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Ng XY, Cao M. Dysfunction of synaptic endocytic trafficking in Parkinson's disease. Neural Regen Res 2024; 19:2649-2660. [PMID: 38595283 PMCID: PMC11168511 DOI: 10.4103/nrr.nrr-d-23-01624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/12/2023] [Accepted: 01/03/2024] [Indexed: 04/11/2024] Open
Abstract
Parkinson's disease is characterized by the selective degeneration of dopamine neurons in the nigrostriatal pathway and dopamine deficiency in the striatum. The precise reasons behind the specific degeneration of these dopamine neurons remain largely elusive. Genetic investigations have identified over 20 causative PARK genes and 90 genomic risk loci associated with both familial and sporadic Parkinson's disease. Notably, several of these genes are linked to the synaptic vesicle recycling process, particularly the clathrin-mediated endocytosis pathway. This suggests that impaired synaptic vesicle recycling might represent an early feature of Parkinson's disease, followed by axonal degeneration and the eventual loss of dopamine cell bodies in the midbrain via a "dying back" mechanism. Recently, several new animal and cellular models with Parkinson's disease-linked mutations affecting the endocytic pathway have been created and extensively characterized. These models faithfully recapitulate certain Parkinson's disease-like features at the animal, circuit, and cellular levels, and exhibit defects in synaptic membrane trafficking, further supporting the findings from human genetics and clinical studies. In this review, we will first summarize the cellular and molecular findings from the models of two Parkinson's disease-linked clathrin uncoating proteins: auxilin (DNAJC6/PARK19) and synaptojanin 1 (SYNJ1/PARK20). The mouse models carrying these two PARK gene mutations phenocopy each other with specific dopamine terminal pathology and display a potent synergistic effect. Subsequently, we will delve into the involvement of several clathrin-mediated endocytosis-related proteins (GAK, endophilin A1, SAC2/INPP5F, synaptotagmin-11), identified as Parkinson's disease risk factors through genome-wide association studies, in Parkinson's disease pathogenesis. We will also explore the direct or indirect roles of some common Parkinson's disease-linked proteins (alpha-synuclein (PARK1/4), Parkin (PARK2), and LRRK2 (PARK8)) in synaptic endocytic trafficking. Additionally, we will discuss the emerging novel functions of these endocytic proteins in downstream membrane traffic pathways, particularly autophagy. Given that synaptic dysfunction is considered as an early event in Parkinson's disease, a deeper understanding of the cellular mechanisms underlying synaptic vesicle endocytic trafficking may unveil novel targets for early diagnosis and the development of interventional therapies for Parkinson's disease. Future research should aim to elucidate why generalized synaptic endocytic dysfunction leads to the selective degeneration of nigrostriatal dopamine neurons in Parkinson's disease.
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Affiliation(s)
- Xin Yi Ng
- Programme in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
| | - Mian Cao
- Programme in Neuroscience and Behavioural Disorders, Duke-NUS Medical School, Singapore, Singapore
- Department of Physiology, National University of Singapore, Singapore, Singapore
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2
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Zalon AJ, Quiriconi DJ, Pitcairn C, Mazzulli JR. α-Synuclein: Multiple pathogenic roles in trafficking and proteostasis pathways in Parkinson's disease. Neuroscientist 2024; 30:612-635. [PMID: 38420922 PMCID: PMC11358363 DOI: 10.1177/10738584241232963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Parkinson's disease (PD) is a common age-related neurodegenerative disorder characterized by the loss of dopaminergic neurons in the midbrain. A hallmark of both familial and sporadic PD is the presence of Lewy body inclusions composed mainly of aggregated α-synuclein (α-syn), a presynaptic protein encoded by the SNCA gene. The mechanisms driving the relationship between α-syn accumulation and neurodegeneration are not completely understood, although recent evidence indicates that multiple branches of the proteostasis pathway are simultaneously perturbed when α-syn aberrantly accumulates within neurons. Studies from patient-derived midbrain cultures that develop α-syn pathology through the endogenous expression of PD-causing mutations show that proteostasis disruption occurs at the level of synthesis/folding in the endoplasmic reticulum (ER), downstream ER-Golgi trafficking, and autophagic-lysosomal clearance. Here, we review the fundamentals of protein transport, highlighting the specific steps where α-syn accumulation may intervene and the downstream effects on proteostasis. Current therapeutic efforts are focused on targeting single pathways or proteins, but the multifaceted pathogenic role of α-syn throughout the proteostasis pathway suggests that manipulating several targets simultaneously will provide more effective disease-modifying therapies for PD and other synucleinopathies.
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Affiliation(s)
- Annie J Zalon
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Drew J Quiriconi
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Caleb Pitcairn
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Joseph R Mazzulli
- The Ken and Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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3
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Mercado G, Kaeufer C, Richter F, Peelaerts W. Infections in the Etiology of Parkinson's Disease and Synucleinopathies: A Renewed Perspective, Mechanistic Insights, and Therapeutic Implications. JOURNAL OF PARKINSON'S DISEASE 2024:JPD240195. [PMID: 39331109 DOI: 10.3233/jpd-240195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/28/2024]
Abstract
Increasing evidence suggests a potential role for infectious pathogens in the etiology of synucleinopathies, a group of age-related neurodegenerative disorders including Parkinson's disease (PD), multiple system atrophy and dementia with Lewy bodies. In this review, we discuss the link between infections and synucleinopathies from a historical perspective, present emerging evidence that supports this link, and address current research challenges with a focus on neuroinflammation. Infectious pathogens can elicit a neuroinflammatory response and modulate genetic risk in PD and related synucleinopathies. The mechanisms of how infections might be linked with synucleinopathies as well as the overlap between the immune cellular pathways affected by virulent pathogens and disease-related genetic risk factors are discussed. Here, an important role for α-synuclein in the immune response against infections is emerging. Critical methodological and knowledge gaps are addressed, and we provide new future perspectives on how to address these gaps. Understanding how infections and neuroinflammation influence synucleinopathies will be essential for the development of early diagnostic tools and novel therapies.
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Affiliation(s)
- Gabriela Mercado
- Division of Neurobiology, Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Kaeufer
- Center for Systems Neuroscience, Hannover, Germany
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Franziska Richter
- Department of Pharmacology, Toxicology and Pharmacy, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wouter Peelaerts
- Laboratory for Virology and Gene Therapy, Department of Pharmacy and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
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4
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Vieira SRL, Mezabrovschi R, Toffoli M, Del Pozo SL, Menozzi E, Mullin S, Yalkic S, Limbachiya N, Koletsi S, Loefflad N, Lopez GJ, Gan-Or Z, Alcalay RN, Sidransky E, Schapira AHV. Consensus Guidance for Genetic Counseling in GBA1 Variants: A Focus on Parkinson's Disease. Mov Disord 2024. [PMID: 39258449 DOI: 10.1002/mds.30006] [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: 06/10/2024] [Accepted: 08/16/2024] [Indexed: 09/12/2024] Open
Abstract
Glucocerebrosidase (GBA1) variants constitute numerically the most common known genetic risk factor for Parkinson's disease (PD) and are distributed worldwide. Access to GBA1 genotyping varies across the world and even regionally within countries. Guidelines for GBA1 variant counseling are evolving. We review the current knowledge of the link between GBA1 and PD, and discuss the practicalities of GBA1 testing. Lastly, we provide a consensus for an approach to counseling people with GBA1 variants, notably the communication of PD risk. © 2024 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Sophia R L Vieira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Roxana Mezabrovschi
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Marco Toffoli
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Sara Lucas Del Pozo
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Elisa Menozzi
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Stephen Mullin
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
- Faculty of Health, University of Plymouth, Plymouth, United Kingdom
| | - Selen Yalkic
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Naomi Limbachiya
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Sofia Koletsi
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
| | - Nadine Loefflad
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
| | - Grisel J Lopez
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ziv Gan-Or
- Department of Neurology and Neurosurgery, The Neuro (Montreal Neurological Institute-Hospital), and Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Roy N Alcalay
- Columbia University Irving Medical Center, New York, New York, USA
- Tel Aviv Sourasky Medical Center, Tel Aviv School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ellen Sidransky
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony H V Schapira
- Department of Clinical and Movement Neurosciences, University College London Queen Square Institute of Neurology, London, United Kingdom
- Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, Maryland, USA
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Yang W, Xu S, Zhou M, Chan P. Aging-related biomarkers for the diagnosis of Parkinson's disease based on bioinformatics analysis and machine learning. Aging (Albany NY) 2024; 16:12191-12208. [PMID: 39264583 PMCID: PMC11424590 DOI: 10.18632/aging.205954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 04/22/2024] [Indexed: 09/13/2024]
Abstract
Parkinson's disease (PD) is a multifactorial disease that lacks reliable biomarkers for its diagnosis. It is now clear that aging is the greatest risk factor for developing PD. Therefore, it is necessary to identify novel biomarkers associated with aging in PD. In this study, we downloaded aging-related genes from the Human Ageing Gene Database. To screen and verify biomarkers for PD, we used whole-blood RNA-Seq data from 11 PD patients and 13 healthy control (HC) subjects as a training dataset and three datasets retrieved from the Gene Expression Omnibus (GEO) database as validation datasets. Using the limma package in R, 1435 differentially expressed genes (DEGs) were found in the training dataset. Of these genes, 29 genes were found to occur in both DEGs and 307 aging-related genes. By using machine learning algorithms (LASSO, RF, SVM, and RR), Venn diagrams, and LASSO regression, four of these genes were determined to be potential PD biomarkers; these were further validated in external validation datasets and by qRT-PCR in the peripheral blood mononuclear cells (PBMCs) of 10 PD patients and 10 HC subjects. Based on the biomarkers, a diagnostic model was developed that had reliable predictive ability for PD. Two of the identified biomarkers demonstrated a meaningful correlation with immune cell infiltration status in the PD patients and HC subjects. In conclusion, four aging-related genes were identified as robust diagnostic biomarkers and may serve as potential targets for PD therapeutics.
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Affiliation(s)
- Weiwei Yang
- Department of Neurobiology, Neurology and Geriatrics, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Disorders, Beijing, China
| | - Shengli Xu
- Department of Neurobiology, Neurology and Geriatrics, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Disorders, Beijing, China
| | - Ming Zhou
- Department of Neurobiology, Neurology and Geriatrics, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Disorders, Beijing, China
| | - Piu Chan
- Department of Neurobiology, Neurology and Geriatrics, Xuanwu Hospital of Capital Medical University, National Clinical Research Center for Geriatric Disorders, Beijing, China
- Clinical Center for Parkinson's Disease, Capital Medical University, Beijing, China
- Key Laboratory for Neurodegenerative Disease of the Ministry of Education, Beijing Key Laboratory for Parkinson's Disease, Parkinson Disease Center of Beijing Institute for Brain Disorders, Beijing, China
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Gao Y, Li Q, Yang L, Zhao H, Wang D, Pesola AJ. Causal Association Between Sedentary Behaviors and Health Outcomes: A Systematic Review and Meta-Analysis of Mendelian Randomization Studies. Sports Med 2024:10.1007/s40279-024-02090-5. [PMID: 39218828 DOI: 10.1007/s40279-024-02090-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND Different types of sedentary behavior are associated with several health outcomes, but the causality of these associations remains unclear. OBJECTIVES To conduct a systematic review and meta-analysis of Mendelian randomization (MR) studies investigating the associations between sedentary behaviors and health outcomes. METHODS A systematic search on PubMed, Embase, Web of Science, Scopus, and PsycINFO up to August 2023 was conducted to identify eligible MR studies. We selected studies that assessed associations of genetically determined sedentary behaviors and health outcomes. A meta-analysis was conducted to examine the causal associations when two or more MR studies were available. We graded the evidence level of each MR association based on the results of the main method and sensitivity analyses in MR studies. RESULTS A total of 31 studies with 168 MR associations between six types of sedentary behavior and 47 health outcomes were included. Results from meta-analyses suggested a total of 47 significant causal associations between sedentary behaviors and health outcomes. Notably, more leisure TV watching is robustly correlated with increased risks of myocardial infarction, coronary artery disease, all-cause ischemic stroke, and type 2 diabetes. Conversely, robust inverse associations were observed between leisure computer use and risks of rheumatoid arthritis, Alzheimer's disease, and gastroesophageal reflux disease. CONCLUSION These findings suggest that different types of sedentary behavior have distinct causal effects on health outcomes. Therefore, interventions should focus not only on reducing sedentary time but also on promoting healthier types of sedentary behavior. PROSPERO REGISTRATION CRD42023453828.
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Affiliation(s)
- Ying Gao
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Qingyang Li
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Luyao Yang
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Hanhua Zhao
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China
| | - Di Wang
- Department of Sports Science, College of Education, Zhejiang University, Hangzhou, China.
| | - Arto J Pesola
- Active Life Lab, South-Eastern Finland University of Applied Sciences, Mikkeli, Finland
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7
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Feng T, Zheng H, Zhang Z, Fan P, Yang X. Mechanism and therapeutic targets of the involvement of a novel lysosomal proton channel TMEM175 in Parkinson's disease. Ageing Res Rev 2024; 100:102373. [PMID: 38960046 DOI: 10.1016/j.arr.2024.102373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/01/2024] [Accepted: 06/04/2024] [Indexed: 07/05/2024]
Abstract
Parkinson's disease (PD), recognized as the second most prevalent neurodegenerative disease in the aging population, presents a significant challenge due to the current lack of effective treatment methods to mitigate its progression. Many pathogenesis of PD are related to lysosomal dysfunction. Moreover, extensive genetic studies have shown a significant correlation between the lysosomal membrane protein TMEM175 and the risk of developing PD. Building on this discovery, TMEM175 has been identified as a novel potassium ion channel. Intriguingly, further investigations have found that potassium ion channels gradually close and transform into hydrion "excretion" channels in the microenvironment of lysosomes. This finding was further substantiated by studies on TMEM175 knockout mice, which exhibited pronounced motor dysfunction in pole climbing and suspension tests, alongside a notable reduction in dopamine neurons within the substantia nigra compacta. Despite these advancements, the current research landscape is not without its controversies. In light of this, the present review endeavors to methodically examine and consolidate a vast array of recent literature on TMEM175. This comprehensive analysis spans from the foundational research on the structure and function of TMEM175 to expansive population genetics studies and mechanism research utilizing cellular and animal models.A thorough understanding of the structure and function of TMEM175, coupled with insights into the intricate mechanisms underpinning lysosomal dysfunction in PD dopaminergic neurons, is imperative. Such knowledge is crucial for pinpointing precise intervention targets, thereby paving the way for novel therapeutic strategies that could potentially alter the neurodegenerative trajectory of PD.
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Affiliation(s)
- Tingting Feng
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China
| | | | - Zhan Zhang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Peidong Fan
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China
| | - Xinling Yang
- Department of Neurology, Second Affiliated Hospital of Xinjiang Medical University, Urumqi 830063, China; Xinjiang Key Laboratory of Nervous System Disease Research, Urumqi 830063,China; Xinjiang Clinical Research Center for Nervous System Diseases, Urumqi 830063, China; Xinjiang Medical University, Urumqi 830017, China.
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8
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Landoulsi Z, Sreelatha AAK, Schulte C, Bobbili DR, Montanucci L, Leu C, Niestroj LM, Hassanin E, Domenighetti C, Pavelka L, Sugier PE, Radivojkov-Blagojevic M, Lichtner P, Portugal B, Edsall C, Kru Ger J, Hernandez DG, Blauwendraat C, Mellick GD, Zimprich A, Pirker W, Tan M, Rogaeva E, Lang AE, Koks S, Taba P, Lesage S, Brice A, Corvol JC, Chartier-Harlin MC, Mutez E, Brockmann K, Deutschländer AB, Hadjigeorgiou GM, Dardiotis E, Stefanis L, Simitsi AM, Valente EM, Petrucci S, Straniero L, Zecchinelli A, Pezzoli G, Brighina L, Ferrarese C, Annesi G, Quattrone A, Gagliardi M, Burbulla LF, Matsuo H, Nakayama A, Hattori N, Nishioka K, Chung SJ, Kim YJ, Kolber P, van de Warrenburg BP, Bloem BR, Singleton AB, Toft M, Pihlstrom L, Guedes LC, Ferreira JJ, Bardien S, Carr J, Tolosa E, Ezquerra M, Pastor P, Wirdefeldt K, Pedersen NL, Ran C, Belin AC, Puschmann A, Clarke CE, Morrison KE, Krainc D, Farrer MJ, Lal D, Elbaz A, Gasser T, Krüger R, Sharma M, May P. Genome-wide association study of copy number variations in Parkinson's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.21.24311915. [PMID: 39228715 PMCID: PMC11370542 DOI: 10.1101/2024.08.21.24311915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Objective Our study investigates the impact of copy number variations (CNVs) on Parkinson's disease (PD) pathogenesis using genome-wide data, aiming to uncover novel genetic mechanisms and improve the understanding of the role of CNVs in sporadic PD. Methods We applied a sliding window approach to perform CNV-GWAS and conducted genome-wide burden analyses on CNV data from 11,035 PD patients (including 2,731 early-onset PD (EOPD)) and 8,901 controls from the COURAGE-PD consortium. Results We identified 14 genome-wide significant CNV loci associated with PD, including one deletion and 13 duplications. Among these, duplications in 7q22.1, 11q12.3 and 7q33 displayed the highest effect. Two significant duplications overlapped with PD-related genes SNCA and VPS13C, but none overlapped with recent significant SNP-based GWAS findings. Five duplications included genes associated with neurological disease, and four overlapping genes were dosage-sensitive and intolerant to loss-of-function variants. Enriched pathways included neurodegeneration, steroid hormone biosynthesis, and lipid metabolism. In early-onset cases, four loci were significantly associated with EOPD, including three known duplications and one novel deletion in PRKN. CNV burden analysis showed a higher prevalence of CNVs in PD-related genes in patients compared to controls (OR=1.56 [1.18-2.09], p=0.0013), with PRKN showing the highest burden (OR=1.47 [1.10-1.98], p=0.026). Patients with CNVs in PRKN had an earlier disease onset. Burden analysis with controls and EOPD patients showed similar results. Interpretation This is the largest CNV-based GWAS in PD identifying novel CNV regions and confirming the significant CNV burden in EOPD, primarily driven by the PRKN gene, warranting further investigation.
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Affiliation(s)
- Zied Landoulsi
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg; L-4367, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Ashwin Ashok Kumar Sreelatha
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Claudia Schulte
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Dheeraj Reddy Bobbili
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg; L-4367, Esch-sur-Alzette, Luxembourg
| | - Ludovica Montanucci
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Costin Leu
- Department of Clinical and Experimental Epilepsy, Institute of Neurology, University College London, London, UK
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Lisa-Marie Niestroj
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, Cologne, Germany
| | - Emadeldin Hassanin
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg; L-4367, Esch-sur-Alzette, Luxembourg
| | - Cloé Domenighetti
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - Lukas Pavelka
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
| | | | | | - Peter Lichtner
- Institute of Human Genetics, Helmholtz Zentrum Munchen, Neuherberg, Germany
| | - Berta Portugal
- Department of Precision Health, Luxembourg Institute of Health, Strassen, Luxembourg
| | - Connor Edsall
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
| | - Jens Kru Ger
- Group of Applied Bioinformatics, University of Tubingen, Tubingen, Germany
| | - Dena G Hernandez
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
| | - Cornelis Blauwendraat
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
| | - George D Mellick
- Griffith Institute for Drug Discovery, Griffith University, Don Young Road, Nathan, Queensland, Australia
| | | | - Walter Pirker
- Department of Neurology, Klinik Ottakring, Vienna Austria
| | - Manuela Tan
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
| | - Anthony E Lang
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, Ontario, Canada
- Edmond J. Safra Program in Parkinson's Disease, Morton and Gloria Shulman Movement Disorders Clinic, Toronto Western Hospital, UHN, Toronto, Ontario, Canada
- Division of Neurology, University of Toronto, Toronto, Ontario, Canada
- Krembil Brain Institute, Toronto, Ontario, Canada
| | - Sulev Koks
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, Australia
- Perron Institute for Neurological and Translational Science, Nedlands, Western Australia, Australia
| | - Pille Taba
- Department of Neurology and Neurosurgery, University of Tartu, Estonia
- Neurology Clinic, Tartu University Hospital, Tartu, Estonia
| | - Suzanne Lesage
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
| | - Jean-Christophe Corvol
- Sorbonne Université, Paris Brain Institute - ICM, Inserm, CNRS, Paris, France
- Assistance Publique Hôpitaux de Paris, Department of Neurology, CIC Neurosciences, Pitié-Salpêtrière Hospital, Paris, France
| | - Marie-Christine Chartier-Harlin
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Lille Neurosciences & Cognition, F-59000 Lille, France
| | - Eugenie Mutez
- Univ. Lille, Inserm, CHU Lille, UMR-S 1172 - JPArc - Centre de Recherche Lille Neurosciences & Cognition, F-59000 Lille, France
| | - Kathrin Brockmann
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Angela B Deutschländer
- Department of Neurology, Ludwig Maximilians University of Munich, Germany
- Department of Neurology, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Neurology and Department of Clinical Genomics, Mayo Clinic Florida, Jacksonville, FL, USA
| | - Georges M Hadjigeorgiou
- Department of Neurology, Medical School, University of Cyprus, Nicosia, Cyprus
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Efthimos Dardiotis
- Department of Neurology, Laboratory of Neurogenetics, University of Thessaly, University Hospital of Larissa, Larissa, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
- 1st Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Athina Maria Simitsi
- 1st Department of Neurology, Eginition Hospital, Medical School, National and Kapodistrian University of Athens, Athens, Greece
| | - Enza Maria Valente
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Mondino Foundation, Pavia, Italy
| | - Simona Petrucci
- UOC Medical Genetics and Advanced Cell Diagnostics, S. Andrea University Hospital, Rome, Italy
- Department of Clinical and Molecular Medicine, Sapienza University of Rome, Italy UOC Medical Genetics and Advanced Cell Diagnostics, S. Andrea University Hospital, Rome, Italy
| | - Letizia Straniero
- Department of Biomedical Sciences - Humanitas University, Milan, Italy
| | - Anna Zecchinelli
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini/CTO, Milano, Italia
| | - Gianni Pezzoli
- Parkinson Institute, Azienda Socio Sanitaria Territoriale (ASST) Gaetano Pini/CTO, Milano, Italia
- Fondazione Grigioni per il Morbo di Parkinson, Milan, Italy
| | - Laura Brighina
- Department of Neurology, San Gerardo Hospital, Milan, Italy
- Center for Neuroscience, University of Milano Bicocca, Monza, Italy
| | - Carlo Ferrarese
- Department of Neurology, San Gerardo Hospital, Milan, Italy
- Center for Neuroscience, University of Milano Bicocca, Monza, Italy
| | - Grazia Annesi
- Institute for Biomedical Research and Innovation, National Research Council, Cosenza, Italy
| | - Andrea Quattrone
- Institute of Neurology, Department of Medical and Surgical Sciences, Magna Graecia University, Catanzaro, Italy
| | - Monica Gagliardi
- Department of Medical and Surgical Sciences, Neuroscience Research Center, Magna Graecia University, Catanzaro, Italy
| | - Lena F Burbulla
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
- Metabolic Biochemistry, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians University, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hirotaka Matsuo
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama 359-8513, Japan
| | - Akiyoshi Nakayama
- Department of Integrative Physiology and Bio-Nano Medicine, National Defense Medical College, Saitama 359-8513, Japan
| | - Nobutaka Hattori
- Department of Neurology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Kenya Nishioka
- Department of Neurology, Juntendo University School of Medicine, Bunkyo-ku, Tokyo 113-8421, Japan
| | - Sun Ju Chung
- Department of Neurology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Yun Joong Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, South Korea
| | - Pierre Kolber
- Centre Hospitalier du Luxembourg, Parkinson Research Clinic, Luxembourg, Luxembourg
| | - Bart Pc van de Warrenburg
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Nijmegen, The Netherlands
| | - Bastiaan R Bloem
- Radboud University Medical Centre, Donders Institute for Brain, Cognition and Behaviour, Department of Neurology, Nijmegen, The Netherlands
| | - Andrew B Singleton
- Molecular Genetics Section, Laboratory of Neurogenetics, NIA, NIH, Bethesda, MD 20892, USA
- Center For Alzheimer's and Related Dementias, NIA, NIH, Bethesda, MD, USA
| | - Mathias Toft
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Lasse Pihlstrom
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Leonor Correia Guedes
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Department of Neurosciences and Mental Health, Neurology, Hospital de Santa Maria, Centro Hospitalar Universitario Lisboa Norte (CHULN), Lisbon, Portugal
| | - Joaquim J Ferreira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
- Laboratory of Clinical Pharmacology and Therapeutics, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
- South African Medical Research Council / Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Jonathan Carr
- Division of Neurology, Department of Medicine, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa
| | - Eduardo Tolosa
- Parkinson's disease &Movement Disorders Unit, Neurology Service, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED: CB06/05/0018-ISCIII) Barcelona, Spain
| | - Mario Ezquerra
- Lab of Parkinson Disease and Other Neurodegenerative Movement Disorders, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Institut de Neurociències, Universitat de Barcelona, ES-08036 Barcelona, Catalonia
| | - Pau Pastor
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
- Movement Disorders Unit, Department of Neurology, Hospital Universitari Mutua de Terrassa, Terrassa, Barcelona, Spain
| | - Karin Wirdefeldt
- Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Caroline Ran
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Andrea C Belin
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Andreas Puschmann
- Lund University, Skåne University Hospital, Department of Clinical Sciences Lund, Neurology, Getingevägen 4, 221 85, Lund, Sweden
| | - Carl E Clarke
- University of Birmingham and Sandwell and West Birmingham Hospitals NHS Trust, United Kingdom
| | - Karen E Morrison
- Faculty of Medicine, Health and Life Sciences, Queens University, Belfast, United Kingdom
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, United States
| | - Matt J Farrer
- Department of Neurology, McKnight Brain Institute, University of Florida, Gainesville, FL, USA
| | - Dennis Lal
- Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Stanley Center for Psychiatric Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Alexis Elbaz
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - Thomas Gasser
- Department for Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tubingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Rejko Krüger
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg; L-4367, Esch-sur-Alzette, Luxembourg
- Transversal Translational Medicine, Luxembourg Institute of Health, Strassen, Luxembourg
- Centre Hospitalier du Luxembourg, Parkinson Research Clinic, Luxembourg, Luxembourg
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tubingen, Germany
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg; L-4367, Esch-sur-Alzette, Luxembourg
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9
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Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F. A microglia clonal inflammatory disorder in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.25.577216. [PMID: 38328106 PMCID: PMC10849735 DOI: 10.1101/2024.01.25.577216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Somatic genetic heterogeneity resulting from post-zygotic DNA mutations is widespread in human tissues and can cause diseases, however few studies have investigated its role in neurodegenerative processes such as Alzheimer's Disease (AD). Here we report the selective enrichment of microglia clones carrying pathogenic variants, that are not present in neuronal, glia/stromal cells, or blood, from patients with AD in comparison to age-matched controls. Notably, microglia-specific AD-associated variants preferentially target the MAPK pathway, including recurrent CBL ring-domain mutations. These variants activate ERK and drive a microglia transcriptional program characterized by a strong neuro-inflammatory response, both in vitro and in patients. Although the natural history of AD-associated microglial clones is difficult to establish in human, microglial expression of a MAPK pathway activating variant was previously shown to cause neurodegeneration in mice, suggesting that AD-associated neuroinflammatory microglial clones may contribute to the neurodegenerative process in patients.
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Affiliation(s)
- Rocio Vicario
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Stamatina Fragkogianni
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Leslie Weber
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Tomi Lazarov
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Yang Hu
- Department of Physiology and Biophysics, Institute for Computational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Samantha Y. Hayashi
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Barbara P. Craddock
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Nicholas D. Socci
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Araitz Alberdi
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ann Baako
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Oyku Ay
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Masato Ogishi
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Estibaliz Lopez-Rodrigo
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Rajya Kappagantula
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Agnes Viale
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Christine A. Iacobuzio-Donahue
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Ting Zhou
- SKI Stem Cell Research Core, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | | | | | | | - Omar Abdel-Wahab
- Human Oncology & Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - Olivier Elemento
- Department of Physiology and Biophysics, Institute for Computational Biomedicine,Weill Cornell New York, NY 10021, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, 10065 NY, USA
| | - W. Todd Miller
- Department of Physiology and Biophysics, Stony Brook University School of Medicine, Stony Brook, NY, 11794-8661
| | - Frederic Geissmann
- Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
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10
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Kim MS, Kim H, Lee G. Precision Medicine in Parkinson's Disease Using Induced Pluripotent Stem Cells. Adv Healthc Mater 2024; 13:e2303041. [PMID: 38269602 DOI: 10.1002/adhm.202303041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Parkinson's disease (PD) is one of the most devastating neurological diseases; however, there is no effective cure yet. The availability of human induced pluripotent stem cells (iPSCs) provides unprecedented opportunities to understand the pathogenic mechanism and identification of new therapy for PD. Here a new model system of PD, including 2D human iPSC-derived midbrain dopaminergic (mDA) neurons, 3D iPSC-derived midbrain organoids (MOs) with cellular complexity, and more advanced microphysiological systems (MPS) with 3D organoids, is introduced. It is believed that successful integrations and applications of iPSC, organoid, and MPS technologies can bring new insight on PD's pathogenesis that will lead to more effective treatments for this debilitating disease.
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Affiliation(s)
- Min Seong Kim
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Hyesoo Kim
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Gabsang Lee
- Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- The Solomon Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
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11
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Li Y, Wen Y, Li Y, Tan X, Gao S, Fan P, Tian W, Wong CC, Chen Y. Rab10-CAV1 mediated intraluminal vesicle transport to migrasomes. Proc Natl Acad Sci U S A 2024; 121:e2319267121. [PMID: 39008679 PMCID: PMC11287133 DOI: 10.1073/pnas.2319267121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 06/12/2024] [Indexed: 07/17/2024] Open
Abstract
Migrasomes, vesicular organelles generated on the retraction fibers of migrating cells, play a crucial role in migracytosis, mediating intercellular communication. The cargoes determine the functional specificity of migrasomes. Migrasomes harbor numerous intraluminal vesicles, a pivotal component of their cargoes. The mechanism underlying the transportation of these intraluminal vesicles to the migrasomes remains enigmatic. In this study, we identified that Rab10 and Caveolin-1 (CAV1) mark the intraluminal vesicles in migrasomes. Transport of Rab10-CAV1 vesicles to migrasomes required the motor protein Myosin Va and adaptor proteins RILPL2. Notably, the phosphorylation of Rab10 by the kinase LRRK2 regulated this process. Moreover, CSF-1 can be transported to migrasomes through this mechanism, subsequently fostering monocyte-macrophage differentiation in skin wound healing, which served as a proof of the physiological importance of this transporting mechanism.
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Affiliation(s)
- Yong Li
- Peking‐Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100084, China
- Center for Precision Medicine Multi-Omics Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Advanced Clinical Medicine, Peking University, Beijing100191, China
| | - Yiling Wen
- Center for Precision Medicine Multi-Omics Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Advanced Clinical Medicine, Peking University, Beijing100191, China
| | - Ying Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing100084, China
| | - Xinyi Tan
- The Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing100101, China
| | - Shuaixin Gao
- Department of Human Sciences & James Comprehensive Cancer Center, The Ohio State University, Columbus, OH43210
| | - Peiyao Fan
- Center for Precision Medicine Multi-Omics Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Advanced Clinical Medicine, Peking University, Beijing100191, China
| | - Wenmin Tian
- Center for Precision Medicine Multi-Omics Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Advanced Clinical Medicine, Peking University, Beijing100191, China
| | - Catherine C.L. Wong
- Peking‐Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing100084, China
- Department of Medical Research Center, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, Beijing100730, China
| | - Yang Chen
- Center for Precision Medicine Multi-Omics Research, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Institute of Advanced Clinical Medicine, Peking University, Beijing100191, China
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12
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Zhao B, Li Y, Fan Z, Wu Z, Shu J, Yang X, Yang Y, Wang X, Li B, Wang X, Copana C, Yang Y, Lin J, Li Y, Stein JL, O'Brien JM, Li T, Zhu H. Eye-brain connections revealed by multimodal retinal and brain imaging genetics. Nat Commun 2024; 15:6064. [PMID: 39025851 PMCID: PMC11258354 DOI: 10.1038/s41467-024-50309-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 07/02/2024] [Indexed: 07/20/2024] Open
Abstract
The retina, an anatomical extension of the brain, forms physiological connections with the visual cortex of the brain. Although retinal structures offer a unique opportunity to assess brain disorders, their relationship to brain structure and function is not well understood. In this study, we conducted a systematic cross-organ genetic architecture analysis of eye-brain connections using retinal and brain imaging endophenotypes. We identified novel phenotypic and genetic links between retinal imaging biomarkers and brain structure and function measures from multimodal magnetic resonance imaging (MRI), with many associations involving the primary visual cortex and visual pathways. Retinal imaging biomarkers shared genetic influences with brain diseases and complex traits in 65 genomic regions, with 18 showing genetic overlap with brain MRI traits. Mendelian randomization suggests bidirectional genetic causal links between retinal structures and neurological and neuropsychiatric disorders, such as Alzheimer's disease. Overall, our findings reveal the genetic basis for eye-brain connections, suggesting that retinal images can help uncover genetic risk factors for brain disorders and disease-related changes in intracranial structure and function.
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Affiliation(s)
- Bingxin Zhao
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA.
- Applied Mathematics and Computational Science Graduate Group, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Center for AI and Data Science for Integrated Diagnostics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Penn Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Population Aging Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Institute for Translational Medicine and Therapeutics, University of Pennsylvania, Philadelphia, PA, 19104, USA.
| | - Yujue Li
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Zirui Fan
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Zhenyi Wu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Juan Shu
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiaochen Yang
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Yilin Yang
- Department of Statistics and Data Science, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Xifeng Wang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Bingxuan Li
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Xiyao Wang
- Department of Computer Science, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos Copana
- Department of Statistics, Purdue University, West Lafayette, IN, 47907, USA
| | - Yue Yang
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jinjie Lin
- Yale School of Management, Yale University, New Haven, CT, 06511, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jason L Stein
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Joan M O'Brien
- Scheie Eye Institute, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Penn Medicine Center for Ophthalmic Genetics in Complex Diseases, Philadelphia, PA, 19104, USA
| | - Tengfei Li
- Department of Radiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Biomedical Research Imaging Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hongtu Zhu
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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13
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Chen YC, Liaw YC, Nfor ON, Hsiao CH, Zhong JH, Wu SL, Liaw YP. Epigenetic associations of GPNMB rs199347 variant with alcohol consumption in Parkinson's disease. Front Psychiatry 2024; 15:1377403. [PMID: 39091454 PMCID: PMC11293056 DOI: 10.3389/fpsyt.2024.1377403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/27/2024] [Indexed: 08/04/2024] Open
Abstract
Introduction Alcohol consumption can induce a neuroinflammatory response and contribute to the progression of neurodegeneration. However, its association with Parkinson's disease (PD), the second most common neurodegenerative disorder, remains undetermined. Recent studies suggest that the glycoprotein non-metastatic melanoma protein B (GPNMB) is a potential biomarker for PD. We evaluated the association of rs199347, a variant of the GPNMB gene, with alcohol consumption and methylation upstream of GPNMB. Methods We retrieved genetic and DNA methylation data obtained from participants enrolled in the Taiwan Biobank (TWB) between 2008 and 2016. After excluding individuals with incomplete or missing information about potential PD risk factors, we included 1,357 participants in our final analyses. We used multiple linear regression to assess the association of GPNMB rs199347 and chronic alcohol consumption (and other potential risk factors) with GPNMB cg17274742 methylation. Results There was no difference between the distribution of GPNMB rs199347 genotypes between chronic alcohol consumers and the other study participants. A significant interaction was observed between the GPNMB rs199347 variant and alcohol consumption (p = 0.0102) concerning cg17274742 methylation. Compared to non-chronic alcohol consumers with the AA genotype, alcohol drinkers with the rs199347 GG genotype had significantly lower levels (hypomethylation) of cg17274742 (p = 0.0187). Conclusion Alcohol consumption among individuals with the rs199347 GG genotype was associated with lower levels of cg17274742 methylation, which could increase expression of the GPNMB gene, an important neuroinflammatory-related risk gene for PD.
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Affiliation(s)
- Yen-Chung Chen
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
| | - Yi-Chia Liaw
- Neurological Institute, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Oswald Ndi Nfor
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Hsuan Hsiao
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Ji-Han Zhong
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
| | - Shey-Lin Wu
- Department of Neurology, Changhua Christian Hospital, Changhua, Taiwan
- Department of Electrical Engineering, National Changhua University of Education, Changhua, Taiwan
| | - Yung-Po Liaw
- Department of Public Health and Institute of Public Health, Chung Shan Medical University, Taichung, Taiwan
- Department of Medical Imaging, Chung Shan Medical University Hospital, Taichung, Taiwan
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
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14
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Bakhite E, Mohamed SK, Lai CH, Subramani K, Marae IS, Abuelhassan S, Soliman AAE, Youssef MSK, Abuelizz HA, Mague JT, Al-Salahi R, El Bakri Y. Synthesis, Crystal Structure, Hirshfeld Surface Analysis, and Computational Approach of a New Pyrazolo[3,4- g]isoquinoline Derivative as Potent against Leucine-Rich Repeat Kinase 2 (LRRK2). ACS OMEGA 2024; 9:30751-30770. [PMID: 39035914 PMCID: PMC11256088 DOI: 10.1021/acsomega.4c03208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/22/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024]
Abstract
Ethyl-2-((8-cyano-3,5,9a-trimethyl-1-(4-oxo-4,5-dihydrothiazol-2-yl)-4-phenyl-3a,4,9,9a-tetrahydro-1H-pyrazolo[3,4-g]isoquinolin-7-yl)thio)acetate (5) was synthesized, and its structure was characterized by IR, MS, and NMR (1H and 13C) and verified by a single-crystal X-ray structure determination. Compound 5 adopts a "pincer" conformation. In the crystal, the hydrogen bonds of -H···O, C-H···O, and O-H···S form thick layers of molecules that are parallel to (101). The layers are linked by C-H···π(ring) interactions. The Hirshfeld surface analysis shows that intermolecular hydrogen bonding plays a more important role than both intramolecular hydrogen bonding and π···π stacking in the crystal. The intramolecular noncovalent interactions in 5 were studied by QTAIM, NCI, and DFT-NBO calculations. Based on structural activity relationship studies, leucine-rich repeat kinase 2 (LRRK2) was found to bind 5 and was further subjected to molecular docking studies, molecular dynamics, and ADMET analysis to probe potential drug candidacy.
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Affiliation(s)
- Etify
A. Bakhite
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | - Shaaban Kamel Mohamed
- Chemistry
and Environmental Division, Manchester Metropolitan
University, Manchester M1 5GD, England
- Chemistry
Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Chin-Hung Lai
- Department
of Medical Applied Chemistry, Chung Shan
Medical University, Taichung 40241, Taiwan
- Department
of Medical Education, Chung Shan Medical
University Hospital, Taichung 40201, Taiwan
| | - Karthikeyan Subramani
- Center
for
Healthcare Advancement, Innovation and Research, Vellore Institute of Technology University, Chennai Campus, Chennai 600127, India
| | - Islam S. Marae
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | - Suzan Abuelhassan
- Department
of Chemistry, Faculty of Science, Assiut
University, Assiut 71516, Egypt
| | | | | | - Hatem A. Abuelizz
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Rashad Al-Salahi
- Department
of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Youness El Bakri
- Department
of Theoretical and Applied Chemistry, South
Ural State University, Lenin prospect 76, Chelyabinsk 454080, Russian Federation
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15
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Yoo M, Bunkowski K, Lie A, Junn E. Regulation of MicroRNA-4697-3p by Parkinson's disease-associated SNP rs329648 and its impact on SNCA112 mRNA. Mol Biol Rep 2024; 51:797. [PMID: 39001947 DOI: 10.1007/s11033-024-09725-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 06/13/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Parkinson's disease (PD) is a common neurodegenerative disorder characterized by a multifaceted genetic foundation. Genome-Wide Association Studies (GWAS) have played a crucial role in pinpointing genetic variants linked to PD susceptibility. Current study aims to delve into the mechanistic aspects through which the PD-associated Single Nucleotide Polymorphism (SNP) rs329648, identified in prior GWAS, influences the pathogenesis of PD. METHODS AND RESULTS Employing the CRISPR/Cas9-mediated genome editing mechanism, we demonstrated the association of the disease-associated allele of rs329648 with increased expression of miR-4697-3p in differentiated SH-SY5Y cells. We revealed that miR-4697-3p contributes to the formation of high molecular weight complexes of α-Synuclein (α-Syn), indicative of α-Syn aggregate formation, as evidenced by Western blot analysis. Furthermore, our study unveiled that miR-4697-3p elevates SNCA112 mRNA levels. The resultant protein product, α-Syn 112, a variant of α-Syn with 112 amino acids, is recognized for augmenting α-Syn aggregation. Notably, this regulatory effect minimally impacts the levels of full-length SNCA140 mRNA, as evidenced by qRT-PCR. Additionally, we observed a correlation between the disease-associated allele and miR-4697-3p with increased cell death, substantiated by assessments including cell viability assays, alterations in cell morphology, and TUNEL assays. CONCLUSION Our research reveals that the disease-associated allele of rs329648 is linked to higher levels of miR-4697-3p. This increase in miR-4697-3p leads to elevated SNCA112 mRNA levels, consequently promoting the formation of α-Syn aggregates. Furthermore, miR-4697-3p appears to play a role in increased cell death, potentially contributing to the pathogenesis of PD.
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Affiliation(s)
- Myungsik Yoo
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Klaudia Bunkowski
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Andrew Lie
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
| | - Eunsung Junn
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA.
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Ashique S, Kumar N, Mishra N, Muthu S, Rajendran RL, Chandrasekaran B, Obeng BF, Hong CM, Krishnan A, Ahn BC, Gangadaran P. Unveiling the role of exosomes as cellular messengers in neurodegenerative diseases and their potential therapeutic implications. Pathol Res Pract 2024; 260:155451. [PMID: 39002435 DOI: 10.1016/j.prp.2024.155451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/15/2024]
Abstract
Exosomes are a subgroup of extracellular vesicles that function as transmitters, allowing cells to communicate more effectively with each other. However, exosomes may have both beneficial and harmful impacts on central nervous system disorders. Hence, the fundamental molecular mechanisms of the origin of illness and its progression are currently being investigated. The involvement of exosomes in the origin and propagation of neurodegenerative illness has been demonstrated recently. Exosomes provide a representation of the intracellular environment since they include various essential bioactive chemicals. The latest studies have demonstrated that exosomes transport several proteins. Additionally, these physiological vesicles are important in the regeneration of nervous tissue and the healing of neuronal lesions. They also offer a microenvironment to stimulate the conformational variation of concerning proteins for aggregation, resulting in neurodegenerative diseases. The biosynthesis, composition, and significance of exosomes as extracellular biomarkers in neurodegenerative disorders are discussed in this article, with a particular emphasis on their neuroprotective effects.
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Affiliation(s)
- Sumel Ashique
- Department of Pharmaceutics, Bengal College of Pharmaceutical Sciences & Research, Durgapur, West Bengal 713212, India; Research Scholar, School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Nitish Kumar
- SRM Modinagar College of Pharmacy, SRM Institute of Science and Technology (Deemed to be University), Delhi-NCR Campus, Modinagar, Ghaziabad, Uttar Pradesh 201204, India
| | - Neeraj Mishra
- Amity Institute of Pharmacy, Amity University Madhya Pradesh (AUMP), Gwalior, Madhya Pradesh 474005, India
| | - Sathish Muthu
- Department of Orthopaedics, Orthopaedic Research Group, Coimbatore, Tamil Nadu 641045, India; Department of Biotechnology, Faculty of Engineering, Karpagam Academy of Higher Education, Coimbatore, Tamil Nadu 641021, India
| | - Ramya Lakshmi Rajendran
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea
| | | | - Brenya Francis Obeng
- Faculty of Science, College of Health and Allied Sciences, School of Medical Sciences, University of Cape Coast, PMB, Cape Coast, Ghana
| | - Chae Moon Hong
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea; Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu 41944, the Republic of Korea
| | - Anand Krishnan
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences, University of the Free State, Bloemfontein 9300, South Africa.
| | - Byeong-Cheol Ahn
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea; BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea; Department of Nuclear Medicine, Kyungpook National University Hospital, Daegu 41944, the Republic of Korea.
| | - Prakash Gangadaran
- Department of Nuclear Medicine, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea; BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, Department of Biomedical Science, School of Medicine, Kyungpook National University, Daegu 41944, the Republic of Korea.
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Deng IB, Follett J, Fox JD, Farrer MJ. Characterization of Dnajc12 knockout mice, a model of hypodopaminergia. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602343. [PMID: 39026821 PMCID: PMC11257452 DOI: 10.1101/2024.07.06.602343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Homozygous DNAJC12 c.79-2A>G (p. V27Wfs*14) loss-of-function mutations were first reported as a cause of young-onset Parkinson's disease. However, bi-allelic autosomal recessive pathogenic variants in DNAJC12 may lead to an alternative constellation of neurological features including infantile dystonia, developmental delay, intellectual disability and neuropsychiatric disorders. DNAJC12 is understood to co-chaperone aromatic amino acid hydroxylases to enhance the synthesis of biogenic amines. In vitro , we confirm overexpressed DNAJC12 forms a complex with tyrosine hydroxylase, the rate-limiting enzyme in dopamine (DA) synthesis. Now we describe a conditional knockout mouse (cDKO) in which loxP sites flanking Dnajc12 exon 2 enable its excision by cre-recombinase to create a constitutive Dnajc12 knock out (DKO). At three months of age, DKO animals exhibit reduced locomotion and exploratory behavior in automated open-field testing. DKO mice also manifest increased plasma phenylalanine levels, a cardinal feature of patients with DNAJC12 pathogenic variants. In striatal tissue, total DA and serotonin, and their metabolites, are reduced. Biochemical alterations in synaptic proteins and tyrosine hydroxylase are also apparent, with enhanced phosphorylation of pSer31 and pSer40 sites that may reflect biological compensation. Electrically-evoked striatal DA is reduced. Most immediately, cDKO and DKO mice present models to develop and refined therapeutic approaches for the treatment of DNAJC12 dystonia and parkinsonism. These models may also enable the pleiotropic functions of biogenic amines (including DA) to be individually investigated in the brain and periphery.
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18
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Wang Q, Gu X, Yang L, Jiang Y, Zhang J, He J. Emerging perspectives on precision therapy for Parkinson's disease: multidimensional evidence leading to a new breakthrough in personalized medicine. Front Aging Neurosci 2024; 16:1417515. [PMID: 39026991 PMCID: PMC11254646 DOI: 10.3389/fnagi.2024.1417515] [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: 04/15/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
PD is a prevalent and progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Genes play a significant role in the onset and progression of the disease. While the complexity and pleiotropy of gene expression networks have posed challenges for gene-targeted therapies, numerous pathways of gene variant expression show promise as therapeutic targets in preclinical studies, with some already in clinical trials. With the recognition of the numerous genes and complex pathways that can influence PD, it may be possible to take a novel approach to choose a treatment for the condition. This approach would be based on the symptoms, genomics, and underlying mechanisms of the disease. We discuss the utilization of emerging genetic and pathological knowledge of PD patients to categorize the disease into subgroups. Our long-term objective is to generate new insights for the therapeutic approach to the disease, aiming to delay and treat it more effectively, and ultimately reduce the burden on individuals and society.
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Affiliation(s)
- Qiaoli Wang
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xuan Gu
- Department of Trauma center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Le Yang
- Department of Endocrinology, The People’s Hospital of Jilin Province, Changchun, China
| | - Yan Jiang
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jiao Zhang
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jinting He
- Department of Neurology, China-Japan Union Hospital of Jilin University, Changchun, China
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19
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Galper J, Mori G, McDonald G, Ahmadi Rastegar D, Pickford R, Lewis SJG, Halliday GM, Kim WS, Dzamko N. Prediction of motor and non-motor Parkinson's disease symptoms using serum lipidomics and machine learning: a 2-year study. NPJ Parkinsons Dis 2024; 10:123. [PMID: 38918434 PMCID: PMC11199659 DOI: 10.1038/s41531-024-00741-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/14/2024] [Indexed: 06/27/2024] Open
Abstract
Identifying biological factors which contribute to the clinical progression of heterogeneous motor and non-motor phenotypes in Parkinson's disease may help to better understand the disease process. Several lipid-related genetic risk factors for Parkinson's disease have been identified, and the serum lipid signature of Parkinson's disease patients is significantly distinguishable from controls. However, the extent to which lipid profiles are associated with clinical outcomes remains unclear. Untargeted high-performance liquid chromatography-tandem mass spectrometry identified >900 serum lipids in Parkinson's disease subjects at baseline (n = 122), and the potential for machine learning models using these lipids to predict motor and non-motor clinical scores after 2 years (n = 67) was assessed. Machine learning models performed best when baseline serum lipids were used to predict the 2-year future Unified Parkinson's disease rating scale part three (UPDRS III) and Geriatric Depression Scale scores (both normalised root mean square error = 0.7). Feature analysis of machine learning models indicated that species of lysophosphatidylethanolamine, phosphatidylcholine, platelet-activating factor, sphingomyelin, diacylglycerol and triacylglycerol were top predictors of both motor and non-motor scores. Serum lipids were overall more important predictors of clinical outcomes than subject sex, age and mutation status of the Parkinson's disease risk gene LRRK2. Furthermore, lipids were found to better predict clinical scales than a panel of 27 serum cytokines previously measured in this cohort (The Michael J. Fox Foundation LRRK2 Clinical Cohort Consortium). These results suggest that lipid changes may be associated with clinical phenotypes in Parkinson's disease.
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Affiliation(s)
- Jasmin Galper
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Giorgia Mori
- Sydney Informatics Hub, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Gordon McDonald
- Sydney Informatics Hub, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Diba Ahmadi Rastegar
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Russell Pickford
- Bioanalytical Mass Spectrometry Facility, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Simon J G Lewis
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Glenda M Halliday
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Woojin S Kim
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia
| | - Nicolas Dzamko
- Brain and Mind Centre and Faculty of Medicine and Health, School of Medical Sciences, University of Sydney, Camperdown, NSW, 2050, Australia.
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20
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Jaykumar AB, Binns D, Taylor CA, Anselmo A, Birnbaum SG, Huber KM, Cobb MH. WNKs regulate mouse behavior and alter central nervous system glucose uptake and insulin signaling. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.09.598125. [PMID: 38915673 PMCID: PMC11195145 DOI: 10.1101/2024.06.09.598125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Certain areas of the brain involved in episodic memory and behavior, such as the hippocampus, express high levels of insulin receptors and glucose transporter-4 (GLUT4) and are responsive to insulin. Insulin and neuronal glucose metabolism improve cognitive functions and regulate mood in humans. Insulin-dependent GLUT4 trafficking has been extensively studied in muscle and adipose tissue, but little work has demonstrated either how it is controlled in insulin-responsive brain regions or its mechanistic connection to cognitive functions. In this study, we demonstrate that inhibition of WNK (With-No-lysine (K)) kinases improves learning and memory in mice. Neuronal inhibition of WNK enhances in vivo hippocampal glucose uptake. Inhibition of WNK enhances insulin signaling output and insulin-dependent GLUT4 trafficking to the plasma membrane in mice primary neuronal cultures and hippocampal slices. Therefore, we propose that the extent of neuronal WNK kinase activity has an important influence on learning, memory and anxiety-related behaviors, in part, by modulation of neuronal insulin signaling.
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Affiliation(s)
- Ankita B. Jaykumar
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Derk Binns
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Clinton A. Taylor
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Anthony Anselmo
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
| | - Shari G. Birnbaum
- Departments of Peter O’Donnell Jr. Brain Institute and Psychiatry, UT Southwestern Medical Center, Dallas, USA
| | | | - Melanie H. Cobb
- Departments of Pharmacology, UT Southwestern Medical Center, Dallas, USA
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21
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Cen J, Hu N, Shen J, Gao Y, Lu H. Pathological Functions of Lysosomal Ion Channels in the Central Nervous System. Int J Mol Sci 2024; 25:6565. [PMID: 38928271 PMCID: PMC11203704 DOI: 10.3390/ijms25126565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/06/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Lysosomes are highly dynamic organelles that maintain cellular homeostasis and regulate fundamental cellular processes by integrating multiple metabolic pathways. Lysosomal ion channels such as TRPML1-3, TPC1/2, ClC6/7, CLN7, and TMEM175 mediate the flux of Ca2+, Cl-, Na+, H+, and K+ across lysosomal membranes in response to osmotic stimulus, nutrient-dependent signals, and cellular stresses. These ion channels serve as the crucial transducers of cell signals and are essential for the regulation of lysosomal biogenesis, motility, membrane contact site formation, and lysosomal homeostasis. In terms of pathophysiology, genetic variations in these channel genes have been associated with the development of lysosomal storage diseases, neurodegenerative diseases, inflammation, and cancer. This review aims to discuss the current understanding of the role of these ion channels in the central nervous system and to assess their potential as drug targets.
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Affiliation(s)
| | | | | | - Yongjing Gao
- Institute of Pain Medicine and Special Environmental Medicine, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China; (J.C.); (N.H.); (J.S.)
| | - Huanjun Lu
- Institute of Pain Medicine and Special Environmental Medicine, Co-Innovation Center of Neuroregeneration, Nantong University, Nantong 226019, China; (J.C.); (N.H.); (J.S.)
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22
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Mato-Blanco X, Kim SK, Jourdon A, Ma S, Tebbenkamp AT, Liu F, Duque A, Vaccarino FM, Sestan N, Colantuoni C, Rakic P, Santpere G, Micali N. Early Developmental Origins of Cortical Disorders Modeled in Human Neural Stem Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.14.598925. [PMID: 38915580 PMCID: PMC11195173 DOI: 10.1101/2024.06.14.598925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The implications of the early phases of human telencephalic development, involving neural stem cells (NSCs), in the etiology of cortical disorders remain elusive. Here, we explored the expression dynamics of cortical and neuropsychiatric disorder-associated genes in datasets generated from human NSCs across telencephalic fate transitions in vitro and in vivo. We identified risk genes expressed in brain organizers and sequential gene regulatory networks across corticogenesis revealing disease-specific critical phases, when NSCs are more vulnerable to gene dysfunctions, and converging signaling across multiple diseases. Moreover, we simulated the impact of risk transcription factor (TF) depletions on different neural cell types spanning the developing human neocortex and observed a spatiotemporal-dependent effect for each perturbation. Finally, single-cell transcriptomics of newly generated autism-affected patient-derived NSCs in vitro revealed recurrent alterations of TFs orchestrating brain patterning and NSC lineage commitment. This work opens new perspectives to explore human brain dysfunctions at the early phases of development.
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Affiliation(s)
- Xoel Mato-Blanco
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Suel-Kee Kim
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alexandre Jourdon
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
| | - Shaojie Ma
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | | | - Fuchen Liu
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Alvaro Duque
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Flora M. Vaccarino
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Nenad Sestan
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Child Study Center, Yale University School of Medicine, New Haven, CT, USA
- Departments of Psychiatry, Genetics and Comparative Medicine, Wu Tsai Institute, Program in Cellular Neuroscience, Neurodegeneration and Repair, Yale School of Medicine, New Haven, CT 06510, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Carlo Colantuoni
- Depts. of Neurology, Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Pasko Rakic
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
- Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
| | - Gabriel Santpere
- Hospital del Mar Research Institute, Parc de Recerca Biomèdica de Barcelona (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Nicola Micali
- Department of Neuroscience, Yale School of Medicine, New Haven, CT 06520, USA
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23
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Guo X, Luo X, Huang X, Zhang Y, Ji J, Wang X, Wang K, Wang J, Pan X, Chen B, Tan Y, Luo X. The Role of 3' Regulatory Region Flanking Kinectin 1 Gene in Schizophrenia. ALPHA PSYCHIATRY 2024; 25:413-420. [PMID: 39148597 PMCID: PMC11322729 DOI: 10.5152/alphapsychiatry.2024.241616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 04/18/2024] [Indexed: 08/17/2024]
Abstract
Objective Schizophrenia is often associated with volumetric reductions in cortices and expansions in basal ganglia, particularly the putamen. Recent genome-wide association studies have highlighted the significance of variants in the 3' regulatory region adjacent to the kinectin 1 gene (KTN1) in regulating gray matter volume (GMV) of the putamen. This study aimed to comprehensively investigate the involvement of this region in schizophrenia. Methods We analyzed 1136 single-nucleotide polymorphisms (SNPs) covering the entire 3' regulatory region in 4 independent dbGaP samples (4604 schizophrenia patients vs. 4884 healthy subjects) and 3 independent Psychiatric Genomics Consortium samples (107 240 cases vs. 210 203 controls) to identify consistent associations. Additionally, we examined the regulatory effects of schizophrenia-associated alleles on KTN1 mRNA expression in 16 brain areas among 348 subjects, as well as GMVs of 7 subcortical nuclei in 38 258 subjects, and surface areas (SA) and thickness (TH) of the entire cortex and 34 cortical areas in 36 936 subjects. Results The major alleles (f > 0.5) of 25 variants increased (β > 0) the risk of schizophrenia across 2 to 5 independent samples (8.4 × 10-4 ≤ P ≤ .049). These schizophrenia-associated alleles significantly elevated (β > 0) GMVs of basal ganglia, including the putamen (6.0 × 10-11 ≤ P ≤ 1.1 × 10-4), caudate (8.7 × 10-4 ≤ P ≤ 9.4 × 10-3), pallidum (P = 6.0 × 10-4), and nucleus accumbens (P = 2.7 × 10-5). Moreover, they potentially augmented (β > 0) the SA of posterior cingulate and insular cortices, as well as the TH of frontal (pars triangularis and medial orbitofrontal), parietal (superior, precuneus, and inferior), and temporal (transverse) cortices, but potentially reduced (β < 0) the SA of the whole, frontal (medial orbitofrontal), and temporal (pole, superior, middle, and entorhinal) cortices, as well as the TH of rostral middle frontal and superior frontal cortices (8.9 × 10-4 ≤ P ≤ .050). Conclusion Our findings identify significant and functionally relevant risk alleles in the 3' regulatory region adjacent to KTN1, implicating their crucial roles in the development of schizophrenia.
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Affiliation(s)
- Xiaoyun Guo
- Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xinqun Luo
- Department of Neurosurgery, The First Affiliated Hospital, Fujian Medical University, Fuzhou, China
| | - Xiaoyi Huang
- Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yong Zhang
- Institute of Mental Health, Tianjin Anding Hospital, Mental Health Center of Tianjin Medical University, Tianjin, China
| | - Jiawu Ji
- Department of Psychiatry, Fujian Medical University Affiliated Fuzhou Neuropsychiatric Hospital, Fuzhou, Fujian, China
| | - Xiaoping Wang
- Department of Neurology, Jiading Branch of Shanghai General Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kesheng Wang
- Department of Family and Community Health, School of Nursing, Health Sciences Center, West Virginia University, Morgantown, WV, USA
| | - Jijun Wang
- Shanghai Mental Health Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xinghua Pan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Southern Medical University, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Guangzhou, China
| | - Bin Chen
- Department of Cardiovascular Medicine, Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fujian Provincial Hospital, Fuzhou, China
| | - Yunlong Tan
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing, China
| | - Xingguang Luo
- Beijing Huilongguan Hospital, Peking University Huilongguan School of Clinical Medicine, Beijing, China
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
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24
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Gustavsson EK, Follett J, Trinh J, Barodia SK, Real R, Liu Z, Grant-Peters M, Fox JD, Appel-Cresswell S, Stoessl AJ, Rajput A, Rajput AH, Auer R, Tilney R, Sturm M, Haack TB, Lesage S, Tesson C, Brice A, Vilariño-Güell C, Ryten M, Goldberg MS, West AB, Hu MT, Morris HR, Sharma M, Gan-Or Z, Samanci B, Lis P, Periñan MT, Amouri R, Ben Sassi S, Hentati F, Tonelli F, Alessi DR, Farrer MJ. RAB32 Ser71Arg in autosomal dominant Parkinson's disease: linkage, association, and functional analyses. Lancet Neurol 2024; 23:603-614. [PMID: 38614108 PMCID: PMC11096864 DOI: 10.1016/s1474-4422(24)00121-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Parkinson's disease is a progressive neurodegenerative disorder with multifactorial causes, among which genetic risk factors play a part. The RAB GTPases are regulators and substrates of LRRK2, and variants in the LRRK2 gene are important risk factors for Parkinson's disease. We aimed to explore genetic variability in RAB GTPases within cases of familial Parkinson's disease. METHODS We did whole-exome sequencing in probands from families in Canada and Tunisia with Parkinson's disease without a genetic cause, who were recruited from the Centre for Applied Neurogenetics (Vancouver, BC, Canada), an international consortium that includes people with Parkinson's disease from 36 sites in 24 countries. 61 RAB GTPases were genetically screened, and candidate variants were genotyped in relatives of the probands to assess disease segregation by linkage analysis. Genotyping was also done to assess variant frequencies in individuals with idiopathic Parkinson's disease and controls, matched for age and sex, who were also from the Centre for Applied Neurogenetics but unrelated to the probands or each other. All participants were aged 18 years or older. The sequencing and genotyping findings were validated by case-control association analyses using bioinformatic data obtained from publicly available clinicogenomic databases (AMP-PD, GP2, and 100 000 Genomes Project) and a private German clinical diagnostic database (University of Tübingen). Clinical and pathological findings were summarised and haplotypes were determined. In-vitro studies were done to investigate protein interactions and enzyme activities. FINDINGS Between June 1, 2010, and May 31, 2017, 130 probands from Canada and Tunisia (47 [36%] female and 83 [64%] male; mean age 72·7 years [SD 11·7; range 38-96]; 109 White European ancestry, 18 north African, two east Asian, and one Hispanic] underwent whole-exome sequencing. 15 variants in RAB GTPase genes were identified, of which the RAB32 variant c.213C>G (Ser71Arg) cosegregated with autosomal dominant Parkinson's disease in three families (nine affected individuals; non-parametric linkage Z score=1·95; p=0·03). 2604 unrelated individuals with Parkinson's disease and 344 matched controls were additionally genotyped, and five more people originating from five countries (Canada, Italy, Poland, Turkey, and Tunisia) were identified with the RAB32 variant. From the database searches, in which 6043 individuals with Parkinson's disease and 62 549 controls were included, another eight individuals were identified with the RAB32 variant from four countries (Canada, Germany, UK, and USA). Overall, the association of RAB32 c.213C>G (Ser71Arg) with Parkinson's disease was significant (odds ratio [OR] 13·17, 95% CI 2·15-87·23; p=0·0055; I2=99·96%). In the people who had the variant, Parkinson's disease presented at age 54·6 years (SD 12·75, range 31-81, n=16), and two-thirds had a family history of parkinsonism. RAB32 Ser71Arg heterozygotes shared a common haplotype, although penetrance was incomplete. Findings in one individual at autopsy showed sparse neurofibrillary tangle pathology in the midbrain and thalamus, without Lewy body pathology. In functional studies, RAB32 Arg71 activated LRRK2 kinase to a level greater than RAB32 Ser71. INTERPRETATION RAB32 Ser71Arg is a novel genetic risk factor for Parkinson's disease, with reduced penetrance. The variant was found in individuals with Parkinson's disease from multiple ethnic groups, with the same haplotype. In-vitro assays show that RAB32 Arg71 activates LRRK2 kinase, which indicates that genetically distinct causes of familial parkinsonism share the same mechanism. The discovery of RAB32 Ser71Arg also suggests several genetically inherited causes of Parkinson's disease originated to control intracellular immunity. This shared aetiology should be considered in future translational research, while the global epidemiology of RAB32 Ser71Arg needs to be assessed to inform genetic counselling. FUNDING National Institutes of Health, the Canada Excellence Research Chairs program, Aligning Science Across Parkinson's, the Michael J Fox Foundation for Parkinson's Research, and the UK Medical Research Council.
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Affiliation(s)
- Emil K Gustavsson
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Jordan Follett
- McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, FL, USA; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Joanne Trinh
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Sandeep K Barodia
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Raquel Real
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Movement Disorders Centre, University College London, London, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Zhiyong Liu
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Melissa Grant-Peters
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Jesse D Fox
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Silke Appel-Cresswell
- Pacific Parkinson's Research Centre, Djavad Mowafaghian Centre for Brain Health, Division of Neurology, University of British Columbia, Vancouver, BC, Canada
| | - A Jon Stoessl
- Pacific Parkinson's Research Centre, Djavad Mowafaghian Centre for Brain Health, Division of Neurology, University of British Columbia, Vancouver, BC, Canada
| | - Alex Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Ali H Rajput
- Movement Disorders Program, Division of Neurology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Roland Auer
- Department of Pathology, University of Saskatchewan and Saskatchewan Health Authority, Saskatoon, SK, Canada
| | - Russel Tilney
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Movement Disorders Centre, University College London, London, UK
| | - Marc Sturm
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute for Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Suzanne Lesage
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, Paris, France
| | - Christelle Tesson
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, Paris, France
| | - Alexis Brice
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, Inserm, CNRS, Paris, France; Assistance Publique Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Département de Neurologie, Centre d'Investigation Clinique Neurosciences, DMU Neuroscience, Paris, France
| | - Carles Vilariño-Güell
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Mina Ryten
- Department of Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, UK; NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Matthew S Goldberg
- Department of Neurology, Center for Neurodegeneration and Experimental Therapeutics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Andrew B West
- Duke Center for Neurodegeneration and Neurotherapeutics, Department of Pharmacology and Cancer Biology, Duke University, Durham, NC, USA
| | - Michele T Hu
- Division of Neurology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Huw R Morris
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, London, UK; UCL Movement Disorders Centre, University College London, London, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Manu Sharma
- Centre for Genetic Epidemiology, Institute for Clinical Epidemiology and Applied Biometry, University of Tübingen, Tübingen, Germany
| | - Ziv Gan-Or
- The Neuro, Montreal Neurological Institute-Hospital, Montreal, QC, Canada; Department of Neurology and Neurosurgery, and Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Bedia Samanci
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Rim Amouri
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis, Tunisia
| | - Samia Ben Sassi
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis, Tunisia
| | - Faycel Hentati
- Service de Neurologie, Institut National de Neurologie, La Rabta, Tunis, Tunisia
| | - Francesca Tonelli
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK; Aligning Science Across Parkinson's Collaborative Research Network, Chevy Chase, MD, USA
| | - Matthew J Farrer
- McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, FL, USA; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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25
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Pedicone C, Weitzman SA, Renton AE, Goate AM. Unraveling the complex role of MAPT-containing H1 and H2 haplotypes in neurodegenerative diseases. Mol Neurodegener 2024; 19:43. [PMID: 38812061 PMCID: PMC11138017 DOI: 10.1186/s13024-024-00731-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 05/11/2024] [Indexed: 05/31/2024] Open
Abstract
A ~ 1 Mb inversion polymorphism exists within the 17q21.31 locus of the human genome as direct (H1) and inverted (H2) haplotype clades. This inversion region demonstrates high linkage disequilibrium, but the frequency of each haplotype differs across ancestries. While the H1 haplotype exists in all populations and shows a normal pattern of genetic variability and recombination, the H2 haplotype is enriched in European ancestry populations, is less frequent in African ancestry populations, and nearly absent in East Asian ancestry populations. H1 is a known risk factor for several neurodegenerative diseases, and has been associated with many other traits, suggesting its importance in cellular phenotypes of the brain and entire body. Conversely, H2 is protective for these diseases, but is associated with predisposition to recurrent microdeletion syndromes and neurodevelopmental disorders such as autism. Many single nucleotide variants and copy number variants define H1/H2 haplotypes and sub-haplotypes, but identifying the causal variant(s) for specific diseases and phenotypes is complex due to the extended linkage equilibrium. In this review, we assess the current knowledge of this inversion region regarding genomic structure, gene expression, cellular phenotypes, and disease association. We discuss recent discoveries and challenges, evaluate gaps in knowledge, and highlight the importance of understanding the effect of the 17q21.31 haplotypes to promote advances in precision medicine and drug discovery for several diseases.
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Affiliation(s)
- Chiara Pedicone
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sarah A Weitzman
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan E Renton
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alison M Goate
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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26
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Fröhlich A, Pfaff AL, Middlehurst B, Hughes LS, Bubb VJ, Quinn JP, Koks S. Deciphering the role of a SINE-VNTR-Alu retrotransposon polymorphism as a biomarker of Parkinson's disease progression. Sci Rep 2024; 14:10932. [PMID: 38740892 DOI: 10.1038/s41598-024-61753-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/09/2024] [Indexed: 05/16/2024] Open
Abstract
SINE-VNTR-Alu (SVA) retrotransposons are transposable elements which represent a source of genetic variation. We previously demonstrated that the presence/absence of a human-specific SVA, termed SVA_67, correlated with the progression of Parkinson's disease (PD). In the present study, we demonstrate that SVA_67 acts as expression quantitative trait loci, thereby exhibiting a strong regulatory effect across the genome using whole genome and transcriptomic data from the Parkinson's progression markers initiative cohort. We further show that SVA_67 is polymorphic for its variable number tandem repeat domain which correlates with both regulatory properties in a luciferase reporter gene assay in vitro and differential expression of multiple genes in vivo. Additionally, this variation's utility as a biomarker is reflected in a correlation with a number of PD progression markers. These experiments highlight the plethora of transcriptomic and phenotypic changes associated with SVA_67 polymorphism which should be considered when investigating the missing heritability of neurodegenerative diseases.
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Affiliation(s)
- Alexander Fröhlich
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
| | - Abigail L Pfaff
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia
| | - Ben Middlehurst
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Lauren S Hughes
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Vivien J Bubb
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - John P Quinn
- Department of Pharmacology and Therapeutics, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| | - Sulev Koks
- Perron Institute for Neurological and Translational Science, Perth, WA, Australia.
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Perth, WA, Australia.
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27
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Schaffner SL, Casazza W, Artaud F, Konwar C, Merrill SM, Domenighetti C, Schulze-Hentrich JM, Lesage S, Brice A, Corvol JC, Mostafavi S, Dennis JK, Elbaz A, Kobor MS. Genetic variation and pesticide exposure influence blood DNA methylation signatures in females with early-stage Parkinson's disease. NPJ Parkinsons Dis 2024; 10:98. [PMID: 38714693 PMCID: PMC11076573 DOI: 10.1038/s41531-024-00704-3] [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: 08/07/2023] [Accepted: 04/05/2024] [Indexed: 05/10/2024] Open
Abstract
Although sex, genetics, and exposures can individually influence risk for sporadic Parkinson's disease (PD), the joint contributions of these factors to the epigenetic etiology of PD have not been comprehensively assessed. Here, we profiled sex-stratified genome-wide blood DNAm patterns, SNP genotype, and pesticide exposure in agricultural workers (71 early-stage PD cases, 147 controls) and explored replication in three independent samples of varying demographics (n = 218, 222, and 872). Using a region-based approach, we found more associations of blood DNAm with PD in females (69 regions) than in males (2 regions, Δβadj| ≥0.03, padj ≤ 0.05). For 48 regions in females, models including genotype or genotype and pesticide exposure substantially improved in explaining interindividual variation in DNAm (padj ≤ 0.05), and accounting for these variables decreased the estimated effect of PD on DNAm. The results suggested that genotype, and to a lesser degree, genotype-exposure interactions contributed to variation in PD-associated DNAm. Our findings should be further explored in larger study populations and in experimental systems, preferably with precise measures of exposure.
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Affiliation(s)
- S L Schaffner
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - W Casazza
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - F Artaud
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - C Konwar
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - S M Merrill
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
| | - C Domenighetti
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - J M Schulze-Hentrich
- Department of Genetics/Epigenetics, Faculty NT, Saarland University, 66041, Saarbrücken, Germany
| | - S Lesage
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - A Brice
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
| | - J C Corvol
- Sorbonne Université, Institut du Cerveau-Paris Brain Institute-ICM, INSERM, CNRS, Assistance Publique Hôpitaux de Paris, Paris, France
- Sorbonne University, Assistance Publique Hôpitaux de Paris, Paris Brain Insitute - ICM, Inserm, CNRS, Department of Neurology and CIC Neurosciences, Pitié-Salpêtrière Hospital, Paris, France
| | - S Mostafavi
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
- Paul Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - J K Dennis
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - A Elbaz
- Université Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, 94805, Villejuif, France
| | - M S Kobor
- Edwin S. H. Leong Centre for Healthy Aging, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada.
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital, Vancouver, BC, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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28
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Schrӧder LF, Peng W, Gao G, Wong YC, Schwake M, Krainc D. VPS13C regulates phospho-Rab10-mediated lysosomal function in human dopaminergic neurons. J Cell Biol 2024; 223:e202304042. [PMID: 38358348 PMCID: PMC10868123 DOI: 10.1083/jcb.202304042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 12/14/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024] Open
Abstract
Loss-of-function mutations in VPS13C are linked to early-onset Parkinson's disease (PD). While VPS13C has been previously studied in non-neuronal cells, the neuronal role of VPS13C in disease-relevant human dopaminergic neurons has not been elucidated. Using live-cell microscopy, we investigated the role of VPS13C in regulating lysosomal dynamics and function in human iPSC-derived dopaminergic neurons. Loss of VPS13C in dopaminergic neurons disrupts lysosomal morphology and dynamics with increased inter-lysosomal contacts, leading to impaired lysosomal motility and cellular distribution, as well as defective lysosomal hydrolytic activity and acidification. We identified Rab10 as a phospho-dependent interactor of VPS13C on lysosomes and observed a decreased phospho-Rab10-mediated lysosomal stress response upon loss of VPS13C. These findings highlight an important role of VPS13C in regulating lysosomal homeostasis in human dopaminergic neurons and suggest that disruptions in Rab10-mediated lysosomal stress response contribute to disease pathogenesis in VPS13C-linked PD.
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Affiliation(s)
- Leonie F. Schrӧder
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Wesley Peng
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ge Gao
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Yvette C. Wong
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Michael Schwake
- Biochemistry III/Faculty of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Dimitri Krainc
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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29
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Rogers M, Obergrussberger A, Kondratskyi A, Fertig N. Using automated patch clamp electrophysiology platforms in ion channel drug discovery: an industry perspective. Expert Opin Drug Discov 2024; 19:523-535. [PMID: 38481119 DOI: 10.1080/17460441.2024.2329104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/06/2024] [Indexed: 04/25/2024]
Abstract
INTRODUCTION Automated patch clamp (APC) is now well established as a mature technology for ion channel drug discovery in academia, biotech and pharma companies, and in contract research organizations (CRO), for a variety of applications including channelopathy research, compound screening, target validation and cardiac safety testing. AREAS COVERED Ion channels are an important class of drugged and approved drug targets. The authors present a review of the current state of ion channel drug discovery along with new and exciting developments in ion channel research involving APC. This includes topics such as native and iPSC-derived cells in ion channel drug discovery, channelopathy research, organellar and biologics in ion channel drug discovery. EXPERT OPINION It is our belief that APC will continue to play a critical role in ion channel drug discovery, not only in 'classical' hit screening, target validation and cardiac safety testing, but extending these applications to include high throughput organellar recordings and optogenetics. In this way, with advancements in APC capabilities and applications, together with high resolution cryo-EM structures, ion channel drug discovery will be re-invigorated, leading to a growing list of ion channel ligands in clinical development.
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Affiliation(s)
- Marc Rogers
- Albion Drug Discovery Services Ltd, Cambridge, UK
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30
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Hernández-Lorenzo L, García-Gutiérrez F, Solbas-Casajús A, Corrochano S, Matías-Guiu JA, Ayala JL. Genetic-based patient stratification in Alzheimer's disease. Sci Rep 2024; 14:9970. [PMID: 38693203 PMCID: PMC11063050 DOI: 10.1038/s41598-024-60707-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/26/2024] [Indexed: 05/03/2024] Open
Abstract
Alzheimer's disease (AD) shows a high pathological and symptomatological heterogeneity. To study this heterogeneity, we have developed a patient stratification technique based on one of the most significant risk factors for the development of AD: genetics. We addressed this challenge by including network biology concepts, mapping genetic variants data into a brain-specific protein-protein interaction (PPI) network, and obtaining individualized PPI scores that we then used as input for a clustering technique. We then phenotyped each obtained cluster regarding genetics, sociodemographics, biomarkers, fluorodeoxyglucose-positron emission tomography (FDG-PET) imaging, and neurocognitive assessments. We found three clusters defined mainly by genetic variants found in MAPT, APP, and APOE, considering known variants associated with AD and other neurodegenerative disease genetic architectures. Profiling of these clusters revealed minimal variation in AD symptoms and pathology, suggesting different biological mechanisms may activate the neurodegeneration and pathobiological patterns behind AD and result in similar clinical and pathological presentations, even a shared disease diagnosis. Lastly, our research highlighted MAPT, APP, and APOE as key genes where these genetic distinctions manifest, suggesting them as potential targets for personalized drug development strategies to address each AD subgroup individually.
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Affiliation(s)
- Laura Hernández-Lorenzo
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain.
| | - Fernando García-Gutiérrez
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
| | - Ana Solbas-Casajús
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
| | - Silvia Corrochano
- Department of Neurology, San Carlos Research Institute (IdSSC), Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Jordi A Matías-Guiu
- Department of Neurology, San Carlos Research Institute (IdSSC), Hospital Clínico San Carlos, 28040, Madrid, Spain
| | - Jose L Ayala
- Department of Computer Architecture and Automation, Computer Science Faculty, Complutense University of Madrid, 28040, Madrid, Spain
- Instituto de Tecnología del Conocimiento, Universidad Complutense de Madrid, 28040, Madrid, Spain
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31
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Miano-Burkhardt A, Alvarez Jerez P, Daida K, Bandres Ciga S, Billingsley KJ. The Role of Structural Variants in the Genetic Architecture of Parkinson's Disease. Int J Mol Sci 2024; 25:4801. [PMID: 38732020 PMCID: PMC11084710 DOI: 10.3390/ijms25094801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/17/2024] [Accepted: 04/22/2024] [Indexed: 05/13/2024] Open
Abstract
Parkinson's disease (PD) significantly impacts millions of individuals worldwide. Although our understanding of the genetic foundations of PD has advanced, a substantial portion of the genetic variation contributing to disease risk remains unknown. Current PD genetic studies have primarily focused on one form of genetic variation, single nucleotide variants (SNVs), while other important forms of genetic variation, such as structural variants (SVs), are mostly ignored due to the complexity of detecting these variants with traditional sequencing methods. Yet, these forms of genetic variation play crucial roles in gene expression and regulation in the human brain and are causative of numerous neurological disorders, including forms of PD. This review aims to provide a comprehensive overview of our current understanding of the involvement of coding and noncoding SVs in the genetic architecture of PD.
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Affiliation(s)
- Abigail Miano-Burkhardt
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Pilar Alvarez Jerez
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kensuke Daida
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Sara Bandres Ciga
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
| | - Kimberley J. Billingsley
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA; (A.M.-B.); (K.D.)
- Center for Alzheimer’s and Related Dementias, National Institute on Aging, Bethesda, MD 20892, USA; (P.A.J.); (S.B.C.)
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32
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Ribarič S. The Contribution of Type 2 Diabetes to Parkinson's Disease Aetiology. Int J Mol Sci 2024; 25:4358. [PMID: 38673943 PMCID: PMC11050090 DOI: 10.3390/ijms25084358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Type 2 diabetes (T2D) and Parkinson's disease (PD) are chronic disorders that have a significant health impact on a global scale. Epidemiological, preclinical, and clinical research underpins the assumption that insulin resistance and chronic inflammation contribute to the overlapping aetiologies of T2D and PD. This narrative review summarises the recent evidence on the contribution of T2D to the initiation and progression of PD brain pathology. It also briefly discusses the rationale and potential of alternative pharmacological interventions for PD treatment.
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Affiliation(s)
- Samo Ribarič
- Institute of Pathophysiology, Faculty of Medicine, University of Ljubljana, Zaloška 4, 1000 Ljubljana, Slovenia
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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] [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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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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35
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Kang H, Lee CJ. Transmembrane proteins with unknown function (TMEMs) as ion channels: electrophysiological properties, structure, and pathophysiological roles. Exp Mol Med 2024; 56:850-860. [PMID: 38556553 PMCID: PMC11059273 DOI: 10.1038/s12276-024-01206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/27/2023] [Accepted: 01/19/2024] [Indexed: 04/02/2024] Open
Abstract
A transmembrane (TMEM) protein with an unknown function is a type of membrane-spanning protein expressed in the plasma membrane or the membranes of intracellular organelles. Recently, several TMEM proteins have been identified as functional ion channels. The structures and functions of these proteins have been extensively studied over the last two decades, starting with TMEM16A (ANO1). In this review, we provide a summary of the electrophysiological properties of known TMEM proteins that function as ion channels, such as TMEM175 (KEL), TMEM206 (PAC), TMEM38 (TRIC), TMEM87A (GolpHCat), TMEM120A (TACAN), TMEM63 (OSCA), TMEM150C (Tentonin3), and TMEM43 (Gapjinc). Additionally, we examine the unique structural features of these channels compared to those of other well-known ion channels. Furthermore, we discuss the diverse physiological roles of these proteins in lysosomal/endosomal/Golgi pH regulation, intracellular Ca2+ regulation, spatial memory, cell migration, adipocyte differentiation, and mechanical pain, as well as their pathophysiological roles in Parkinson's disease, cancer, osteogenesis imperfecta, infantile hypomyelination, cardiomyopathy, and auditory neuropathy spectrum disorder. This review highlights the potential for the discovery of novel ion channels within the TMEM protein family and the development of new therapeutic targets for related channelopathies.
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Affiliation(s)
- Hyunji Kang
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea
| | - C Justin Lee
- Center for Cognition and Sociality, Life Science Cluster, Institute for Basic Science (IBS), 55 Expo-ro, Yuseong-gu, Daejeon, 34126, Republic of Korea.
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36
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Gao X, Fu J, Yu D, Lu F, Liu S. Integrated network pharmacology and phosphoproteomic analyses of Baichanting in Parkinson's disease model mice. Heliyon 2024; 10:e26916. [PMID: 38509878 PMCID: PMC10951462 DOI: 10.1016/j.heliyon.2024.e26916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/21/2024] [Accepted: 02/21/2024] [Indexed: 03/22/2024] Open
Abstract
The incidence rate of Parkinson's disease (PD) is increasing yearly. Neuronal apoptosis caused by abnormal protein phosphorylation is closely related to the pathogenesis of Parkinson's disease. At present, few PD-specific apoptosis pathways have been revealed. To investigate the effect of Baichanting (BCT) on apoptosis from the perspective of protein phosphorylation, α-syn transgenic mice were selected to observe the behavioral changes of the mice, and the apoptosis of substantia nigra cells were detected by the HE method and TUNEL method. Network pharmacology combined with phosphorylation proteomics was used to find relevant targets for BCT treatment of PD and was further verified by PRM and western blotting. BCT improved the morphology of neurons in the substantia nigra and reduced neuronal apoptosis. The main enriched pathways in the network pharmacology results were apoptosis, the p53 signaling pathway and autophagy. Western blot results showed that BCT significantly regulated the protein expression levels of BAX, Caspase-3, LC3B, P53 and mTOR and upregulated autophagy to alleviate apoptosis. Using phosphorylated proteomics and PRM validation, we found that Pak5, Grin2b, Scn1a, BcaN, L1cam and Braf are closely correlated with the targets of the web-based pharmacological screen and may be involved in p53/mTOR-mediated autophagy and apoptosis pathways. BCT can inhibit the activation of the p53/mTOR signaling pathway, thereby enhancing the autophagy function of cells, and reducing the apoptosis of neurons which is the main mechanism of its neuroprotective effect.
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Affiliation(s)
- Xin Gao
- Heilongjiang University of Chinese Medicine, College of Pharmacy, Harbin, 150040, China
| | - Jiaqi Fu
- Heilongjiang University of Chinese Medicine, College of Pharmacy, Harbin, 150040, China
| | - DongHua Yu
- Heilongjiang University of Chinese Medicine, Research Institute of Chinese Medicine, Harbin, 150040, China
| | - Fang Lu
- Heilongjiang University of Chinese Medicine, Research Institute of Chinese Medicine, Harbin, 150040, China
| | - Shumin Liu
- Heilongjiang University of Chinese Medicine, Research Institute of Chinese Medicine, Harbin, 150040, China
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37
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Kraus F, He Y, Swarup S, Overmyer KA, Jiang Y, Brenner J, Capitanio C, Bieber A, Jen A, Nightingale NM, Anderson BJ, Lee C, Paulo JA, Smith IR, Plitzko JM, Schulman BA, Wilfling F, Coon JJ, Wade Harper J. Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.26.586828. [PMID: 38585873 PMCID: PMC10996675 DOI: 10.1101/2024.03.26.586828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneously quantify HeLa cell proteomes and lipidomes from more than two dozen LSD mutants, revealing diverse molecular phenotypes. Defects in delivery of ferritin and its autophagic receptor NCOA4 to lysosomes (ferritinophagy) were pronounced in NPC2-/- cells, which correlated with increased lyso-phosphatidylcholine species and multi-lamellar membrane structures visualized by cryo-electron-tomography. Ferritinophagy defects correlated with loss of mitochondrial cristae, MICOS-complex components, and electron transport chain complexes rich in iron-sulfur cluster proteins. Strikingly, mitochondrial defects were alleviated when iron was provided through the transferrin system. This resource reveals how defects in lysosomal function can impact mitochondrial homeostasis in trans and highlights nMOST as a discovery tool for illuminating molecular phenotypes across LSDs.
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Affiliation(s)
- Felix Kraus
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- equal contribution
| | - Yuchen He
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- equal contribution
| | - Sharan Swarup
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- equal contribution
| | - Katherine A Overmyer
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yizhi Jiang
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Johann Brenner
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Cristina Capitanio
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Anna Bieber
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Annie Jen
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Nightingale
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Benton J Anderson
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Chan Lee
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - Joao A Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ian R Smith
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jürgen M Plitzko
- CryoEM Technology, Max Planck Institute of Biochemistry, Munich, Germany
| | - Brenda A Schulman
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Florian Wilfling
- Mechanisms of Cellular Quality Control, Max Planck Institute of Biophysics, Frankfurt, Germany
| | - Joshua J Coon
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53715, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - J Wade Harper
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
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Wu YS, Zheng WH, Liu TH, Sun Y, Xu YT, Shao LZ, Cai QY, Tang YQ. Joint-tissue integrative analysis identifies high-risk genes for Parkinson's disease. Front Neurosci 2024; 18:1309684. [PMID: 38576865 PMCID: PMC10991821 DOI: 10.3389/fnins.2024.1309684] [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: 10/08/2023] [Accepted: 02/22/2024] [Indexed: 04/06/2024] Open
Abstract
The loss of dopaminergic neurons in the substantia nigra and the abnormal accumulation of synuclein proteins and neurotransmitters in Lewy bodies constitute the primary symptoms of Parkinson's disease (PD). Besides environmental factors, scholars are in the early stages of comprehending the genetic factors involved in the pathogenic mechanism of PD. Although genome-wide association studies (GWAS) have unveiled numerous genetic variants associated with PD, precisely pinpointing the causal variants remains challenging due to strong linkage disequilibrium (LD) among them. Addressing this issue, expression quantitative trait locus (eQTL) cohorts were employed in a transcriptome-wide association study (TWAS) to infer the genetic correlation between gene expression and a particular trait. Utilizing the TWAS theory alongside the enhanced Joint-Tissue Imputation (JTI) technique and Mendelian Randomization (MR) framework (MR-JTI), we identified a total of 159 PD-associated genes by amalgamating LD score, GTEx eQTL data, and GWAS summary statistic data from a substantial cohort. Subsequently, Fisher's exact test was conducted on these PD-associated genes using 5,152 differentially expressed genes sourced from 12 PD-related datasets. Ultimately, 29 highly credible PD-associated genes, including CTX1B, SCNA, and ARSA, were uncovered. Furthermore, GO and KEGG enrichment analyses indicated that these genes primarily function in tissue synthesis, regulation of neuron projection development, vesicle organization and transportation, and lysosomal impact. The potential PD-associated genes identified in this study not only offer fresh insights into the disease's pathophysiology but also suggest potential biomarkers for early disease detection.
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Affiliation(s)
- Ya-Shi Wu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Wen-Han Zheng
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Tai-Hang Liu
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yan Sun
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Yu-Ting Xu
- Department of Cell Biology and Medical Genetics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Li-Zhen Shao
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Qin-Yu Cai
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
| | - Ya Qin Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Chongqing Medical University, Chongqing, China
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Sekimitsu S, Shweikh Y, Shareef S, Zhao Y, Elze T, Segrè A, Wiggs J, Zebardast N. Association of retinal optical coherence tomography metrics and polygenic risk scores with cognitive function and future cognitive decline. Br J Ophthalmol 2024; 108:599-606. [PMID: 36990674 DOI: 10.1136/bjo-2022-322762] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
Abstract
PURPOSE To evaluate the potential of retinal optical coherence tomography (OCT) measurements and polygenic risk scores (PRS) to identify people at risk of cognitive impairment. METHODS Using OCT images from 50 342 UK Biobank participants, we examined associations between retinal layer thickness and genetic risk for neurodegenerative disease and combined these metrics with PRS to predict baseline cognitive function and future cognitive deterioration. Multivariate Cox proportional hazard models were used to predict cognitive performance. P values for retinal thickness analyses are false-discovery-rate-adjusted. RESULTS Higher Alzheimer's disease PRS was associated with a thicker inner nuclear layer (INL), chorio-scleral interface (CSI) and inner plexiform layer (IPL) (all p<0.05). Higher Parkinson's disease PRS was associated with thinner outer plexiform layer (p<0.001). Worse baseline cognitive performance was associated with thinner retinal nerve fibre layer (RNFL) (aOR=1.038, 95% CI (1.029 to 1.047), p<0.001) and photoreceptor (PR) segment (aOR=1.035, 95% CI (1.019 to 1.051), p<0.001), ganglion cell complex (aOR=1.007, 95% CI (1.002 to 1.013), p=0.004) and thicker ganglion cell layer (aOR=0.981, 95% CI (0.967 to 0.995), p=0.009), IPL (aOR=0.976, 95% CI (0.961 to 0.992), p=0.003), INL (aOR=0.923, 95% CI (0.905 to 0.941), p<0.001) and CSI (aOR=0.998, 95% CI (0.997 to 0.999), p<0.001). Worse future cognitive performance was associated with thicker IPL (aOR=0.945, 95% CI (0.915 to 0.999), p=0.045) and CSI (aOR=0.996, 95% CI (0.993 to 0.999) 95% CI, p=0.014). Prediction of cognitive decline was significantly improved with the addition of PRS and retinal measurements. CONCLUSIONS AND RELEVANCE Retinal OCT measurements are significantly associated with genetic risk of neurodegenerative disease and may serve as biomarkers predictive of future cognitive impairment.
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Affiliation(s)
| | - Yusrah Shweikh
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Sussex Eye Hospital, University Hospitals Sussex NHS Foundation Trust, Sussex, UK
| | - Sarah Shareef
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
| | - Yan Zhao
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Tobias Elze
- Schepens Eye Research Institute, Harvard Medical School, Boston, Massachusetts, USA
| | - Ayellet Segrè
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Janey Wiggs
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
| | - Nazlee Zebardast
- Department of Ophthalmology, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, USA
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Gaynor-Gillett SC, Cheng L, Shi M, Liu J, Wang G, Spector M, Flaherty M, Wall M, Hwang A, Gu M, Chen Z, Chen Y, Consortium P, Moran JR, Zhang J, Lee D, Gerstein M, Geschwind D, White KP. Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585066. [PMID: 38562832 PMCID: PMC10983874 DOI: 10.1101/2024.03.14.585066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.
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Affiliation(s)
- Sophia C. Gaynor-Gillett
- Tempus Labs, Inc.; Chicago, IL, 60654, USA
- Department of Biology, Cornell College; Mount Vernon, IA, 52314, USA
| | | | - Manman Shi
- Tempus Labs, Inc.; Chicago, IL, 60654, USA
| | - Jason Liu
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Gaoyuan Wang
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | | | | | | | - Ahyeon Hwang
- Department of Computer Science, University of California Irvine; Irvine, CA, 92697, USA
| | - Mengting Gu
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Zhanlin Chen
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | - Yuhang Chen
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
| | | | | | - Jing Zhang
- Department of Computer Science, University of California Irvine; Irvine, CA, 92697, USA
| | - Donghoon Lee
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai; New York, NY, 10029, USA
| | - Mark Gerstein
- Computational Biology and Bioinformatics Program, Yale University; New Haven, CT, 06511, USA
- Department of Statistics and Data Science, Yale University; New Haven, CT, 06511, USA
- Department of Molecular Biophysics and Biochemistry, Yale University; New Haven, CT, 06511, USA
- Department of Computer Science, Yale University; New Haven, CT, 06511, USA
| | - Daniel Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
- Department of Psychiatry and Semel Institute, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, CA, 90095, USA
| | - Kevin P. White
- Yong Loo Lin School of Medicine, National University of Singapore; Singapore, 117597
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Sun Z, Kantor B, Chiba-Falek O. Neuronal-type-specific epigenome editing to decrease SNCA expression: Implications for precision medicine in synucleinopathies. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102084. [PMID: 38130373 PMCID: PMC10732167 DOI: 10.1016/j.omtn.2023.102084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 11/22/2023] [Indexed: 12/23/2023]
Abstract
Overexpression of SNCA has been implicated in the pathogenesis of synucleinopathies, particularly Parkinson's disease (PD) and dementia with Lewy bodies (DLB). While PD and DLB share some clinical and pathological similarities, each disease presents distinct characteristics, including the primary affected brain region and neuronal type. We aimed to develop neuronal-type-specific SNCA-targeted epigenome therapies for synucleinopathies. The system is based on an all-in-one lentiviral vector comprised of CRISPR-dSaCas9 and guide RNA (gRNA) targeted at SNCA intron 1 fused with a synthetic repressor molecule of Krüppel-associated box (KRAB)/ methyl CpG binding protein 2 (MeCp2) transcription repression domain (TRD). To achieve neuronal-type specificity for dopaminergic and cholinergic neurons, the system was driven by tyrosine hydroxylase (TH) and choline acetyltransferase (ChAT) promoters, respectively. Delivering the system into human induced pluripotent stem cell (hiPSC)-derived dopaminergic and cholinergic neurons from a patient with the SNCA triplication resulted in efficient and neuronal-type-specific downregulation of SNCA-mRNA and protein. Furthermore, the reduction in SNCA levels by the gRNA-dSaCas9-repressor system rescued disease-related cellular phenotypes including Ser129-phophorylated α-synuclein, neuronal viability, and mitochondrial dysfunction. We established a novel neuronal-type-specific SNCA-targeted epigenome therapy and provided in vitro proof of concept using human-based disease models. Our results support the therapeutic potential of our system for PD and DLB and provide the foundation for further preclinical studies in animal models toward investigational new drug (IND) enablement and clinical trials.
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Affiliation(s)
| | - Boris Kantor
- Viral Vector Core, Department of Neurobiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ornit Chiba-Falek
- Division of Translational Brain Sciences, Department of Neurology, Duke University School of Medicine, Durham, NC 27710, USA
- Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC 27710, USA
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Lechner SA, Barnett DGS, Gammie SC, Kelm-Nelson CA. Prodromal Parkinson disease signs are predicted by a whole-blood inflammatory transcriptional signature in young Pink1 -/- rats. BMC Neurosci 2024; 25:11. [PMID: 38438964 PMCID: PMC10910737 DOI: 10.1186/s12868-024-00857-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/20/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Parkinson disease (PD) is the fastest growing neurodegenerative disease. The molecular pathology of PD in the prodromal phase is poorly understood; as such, there are no specific prognostic or diagnostic tests. A validated Pink1 genetic knockout rat was used to model early-onset and progressive PD. Male Pink1-/- rats exhibit progressive declines in ultrasonic vocalizations as well as hindlimb and forelimb motor deficits by mid-to-late adulthood. Previous RNA-sequencing work identified upregulation of genes involved in disease pathways and inflammation within the brainstem and vocal fold muscle. The purpose of this study was to identify gene pathways within the whole blood of young Pink1-/- rats (3 months of age) and to link gene expression to early acoustical changes. To accomplish this, limb motor testing (open field and cylinder tests) and ultrasonic vocalization data were collected, immediately followed by the collection of whole blood and RNA extraction. Illumina® Total RNA-Seq TruSeq platform was used to profile differential expression of genes. Statistically significant genes were identified and Weighted Gene Co-expression Network Analysis was used to construct co-expression networks and modules from the whole blood gene expression dataset as well as the open field, cylinder, and USV acoustical dataset. ENRICHR was used to identify the top up-regulated biological pathways. RESULTS The data suggest that inflammation and interferon signaling upregulation in the whole blood is present during early PD. We also identified genes involved in the dysregulation of ribosomal protein and RNA processing gene expression as well as prion protein gene expression. CONCLUSIONS These data identified several potential blood biomarkers and pathways that may be linked to anxiety and vocalization acoustic parameters and are key candidates for future drug-repurposing work and comparison to human datasets.
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Affiliation(s)
- Sarah A Lechner
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, Medical Sciences Center, University of Wisconsin-Madison, 1300 University Avenue, 416, Madison, WI, 53706, USA
| | - David G S Barnett
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, Medical Sciences Center, University of Wisconsin-Madison, 1300 University Avenue, 416, Madison, WI, 53706, USA
| | - Stephen C Gammie
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Cynthia A Kelm-Nelson
- Department of Surgery, Division of Otolaryngology-Head and Neck Surgery, Medical Sciences Center, University of Wisconsin-Madison, 1300 University Avenue, 416, Madison, WI, 53706, USA.
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Li C, Ke B, Chen J, Xiao Y, Wang S, Jiang R, Zheng X, Lin J, Huang J, Shang H. Systemic inflammation and risk of Parkinson's disease: A prospective cohort study and genetic analysis. Brain Behav Immun 2024; 117:447-455. [PMID: 38336023 DOI: 10.1016/j.bbi.2024.02.013] [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: 10/23/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND Multiple evidence has suggested the complex interplay between Parkinson's disease (PD) and systemic inflammation marked by C-reactive protein (CRP) and interleukin 6 (IL-6). Nevertheless, the findings across studies have shown inconsistency, and the direction of the effect remains controversial. Here, we aimed to explore the link between CRP and IL-6 and the risk of PD. METHODS Based on data from the UK Biobank, we investigated the association between baseline CRP and IL-6 and the risk of incident PD with Cox proportional hazards regression analysis. We further performed extensive genetic analyses including genetic correlation, polygenic risk score (PRS), and pleiotropic enrichment based on summary statistics from previous genome-wide association studies. RESULTS A higher level of CRP at baseline was associated with a lower risk of PD (HR = 0.85, 95 % CI: 0.79-0.90, P = 4.23E-07). The results remained consistent in the subgroup analyses stratified by sex, age and body mass index. From the genetic perspective, a significant negative genetic correlation was identified between CRP and PD risk (correlation: -0.14, P = 6.31E-05). Higher PRS of CRP was associated with a lower risk of PD (P = 0.015, beta = -0.04, SE = 0.017). Moreover, we observed significant pleiotropic enrichment for PD conditional on CRP, and identified 13 risk loci for PD, some of which are implicated in immune functionality and have been linked to PD, including CTSB, HNF4A, PPM1G, ACMSD, and NCOR1. In contrast, no significant association was identified between IL-6 and PD. CONCLUSIONS Systemic inflammation at baseline measured by CRP level is associated with decreased future risk of PD. These discoveries contribute to a deeper comprehension of the role of inflammation in the risk of PD, and hold implications for the design of therapeutic interventions in clinical trials.
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Affiliation(s)
- Chunyu Li
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Bin Ke
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jianhai Chen
- Department of Ecology and Evolution, Biological Sciences Division, the University of Chicago, United States
| | - Yi Xiao
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Shichan Wang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Rirui Jiang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoting Zheng
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Junyu Lin
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Jingxuan Huang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huifang Shang
- Department of Neurology, Laboratory of Neurodegenerative Disorders, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan, China.
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Kwok AJ, Lu J, Huang J, Ip BY, Mok VCT, Lai HM, Ko H. High-resolution omics of vascular ageing and inflammatory pathways in neurodegeneration. Semin Cell Dev Biol 2024; 155:30-49. [PMID: 37380595 DOI: 10.1016/j.semcdb.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/07/2023] [Indexed: 06/30/2023]
Abstract
High-resolution omics, particularly single-cell and spatial transcriptomic profiling, are rapidly enhancing our comprehension of the normal molecular diversity of gliovascular cells, as well as their age-related changes that contribute to neurodegeneration. With more omic profiling studies being conducted, it is becoming increasingly essential to synthesise valuable information from the rapidly accumulating findings. In this review, we present an overview of the molecular features of neurovascular and glial cells that have been recently discovered through omic profiling, with a focus on those that have potentially significant functional implications and/or show cross-species differences between human and mouse, and that are linked to vascular deficits and inflammatory pathways in ageing and neurodegenerative disorders. Additionally, we highlight the translational applications of omic profiling, and discuss omic-based strategies to accelerate biomarker discovery and facilitate disease course-modifying therapeutics development for neurodegenerative conditions.
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Affiliation(s)
- Andrew J Kwok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Jianning Lu
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junzhe Huang
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Bonaventure Y Ip
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vincent C T Mok
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Hei Ming Lai
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
| | - Ho Ko
- Division of Neurology, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Margaret K. L. Cheung Research Centre for Management of Parkinsonism, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Lau Tat-chuen Research Centre of Brain Degenerative Diseases in Chinese, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China; Gerald Choa Neuroscience Institute, The Chinese University of Hong Kong, Hong Kong SAR, China.
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Basavarajappa BS, Subbanna S. Unlocking the epigenetic symphony: histone acetylation's impact on neurobehavioral change in neurodegenerative disorders. Epigenomics 2024; 16:331-358. [PMID: 38321930 PMCID: PMC10910622 DOI: 10.2217/epi-2023-0428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024] Open
Abstract
Recent genomics and epigenetic advances have empowered the exploration of DNA/RNA methylation and histone modifications crucial for gene expression in response to stress, aging and disease. Interest in understanding neuronal plasticity's epigenetic mechanisms, influencing brain rewiring amid development, aging and neurodegenerative disorders, continues to grow. Histone acetylation dysregulation, a commonality in diverse brain disorders, has become a therapeutic focus. Histone acetyltransferases and histone deacetylases have emerged as promising targets for neurodegenerative disorder treatment. This review delves into histone acetylation regulation, potential therapies and future perspectives for disorders like Alzheimer's, Parkinson's and Huntington's. Exploring genetic-environmental interplay through models and studies reveals molecular changes, behavioral insights and early intervention possibilities targeting the epigenome in at-risk individuals.
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Affiliation(s)
- Balapal S Basavarajappa
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
- Molecular Imaging & Neuropathology Area, New York State Psychiatric Institute, NY 10032, USA
- Department of Psychiatry, Columbia University Irving Medical Center, NY 10032, USA
- Department of Psychiatry, New York University Langone Medical Center, NY 10016, USA
| | - Shivakumar Subbanna
- Center for Dementia Research, Nathan Kline Institute for Psychiatric Research, Orangeburg, NY 10962, USA
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Pena N, Richbourg T, Gonzalez-Hunt CP, Qi R, Wren P, Barlow C, Shanks NF, Carlisle HJ, Sanders LH. G2019S selective LRRK2 kinase inhibitor abrogates mitochondrial DNA damage. NPJ Parkinsons Dis 2024; 10:49. [PMID: 38429321 PMCID: PMC10907374 DOI: 10.1038/s41531-024-00660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/14/2024] [Indexed: 03/03/2024] Open
Abstract
Pathogenic mutations in LRRK2 cause Parkinson's disease (PD). The G2019S variant is the most common, which results in abnormally high kinase activity. Compounds that target LRRK2 kinase activity are currently being developed and tested in clinical trials. We recently found that G2019S LRRK2 causes mitochondrial DNA (mtDNA) damage and treatment with multiple classes of LRRK2 kinase inhibitors at concentrations associated with dephosphorylation of LRRK2 reversed mtDNA damage to healthy control levels. Because maintaining the normal function of LRRK2 in heterozygous G2019S LRRK2 carriers while specifically targeting the G2019S LRRK2 activity could have an advantageous safety profile, we explored the efficacy of a G2019S mutant selective LRRK2 inhibitor to reverse mtDNA damage in G2019S LRRK2 models and patient cells relative to non-selective LRRK2 inhibitors. Potency of LRRK2 kinase inhibition by EB-42168, a G2019S mutant LRRK2 kinase inhibitor, and MLi-2, a non-selective inhibitor, was determined by measuring phosphorylation of LRRK2 at Ser935 and/or Ser1292 using quantitative western immunoblot analysis. The Mito DNADX assay, which allows for the accurate real-time quantification of mtDNA damage in a 96-well platform, was performed in parallel. We confirmed that EB-42168 selectively inhibits LRRK2 phosphorylation on G2019S LRRK2 relative to wild-type LRRK2. On the other hand, MLi-2 was equipotent for wild-type and G2019S LRRK2. Acute treatment with EB-42168 inhibited LRRK2 phosphorylation and also restored mtDNA damage to healthy control levels. We further investigated the relationship between LRRK2 kinase activity, mtDNA damage and mitophagy. Levels of mtDNA damage caused by G2019S LRRK2 were fully re-established within 2 h of a LRRK2 inhibitor wash out and recovery experiment, indicating the mtDNA damage phenotype is highly dynamic. G2019S LRRK2 mitophagy defects were not alleviated with LRRK2 kinase inhibition, suggesting that mitophagy is not mechanistically regulating LRRK2 kinase-mediated reversal of mtDNA damage in this acute timeframe. Abrogation of mtDNA damage with the mutant selective tool inhibitor EB-42168 demonstrates the potential of a precision medicine approach for LRRK2 G2019S PD. Levels of mtDNA damage may serve as a potential pharmacodynamic biomarker of altered kinase activity that could be useful for small molecule development and clinical trials.
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Affiliation(s)
- Nicholas Pena
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Tara Richbourg
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Claudia P Gonzalez-Hunt
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Rui Qi
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA
| | - Paul Wren
- ESCAPE Bio, Inc., South San Francisco, CA, 94080, USA
| | | | | | | | - Laurie H Sanders
- Departments of Neurology and Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Center for Neurodegeneration and Neurotherapeutics, Duke University, Durham, NC, USA.
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Farrow SL, Gokuladhas S, Schierding W, Pudjihartono M, Perry JK, Cooper AA, O'Sullivan JM. Identification of 27 allele-specific regulatory variants in Parkinson's disease using a massively parallel reporter assay. NPJ Parkinsons Dis 2024; 10:44. [PMID: 38413607 PMCID: PMC10899198 DOI: 10.1038/s41531-024-00659-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Genome wide association studies (GWAS) have identified a number of genomic loci that are associated with Parkinson's disease (PD) risk. However, the majority of these variants lie in non-coding regions, and thus the mechanisms by which they influence disease development, and/or potential subtypes, remain largely elusive. To address this, we used a massively parallel reporter assay (MPRA) to screen the regulatory function of 5254 variants that have a known or putative connection to PD. We identified 138 loci with enhancer activity, of which 27 exhibited allele-specific regulatory activity in HEK293 cells. The identified regulatory variant(s) typically did not match the original tag variant within the PD associated locus, supporting the need for deeper exploration of these loci. The existence of allele specific transcriptional impacts within HEK293 cells, confirms that at least a subset of the PD associated regions mark functional gene regulatory elements. Future functional studies that confirm the putative targets of the empirically verified regulatory variants will be crucial for gaining a greater understanding of how gene regulatory network(s) modulate PD risk.
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Affiliation(s)
- Sophie L Farrow
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
| | | | - William Schierding
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
- Department of Ophthalmology, The University of Auckland, Auckland, New Zealand
| | | | - Jo K Perry
- Liggins Institute, The University of Auckland, Auckland, New Zealand
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand
| | - Antony A Cooper
- Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Justin M O'Sullivan
- Liggins Institute, The University of Auckland, Auckland, New Zealand.
- The Maurice Wilkins Centre, The University of Auckland, Auckland, New Zealand.
- Australian Parkinsons Mission, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Singapore Institute for Clinical Sciences, Agency for Science Technology and Research, Singapore, Singapore.
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, United Kingdom.
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Karunakaran KB, Jain S, Brahmachari SK, Balakrishnan N, Ganapathiraju MK. Parkinson's disease and schizophrenia interactomes contain temporally distinct gene clusters underlying comorbid mechanisms and unique disease processes. SCHIZOPHRENIA (HEIDELBERG, GERMANY) 2024; 10:26. [PMID: 38413605 PMCID: PMC10899210 DOI: 10.1038/s41537-024-00439-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Genome-wide association studies suggest significant overlaps in Parkinson's disease (PD) and schizophrenia (SZ) risks, but the underlying mechanisms remain elusive. The protein-protein interaction network ('interactome') plays a crucial role in PD and SZ and can incorporate their spatiotemporal specificities. Therefore, to study the linked biology of PD and SZ, we compiled PD- and SZ-associated genes from the DisGeNET database, and constructed their interactomes using BioGRID and HPRD. We examined the interactomes using clustering and enrichment analyses, in conjunction with the transcriptomic data of 26 brain regions spanning foetal stages to adulthood available in the BrainSpan Atlas. PD and SZ interactomes formed four gene clusters with distinct temporal identities (Disease Gene Networks or 'DGNs'1-4). DGN1 had unique SZ interactome genes highly expressed across developmental stages, corresponding to a neurodevelopmental SZ subtype. DGN2, containing unique SZ interactome genes expressed from early infancy to adulthood, correlated with an inflammation-driven SZ subtype and adult SZ risk. DGN3 contained unique PD interactome genes expressed in late infancy, early and late childhood, and adulthood, and involved in mitochondrial pathways. DGN4, containing prenatally-expressed genes common to both the interactomes, involved in stem cell pluripotency and overlapping with the interactome of 22q11 deletion syndrome (comorbid psychosis and Parkinsonism), potentially regulates neurodevelopmental mechanisms in PD-SZ comorbidity. Our findings suggest that disrupted neurodevelopment (regulated by DGN4) could expose risk windows in PD and SZ, later elevating disease risk through inflammation (DGN2). Alternatively, variant clustering in DGNs may produce disease subtypes, e.g., PD-SZ comorbidity with DGN4, and early/late-onset SZ with DGN1/DGN2.
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Affiliation(s)
- Kalyani B Karunakaran
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India.
- Institute for the Advanced Study of Human Biology, Kyoto University, Kyoto, Japan.
| | - Sanjeev Jain
- National Institute of Mental Health and Neuro-Sciences (NIMHANS), Bangalore, India.
| | | | - N Balakrishnan
- Supercomputer Education and Research Centre, Indian Institute of Science, Bangalore, India
| | - Madhavi K Ganapathiraju
- Department of Computer Science, Carnegie Mellon University Qatar, Doha, Qatar.
- Department of Biomedical Informatics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA.
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Kearney PJ, Zhang Y, Liang M, Tan Y, Kahuno E, Conklin TL, Fagan RR, Pavchinskiy RG, Shaffer SA, Yue Z, Melikian HE. Silencing Parkinson's risk allele Rit2 sex-specifically compromises motor function and dopamine neuron viability. NPJ Parkinsons Dis 2024; 10:41. [PMID: 38395968 PMCID: PMC10891080 DOI: 10.1038/s41531-024-00648-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disease and arises from dopamine (DA) neuron death selectively in the substantia nigra pars compacta (SNc). Rit2 is a reported PD risk allele, and recent single cell transcriptomic studies identified a major RIT2 cluster in PD DA neurons, potentially linking Rit2 expression loss to a PD patient cohort. However, it is still unknown whether Rit2 loss itself impacts DA neuron function and/or viability. Here we report that conditional Rit2 silencing in mouse DA neurons drove motor dysfunction that occurred earlier in males than females and was rescued at early stages by either inhibiting the DA transporter (DAT) or with L-DOPA treatment. Motor dysfunction was accompanied by decreased DA release, striatal DA content, phenotypic DAergic markers, DA neurons, and DAergic terminals, with increased pSer129-alpha synuclein and pSer935-LRRK2 expression. These results provide clear evidence that Rit2 loss is causal for SNc cell death and motor dysfunction, and reveal key sex-specific differences in the response to Rit2 loss.
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Affiliation(s)
- Patrick J Kearney
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA
- University of California, San Diego, CA, USA
| | - Yuanxi Zhang
- Department of Neurology and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Marianna Liang
- Department of Neurology and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yanglan Tan
- Mass Spectrometry Facility, Department of Biochemistry and Molecular Biotechnology, UMASS Chan Medical School, Worcester, MA, USA
- DMPK Group, Merck, S. San Francisco, CA, USA
| | - Elizabeth Kahuno
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA
| | - Tucker L Conklin
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA
- Regeneron, Albany, NY, USA
| | - Rita R Fagan
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA
- University of California, San Francisco, CA, USA
| | - Rebecca G Pavchinskiy
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA
| | - Scott A Shaffer
- Mass Spectrometry Facility, Department of Biochemistry and Molecular Biotechnology, UMASS Chan Medical School, Worcester, MA, USA
| | - Zhenyu Yue
- Department of Neurology and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Haley E Melikian
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, UMASS Chan Medical School, Worcester, MA, USA.
- Graduate Program in Neuroscience, Morningside Graduate School of Biomedical Sciences, UMass Chan Medical School, Worcester, MA, USA.
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He R, Zeng Y, Wang C, Chen L, Cai G, Chen Y, Wang Y, Ye Q, Chen X. Associative role of HLA-DRB1 as a protective factor for susceptibility and progression of Parkinson's disease: a Chinese cross-sectional and longitudinal study. Front Aging Neurosci 2024; 16:1361492. [PMID: 38586829 PMCID: PMC10995924 DOI: 10.3389/fnagi.2024.1361492] [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: 12/26/2023] [Accepted: 02/13/2024] [Indexed: 04/09/2024] Open
Abstract
Background Previous genome-wide association studies investigating the relationship between the HLA-DRB1 and the risk of Parkinson's disease (PD) have shown limited racial diversity and have not explored clinical heterogeneity extensively. Methods The study consisted of three parts: a case-control study, a cross-sectional study, and a longitudinal cohort study. The case-control study included 477 PD patients and 477 healthy controls to explore the relationship between rs660895 and PD susceptibility. The cross-sectional study utilized baseline data from 429 PD patients to examine the correlation between rs660895 and PD features. The longitudinal study included 388 PD patients who completed a 3-year follow-up to investigate the effects of rs660895 on PD progression. Results In the case-control study, HLA-DRB1 rs660895-G allele was associated with a decreased risk of PD in allele model (adjusted OR=0.72, p = 0.003) and dominant model (AG + GG vs. AA: adjusted OR = 0.67, p = 0.003). In the cross-sectional analysis, there was no association between rs660895 and the onset age, motor phenotype, or initial motor symptoms. In the longitudinal analysis, PD patients with the G allele exhibited a slower progression of motor symptoms (MDS-UPDRS-III total score: β = -5.42, p < 0.001, interaction ptime × genotype < 0.001) and non-motor symptoms (NMSS score: β = -4.78, p = 0.030, interaction ptime × genotype < 0.001). Conclusion Our findings support HLA-DRB1 rs660895-G allele is a protective genetic factor for PD risk in Chinese population. Furthermore, we also provide new evidence for the protective effect of rs660895-G allele in PD progression.
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Affiliation(s)
- Raoli He
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Yuqi Zeng
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Chaodong Wang
- Department of Neurology, National Clinical Research Center for Geriatric Diseases, Xuanwu Hospital of Capital Medical University, Beijing, China
| | - Lina Chen
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Guoen Cai
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Ying Chen
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Yingqing Wang
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Qinyong Ye
- Department of Neurology, Fujian Medical University Union Hospital, Fuzhou, China
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
| | - Xiaochun Chen
- Fujian Key Laboratory of Molecular Neurology and Institute of Neuroscience, Fujian Medical University, Fuzhou, China
- Institute of Clinical Neurology, Fujian Medical University, Fuzhou, China
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