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Saleh MA, Amer-Sarsour F, Berant A, Pasmanik-Chor M, Kobo H, Sharabi Y, Vatine GD, Ashkenazi A. Chronic and acute exposure to rotenone reveals distinct Parkinson's disease-related phenotypes in human iPSC-derived peripheral neurons. Free Radic Biol Med 2024; 213:164-173. [PMID: 38246514 DOI: 10.1016/j.freeradbiomed.2024.01.016] [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: 11/26/2023] [Accepted: 01/12/2024] [Indexed: 01/23/2024]
Abstract
Peripheral autonomic nervous system (P-ANS) dysfunction is a critical non-motor phenotype of Parkinson's disease (PD). The majority of PD cases are sporadic and lack identified PD-associated genes involved. Epidemiological and animal model studies suggest an association with pesticides and other environmental toxins. However, the cellular mechanisms underlying toxin induced P-ANS dysfunctions remain unclear. Here, we mapped the global transcriptome changes in human induced pluripotent stem cell (iPSC) derived P-ANS sympathetic neurons during inhibition of the mitochondrial respiratory chain by the PD-related pesticide, rotenone. We revealed distinct transcriptome profiles between acute and chronic exposure to rotenone. In the acute stage, there was a down regulation of specific cation channel genes, known to mediate electrophysiological activity, while in the chronic stage, the human P-ANS neurons exhibited dysregulation of anti-apoptotic and Golgi apparatus-related pathways. Moreover, we identified the sodium voltage-gated channel subunit SCN3A/Nav1.3 as a potential biomarker in human P-ANS neurons associated with PD. Our analysis of the rotenone-altered coding and non-coding transcriptome of human P-ANS neurons may thus provide insight into the pathological signaling events in the sympathetic neurons during PD progression.
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Affiliation(s)
- Mahmood Ali Saleh
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel; The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Fatima Amer-Sarsour
- The Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Asaf Berant
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel; The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel
| | - Metsada Pasmanik-Chor
- Bioinformatics Unit, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Hila Kobo
- Genomics Research Unit, George Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Yehonatan Sharabi
- Hypertension Unit, Department of Medicine, Sheba Medical Center, Tel Hashomer and Faculty of Medicine, Tel Aviv University, Israel
| | - Gad D Vatine
- The Department of Physiology and Cell Biology, Faculty of Health Sciences, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel; The Regenerative Medicine and Stem Cell (RMSC) Research Center, Ben-Gurion University of the Negev, 8410501, Beer Sheva, Israel.
| | - Avraham Ashkenazi
- The Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel; Sagol School of Neuroscience, Tel Aviv University, 6997801, Tel Aviv, Israel.
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Gagliardi M, Procopio R, Talarico M, Quattrone A, Arabia G, Morelli M, D'Amelio M, Malanga D, Bonapace G, Quattrone A, Annesi G. ANXA1 mutation analysis in Italian patients with early onset PD. Neurobiol Aging 2023; 125:123-124. [PMID: 36828691 DOI: 10.1016/j.neurobiolaging.2023.01.014] [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: 11/03/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 01/30/2023]
Abstract
Recently, a novel pathogenic variant in Annexin A1 protein (c.4G > A, p.Ala2Thr) has been identified in an Iranian consanguineous family with autosomal recessive parkinsonism. The deficiencies of ANXA1 could lead to extracellular SNCA accumulation, defects in intracellular signaling pathways and synaptic plasticity causing parkinsonism. The aim of this study was to identify rare ANXA1 variants in 95 early-onset PD patients from South Italy. Sequencing analysis of ANXA1 gene revealed only 2 synonymous variants in PD patients (rs1050305, rs149033255). Therefore, we conclude that the recently published ANXA1 mutation is not a common cause of EOPD in Southern Italy.
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Affiliation(s)
- Monica Gagliardi
- Department of Medical and Surgical Sciences, Neuroscience Research Center, Magna Graecia University, Catanzaro, Italy.
| | - Radha Procopio
- Department of Medical and Surgical Sciences, Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Mariagrazia Talarico
- Department of Medical and Surgical Sciences, Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Andrea Quattrone
- Department of Medical and Surgical Sciences, Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Gennarina Arabia
- Department of Medical and Surgical Sciences, Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Maurizio Morelli
- Department of Medical and Surgical Sciences, Institute of Neurology, Magna Graecia University, Catanzaro, Italy
| | - Marco D'Amelio
- Department of Biomedicine, Neurosciences and Advanced Diagnostics, University of Palermo, Palermo, Italy
| | - Donatella Malanga
- Department of Experimental and Clinical Medicine, Laboratory of Molecular Oncology, Magna Graecia University, Catanzaro, Italy; Interdepartmental Center of Services (CIS), Magna Graecia University, Catanzaro, Italy
| | - Giuseppe Bonapace
- Faculty of Medicine, Pediatrics, Magna Graecia University, Catanzaro, Italy
| | - Aldo Quattrone
- Department of Medical and Surgical Sciences, Neuroscience Research Center, Magna Graecia University, Catanzaro, Italy; Institute for Biomedical Research and Innovation, National Research Council, Cosenza, Italy
| | - Grazia Annesi
- Institute for Biomedical Research and Innovation, National Research Council, Cosenza, Italy
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3
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Shadrina MI, Slominsky PA. Genetic Architecture of Parkinson's Disease. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:417-433. [PMID: 37076287 DOI: 10.1134/s0006297923030100] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 03/28/2023]
Abstract
Year 2022 marks 25 years since the first mutation in familial autosomal dominant Parkinson's disease was identified. Over the years, our understanding of the role of genetic factors in the pathogenesis of familial and idiopathic forms of Parkinson's disease has expanded significantly - a number of genes for the familial form of the disease have been identified, and DNA markers for an increased risk of developing its sporadic form have been found. But, despite all the success achieved, we are far from an accurate assessment of the contribution of genetic and, even more so, epigenetic factors to the disease development. The review summarizes the information accumulated to date on the genetic architecture of Parkinson's disease and formulates issues that need to be addressed, which are primarily related to the assessment of epigenetic factors in the disease pathogenesis.
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Affiliation(s)
- Maria I Shadrina
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia.
| | - Petr A Slominsky
- Institute of Molecular Genetics, Kurchatov Institute National Research Centre, Moscow, 123182, Russia
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4
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Pillay NS, Ross OA, Christoffels A, Bardien S. Current Status of Next-Generation Sequencing Approaches for Candidate Gene Discovery in Familial Parkinson´s Disease. Front Genet 2022; 13:781816. [PMID: 35299952 PMCID: PMC8921601 DOI: 10.3389/fgene.2022.781816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
Parkinson's disease is a neurodegenerative disorder with a heterogeneous genetic etiology. The advent of next-generation sequencing (NGS) technologies has aided novel gene discovery in several complex diseases, including PD. This Perspective article aimed to explore the use of NGS approaches to identify novel loci in familial PD, and to consider their current relevance. A total of 17 studies, spanning various populations (including Asian, Middle Eastern and European ancestry), were identified. All the studies used whole-exome sequencing (WES), with only one study incorporating both WES and whole-genome sequencing. It is worth noting how additional genetic analyses (including linkage analysis, haplotyping and homozygosity mapping) were incorporated to enhance the efficacy of some studies. Also, the use of consanguineous families and the specific search for de novo mutations appeared to facilitate the finding of causal mutations. Across the studies, similarities and differences in downstream analysis methods and the types of bioinformatic tools used, were observed. Although these studies serve as a practical guide for novel gene discovery in familial PD, these approaches have not significantly resolved the "missing heritability" of PD. We speculate that what is needed is the use of third-generation sequencing technologies to identify complex genomic rearrangements and new sequence variation, missed with existing methods. Additionally, the study of ancestrally diverse populations (in particular those of Black African ancestry), with the concomitant optimization and tailoring of sequencing and analytic workflows to these populations, are critical. Only then, will this pave the way for exciting new discoveries in the field.
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Affiliation(s)
- Nikita Simone Pillay
- South African National Bioinformatics Institute (SANBI), South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
| | - Owen A. Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, United States
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, United States
| | - Alan Christoffels
- South African National Bioinformatics Institute (SANBI), South African Medical Research Council Bioinformatics Unit, University of the Western Cape, Bellville, South Africa
- Africa Centres for Disease Control and Prevention, African Union Headquarters, Addis Ababa, Ethiopia
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council/Stellenbosch University Genomics of Brain Disorders Research Unit, Cape Town, South Africa
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5
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Filatova EV, Krylova NS, Vlasov IN, Maslova MS, Poteshkina NG, Slominsky PA, Shadrina MI. Targeted exome analysis of Russian patients with hypertrophic cardiomyopathy. Mol Genet Genomic Med 2021; 9:e1808. [PMID: 34598319 PMCID: PMC8606207 DOI: 10.1002/mgg3.1808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 08/23/2021] [Accepted: 08/27/2021] [Indexed: 11/20/2022] Open
Abstract
Background Hypertrophic cardiomyopathy (HCM), described as the presence of hypertrophy of left ventricular, is the most prevalent heritable cardiovascular disease with predominantly an autosomal dominant type of inheritance. However, pathogenic alleles are not identified in at least 25% of patients with HCM, and the spectrum of pathogenic variants that contribute to the development of HCM in Russia has not been fully described. Therefore, the goal of our study was to identify genetic variants associated with the etiopathogenesis of HCM in Russian patients. Methods The study cohort included 98 unrelated adult patients with HCM. We performed targeted exome sequencing, an analysis using various algorithms for prediction of the impact of variants on protein structure and the prediction of pathogenicity using ACMG Guidelines. Results The frequency of pathogenic and likely pathogenic variants in all HCM‐related genes was 8% in our patients. We also identified 20 variants of uncertain significance in all HCM‐related genes. Conclusions The prevalence of individual pathogenic variants in HCM‐related genes in Russian population appears to be lower than in general European population, which could be explained by ethnic features of Russian population, age characteristics of our sample, or unidentified pathogenic variants in genes previously not linked with HCM.
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Affiliation(s)
- Elena V Filatova
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Natalia S Krylova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan N Vlasov
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Maria S Maslova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | | | - Petr A Slominsky
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
| | - Maria I Shadrina
- Institute of Molecular Genetics of National Research Centre, Moscow, Russia
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Ithal D, Sukumaran SK, Bhattacharjee D, Vemula A, Nadella R, Mahadevan J, Sud R, Viswanath B, Purushottam M, Jain S. Exome hits demystified: The next frontier. Asian J Psychiatr 2021; 59:102640. [PMID: 33892377 DOI: 10.1016/j.ajp.2021.102640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/26/2021] [Indexed: 12/13/2022]
Abstract
Severe mental illnesses such as schizophrenia and bipolar disorder have complex inheritance patterns, involving both common and rare variants. Whole exome sequencing is a promising approach to find out the rare genetic variants. We had previously reported several rare variants in multiplex families with severe mental illnesses. The current article tries to summarise the biological processes and pattern of expression of genes harbouring the aforementioned variants, linking them to known clinical manifestations through a methodical narrative review. Of the 28 genes considered for this review from 7 families with multiple affected individuals, 6 genes are implicated in various neuropsychiatric manifestations including some variations in the brain morphology assessed by magnetic resonance imaging. Another 15 genes, though associated with neuropsychiatric manifestations, did not have established brain morphological changes whereas the remaining 7 genes did not have any previously recorded neuropsychiatric manifestations at all. Wnt/b-catenin signaling pathway was associated with 6 of these genes and PI3K/AKT, calcium signaling, ERK, RhoA and notch signaling pathways had at least 2 gene associations. We present a comprehensive review of biological and clinical knowledge about the genes previously reported in multiplex families with severe mental illness. A 'disease in dish approach' can be helpful to further explore the fundamental mechanisms.
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Affiliation(s)
- Dhruva Ithal
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Salil K Sukumaran
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Debanjan Bhattacharjee
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Alekhya Vemula
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Ravi Nadella
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Jayant Mahadevan
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Reeteka Sud
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Biju Viswanath
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
| | - Meera Purushottam
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India.
| | - Sanjeev Jain
- Department of Psychiatry, National Institute of Mental Health and Neuro Sciences, Bengaluru, Karnataka, India
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7
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Sazonova MA, Sinyov VV, Ryzhkova AI, Sazonova MD, Kirichenko TV, Khotina VA, Khasanova ZB, Doroschuk NA, Karagodin VP, Orekhov AN, Sobenin IA. Some Molecular and Cellular Stress Mechanisms Associated with Neurodegenerative Diseases and Atherosclerosis. Int J Mol Sci 2021; 22:E699. [PMID: 33445687 PMCID: PMC7828120 DOI: 10.3390/ijms22020699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/14/2022] Open
Abstract
Chronic stress is a combination of nonspecific adaptive reactions of the body to the influence of various adverse stress factors which disrupt its homeostasis, and it is also a corresponding state of the organism's nervous system (or the body in general). We hypothesized that chronic stress may be one of the causes occurence of several molecular and cellular types of stress. We analyzed literary sources and considered most of these types of stress in our review article. We examined genes and mutations of nuclear and mitochondrial genomes and also molecular variants which lead to various types of stress. The end result of chronic stress can be metabolic disturbance in humans and animals, leading to accumulation of reactive oxygen species (ROS), oxidative stress, energy deficiency in cells (due to a decrease in ATP synthesis) and mitochondrial dysfunction. These changes can last for the lifetime and lead to severe pathologies, including neurodegenerative diseases and atherosclerosis. The analysis of literature allowed us to conclude that under the influence of chronic stress, metabolism in the human body can be disrupted, mutations of the mitochondrial and nuclear genome and dysfunction of cells and their compartments can occur. As a result of these processes, oxidative, genotoxic, and cellular stress can occur. Therefore, chronic stress can be one of the causes forthe occurrence and development of neurodegenerative diseases and atherosclerosis. In particular, chronic stress can play a large role in the occurrence and development of oxidative, genotoxic, and cellular types of stress.
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Affiliation(s)
- Margarita A. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Vasily V. Sinyov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Anastasia I. Ryzhkova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
| | - Marina D. Sazonova
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
| | - Tatiana V. Kirichenko
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
| | - Victoria A. Khotina
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
| | - Zukhra B. Khasanova
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Natalya A. Doroschuk
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
| | - Vasily P. Karagodin
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Department of Commodity Science and Expertise, Plekhanov Russian University of Economics, 125993 Moscow, Russia
| | - Alexander N. Orekhov
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Cellular and Molecular Pathology of Cardiovascular System, Research Institute of Human Morphology, 117418 Moscow, Russia
- Institute for Atherosclerosis Research, Skolkovo Innovative Centre, 143024 Moscow, Russia
| | - Igor A. Sobenin
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia; (V.V.S.); (A.I.R.); (M.D.S.); (T.V.K.); (V.A.K.); (V.P.K.); (A.N.O.); (I.A.S.)
- Laboratory of Medical Genetics, National Medical Research Center of Cardiology, 121552 Moscow, Russia; (Z.B.K.); (N.A.D.)
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Lan S, Li H, Liu Y, Xu J, Huang Z, Yan S, Zhang Q, Cheng Y. A Novel ROS1-FBXL17 Fusion Co-Existing with CD74-ROS1 Fusion May Improve Sensitivity to Crizotinib and Prolong Progression-Free Survival of Patients with Lung Adenocarcinoma. Onco Targets Ther 2020; 13:11499-11504. [PMID: 33204104 PMCID: PMC7667179 DOI: 10.2147/ott.s278907] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/21/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose The rearrangement of ROS1 (C-ros oncogene 1) is an important driver of non-small cell lung cancer (NSCLC). Currently, only approximately 24 ROS1 fusion partners have been shown to be sensitive to crizotinib. Although fusion partner determination is not required to treat patients with tyrosine kinase inhibitor, the correlation between ROS1 phenotypes and efficacies still needs more researches. Furthermore, non-reciprocal/reciprocal ROS1 translocations are rare and have not yet been reported. Thus, more novel ROS1 fusion partners and non-reciprocal/reciprocal fusions need to be provided and supplemented to guide targeted therapy and prognosis for patients. Case Presentation Targeted next-generation sequencing panel was used to identify ROS1 rearrangements in a Chinese patient with advanced lung adenocarcinoma. We identified a non-reciprocal/reciprocal ROS1 translocation which contained a novel ROS1-FBXL17 (F-box and leucine-rich repeat protein 17) fusion co-existing with the CD74-ROS1 fusion and the patient was sensitive to crizotinib. The ROS1 rearrangement was then validated using RT-qPCR. The progression-free survival (PFS) was 15.7 months which exceeded the highest PFS level (14.2 months) in the Chinese population reported recently. Thus, this non-reciprocal/reciprocal ROS1 translocation patient had an excellent efficacy to crizotinib which was different from that in ALK. And it may be possible that the ROS1-FBXL17 fusion in this patient synergistically promotes the sensitivity of the CD74-RSO1 fusion to crizotinib. Conclusion The ROS1-FBXL17 fusion may be a novel driver of NSCLC and we provide a non-reciprocal/reciprocal ROS1 translocation mode very sensitive to crizotinib. Our study adds new data to the ROS1 fusion database and provides a reference strategy for the clinical treatment of patients with double ROS1 fusions or non-reciprocal/reciprocal ROS1 translocation.
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Affiliation(s)
- Shaowei Lan
- Translational Oncology Research Lab, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China.,Jilin Provincial Key Laboratory of Molecular Diagnostics for Lung Cancer, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Hui Li
- Translational Oncology Research Lab, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China.,Jilin Provincial Key Laboratory of Molecular Diagnostics for Lung Cancer, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Ying Liu
- Department of Medical Thoracic Oncology, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Jinhua Xu
- Department of Medical Thoracic Oncology, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Zhicheng Huang
- Department of Radiology, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Shi Yan
- Translational Oncology Research Lab, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China.,Jilin Provincial Key Laboratory of Molecular Diagnostics for Lung Cancer, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
| | - Qiang Zhang
- Burning Rock Biotech, Guangzhou 510000, People's Republic of China
| | - Ying Cheng
- Translational Oncology Research Lab, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China.,Jilin Provincial Key Laboratory of Molecular Diagnostics for Lung Cancer, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China.,Department of Medical Thoracic Oncology, Jilin Provincial Cancer Hospital, Changchun 130012, People's Republic of China
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9
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Explorative Combined Lipid and Transcriptomic Profiling of Substantia Nigra and Putamen in Parkinson's Disease. Cells 2020; 9:cells9091966. [PMID: 32858884 PMCID: PMC7564986 DOI: 10.3390/cells9091966] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/19/2022] Open
Abstract
Parkinson’s disease (PD) is characterized by the loss of dopaminergic neurons from the substantia nigra (SN) that project to the dorsal striatum (caudate-putamen). To better understand the molecular mechanisms underlying PD, we performed combined lipid profiling and RNA sequencing of SN and putamen samples from PD patients and age-matched controls. SN lipid analysis pointed to a neuroinflammatory component and included elevated levels of the endosomal lipid Bis (Monoacylglycero)Phosphate 42:8, while two of the three depleted putamen lipids were saturated sphingomyelin species. Remarkably, we observed gender-related differences in the SN and putamen lipid profiles. Transcriptome analysis revealed that the top-enriched pathways among the 354 differentially expressed genes (DEGs) in the SN were “protein folding” and “neurotransmitter transport”, and among the 261 DEGs from putamen “synapse organization”. Furthermore, we identified pathways, e.g., “glutamate signaling”, and genes, encoding, e.g., an angiotensin receptor subtype or a proprotein convertase, that have not been previously linked to PD. The identification of 33 genes that were common among the SN and putamen DEGs, which included the α-synuclein paralog β-synuclein, may contribute to the understanding of general PD mechanisms. Thus, our proof-of-concept data highlights new genes, pathways and lipids that have not been explored before in the context of PD.
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10
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Farajollahi Z, Razmara E, Heidari E, Jafarinia E, Garshasbi M. A novel variant of ST3GAL3 causes non-syndromic autosomal recessive intellectual disability in Iranian patients. J Gene Med 2020; 22:e3253. [PMID: 32666583 DOI: 10.1002/jgm.3253] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/01/2020] [Accepted: 07/09/2020] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND The number of reported genes causing non-syndromic autosomal recessive intellectual disability (NS-ARID) is increasing. For example, mutations in the ST3GAL3 gene have been reported to be associated with NS-ARID. In the present study, we aimed to determine the genetic cause of the NS-ARID in a five-generation consanguineous Iranian family. METHODS We subjected four patients with an initial diagnosis of NS-ID in an Iranian family. To identify the possible genetic cause(s), whole-exome sequencing was performed on the proband and Sanger sequencing was applied to investigate co-segregation analysis. Using in silico predictive tools, the possible impacts of the variant on the structure and function of ST3Gal-III were predicted. RESULTS The common clinical features were detected in all affected members who were suffering from a severe ID. Using whole-exome sequencing, a novel variant, c.704C>T or p.(Thr235Met), in exon 9 of the ST3GAL3 gene (NM_001270461.2, OMIM# 606494) was identified and verified by Sanger sequencing. This variant is located next to the VS motif of ST3Gal-III, which is a vital part of the catalytical domains. CONCLUSIONS In the present study, we identified a novel missense variant, c.704C>T or p.(Thr235Met), in the ST3GAL3. To our knowledge, is the third variant in this gene to be associated with NS-ARID. Our findings highlight the need for further investigations into the mechanisms by which variants in ST3GAL3 contribute to neurological dysfunction.
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Affiliation(s)
- Zahra Farajollahi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Razmara
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Erfan Heidari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ehsan Jafarinia
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Masoud Garshasbi
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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11
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Trifonova OP, Maslov DL, Balashova EE, Urazgildeeva GR, Abaimov DA, Fedotova EY, Poleschuk VV, Illarioshkin SN, Lokhov PG. Parkinson's Disease: Available Clinical and Promising Omics Tests for Diagnostics, Disease Risk Assessment, and Pharmacotherapy Personalization. Diagnostics (Basel) 2020; 10:E339. [PMID: 32466249 PMCID: PMC7277996 DOI: 10.3390/diagnostics10050339] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/15/2022] Open
Abstract
Parkinson's disease is the second most frequent neurodegenerative disease, representing a significant medical and socio-economic problem. Modern medicine still has no answer to the question of why Parkinson's disease develops and whether it is possible to develop an effective system of prevention. Therefore, active work is currently underway to find ways to assess the risks of the disease, as well as a means to extend the life of patients and improve its quality. Modern studies aim to create a method of assessing the risk of occurrence of Parkinson's disease (PD), to search for the specific ways of correction of biochemical disorders occurring in the prodromal stage of Parkinson's disease, and to personalize approaches to antiparkinsonian pharmacotherapy. In this review, we summarized all available clinically approved tests and techniques for PD diagnostics. Then, we reviewed major improvements and recent advancements in genomics, transcriptomics, and proteomics studies and application of metabolomics in PD research, and discussed the major metabolomics findings for diagnostics and therapy of the disease.
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Affiliation(s)
- Oxana P. Trifonova
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Dmitri L. Maslov
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Elena E. Balashova
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
| | - Guzel R. Urazgildeeva
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Denis A. Abaimov
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Ekaterina Yu. Fedotova
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Vsevolod V. Poleschuk
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Sergey N. Illarioshkin
- 5th Neurological Department (Department of Neurogenetics), Research Centre of Neurology, Volokolamskoe shosse, 80, 125367 Moscow, Russia; (G.R.U.); (D.A.A.); (E.Y.F.); (V.V.P.); (S.N.I.)
| | - Petr G. Lokhov
- Laboratory of mass spectrometry-based metabolomics diagnostics, Institute of Biomedical Chemistry, 10 building 8, Pogodinskaya street, 119121 Moscow, Russia; (D.L.M.); (E.E.B.); (P.G.L.)
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12
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Ohnmacht J, May P, Sinkkonen L, Krüger R. Missing heritability in Parkinson's disease: the emerging role of non-coding genetic variation. J Neural Transm (Vienna) 2020; 127:729-748. [PMID: 32248367 PMCID: PMC7242266 DOI: 10.1007/s00702-020-02184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/24/2020] [Indexed: 02/01/2023]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder caused by a complex interplay of genetic and environmental factors. For the stratification of PD patients and the development of advanced clinical trials, including causative treatments, a better understanding of the underlying genetic architecture of PD is required. Despite substantial efforts, genome-wide association studies have not been able to explain most of the observed heritability. The majority of PD-associated genetic variants are located in non-coding regions of the genome. A systematic assessment of their functional role is hampered by our incomplete understanding of genotype-phenotype correlations, for example through differential regulation of gene expression. Here, the recent progress and remaining challenges for the elucidation of the role of non-coding genetic variants is reviewed with a focus on PD as a complex disease with multifactorial origins. The function of gene regulatory elements and the impact of non-coding variants on them, and the means to map these elements on a genome-wide level, will be delineated. Moreover, examples of how the integration of functional genomic annotations can serve to identify disease-associated pathways and to prioritize disease- and cell type-specific regulatory variants will be given. Finally, strategies for functional validation and considerations for suitable model systems are outlined. Together this emphasizes the contribution of rare and common genetic variants to the complex pathogenesis of PD and points to remaining challenges for the dissection of genetic complexity that may allow for better stratification, improved diagnostics and more targeted treatments for PD in the future.
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Affiliation(s)
- Jochen Ohnmacht
- LCSB, University of Luxembourg, Belvaux, Luxembourg
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Patrick May
- LCSB, University of Luxembourg, Belvaux, Luxembourg
| | - Lasse Sinkkonen
- Department of Life Sciences and Medicine (DLSM), University of Luxembourg, Belvaux, Luxembourg
| | - Rejko Krüger
- LCSB, University of Luxembourg, Belvaux, Luxembourg.
- Luxembourg Institute of Health (LIH), Transversal Translational Medicine, Strassen, Luxembourg.
- Parkinson Research Clinic, Centre Hospitalier de Luxembourg (CHL), Luxembourg, Luxembourg.
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13
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Gialluisi A, Reccia MG, Tirozzi A, Nutile T, Lombardi A, De Sanctis C, Varanese S, Pietracupa S, Modugno N, Simeone A, Ciullo M, Esposito T. Whole Exome Sequencing Study of Parkinson Disease and Related Endophenotypes in the Italian Population. Front Neurol 2020; 10:1362. [PMID: 31998221 PMCID: PMC6965311 DOI: 10.3389/fneur.2019.01362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Accepted: 12/10/2019] [Indexed: 12/30/2022] Open
Abstract
Parkinson Disease (PD) is a complex neurodegenerative disorder characterized by large genetic heterogeneity and missing heritability. Since the genetic background of PD can partly vary among ethnicities and neurological scales have been scarcely investigated in a PD setting, we performed an exploratory Whole Exome Sequencing (WES) analysis of 123 PD patients from mainland Italy, investigating scales assessing motor (UPDRS), cognitive (MoCA), and other non-motor symptoms (NMS). We performed variant prioritization, followed by targeted association testing of prioritized variants in 446 PD cases and 211 controls. Then we ran Exome-Wide Association Scans (EWAS) within sequenced PD cases (N = 113), testing both motor and non-motor PD endophenotypes, as well as their associations with Polygenic Risk Scores (PRS) influencing brain subcortical volumes. We identified a variant associated with PD, rs201330591 in GTF2H2 (5q13; alternative T allele: OR [CI] = 8.16[1.08; 61.52], FDR = 0.048), which was not replicated in an independent cohort of European ancestry (1,148 PD cases, 503 controls). In the EWAS, polygenic analyses revealed statistically significant multivariable associations of amygdala- [β(SE) = -0.039(0.013); FDR = 0.039] and caudate-PRS [0.043(0.013); 0.028] with motor symptoms. All subcortical PRSs in a multivariable model notably increased the variance explained in motor (adjusted-R2 = 38.6%), cognitive (32.2%) and other non-motor symptoms (28.9%), compared to baseline models (~20%). Although, the small sample size warrants further replications, these findings suggest shared genetic architecture between PD symptoms and subcortical structures, and provide interesting clues on PD genetic and neuroimaging features.
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Affiliation(s)
| | | | | | - Teresa Nutile
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | | | | | | | | | | | | | - Antonio Simeone
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Marina Ciullo
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
| | - Teresa Esposito
- IRCCS Neuromed, Pozzilli, Italy
- Institute of Genetics and Biophysics, National Research Council, Naples, Italy
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14
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Illés A, Csabán D, Grosz Z, Balicza P, Gézsi A, Molnár V, Bencsik R, Gál A, Klivényi P, Molnar MJ. The Role of Genetic Testing in the Clinical Practice and Research of Early-Onset Parkinsonian Disorders in a Hungarian Cohort: Increasing Challenge in Genetic Counselling, Improving Chances in Stratification for Clinical Trials. Front Genet 2019; 10:1061. [PMID: 31737044 PMCID: PMC6837163 DOI: 10.3389/fgene.2019.01061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/03/2019] [Indexed: 12/27/2022] Open
Abstract
The genetic analysis of early-onset Parkinsonian disorder (EOPD) is part of the clinical diagnostics. Several genes have been implicated in the genetic background of Parkinsonism, which is clinically indistinguishable from idiopathic Parkinson's disease. The identification of patient's genotype could support clinical decision-making process and also track and analyse outcomes in a comprehensive fashion. The aim of our study was to analyse the genetic background of EOPD in a Hungarian cohort and to evaluate the clinical usefulness of different genetic investigations. The age of onset was between 25 and 50 years. To identify genetic alterations, multiplex ligation-dependent probe amplification (n = 142), Sanger sequencing of the most common PD-associated genes (n = 142), and next-generation sequencing (n = 54) of 127 genes which were previously associated to neurodegenerative disorders were carried out. The genetic analysis identified several heterozygous damaging substitutions in PD-associated genes (C19orf12, DNAJC6, DNAJC13, EIF4G1, LRRK2, PRKN, PINK1, PLA2G6, SYNJ1). CNVs in PRKN and SNCA genes were found in five patients. In our cohort, nine previously published genetic risk factors were detected in three genes (GBA, LRRK2, and PINK1). In nine cases, two or three coexisting pathogenic mutations and risk variants were identified. Advances of sequencing technologies make it possible to aid diagnostics of PD by widening the scope of analysis to genes which were previously linked to other neurodegenerative disorders. Our data suggested that rare damaging variants are enriched versus neutral variants, among PD patients in the Hungarian population, which raise the possibility of an oligogenic effect. Heterozygous mutations of multiple recessive genes involved in the same pathway may perturb the molecular process linked to PD pathogenesis. Comprehensive genetic assessment of individual patients can rarely reveal monogenic cause in EOPD, although it may identify the involvement of multiple PD-associated genes in the background of the disease and may facilitate the better understanding of clinically distinct phenocopies. Due to the genetic complexity of the disease, genetic counselling and management is getting more challenging. Clinical geneticist should be prepared for counselling of patients with coexisting disease-causing mutations and susceptibility factors. At the same time, genomic-based stratification has increasing importance in future clinical trials.
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Affiliation(s)
- Anett Illés
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Dóra Csabán
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Zoltán Grosz
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Péter Balicza
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - András Gézsi
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Viktor Molnár
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Renáta Bencsik
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Anikó Gál
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
| | - Péter Klivényi
- Department of Neurology, University of Szeged, Szeged, Hungary
| | - Maria Judit Molnar
- Institute of Genomic Medicine and Rare Disorders, Semmelweis University, Budapest, Hungary
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15
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Olsen AL, Feany MB. Glial α-synuclein promotes neurodegeneration characterized by a distinct transcriptional program in vivo. Glia 2019; 67:1933-1957. [PMID: 31267577 DOI: 10.1002/glia.23671] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/29/2019] [Accepted: 06/18/2019] [Indexed: 12/15/2022]
Abstract
α-Synucleinopathies are neurodegenerative diseases that are characterized pathologically by α-synuclein inclusions in neurons and glia. The pathologic contribution of glial α-synuclein in these diseases is not well understood. Glial α-synuclein may be of particular importance in multiple system atrophy (MSA), which is defined pathologically by glial cytoplasmic α-synuclein inclusions. We have previously described Drosophila models of neuronal α-synucleinopathy, which recapitulate key features of the human disorders. We have now expanded our model to express human α-synuclein in glia. We demonstrate that expression of α-synuclein in glia alone results in α-synuclein aggregation, death of dopaminergic neurons, impaired locomotor function, and autonomic dysfunction. Furthermore, co-expression of α-synuclein in both neurons and glia worsens these phenotypes as compared to expression of α-synuclein in neurons alone. We identify unique transcriptomic signatures induced by glial as opposed to neuronal α-synuclein. These results suggest that glial α-synuclein may contribute to the burden of pathology in the α-synucleinopathies through a cell type-specific transcriptional program. This new Drosophila model system enables further mechanistic studies dissecting the contribution of glial and neuronal α-synuclein in vivo, potentially shedding light on mechanisms of disease that are especially relevant in MSA but also the α-synucleinopathies more broadly.
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Affiliation(s)
- Abby L Olsen
- Department of Neurology, Brigham and Women's Hospital, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Mel B Feany
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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