular axis. Here we want to deepen our knowledge on the gut-brain axis, with particular emphasis on the connection between microbial dysbiosis, leaky gut, cerebral and gut vascular barriers, and neurodegenerative diseases. The firm association between microbial dysbiosis and impairment of the vascular gut-brain axis will be summarized in the context of protection, amelioration or boosting of Alzheimer, Parkinson, Major depressive and Anxiety disorders. Understanding the relationship between disease pathophysiology, mucosal barrier function and host-microbe interaction will foster the use of the microbiome as biomarker for health and disease as well as a target for therapeutic and nutritional advances.
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Affiliation(s)
- Sara Carloni
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 20072 Pieve Emanuele, MI, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy.
| | - Maria Rescigno
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 20072 Pieve Emanuele, MI, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, MI, Italy.
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7
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Petkova-Kirova P, Baas S, Wagenpfeil G, Hartz P, Unger MM, Bernhardt R. SNPs in cytochrome P450 genes decide on the fate of individuals with genetic predisposition to Parkinson's disease. Front Pharmacol 2023; 14:1244516. [PMID: 37601072 PMCID: PMC10436510 DOI: 10.3389/fphar.2023.1244516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 07/21/2023] [Indexed: 08/22/2023] Open
Abstract
Parkinson's disease (PD) is one of the most frequent neurological diseases affecting millions of people worldwide. While the majority of PD cases are of unknown origin (idiopathic), about 5%-10% are familial and linked to mutations in different known genes. However, there are also people with a genetic predisposition to PD who do not develop the disease. To elucidate factors leading to the manifestation of PD we compared the occurrence of single nucleotide polymorphisms (SNPs) in various cytochrome P450 (P450) genes in people with a genetic predisposition and suffering from PD (GPD) to that of people, who are genetically predisposed, but show no symptoms of the disease (GUN). We used the PPMI (Parkinson's Progression Markers Initiative) database and the gene sequences of all 57 P450s as well as their three redox partners. Corresponding odds ratios (OR) and confidence intervals (CI) were calculated to assess the incidence of the various SNPs in the two groups of individuals and consequently their relation to PD. We identified for the first time SNPs that are significantly (up to 10fold!) over- or under-represented in GPD patients compared to GUN. SNPs with OR > 5 were found in 10 P450s being involved in eicosanoid, vitamin A and D metabolism as well as cholesterol degradation pointing to an important role of endogenous factors for the manifestation of PD clinical symptoms. Moreover, 12 P450s belonging to all P450 substrate classes as well as POR have SNPs that are significantly under-represented (OR < 0.2) in GPD compared to GUN, indicating a protective role of those SNPs and the corresponding P450s regarding disease advancement. To the best of our knowledge our data for the first time demonstrate an association between known PD predisposition genes and SNPs in other genes, shown here for different P450 genes and for their redox partner POR, which promote the manifestation of the disease in familial PD. Our results thus shed light onto the pathogenesis of PD, especially the switch from GUN to GPD and might further help to advance novel strategies for preventing the development or progression of the disease.
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Affiliation(s)
- Polina Petkova-Kirova
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Gudrun Wagenpfeil
- Institut für Medizinische Biometrie, Epidemiologie und Medizinische Informatik, Universität des Saarlandes, Homburg, Germany
| | - Philip Hartz
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
| | | | - Rita Bernhardt
- Institut für Biochemie, Fachbereich Biologie, Naturwissenschaftlich-Technische Fakultät, Universität des Saarlandes, Saarbrücken, Germany
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8
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García-Marín LM, Reyes-Pérez P, Diaz-Torres S, Medina-Rivera A, Martin NG, Mitchell BL, Rentería ME. Shared molecular genetic factors influence subcortical brain morphometry and Parkinson's disease risk. NPJ Parkinsons Dis 2023; 9:73. [PMID: 37164954 PMCID: PMC10172359 DOI: 10.1038/s41531-023-00515-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 04/28/2023] [Indexed: 05/12/2023] Open
Abstract
Parkinson's disease (PD) is a late-onset and genetically complex neurodegenerative disorder. Here we sought to identify genes and molecular pathways underlying the associations between PD and the volume of ten brain structures measured through magnetic resonance imaging (MRI) scans. We leveraged genome-wide genetic data from several cohorts, including the International Parkinson's Disease Genomics Consortium (IPDG), the UK Biobank, the Adolescent Brain Cognitive Development (ABCD) study, the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE), the Enhancing Neuroimaging Genetics through Meta-Analyses (ENIGMA), and 23andMe. We observed significant positive genetic correlations between PD and intracranial and subcortical brain volumes. Genome-wide association studies (GWAS) - pairwise analyses identified 210 genomic segments with shared aetiology between PD and at least one of these brain structures. Pathway enrichment results highlight potential links with chronic inflammation, the hypothalamic-pituitary-adrenal pathway, mitophagy, disrupted vesicle-trafficking, calcium-dependent, and autophagic pathways. Investigations for putative causal genetic effects suggest that a larger putamen volume could influence PD risk, independently of the potential causal genetic effects of intracranial volume (ICV) on PD. Our findings suggest that genetic variants influencing larger intracranial and subcortical brain volumes, possibly during earlier stages of life, influence the risk of developing PD later in life.
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Affiliation(s)
- Luis M García-Marín
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia.
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia.
- Laboratorio Internacional de Investigación del Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México.
| | - Paula Reyes-Pérez
- Laboratorio Internacional de Investigación del Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Santiago Diaz-Torres
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Alejandra Medina-Rivera
- Laboratorio Internacional de Investigación del Genoma Humano, Universidad Nacional Autónoma de México, Juriquilla, Querétaro, México
| | - Nicholas G Martin
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Brittany L Mitchell
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
| | - Miguel E Rentería
- Mental Health and Neuroscience Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, QLD, Australia
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9
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Li J, Amoh BK, McCormick E, Tarkunde A, Zhu KF, Perez A, Mair M, Moore J, Shulman JM, Al-Ramahi I, Botas J. Integration of transcriptome-wide association study with neuronal dysfunction assays provides functional genomics evidence for Parkinson's disease genes. Hum Mol Genet 2023; 32:685-695. [PMID: 36173927 PMCID: PMC9896475 DOI: 10.1093/hmg/ddac230] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 02/07/2023] Open
Abstract
Genome-wide association studies (GWAS) have markedly advanced our understanding of the genetics of Parkinson's disease (PD), but they currently do not account for the full heritability of PD. In many cases it is difficult to unambiguously identify a specific gene within each locus because GWAS does not provide functional information on the identified candidate loci. Here we present an integrative approach that combines transcriptome-wide association study (TWAS) with high-throughput neuronal dysfunction analyses in Drosophila to discover and validate candidate PD genes. We identified 160 candidate genes whose misexpression is associated with PD risk via TWAS. Candidates were validated using orthogonal in silico methods and found to be functionally related to PD-associated pathways (i.e. endolysosome). We then mimicked these TWAS-predicted transcriptomic alterations in a Drosophila PD model and discovered that 50 candidates can modulate α-Synuclein(α-Syn)-induced neurodegeneration, allowing us to nominate new genes in previously known PD loci. We also uncovered additional novel PD candidate genes within GWAS suggestive loci (e.g. TTC19, ADORA2B, LZTS3, NRBP1, HN1L), which are also supported by clinical and functional evidence. These findings deepen our understanding of PD, and support applying our integrative approach to other complex trait disorders.
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Affiliation(s)
- Jiayang Li
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Bismark Kojo Amoh
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Emma McCormick
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Akash Tarkunde
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Katy Fan Zhu
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Alma Perez
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Megan Mair
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Justin Moore
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
| | - Joshua M Shulman
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Ismael Al-Ramahi
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
| | - Juan Botas
- Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Center for Alzheimer’s and Neurodegenerative Diseases, Baylor College of Medicine, Houston, TX, USA
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10
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Soudyab M, Shariati M, Esfehani RJ, Shalaei N, Vafadar S, Nouri V, Zech M, Winkelmann J, Shoeibi A, Sadr-Nabavi A. Whole-Exome Sequencing Study of Consanguineous Parkinson's Disease Families and Related Phenotypes: Report of Twelve Novel Variants. J Mol Neurosci 2022; 72:2486-2496. [PMID: 36520381 DOI: 10.1007/s12031-022-02085-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 11/15/2022] [Indexed: 12/23/2022]
Abstract
Parkinson's disease (PD) is a common progressive neurodegenerative disorder with motor and nonmotor symptoms. Recent studies demonstrate various susceptibility loci and candidate genes for familial forms of the disease. However, the genetic basis of the familial form of early-onset PD (EOPD) is not widely studied in the Iranian population. Therefore, the present study aimed to investigate the possible causative genetic variants responsible for developing EOPD among Iranian patients. Iranian patients with a clinical diagnosis of Parkinson's disease were evaluated, and 12 consanguineous families with at least two affected individuals with early-onset PD (EOPD) were chosen to enroll in the present study. An expert neurologist group examined these families. Whole-exome sequencing (WES) was performed on PD patients, and the possible causative genetic variants related to the development of PD were reported. Exome sequencing (WES) was performed on every PD patient and revealed that patients had novel genetic variants in PRKN, PARK7, and PINK1 genes. All the genetic variants were in homozygous status and none of these variants were previously reported in the literature. Moreover, these genetic variants were "pathogenic" based on bioinformatic studies and according to the American College of Medical Genetics (ACMG). The present research revealed some novel variants for EOPD among the Iranian population. Further functional studies are warranted to confirm the pathogenicity of these novel variants and establish their clinical application for the early diagnosis of EOPD.
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Affiliation(s)
- Mohammad Soudyab
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Shariati
- Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran
| | | | - Neda Shalaei
- Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Shabnam Vafadar
- Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Vahid Nouri
- Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institut Für Humangenetik, Technische Universität München, Munich, Germany
| | - Julianne Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany.,Institut Für Humangenetik, Technische Universität München, Munich, Germany.,Lehrstuhl Für Neurogenetik, Technische Universität München, Munich, Germany.,Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Ali Shoeibi
- Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Ariane Sadr-Nabavi
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran. .,Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran. .,Academic Center for Education, Culture, and Research (ACECR)-Khorasan Razavi, Mashhad, Iran. .,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany. .,Institut Für Humangenetik, Technische Universität München, Munich, Germany.
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11
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Pavelka L, Rauschenberger A, Landoulsi Z, Pachchek S, May P, Glaab E, Krüger R, Acharya G, Aguayo G, Alexandre M, Ali M, Allen D, Ammerlann W, Balling R, Bassis M, Beaumont K, Becker R, Bellora C, Berchem G, Berg D, Bisdorff A, Brockmann K, Calmes J, Castillo L, Contesotto G, Diederich N, Dondelinger R, Esteves D, Fagherazzi G, Ferrand JY, Gantenbein M, Gasser T, Gawron P, Ghosh S, Glaab E, Gomes C, De Lope EG, Goncharenko N, Graas J, Graziano M, Groues V, Grünewald A, Gu W, Hammot G, Hanff AM, Hansen L, Hansen M, Heneka M, Henry E, Herbrink S, Herenne E, Herzinger S, Heymann M, Hu M, Hundt A, Jacoby N, Lebioda JJ, Jaroz Y, Klopfenstein Q, Krüger R, Lambert P, Landoulsi Z, Lentz R, Liepelt I, Liszka R, Longhino L, Lorentz V, Lupu PC, Mackay C, Maetzler W, Marcus K, Marques G, Marques T, May P, Mcintyre D, Mediouni C, Meisch F, Menster M, Minelli M, Mittelbronn M, Mollenhauer B, Mommaerts K, Moreno C, Moudio S, Mühlschlegel F, Nati R, Nehrbass U, Nickels S, Nicolai B, Nicolay JP, Oertel W, Ostaszewski M, Pachchek S, Pauly C, Pauly L, Pavelka L, Perquin M, Lima RR, Rauschenberger A, Rawal R, Bobbili DR, Rosales E, Rosety I, Rump K, Sandt E, Satagopam V, Schlesser M, Schmitt M, Schmitz S, Schneider R, Schwamborn J, Sharify A, Soboleva E, Sokolowska K, Terwindt O, Thien H, Thiry E, Loo RTJ, Trefois C, Trouet J, Tsurkalenko O, Vaillant M, Valenti M, Boas LV, Vyas M, Wade-Martins R, Wilmes P. Age at onset as stratifier in idiopathic Parkinson’s disease – effect of ageing and polygenic risk score on clinical phenotypes. NPJ Parkinsons Dis 2022; 8:102. [PMID: 35945230 PMCID: PMC9363416 DOI: 10.1038/s41531-022-00342-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 05/30/2022] [Indexed: 12/23/2022] Open
Abstract
Several phenotypic differences observed in Parkinson’s disease (PD) patients have been linked to age at onset (AAO). We endeavoured to find out whether these differences are due to the ageing process itself by using a combined dataset of idiopathic PD (n = 430) and healthy controls (HC; n = 556) excluding carriers of known PD-linked genetic mutations in both groups. We found several significant effects of AAO on motor and non-motor symptoms in PD, but when comparing the effects of age on these symptoms with HC (using age at assessment, AAA), only positive associations of AAA with burden of motor symptoms and cognitive impairment were significantly different between PD vs HC. Furthermore, we explored a potential effect of polygenic risk score (PRS) on clinical phenotype and identified a significant inverse correlation of AAO and PRS in PD. No significant association between PRS and severity of clinical symptoms was found. We conclude that the observed non-motor phenotypic differences in PD based on AAO are largely driven by the ageing process itself and not by a specific profile of neurodegeneration linked to AAO in the idiopathic PD patients.
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12
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Normal and Pathological NRF2 Signalling in the Central Nervous System. Antioxidants (Basel) 2022; 11:antiox11081426. [PMID: 35892629 PMCID: PMC9394413 DOI: 10.3390/antiox11081426] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
The nuclear factor erythroid 2-related factor 2 (NRF2) was originally described as a master regulator of antioxidant cellular response, but in the time since, numerous important biological functions linked to cell survival, cellular detoxification, metabolism, autophagy, proteostasis, inflammation, immunity, and differentiation have been attributed to this pleiotropic transcription factor that regulates hundreds of genes. After 40 years of in-depth research and key discoveries, NRF2 is now at the center of a vast regulatory network, revealing NRF2 signalling as increasingly complex. It is widely recognized that reactive oxygen species (ROS) play a key role in human physiological and pathological processes such as ageing, obesity, diabetes, cancer, and neurodegenerative diseases. The high oxygen consumption associated with high levels of free iron and oxidizable unsaturated lipids make the brain particularly vulnerable to oxidative stress. A good stability of NRF2 activity is thus crucial to maintain the redox balance and therefore brain homeostasis. In this review, we have gathered recent data about the contribution of the NRF2 pathway in the healthy brain as well as during metabolic diseases, cancer, ageing, and ageing-related neurodegenerative diseases. We also discuss promising therapeutic strategies and the need for better understanding of cell-type-specific functions of NRF2 in these different fields.
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13
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Prahl J, Coetzee GA. Genetic Elements at the Alpha-Synuclein Locus. Front Neurosci 2022; 16:889802. [PMID: 35898413 PMCID: PMC9309432 DOI: 10.3389/fnins.2022.889802] [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: 03/04/2022] [Accepted: 06/24/2022] [Indexed: 11/30/2022] Open
Abstract
Genome-wide association studies have consistently shown that the alpha-synuclein locus is significantly associated with Parkinson’s disease. The mechanism by which this locus modulates the disease pathology and etiology remains largely under-investigated. This is due to the assumption that SNCA is the only driver of the functional aspects of several single nucleotide polymorphism (SNP) risk-signals at this locus. Recent evidence has shown that the risk associated with the top GWAS-identified variant within this locus is independent of SNCA expression, calling into question the validity of assigning function to the nearest gene, SNCA. In this review, we examine additional genes and risk variants present at the SNCA locus and how they may contribute to Parkinson’s disease. Using the SNCA locus as an example, we hope to demonstrate that deeper and detailed functional validations are required for high impact disease-linked variants.
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14
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Schilder BM, Navarro E, Raj T. Multi-omic insights into Parkinson's Disease: From genetic associations to functional mechanisms. Neurobiol Dis 2021; 163:105580. [PMID: 34871738 PMCID: PMC10101343 DOI: 10.1016/j.nbd.2021.105580] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 11/17/2021] [Accepted: 12/02/2021] [Indexed: 02/07/2023] Open
Abstract
Genome-Wide Association Studies (GWAS) have elucidated the genetic components of Parkinson's Disease (PD). However, because the vast majority of GWAS association signals fall within non-coding regions, translating these results into an interpretable, mechanistic understanding of the disease etiology remains a major challenge in the field. In this review, we provide an overview of the approaches to prioritize putative causal variants and genes as well as summarise the primary findings of previous studies. We then discuss recent efforts to integrate multi-omics data to identify likely pathogenic cell types and biological pathways implicated in PD pathogenesis. We have compiled full summary statistics of cell-type, tissue, and phentoype enrichment analyses from multiple studies of PD GWAS and provided them in a standardized format as a resource for the research community (https://github.com/RajLabMSSM/PD_omics_review). Finally, we discuss the experimental, computational, and conceptual advances that will be necessary to fully elucidate the effects of functional variants and genes on cellular dysregulation and disease risk.
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Affiliation(s)
- Brian M Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; UK Dementia Research Institute at Imperial College London, London, United Kingdom.
| | - Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Sección Departamental de Bioquímica y Biología Molecular, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Ronald M. Loeb Center for Alzheimer's disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States; Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States.
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15
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Gui Y, Grzyb K, Thomas MH, Ohnmacht J, Garcia P, Buttini M, Skupin A, Sauter T, Sinkkonen L. Single-nuclei chromatin profiling of ventral midbrain reveals cell identity transcription factors and cell-type-specific gene regulatory variation. Epigenetics Chromatin 2021; 14:43. [PMID: 34503558 PMCID: PMC8427957 DOI: 10.1186/s13072-021-00418-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 08/24/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Cell types in ventral midbrain are involved in diseases with variable genetic susceptibility, such as Parkinson's disease and schizophrenia. Many genetic variants affect regulatory regions and alter gene expression in a cell-type-specific manner depending on the chromatin structure and accessibility. RESULTS We report 20,658 single-nuclei chromatin accessibility profiles of ventral midbrain from two genetically and phenotypically distinct mouse strains. We distinguish ten cell types based on chromatin profiles and analysis of accessible regions controlling cell identity genes highlights cell-type-specific key transcription factors. Regulatory variation segregating the mouse strains manifests more on transcriptome than chromatin level. However, cell-type-level data reveals changes not captured at tissue level. To discover the scope and cell-type specificity of cis-acting variation in midbrain gene expression, we identify putative regulatory variants and show them to be enriched at differentially expressed loci. Finally, we find TCF7L2 to mediate trans-acting variation selectively in midbrain neurons. CONCLUSIONS Our data set provides an extensive resource to study gene regulation in mesencephalon and provides insights into control of cell identity in the midbrain and identifies cell-type-specific regulatory variation possibly underlying phenotypic and behavioural differences between mouse strains.
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Affiliation(s)
- Yujuan Gui
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Mélanie H Thomas
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Jochen Ohnmacht
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Pierre Garcia
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Manuel Buttini
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Thomas Sauter
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg.
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16
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Navarro E, Udine E, de Paiva Lopes K, Parks M, Riboldi G, Schilder BM, Humphrey J, Snijders GJL, Vialle RA, Zhuang M, Sikder T, Argyrou C, Allan A, Chao MJ, Farrell K, Henderson B, Simon S, Raymond D, Elango S, Ortega RA, Shanker V, Swan M, Zhu CW, Ramdhani R, Walker RH, Tse W, Sano M, Pereira AC, Ahfeldt T, Goate AM, Bressman S, Crary JF, de Witte L, Frucht S, Saunders-Pullman R, Raj T. Dysregulation of mitochondrial and proteolysosomal genes in Parkinson's disease myeloid cells. NATURE AGING 2021; 1:850-863. [PMID: 35005630 PMCID: PMC8728893 DOI: 10.1038/s43587-021-00110-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 08/05/2021] [Indexed: 12/11/2022]
Abstract
An increasing number of identified Parkinson's disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their role in pathology is not understood. We hypothesize that PD susceptibility genes modulate disease risk by influencing gene expression within immune cells. To address this, we have generated transcriptomic profiles of monocytes from 230 individuals with sporadic PD and healthy subjects. We observed a dysregulation of mitochondrial and proteasomal pathways. We also generated transcriptomic profiles of primary microglia from brains of 55 subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified 17 PD susceptibility genes whose expression, relative to each risk allele, is altered in monocytes. These findings reveal widespread transcriptomic alterations in PD monocytes, with some being distinct from microglia, and facilitate efforts to understand the roles of myeloid cells in PD as well as the development of biomarkers.
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Affiliation(s)
- Elisa Navarro
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Evan Udine
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Katia de Paiva Lopes
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Madison Parks
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Giulietta Riboldi
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
- Universita degli Studi di Milano, Molecular and Translational Medicine, Milan, Italy
| | - Brian M. Schilder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Jack Humphrey
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Gijsje J. L. Snijders
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Ricardo A. Vialle
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Maojuan Zhuang
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tamjeed Sikder
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Charalambos Argyrou
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Amanda Allan
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Michael J. Chao
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Kurt Farrell
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Brooklyn Henderson
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Sarah Simon
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Deborah Raymond
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Sonya Elango
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Roberto A. Ortega
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Vicki Shanker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Matthew Swan
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Carolyn W. Zhu
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ritesh Ramdhani
- Department of Neurology, Zucker School of Medicine at Hofstra Northwell, New York, NY, United States of America
| | - Ruth H. Walker
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, James J. Peters VA Medical Center, Bronx, NY, United States of America
| | - Winona Tse
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Mary Sano
- Department of Geriatrics and Palliative Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Geriatric Research, Education and Clinical Centers (GRECC), James J. Peters VA Medical Center, Bronx, New York, NY, United States of America
- Alzheimer's Disease Research Center (ADRC), Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Ana C. Pereira
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alison M. Goate
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Susan Bressman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - John F. Crary
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Lotje de Witte
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, United States of America
- Mental Illness Research Education Clinical, Centers of Excellence, VA, Mental Health, Veterans, Bronx, United States of America
| | - Steven Frucht
- The Marlene and Paolo Fresco Institute for Parkinson's Disease and Movement Disorders, New York University Langone Health, New York, NY, United States of America
| | - Rachel Saunders-Pullman
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Neurology, Mount Sinai Beth Israel, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Towfique Raj
- Nash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Ronald M. Loeb Center for Alzheimer’s disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Genetics and Genomic Sciences & Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Estelle and Daniel Maggin Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
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17
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Kim S, Shin JY, Kwon NJ, Kim CU, Kim C, Lee CS, Seo JS. Evaluation of low-pass genome sequencing in polygenic risk score calculation for Parkinson's disease. Hum Genomics 2021; 15:58. [PMID: 34454617 PMCID: PMC8403377 DOI: 10.1186/s40246-021-00357-w] [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: 06/25/2021] [Accepted: 08/22/2021] [Indexed: 12/02/2022] Open
Abstract
Background Low-pass sequencing (LPS) has been extensively investigated for applicability to various genetic studies due to its advantages over genotype array data including cost-effectiveness. Predicting the risk of complex diseases such as Parkinson’s disease (PD) using polygenic risk score (PRS) based on the genetic variations has shown decent prediction accuracy. Although ultra-LPS has been shown to be effective in PRS calculation, array data has been favored to the majority of PRS analysis, especially for PD.
Results Using eight high-coverage WGS, we assessed imputation approaches for downsampled LPS data ranging from 0.5 × to 7.0 × . We demonstrated that uncertain genotype calls of LPS diminished imputation accuracy, and an imputation approach using genotype likelihoods was plausible for LPS. Additionally, comparing imputation accuracies between LPS and simulated array illustrated that LPS had higher accuracies particularly at rare frequencies. To evaluate ultra-low coverage data in PRS calculation for PD, we prepared low-coverage WGS and genotype array of 87 PD cases and 101 controls. Genotype imputation of array and downsampled LPS were conducted using a population-specific reference panel, and we calculated risk scores based on the PD-associated SNPs from an East Asian meta-GWAS. The PRS models discriminated cases and controls as previously reported when both LPS and genotype array were used. Also strong correlations in PRS models for PD between LPS and genotype array were discovered. Conclusions Overall, this study highlights the potentials of LPS under 1.0 × followed by genotype imputation in PRS calculation and suggests LPS as attractive alternatives to genotype array in the area of precision medicine for PD. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00357-w.
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Affiliation(s)
- Sungjae Kim
- Precision Medicine Institute, Seoul, 08511, Republic of Korea.,Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, 03080, Republic of Korea
| | - Jong-Yeon Shin
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | - Nak-Jung Kwon
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | | | - Changhoon Kim
- Precision Medicine Institute, Seoul, 08511, Republic of Korea
| | - Chong Sik Lee
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, 88 Olympic-ro 43-gil, Pungnap 2(i)-dong, Songpa-gu, Seoul, 05505, Republic of Korea.
| | - Jeong-Sun Seo
- Precision Medicine Institute, Seoul, 08511, Republic of Korea. .,Asian Genome Institute, Seoul National University Bundang Hospital, 172 Dolma-ro, Seongnam, Bundang-gu, Gyeonggi-do, 13605, Republic of Korea.
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18
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Coccia E, Ahfeldt T. Towards physiologically relevant human pluripotent stem cell (hPSC) models of Parkinson's disease. Stem Cell Res Ther 2021; 12:253. [PMID: 33926571 PMCID: PMC8082939 DOI: 10.1186/s13287-021-02326-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/05/2021] [Indexed: 02/06/2023] Open
Abstract
The derivation of human embryonic stem cells followed by the discovery of induced pluripotent stem cells and leaps in genome editing approaches have continuously fueled enthusiasm for the development of new models of neurodegenerative diseases such as Parkinson's disease (PD). PD is characterized by the relative selective loss of dopaminergic neurons (DNs) in specific areas of substantia nigra pars compacta (SNpc). While degeneration in late stages can be widespread, there is stereotypic early degeneration of these uniquely vulnerable neurons. Various causes of selective vulnerability have been investigated but much remains unclear. Most studies have sought to identify cell autonomous properties of the most vulnerable neurons. However, recent findings from genetic studies and model systems have added to our understanding of non-cell autonomous contributions including regional-specific neuro-immune interactions with astrocytes, resident or damage-activated microglia, neuro-glia cell metabolic interactions, involvement of endothelial cells, and damage to the vascular system. All of these contribute to specific vulnerability and, along with aging and environmental factors, might be integrated in a complex stressor-threshold model of neurodegeneration. In this forward-looking review, we synthesize recent advances in the field of PD modeling using human pluripotent stem cells, with an emphasis on organoid and complex co-culture models of the nigrostriatal niche, with emerging CRISPR applications to edit or perturb expression of causal PD genes and associated risk factors, such as GBA, to understand the impact of these genes on relevant phenotypes.
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Affiliation(s)
- Elena Coccia
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US
| | - Tim Ahfeldt
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
- Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, US.
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19
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Advancing Personalized Medicine in Common Forms of Parkinson's Disease through Genetics: Current Therapeutics and the Future of Individualized Management. J Pers Med 2021; 11:jpm11030169. [PMID: 33804504 PMCID: PMC7998972 DOI: 10.3390/jpm11030169] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023] Open
Abstract
Parkinson’s disease (PD) is a condition with heterogeneous clinical manifestations that vary in age at onset, rate of progression, disease course, severity, motor and non-motor symptoms, and a variable response to antiparkinsonian drugs. It is considered that there are multiple PD etiological subtypes, some of which could be predicted by genetics. The characterization and prediction of these distinct molecular entities provides a growing opportunity to use individualized management and personalized therapies. Dissecting the genetic architecture of PD is a critical step in identifying therapeutic targets, and genetics represents a step forward to sub-categorize and predict PD risk and progression. A better understanding and separation of genetic subtypes has immediate implications in clinical trial design by unraveling the different flavors of clinical presentation and development. Personalized medicine is a nascent area of research and represents a paramount challenge in the treatment and cure of PD. This manuscript summarizes the current state of precision medicine in the PD field and discusses how genetics has become the engine to gain insights into disease during our constant effort to develop potential etiological based interventions.
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20
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Müller‐Nedebock AC, Westhuizen FH, Kõks S, Bardien S. Nuclear Genes Associated with Mitochondrial
DNA
Processes as Contributors to Parkinson's Disease Risk. Mov Disord 2021; 36:815-831. [DOI: 10.1002/mds.28475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 12/07/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022] Open
Affiliation(s)
- Amica C. Müller‐Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | | | - Sulev Kõks
- Perron Institute for Neurological and Translational Science Nedlands Western Australia Australia
- Centre for Molecular Medicine and Innovative Therapeutics Murdoch University Murdoch Western Australia Australia
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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21
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Okechukwu C. Deciphering and manipulating the epigenome for the treatment of Parkinson’s and Alzheimer’s disease. MGM JOURNAL OF MEDICAL SCIENCES 2021. [DOI: 10.4103/mgmj.mgmj_90_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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22
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Golbe L. A new sorting hat for Parkinson disease. Neurology 2020; 95:805-806. [DOI: 10.1212/wnl.0000000000010819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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23
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Hall A, Bandres-Ciga S, Diez-Fairen M, Quinn JP, Billingsley KJ. Genetic Risk Profiling in Parkinson's Disease and Utilizing Genetics to Gain Insight into Disease-Related Biological Pathways. Int J Mol Sci 2020; 21:E7332. [PMID: 33020390 PMCID: PMC7584037 DOI: 10.3390/ijms21197332] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 12/18/2022] Open
Abstract
Parkinson's disease (PD) is a complex disorder underpinned by both environmental and genetic factors. The latter only began to be understood around two decades ago, but since then great inroads have rapidly been made into deconvoluting the genetic component of PD. In particular, recent large-scale projects such as genome-wide association (GWA) studies have provided insight into the genetic risk factors associated with genetically ''complex'' PD (PD that cannot readily be attributed to single deleterious mutations). Here, we discuss the plethora of genetic information provided by PD GWA studies and how this may be utilized to generate polygenic risk scores (PRS), which may be used in the prediction of risk and trajectory of PD. We also comment on how pathway-specific genetic profiling can be used to gain insight into PD-related biological pathways, and how this may be further utilized to nominate causal PD genes and potentially druggable therapeutic targets. Finally, we outline the current limits of our understanding of PD genetics and the potential contribution of variation currently uncaptured in genetic studies, focusing here on uncatalogued structural variants.
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Affiliation(s)
- Ashley Hall
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, L69 7BE, UK; (A.H.); (J.P.Q.)
| | - Sara Bandres-Ciga
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Monica Diez-Fairen
- Neurogenetics Group, University Hospital MutuaTerrassa, Sant Antoni 19, 08221 Terrassa, Barcelona, Spain;
| | - John P. Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular & Integrative Biology, University of Liverpool, L69 7BE, UK; (A.H.); (J.P.Q.)
| | - Kimberley J. Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA;
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24
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Epigenetics in Lewy Body Diseases: Impact on Gene Expression, Utility as a Biomarker, and Possibilities for Therapy. Int J Mol Sci 2020; 21:ijms21134718. [PMID: 32630630 PMCID: PMC7369933 DOI: 10.3390/ijms21134718] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Lewy body disorders (LBD) include Parkinson's disease (PD) and dementia with Lewy bodies (DLB). They are synucleinopathies with a heterogeneous clinical manifestation. As a cause of neuropathological overlap with other neurodegenerative diseases, the establishment of a correct clinical diagnosis is still challenging, and clinical management may be difficult. The combination of genetic variation and epigenetic changes comprising gene expression-modulating DNA methylation and histone alterations modifies the phenotype, disease course, and susceptibility to disease. In this review, we summarize the results achieved in the deciphering of the LBD epigenome. To provide an appropriate context, first LBD genetics is briefly outlined. Afterwards, a detailed review of epigenetic modifications identified for LBD in human cells, postmortem, and peripheral tissues is provided. We also focus on the difficulty of identifying epigenome-related biomarker candidates and discuss the results obtained so far. Additionally, epigenetic changes as therapeutic targets, as well as different epigenome-based treatments, are revised. The number of studies focusing on PD is relatively limited and practically inexistent for DLB. There is a lack of replication studies, and some results are even contradictory, probably due to differences in sample collection and analytical techniques. In summary, we show the current achievements and directions for future research.
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