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Moisoi N. Mitochondrial proteases modulate mitochondrial stress signalling and cellular homeostasis in health and disease. Biochimie 2024:S0300-9084(24)00141-X. [PMID: 38906365 DOI: 10.1016/j.biochi.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/23/2024]
Abstract
Maintenance of mitochondrial homeostasis requires a plethora of coordinated quality control and adaptations' mechanisms in which mitochondrial proteases play a key role. Their activation or loss of function reverberate beyond local mitochondrial biochemical and metabolic remodelling into coordinated cellular pathways and stress responses that feedback onto the mitochondrial functionality and adaptability. Mitochondrial proteolysis modulates molecular and organellar quality control, metabolic adaptations, lipid homeostasis and regulates transcriptional stress responses. Defective mitochondrial proteolysis results in disease conditions most notably, mitochondrial diseases, neurodegeneration and cancer. Here, it will be discussed how mitochondrial proteases and mitochondria stress signalling impact cellular homeostasis and determine the cellular decision to survive or die, how these processes may impact disease etiopathology, and how modulation of proteolysis may offer novel therapeutic strategies.
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Affiliation(s)
- Nicoleta Moisoi
- Leicester School of Pharmacy, Leicester Institute for Pharmaceutical Health and Social Care Innovations, Faculty of Health and Life Sciences, De Montfort University, The Gateway, Hawthorn Building 1.03, LE1 9BH, Leicester, UK.
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2
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Kobayashi A, Kitagawa Y, Nasser A, Wakimoto H, Yamada K, Tanaka S. Emerging Roles and Mechanisms of RNA Modifications in Neurodegenerative Diseases and Glioma. Cells 2024; 13:457. [PMID: 38474421 DOI: 10.3390/cells13050457] [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: 01/16/2024] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Despite a long history of research, neurodegenerative diseases and malignant brain tumor gliomas are both considered incurable, facing challenges in the development of treatments. Recent evidence suggests that RNA modifications, previously considered as static components of intracellular RNAs, are in fact dynamically regulated across various RNA species in cells and play a critical role in major biological processes in the nervous system. Innovations in next-generation sequencing have enabled the accurate detection of modifications on bases and sugars within various RNA molecules. These RNA modifications influence the stability and transportation of RNA, and crucially affect its translation. This review delves into existing knowledge on RNA modifications to offer a comprehensive inventory of these modifications across different RNA species. The detailed regulatory functions and roles of RNA modifications within the nervous system are discussed with a focus on neurodegenerative diseases and gliomas. This article presents a comprehensive overview of the fundamental mechanisms and emerging roles of RNA modifications in these diseases, which can facilitate the creation of innovative diagnostics and therapeutics for these conditions.
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Affiliation(s)
- Ami Kobayashi
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Yosuke Kitagawa
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ali Nasser
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Hiroaki Wakimoto
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Keisuke Yamada
- Department of Neurosurgery, The University of Tokyo, Tokyo 113-0075, Japan
| | - Shota Tanaka
- Department of Neurosurgery, The University of Tokyo, Tokyo 113-0075, Japan
- Department of Neurosurgery, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama 700-8558, Japan
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Zhou R, Niu K, Wang C, He J, Huang W, Li T, Lan H, Zhang Y, Dang X, Mao L. Human-specific CHRFAM7A primes macrophages for a heightened pro-inflammatory response at the earlier stage of inflammation. Cell Biol Int 2023; 47:1926-1941. [PMID: 37655479 DOI: 10.1002/cbin.12083] [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: 10/01/2022] [Revised: 07/11/2023] [Accepted: 08/12/2023] [Indexed: 09/02/2023]
Abstract
α7-Nicotinic acetylcholine receptor (α7-nAChR) is the key effector molecule of the cholinergic anti-inflammatory pathway. Evolution has evolved a uniquely human α7-nAChR encoded by CHRFAM7A. It has been demonstrated that CHRFAM7A dominant negatively regulates the functions of α7-nAChR. However, its role in inflammation remains to be fully characterized. CHRFAM7A transgenic (Tg) mice were phenotypically normal and their peritoneal macrophages exhibited decreased ligand-binding capability and, importantly, an activated gene expression profile of pro-inflammatory cytokines. Surprisingly, when challenged with sepsis, the Tg mice showed no survival disadvantage relative to their wild-type (Wt) counterparts. Further analysis showed that the complete blood count and serum levels of pro-inflammatory cytokines were comparable at resting state, but the degrees of leukocyte mobilization and the increase of pro-inflammatory cytokines were significantly higher in Tg than Wt mice at the early stage of sepsis. In vitro, peritoneal macrophages of the Tg mice exhibited an exaggerated response to lipopolysaccharides (LPSs), especially at the earlier time points and at lower dosages of LPS. Remarkably, monocytes from CHRFAM7A-carrier showed similar dynamic changes of the pro-inflammatory cytokines to that observed in the Tg mice upon LPS challenge. Our results suggest that CHRFAM7A increases the mobilization of leukocytes and primes macrophages that confer an enhanced immune response at the early stage of inflammation, which may lead to prompt pathogen clearance, an evolutionary advantage in less severe inflammatory conditions.
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Affiliation(s)
- Rui Zhou
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Keran Niu
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Chaoying Wang
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Jianghui He
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Wenjun Huang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Tao Li
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Huan Lan
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Yanmin Zhang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
- Department of Cardiology, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xitong Dang
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
| | - Liang Mao
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Luzhou, China
- Department of Cardiology, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Lee WP, Wang H, Dombroski B, Cheng PL, Tucci A, Si YQ, Farrell J, Tzeng JY, Leung YY, Malamon J, Wang LS, Vardarajan B, Farrer L, Schellenberg G. Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects. RESEARCH SQUARE 2023:rs.3.rs-3353179. [PMID: 37886469 PMCID: PMC10602095 DOI: 10.21203/rs.3.rs-3353179/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Structural variations (SVs) are important contributors to the genetics of human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. We analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (N = 16,905) and identified 400,234 (168,223 high-quality) SVs. Laboratory validation yielded a sensitivity of 82% (85% for high-quality). We found a significant burden of deletions and duplications in AD cases, particularly for singletons and homozygous events. On AD genes, we observed the ultra-rare SVs associated with the disease, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1. Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, exemplified by a 5k deletion in complete LD with rs143080277 in NCK2. We also identified 16 SVs associated with AD and 13 SVs linked to AD-related pathological/cognitive endophenotypes. This study highlights the pivotal role of SVs in shaping our understanding of AD genetics.
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Wang H, Dombroski BA, Cheng PL, Tucci A, Si YQ, Farrell JJ, Tzeng JY, Leung YY, Malamon JS, Wang LS, Vardarajan BN, Farrer LA, Schellenberg GD, Lee WP. Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.13.23295505. [PMID: 37745545 PMCID: PMC10516060 DOI: 10.1101/2023.09.13.23295505] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Structural variations (SVs) are important contributors to the genetics of numerous human diseases. However, their role in Alzheimer's disease (AD) remains largely unstudied due to challenges in accurately detecting SVs. Here, we analyzed whole-genome sequencing data from the Alzheimer's Disease Sequencing Project (ADSP, N=16,905 subjects) and identified 400,234 (168,223 high-quality) SVs. We found a significant burden of deletions and duplications in AD cases (OR=1.05, P=0.03), particularly for singletons (OR=1.12, P=0.0002) and homozygous events (OR=1.10, P<0.0004). On AD genes, the ultra-rare SVs, including protein-altering SVs in ABCA7, APP, PLCG2, and SORL1, were associated with AD (SKAT-O P=0.004). Twenty-one SVs are in linkage disequilibrium (LD) with known AD-risk variants, e.g., a deletion (chr2:105731359-105736864) in complete LD (R2=0.99) with rs143080277 (chr2:105749599) in NCK2. We also identified 16 SVs associated with AD and 13 SVs associated with AD-related pathological/cognitive endophenotypes. Our findings demonstrate the broad impact of SVs on AD genetics.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Beth A Dombroski
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Po-Liang Cheng
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Albert Tucci
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - Ya-Qin Si
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - John J Farrell
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, MA 02118, USA
| | - Jung-Ying Tzeng
- Bioinformatics Research Center, North Carolina State University, NC 27695, USA
| | - Yuk Yee Leung
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - John S Malamon
- Department of Surgery, Scholl of Medicine, University of Colorado, CO 80045, USA
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, NY 10032, USA
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, NY 10032, USA
| | - Lindsay A Farrer
- Department of Medicine (Biomedical Genetics), Boston University School of Medicine, MA 02118, USA
- Department of Neurology, Boston University School of Medicine, MA 02118, USA
- Department of Ophthalmology, Boston University School of Medicine, MA 02118, USA
- Department of Biostatistics, Boston University School of Public Health, MA 02118, USA
- Department of Epidemiology, Boston University School of Public Health, MA 02118, USA
| | - Gerard D Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, PA 19104, USA
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Lambert JC, Ramirez A, Grenier-Boley B, Bellenguez C. Step by step: towards a better understanding of the genetic architecture of Alzheimer's disease. Mol Psychiatry 2023; 28:2716-2727. [PMID: 37131074 PMCID: PMC10615767 DOI: 10.1038/s41380-023-02076-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is considered to have a large genetic component. Our knowledge of this component has progressed over the last 10 years, thanks notably to the advent of genome-wide association studies and the establishment of large consortia that make it possible to analyze hundreds of thousands of cases and controls. The characterization of dozens of chromosomal regions associated with the risk of developing AD and (in some loci) the causal genes responsible for the observed disease signal has confirmed the involvement of major pathophysiological pathways (such as amyloid precursor protein metabolism) and opened up new perspectives (such as the central role of microglia and inflammation). Furthermore, large-scale sequencing projects are starting to reveal the major impact of rare variants - even in genes like APOE - on the AD risk. This increasingly comprehensive knowledge is now being disseminated through translational research; in particular, the development of genetic risk/polygenic risk scores is helping to identify the subpopulations more at risk or less at risk of developing AD. Although it is difficult to assess the efforts still needed to comprehensively characterize the genetic component of AD, several lines of research can be improved or initiated. Ultimately, genetics (in combination with other biomarkers) might help to redefine the boundaries and relationships between various neurodegenerative diseases.
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Affiliation(s)
- Jean-Charles Lambert
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France.
| | - Alfredo Ramirez
- Division of Neurogenetics and Molecular Psychiatry, Department of Psychiatry and Psychotherapy, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- Department of Neurodegenerative diseases and Geriatric Psychiatry, University Hospital Bonn, Medical Faculty, Bonn, Germany
- Department of Psychiatry & Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Cluster of Excellence Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Benjamin Grenier-Boley
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
| | - Céline Bellenguez
- Univ. Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167-RID-AGE Facteurs de risque et déterminants moléculaires des maladies liées au vieillissement, Lille, France
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Ma Y, Liang RM, Ma N, Mi XJ, Cheng ZY, Zhang ZJ, Lu BS, Li PA. Immp2l Mutation Induces Mitochondrial Membrane Depolarization and Complex III Activity Suppression after Middle Cerebral Artery Occlusion in Mice. Curr Med Sci 2023:10.1007/s11596-023-2726-5. [PMID: 37243806 DOI: 10.1007/s11596-023-2726-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/23/2022] [Indexed: 05/29/2023]
Abstract
OBJECTIVE We previously reported that mutations in inner mitochondrial membrane peptidase 2-like (Immp2l) increase infarct volume, enhance superoxide production, and suppress mitochondrial respiration after transient cerebral focal ischemia and reperfusion injury. The present study investigated the impact of heterozygous Immp2l mutation on mitochondria function after ischemia and reperfusion injury in mice. METHODS Mice were subjected to middle cerebral artery occlusion for 1 h followed by 0, 1, 5, and 24 h of reperfusion. The effects of Immp2l+/- on mitochondrial membrane potential, mitochondrial respiratory complex III activity, caspase-3, and apoptosis-inducing factor (AIF) translocation were examined. RESULTS Immp2l+/- increased ischemic brain damage and the number of TUNEL-positive cells compared with wild-type mice. Immp2l+/- led to mitochondrial damage, mitochondrial membrane potential depolarization, mitochondrial respiratory complex III activity suppression, caspase-3 activation, and AIF nuclear translocation. CONCLUSION The adverse impact of Immp2l+/- on the brain after ischemia and reperfusion might be related to mitochondrial damage that involves depolarization of the mitochondrial membrane potential, inhibition of the mitochondrial respiratory complex III, and activation of mitochondria-mediated cell death pathways. These results suggest that patients with stroke carrying Immp2l+/- might have worse and more severe infarcts, followed by a worse prognosis than those without Immp2l mutations.
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Affiliation(s)
- Yi Ma
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, 750004, China.
- Department of Ningxia Key Laboratory of Cerebrocranial Diseases, Ningxia Medical University, Yinchuan, 750004, China.
| | - Rui-Min Liang
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Ning Ma
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Xiao-Juan Mi
- Department of Pathology, School of Basic Medicine, Ningxia Medical University, Yinchuan, 750004, China
| | - Zheng-Yi Cheng
- Department of Pathology, Xi'an No. 3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, 710018, China
| | - Zi-Jing Zhang
- Department of Anesthesiology, Ningxia Chinese Medicine Research Center, Yinchuan, 750004, China
| | - Bai-Song Lu
- Institute for Regenerative Medicine, Wake Forest University School of Medicine, Winston-Salem, 27110, USA
| | - P Andy Li
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technological Enterprise (BRITE), North Carolina Central University, Durham, 27707, USA.
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Wang H, Wang LS, Schellenberg G, Lee WP. The role of structural variations in Alzheimer's disease and other neurodegenerative diseases. Front Aging Neurosci 2023; 14:1073905. [PMID: 36846102 PMCID: PMC9944073 DOI: 10.3389/fnagi.2022.1073905] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 12/31/2022] [Indexed: 02/10/2023] Open
Abstract
Dozens of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease (AD) have been discovered by large scale genome-wide association studies (GWASs). However, only a small portion of the genetic component of AD can be explained by SNPs observed from GWAS. Structural variation (SV) can be a major contributor to the missing heritability of AD; while SV in AD remains largely unexplored as the accurate detection of SVs from the widely used array-based and short-read technology are still far from perfect. Here, we briefly summarized the strengths and weaknesses of available SV detection methods. We reviewed the current landscape of SV analysis in AD and SVs that have been found associated with AD. Particularly, the importance of currently less explored SVs, including insertions, inversions, short tandem repeats, and transposable elements in neurodegenerative diseases were highlighted.
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Affiliation(s)
- Hui Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Li-San Wang
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Gerard Schellenberg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Wan-Ping Lee
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
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Peng W, Mao L, Dang X. The emergence of the uniquely human α7 nicotinic acetylcholine receptor gene and its roles in inflammation. Gene 2022; 842:146777. [PMID: 35952843 DOI: 10.1016/j.gene.2022.146777] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/23/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022]
Abstract
The uniquely human CHRFAM7A gene is evolved from the fusion of two partially duplicated genes, ULK4 and CHRNA7. Transcription of CHRFAM7A gene produces a 1256-bp open reading frame (ORF) that encodes duplicate α7-nAChR (dup-α7-nAChR), in which a 27-aminoacid peptide derived from ULK4 gene replaces the 146-aminoacid N-terminal extracellular domain of α7-nAChR, and the rest protein domains are exactly the same as those of α7-nAChR. In vitro, dup-α7-nAChR has been shown to form hetero-pentamer with α7-nAChR and dominant-negatively inhibits the channel functions of the latter. α7-nAChR has been shown to participate in many pathophysiological processes such as cognition, memory, neuronal degenerative disease, psychological disease, and inflammatory diseases, among others, and thus has been extensively exploited as potential therapeutic targets for many diseases. Unfortunately, many lead compounds that showed potent therapeutic effect in preclinical animal models failed clinical trials, suggesting the possibility that the contribution of the uniquely human CHRFAM7A gene may not be accounted for in the preclinical research. Here, we review the emergence of CHRFAM7A gene and its transcriptional regulation, the regulatory roles of CHRFAM7A gene in α7-nAChR-mediated cholinergic anti-inflammatory pathway, and the potential implications of CHRFAM7A gene in translational research and drug discovery.
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Affiliation(s)
- Wanling Peng
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, India
| | - Liang Mao
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, India
| | - Xitong Dang
- The Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiological Key Laboratory of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, India; Department of Cardiovascular Medicine, The 1st Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou 646000, China.
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10
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Ming C, Wang M, Wang Q, Neff R, Wang E, Shen Q, Reddy JS, Wang X, Allen M, Ertekin‐Taner N, De Jager PL, Bennett DA, Haroutunian V, Schadt E, Zhang B. Whole genome sequencing-based copy number variations reveal novel pathways and targets in Alzheimer's disease. Alzheimers Dement 2022; 18:1846-1867. [PMID: 34918867 PMCID: PMC9264340 DOI: 10.1002/alz.12507] [Citation(s) in RCA: 10] [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: 04/02/2021] [Revised: 09/21/2021] [Accepted: 09/21/2021] [Indexed: 01/28/2023]
Abstract
INTRODUCTION A few copy number variations (CNVs) have been reported for Alzheimer's disease (AD). However, there is a lack of a systematic investigation of CNVs in AD based on whole genome sequencing (WGS) data. METHODS We used four methods to identify consensus CNVs from the WGS data of 1,411 individuals and further investigated their functional roles in AD using the matched transcriptomic and clinicopathological data. RESULTS We identified 3,012 rare AD-specific CNVs whose residing genes are enriched for cellular glucuronidation and neuron projection pathways. Genes whose mRNA expressions are significantly correlated with common CNVs are involved in major histocompatibility complex class II receptor activity. Integration of CNVs, gene expression, and clinical and pathological traits further pinpoints a key CNV that potentially regulates immune response in AD. DISCUSSION We identify CNVs as potential genetic regulators of immune response in AD. The identified CNVs and their downstream gene networks reveal novel pathways and targets for AD.
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Affiliation(s)
- Chen Ming
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Minghui Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Qian Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Ryan Neff
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Erming Wang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Qi Shen
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Joseph S. Reddy
- Department of Quantitative Health SciencesMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Xue Wang
- Department of Quantitative Health SciencesMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Mariet Allen
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Nilüfer Ertekin‐Taner
- Department of NeuroscienceMayo Clinic FloridaJacksonvilleFloridaUSA
- Department of NeurologyMayo Clinic FloridaJacksonvilleFloridaUSA
| | - Philip L. De Jager
- Center for Translational & Computational NeuroimmunologyDepartment of Neurology and the Taub InstituteColumbia University Medical CenterNew YorkNew YorkUSA
- The Broad Institute of MIT and HarvardCambridgeMassachusettsUSA
| | - David A. Bennett
- Rush Alzheimer's Disease CenterRush University Medical CenterChicagoIllinoisUSA
| | - Vahram Haroutunian
- Nash Family Department of NeuroscienceIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Department of PsychiatryIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Alzheimer's Disease Research CenterIcahn School of Medicine at Mount SinaiNew YorkNew York
- PsychiatryJJ Peters VA Medical CenterBronxNew YorkUSA
| | - Eric Schadt
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Bin Zhang
- Department of Genetics and Genomic SciencesIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Mount Sinai Center for Transformative Disease ModelingIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
- Icahn Institute of Genomics and Multiscale BiologyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
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11
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Ji F, Zhu X, Liao H, Ouyang L, Huang Y, Syeda MZ, Ying S. New Era of Mapping and Understanding Common Fragile Sites: An Updated Review on Origin of Chromosome Fragility. Front Genet 2022; 13:906957. [PMID: 35669181 PMCID: PMC9164283 DOI: 10.3389/fgene.2022.906957] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 04/25/2022] [Indexed: 11/13/2022] Open
Abstract
Common fragile sites (CFSs) are specific genomic loci prone to forming gaps or breakages upon replication perturbation, which correlate well with chromosomal rearrangement and copy number variation. CFSs have been actively studied due to their important pathophysiological relevance in different diseases such as cancer and neurological disorders. The genetic locations and sequences of CFSs are crucial to understanding the origin of such unstable sites, which require reliable mapping and characterizing approaches. In this review, we will inspect the evolving techniques for CFSs mapping, especially genome-wide mapping and sequencing of CFSs based on current knowledge of CFSs. We will also revisit the well-established hypotheses on the origin of CFSs fragility, incorporating novel findings from the comprehensive analysis of finely mapped CFSs regarding their locations, sequences, and replication/transcription, etc. This review will present the most up-to-date picture of CFSs and, potentially, a new framework for future research of CFSs.
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Affiliation(s)
- Fang Ji
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Xinli Zhu
- Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Hongwei Liao
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Liujian Ouyang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingfei Huang
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Madiha Zahra Syeda
- Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
| | - Songmin Ying
- International Institutes of Medicine, The Fourth Affiliated Hospital of Zhejiang University School of Medicine, Yiwu, China.,Department of Pharmacology and Department of Respiratory and Critical Care Medicine of the Second Affiliated Hospital, Key Laboratory of Respiratory Disease of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou, China
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12
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Molière A, Beer KB, Wehman AM. Dopey proteins are essential but overlooked regulators of membrane trafficking. J Cell Sci 2022; 135:274973. [PMID: 35388894 DOI: 10.1242/jcs.259628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
Dopey family proteins play crucial roles in diverse processes from morphogenesis to neural function and are conserved from yeast to mammals. Understanding the mechanisms behind these critical functions could have major clinical significance, as dysregulation of Dopey proteins has been linked to the cognitive defects in Down syndrome, as well as neurological diseases. Dopey proteins form a complex with the non-essential GEF-like protein Mon2 and an essential lipid flippase from the P4-ATPase family. Different combinations of Dopey, Mon2 and flippases have been linked to regulating membrane remodeling, from endosomal recycling to extracellular vesicle formation, through their interactions with lipids and other membrane trafficking regulators, such as ARL1, SNX3 and the kinesin-1 light chain KLC2. Despite these important functions and their likely clinical significance, Dopey proteins remain understudied and their roles elusive. Here, we review the major scientific discoveries relating to Dopey proteins and detail key open questions regarding their function to draw attention to these fascinating enigmas.
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Affiliation(s)
- Adrian Molière
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA
| | - Katharina B Beer
- Rudolf Virchow Center, Julius Maximilian University of Würzburg, D-97080, Würzburg, Germany
| | - Ann M Wehman
- Department of Biological Sciences, University of Denver, Denver, CO 80208, USA.,Rudolf Virchow Center, Julius Maximilian University of Würzburg, D-97080, Würzburg, Germany
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13
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Di Lascio S, Fornasari D, Benfante R. The Human-Restricted Isoform of the α7 nAChR, CHRFAM7A: A Double-Edged Sword in Neurological and Inflammatory Disorders. Int J Mol Sci 2022; 23:ijms23073463. [PMID: 35408823 PMCID: PMC8998457 DOI: 10.3390/ijms23073463] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/13/2022] [Accepted: 03/21/2022] [Indexed: 12/13/2022] Open
Abstract
CHRFAM7A is a relatively recent and exclusively human gene arising from the partial duplication of exons 5 to 10 of the α7 neuronal nicotinic acetylcholine receptor subunit (α7 nAChR) encoding gene, CHRNA7. CHRNA7 is related to several disorders that involve cognitive deficits, including neuropsychiatric, neurodegenerative, and inflammatory disorders. In extra-neuronal tissues, α7nAChR plays an important role in proliferation, differentiation, migration, adhesion, cell contact, apoptosis, angiogenesis, and tumor progression, as well as in the modulation of the inflammatory response through the “cholinergic anti-inflammatory pathway”. CHRFAM7A translates the dupα7 protein in a multitude of cell lines and heterologous systems, while maintaining processing and trafficking that are very similar to the full-length form. It does not form functional ion channel receptors alone. In the presence of CHRNA7 gene products, dupα7 can assemble and form heteromeric receptors that, in order to be functional, should include at least two α7 subunits to form the agonist binding site. When incorporated into the receptor, in vitro and in vivo data showed that dupα7 negatively modulated α7 activity, probably due to a reduction in the number of ACh binding sites. Very recent data in the literature report that the presence of the duplicated gene may be responsible for the translational gap in several human diseases. Here, we will review the studies that have been conducted on CHRFAM7A in different pathologies, with the intent of providing evidence regarding when and how the expression of this duplicated gene may be beneficial or detrimental in the pathogenesis, and eventually in the therapeutic response, to CHRNA7-related neurological and non-neurological diseases.
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Affiliation(s)
- Simona Di Lascio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
| | - Diego Fornasari
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
| | - Roberta Benfante
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, 20129 Milan, Italy; (S.D.L.); (D.F.)
- CNR Institute of Neuroscience, 20845 Vedano al Lambro, Italy
- NeuroMi, Milan Center for Neuroscience, University of Milano Bicocca, 20126 Milan, Italy
- Correspondence:
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14
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Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
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Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
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15
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Kunová N, Havalová H, Ondrovičová G, Stojkovičová B, Bauer JA, Bauerová-Hlinková V, Pevala V, Kutejová E. Mitochondrial Processing Peptidases-Structure, Function and the Role in Human Diseases. Int J Mol Sci 2022; 23:1297. [PMID: 35163221 PMCID: PMC8835746 DOI: 10.3390/ijms23031297] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial proteins are encoded by both nuclear and mitochondrial DNA. While some of the essential subunits of the oxidative phosphorylation (OXPHOS) complexes responsible for cellular ATP production are synthesized directly in the mitochondria, most mitochondrial proteins are first translated in the cytosol and then imported into the organelle using a sophisticated transport system. These proteins are directed mainly by targeting presequences at their N-termini. These presequences need to be cleaved to allow the proper folding and assembly of the pre-proteins into functional protein complexes. In the mitochondria, the presequences are removed by several processing peptidases, including the mitochondrial processing peptidase (MPP), the inner membrane processing peptidase (IMP), the inter-membrane processing peptidase (MIP), and the mitochondrial rhomboid protease (Pcp1/PARL). Their proper functioning is essential for mitochondrial homeostasis as the disruption of any of them is lethal in yeast and severely impacts the lifespan and survival in humans. In this review, we focus on characterizing the structure, function, and substrate specificities of mitochondrial processing peptidases, as well as the connection of their malfunctions to severe human diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Eva Kutejová
- Department of Biochemistry and Protein Structure, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská Cesta 21, 845 51 Bratislava, Slovakia; (H.H.); (G.O.); (B.S.); (J.A.B.); (V.B.-H.); (V.P.)
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16
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Dehghani N, Guven G, Kun-Rodrigues C, Gouveia C, Foster K, Hanagasi H, Lohmann E, Samanci B, Gurvit H, Bilgic B, Bras J, Guerreiro R. A comprehensive analysis of copy number variation in a Turkish dementia cohort. Hum Genomics 2021; 15:48. [PMID: 34321086 PMCID: PMC8317312 DOI: 10.1186/s40246-021-00346-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Copy number variants (CNVs) include deletions or multiplications spanning genomic regions. These regions vary in size and may span genes known to play a role in human diseases. As examples, duplications and triplications of SNCA have been shown to cause forms of Parkinson's disease, while duplications of APP cause early onset Alzheimer's disease (AD). RESULTS Here, we performed a systematic analysis of CNVs in a Turkish dementia cohort in order to further characterize the genetic causes of dementia in this population. One hundred twenty-four Turkish individuals, either at risk of dementia due to family history, diagnosed with mild cognitive impairment, AD, or frontotemporal dementia, were whole-genome genotyped and CNVs were detected. We integrated family analysis with a comprehensive assessment of potentially disease-associated CNVs in this Turkish dementia cohort. We also utilized both dementia and non-dementia individuals from the UK Biobank in order to further elucidate the potential role of the identified CNVs in neurodegenerative diseases. We report CNVs overlapping the previously implicated genes ZNF804A, SNORA70B, USP34, XPO1, and a locus on chromosome 9 which includes a cluster of olfactory receptors and ABCA1. Additionally, we also describe novel CNVs potentially associated with dementia, overlapping the genes AFG1L, SNX3, VWDE, and BC039545. CONCLUSIONS Genotyping data from understudied populations can be utilized to identify copy number variation which may contribute to dementia.
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Affiliation(s)
- Nadia Dehghani
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Gamze Guven
- Department of Genetics, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Turkey
| | - Celia Kun-Rodrigues
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Catarina Gouveia
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Kalina Foster
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
- Neuroscience Department, Michigan State University College of Natural Science, East Lansing, MI, USA
| | - Hasmet Hanagasi
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Ebba Lohmann
- Department of Neurodegenerative Diseases, Hertie Institute for Clinical Brain Research, University of Tübingen, Tübingen, Germany
- DZNE, German Center for Neurodegenerative Diseases, Tübingen, Germany
| | - Bedia Samanci
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Hakan Gurvit
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Basar Bilgic
- Behavioural Neurology and Movement Disorders Unit, Department of Neurology, Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | - Jose Bras
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, Michigan, USA.
- Division of Psychiatry and Behavioral Medicine, Michigan State University College of Human Medicine, Grand Rapids, MI, USA.
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17
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Ravanidis S, Bougea A, Karampatsi D, Papagiannakis N, Maniati M, Stefanis L, Doxakis E. Differentially Expressed Circular RNAs in Peripheral Blood Mononuclear Cells of Patients with Parkinson's Disease. Mov Disord 2021; 36:1170-1179. [PMID: 33433033 PMCID: PMC8248110 DOI: 10.1002/mds.28467] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/18/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
Background New noninvasive and affordable molecular approaches that will complement current practices and increase the accuracy of Parkinson's disease (PD) diagnosis are urgently needed. Circular RNAs (circRNAs) are stable noncoding RNAs that accumulate with aging in neurons and are increasingly shown to regulate all aspects of neuronal development and function. Objectives Τhe aims of this study were to identify differentially expressed circRNAs in blood mononuclear cells of patients with idiopathic PD and explore the competing endogenous RNA networks affected. Methods Eighty‐seven circRNAs were initially selected based on relatively high gene expression in the human brain. More than half of these were readily detectable in blood mononuclear cells using real‐time reverse transcription‐polymerase chain reaction. Comparative expression analysis was then performed in blood mononuclear cells from 60 control subjects and 60 idiopathic subjects with PD. Results Six circRNAs were significantly down‐regulated in patients with PD. The classifier that best distinguished PD consisted of four circRNAs with an area under the curve of 0.84. Cross‐linking immunoprecipitation‐sequencing data revealed that the RNA‐binding proteins bound by most of the deregulated circRNAs include the neurodegeneration‐associated FUS, TDP43, FMR1, and ATXN2. MicroRNAs predicted to be sequestered by most deregulated circRNAs have the Gene Ontology categories “protein modification” and “transcription factor activity” mostly enriched. Conclusions This is the first study that identifies specific circRNAs that may serve as diagnostic biomarkers for PD. Because they are highly expressed in the brain and are derived from genes with essential brain functions, they may also hint on the PD pathways affected. © 2021 Biomedical Research Foundation, Academy of Athens. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Stylianos Ravanidis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Anastasia Bougea
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Dimitra Karampatsi
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Nikolaos Papagiannakis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Matina Maniati
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Leonidas Stefanis
- Center of Clinical Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece.,First Department of Neurology, National and Kapodistrian University of Athens Medical School, Athens, Greece
| | - Epaminondas Doxakis
- Center of Basic Research, Biomedical Research Foundation, Academy of Athens, Athens, Greece
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18
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El Bitar F, Al Sudairy N, Qadi N, Al Rajeh S, Alghamdi F, Al Amari H, Al Dawsari G, Alsubaie S, Al Sudairi M, Abdulaziz S, Al Tassan N. A Comprehensive Analysis of Unique and Recurrent Copy Number Variations in Alzheimer's Disease and its Related Disorders. Curr Alzheimer Res 2020; 17:926-938. [PMID: 33256577 DOI: 10.2174/1567205017666201130111424] [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: 04/25/2020] [Revised: 08/20/2020] [Accepted: 10/29/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Copy number variations (CNVs) play an important role in the genetic etiology of various neurological disorders, including Alzheimer's disease (AD). Type 2 diabetes mellitus (T2DM) and major depressive disorder (MDD) were shown to have share mechanisms and signaling pathways with AD. OBJECTIVE We aimed to assess CNVs regions that may harbor genes contributing to AD, T2DM, and MDD in 67 Saudi familial and sporadic AD patients, with no alterations in the known genes of AD and genotyped previously for APOE. METHODS DNA was analyzed using the CytoScan-HD array. Two layers of filtering criteria were applied. All the identified CNVs were checked in the Database of Genomic Variants (DGV). RESULTS A total of 1086 CNVs (565 gains and 521 losses) were identified in our study. We found 73 CNVs harboring genes that may be associated with AD, T2DM or MDD. Nineteen CNVs were novel. Most importantly, 42 CNVs were unique in our studied cohort existing only in one patient. Two large gains on chromosomes 1 and 13 harbored genes implicated in the studied disorders. We identified CNVs in genes that encode proteins involved in the metabolism of amyloid-β peptide (AGRN, APBA2, CR1, CR2, IGF2R, KIAA0125, MBP, RER1, RTN4R, VDR and WISPI) or Tau proteins (CACNAIC, CELF2, DUSP22, HTRA1 and SLC2A14). CONCLUSION The present work provided information on the presence of CNVs related to AD, T2DM, and MDD in Saudi Alzheimer's patients.
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Affiliation(s)
- Fadia El Bitar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nourah Al Sudairy
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Najeeb Qadi
- Department of Neurosciences, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | | | - Fatimah Alghamdi
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hala Al Amari
- Institute of Biology and Environmental Research, National Center for Biotechnology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ghadeer Al Dawsari
- Institute of Biology and Environmental Research, National Center for Genomics Technology, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sahar Alsubaie
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mishael Al Sudairi
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sara Abdulaziz
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nada Al Tassan
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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19
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Suh J, Romano DM, Nitschke L, Herrick SP, DiMarzio BA, Dzhala V, Bae JS, Oram MK, Zheng Y, Hooli B, Mullin K, Gennarino VA, Wasco W, Schmahmann JD, Albers MW, Zoghbi HY, Tanzi RE. Loss of Ataxin-1 Potentiates Alzheimer's Pathogenesis by Elevating Cerebral BACE1 Transcription. Cell 2020; 178:1159-1175.e17. [PMID: 31442405 DOI: 10.1016/j.cell.2019.07.043] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 12/21/2018] [Accepted: 07/24/2019] [Indexed: 01/28/2023]
Abstract
Expansion of CAG trinucleotide repeats in ATXN1 causes spinocerebellar ataxia type 1 (SCA1), a neurodegenerative disease that impairs coordination and cognition. While ATXN1 is associated with increased Alzheimer's disease (AD) risk, CAG repeat number in AD patients is not changed. Here, we investigated the consequences of ataxin-1 loss of function and discovered that knockout of Atxn1 reduced CIC-ETV4/5-mediated inhibition of Bace1 transcription, leading to increased BACE1 levels and enhanced amyloidogenic cleavage of APP, selectively in AD-vulnerable brain regions. Elevated BACE1 expression exacerbated Aβ deposition and gliosis in AD mouse models and impaired hippocampal neurogenesis and olfactory axonal targeting. In SCA1 mice, polyglutamine-expanded mutant ataxin-1 led to the increase of BACE1 post-transcriptionally, both in cerebrum and cerebellum, and caused axonal-targeting deficit and neurodegeneration in the hippocampal CA2 region. These findings suggest that loss of ataxin-1 elevates BACE1 expression and Aβ pathology, rendering it a potential contributor to AD risk and pathogenesis.
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Affiliation(s)
- Jaehong Suh
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA.
| | - Donna M Romano
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Larissa Nitschke
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Scott P Herrick
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Britt A DiMarzio
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Volodymyr Dzhala
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Jun-Seok Bae
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Mary K Oram
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Yuejiao Zheng
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Basavaraj Hooli
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Kristina Mullin
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Vincenzo A Gennarino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA
| | - Wilma Wasco
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Jeremy D Schmahmann
- Ataxia Unit, Cognitive Behavioral Neurology Unit, Laboratory for Neuroanatomy and Cerebellar Neurobiology, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Mark W Albers
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA
| | - Huda Y Zoghbi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute at Texas Children's Hospital, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, McCance Center for Brain Health, MassGeneral Institute of Neurodegenerative Disease, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA.
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20
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Ziegler GC, Almos P, McNeill RV, Jansch C, Lesch KP. Cellular effects and clinical implications of SLC2A3 copy number variation. J Cell Physiol 2020; 235:9021-9036. [PMID: 32372501 DOI: 10.1002/jcp.29753] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 04/04/2020] [Accepted: 04/21/2020] [Indexed: 12/19/2022]
Abstract
SLC2A3 encodes the predominantly neuronal glucose transporter 3 (GLUT3), which facilitates diffusion of glucose across plasma membranes. The human brain depends on a steady glucose supply for ATP generation, which consequently fuels critical biochemical processes, such as axonal transport and neurotransmitter release. Besides its role in the central nervous system, GLUT3 is also expressed in nonneural organs, such as the heart and white blood cells, where it is equally involved in energy metabolism. In cancer cells, GLUT3 overexpression contributes to the Warburg effect by answering the cell's increased glycolytic demands. The SLC2A3 gene locus at chromosome 12p13.31 is unstable and prone to non-allelic homologous recombination events, generating multiple copy number variants (CNVs) of SLC2A3 which account for alterations in SLC2A3 expression. Recent associations of SLC2A3 CNVs with different clinical phenotypes warrant investigation of the potential influence of these structural variants on pathomechanisms of neuropsychiatric, cardiovascular, and immune diseases. In this review, we accumulate and discuss the evidence how SLC2A3 gene dosage may exert diverse protective or detrimental effects depending on the pathological condition. Cellular states which lead to increased energetic demand, such as organ development, proliferation, and cellular degeneration, appear particularly susceptible to alterations in SLC2A3 copy number. We conclude that better understanding of the impact of SLC2A3 variation on disease etiology may potentially provide novel therapeutic approaches specifically targeting this GLUT.
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Affiliation(s)
- Georg C Ziegler
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Germany.,Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Würzburg, Germany
| | - Peter Almos
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Germany.,Department of Psychiatry, University of Szeged, Hungary
| | - Rhiannon V McNeill
- Department of Psychiatry, Psychosomatics and Psychotherapy, Center of Mental Health, University of Würzburg, Germany
| | - Charline Jansch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Germany
| | - Klaus-Peter Lesch
- Division of Molecular Psychiatry, Center of Mental Health, University of Würzburg, Germany.,Department of Psychiatry and Neuropsychology, School of Mental Health and Neuroscience, Maastricht University, Maastricht, The Netherlands.,Laboratory of Psychiatric Neurobiology, Institute of Molecular Medicine, I.M. Sechenov First Moscow State Medical University, Moscow, Russia
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21
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Cosemans N, Vandenhove L, Vogels A, Devriendt K, Van Esch H, Van Buggenhout G, Olivié H, de Ravel T, Ortibus E, Legius E, Aerssens P, Breckpot J, R Vermeesch J, Shen S, Fitzgerald J, Gallagher L, Peeters H. The clinical relevance of intragenic NRXN1 deletions. J Med Genet 2020; 57:347-355. [PMID: 31932357 DOI: 10.1136/jmedgenet-2019-106448] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 11/02/2019] [Accepted: 11/17/2019] [Indexed: 11/03/2022]
Abstract
BACKGROUND Intragenic NRXN1 deletions are susceptibility variants for neurodevelopmental disorders; however, their clinical interpretation is often unclear. Therefore, a literature study and an analysis of 43 previously unpublished deletions are provided. METHODS The literature cohort covered 629 heterozygous NRXN1 deletions: 148 in controls, 341 in probands and 140 in carrier relatives, and was used for clinical hypothesis testing. Exact breakpoint determination was performed for 43 in-house deletions. RESULTS The prevalence of exonic NRXN1 deletions in controls was ~1/3000 as compared with ~1/800 in patients with neurodevelopmental/neuropsychiatric disorders. The differential distribution of deletions across the gene between controls and probands allowed to distinguish distinct areas within the gene. Exon 6-24 deletions appeared only twice in over 100000 control individuals, had an estimated penetrance for neurodevelopmental disorders of 32.43%, a de novo rate of 50% and segregated mainly with intellectual disability (ID) and schizophrenia. In contrast, exon 1-5 deletions appeared in 20 control individuals, had an estimated penetrance of 12.59%, a de novo rate of 32.5% and were reported with a broad range of neurodevelopmental phenotypes. Exact breakpoint determination revealed six recurrent intron 5 deletions. CONCLUSION Exon 6-24 deletions have a high penetrance and are mainly associated with ID and schizophrenia. In contrast, the actual contribution of exon 1-5 deletions to a neurodevelopmental/neuropsychiatric disorder in an individual patient and family remains very difficult to assess. To enhance the clinical interpretation, this study provides practical considerations for counselling and an interactive table for comparing a deletion of interest with the available literature data.
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Affiliation(s)
- Nele Cosemans
- Department of Human Genetics, KU Leuven, Leuven, Belgium.,Leuven Autism Research (LAuRes), KU Leuven, Leuven, Belgium
| | | | - Annick Vogels
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Hilde Van Esch
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Hilde Olivié
- Center for Developmental Disabilities Leuven, Leuven, Belgium
| | - Thomy de Ravel
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Els Ortibus
- Center for Developmental Disabilities Leuven, Leuven, Belgium.,Department of Development and Regeneration, KU Leuven, Leuven, Belgium
| | - Eric Legius
- Department of Human Genetics, KU Leuven, Leuven, Belgium.,Leuven Autism Research (LAuRes), KU Leuven, Leuven, Belgium
| | | | | | | | - Sanbing Shen
- Regenerative Medicine Institute, School of Medicine, BioMedical Sciences Building, National University of Ireland (NUI), Galway, Ireland
| | | | - Louise Gallagher
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin, Ireland
| | - Hilde Peeters
- Department of Human Genetics, KU Leuven, Leuven, Belgium .,Leuven Autism Research (LAuRes), KU Leuven, Leuven, Belgium
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22
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Hu Z, Xiao X, Zhang Z, Li M. Genetic insights and neurobiological implications from NRXN1 in neuropsychiatric disorders. Mol Psychiatry 2019; 24:1400-1414. [PMID: 31138894 DOI: 10.1038/s41380-019-0438-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Revised: 03/31/2019] [Accepted: 04/29/2019] [Indexed: 02/08/2023]
Abstract
Many neuropsychiatric and neurodevelopmental disorders commonly share genetic risk factors. To date, the mechanisms driving the pathogenesis of these disorders, particularly how genetic variations affect the function of risk genes and contribute to disease symptoms, remain largely unknown. Neurexins are a family of synaptic adhesion molecules, which play important roles in the formation and establishment of synaptic structure, as well as maintenance of synaptic function. Accumulating genomic findings reveal that genetic variations within genes encoding neurexins are associated with a variety of psychiatric conditions such as schizophrenia, autism spectrum disorder, and some developmental abnormalities. In this review, we focus on NRXN1, one of the most compelling psychiatric risk genes of the neurexin family. We performed a comprehensive survey and analysis of current genetic and molecular data including both common and rare alleles within NRXN1 associated with psychiatric illnesses, thus providing insights into the genetic risk conferred by NRXN1. We also summarized the neurobiological evidences, supporting the function of NRXN1 and its protein products in synaptic formation, organization, transmission and plasticity, as well as disease-relevant behaviors, and assessed the mechanistic link between the mutations of NRXN1 and synaptic and behavioral pathology in neuropsychiatric disorders.
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Affiliation(s)
- Zhonghua Hu
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China. .,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China. .,Department of Psychiatry, the Second Xiangya Hospital, Central South University, Changsha, Hunan, China. .,National Clinical Research Center on Mental Disorders, Changsha, Hunan, China.
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhuohua Zhang
- Institute of Molecular Precision Medicine and Hunan Key Laboratory of Molecular Precision Medicine, Xiangya Hospital, Central South University, Changsha, Hunan, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
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23
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Jiang Y, Yuan H, Huang L, Hou X, Zhou R, Dang X. Global proteomic profiling of the uniquely human CHRFAM7A gene in transgenic mouse brain. Gene 2019; 714:143996. [PMID: 31348980 DOI: 10.1016/j.gene.2019.143996] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/19/2019] [Accepted: 07/22/2019] [Indexed: 01/08/2023]
Abstract
The uniquely human α7-nAChR gene (CHRFAM7A) is evolved from the fusion of two partially duplicated genes, FAM7 and α7-nAChR gene (CHRNA7), and is inserted on same chromosome 15, 5' end of the CHRNA7 gene. Transcription of CHRFAM7A gene produces a 1256-bp open reading frame encoding dup-α7-nAChR, where a 27-aminoacid residues from FAM7 replaced the 146-aminoacid residues of the N-terminal extracellular ligand binding domain of α7-nAChR. In vitro, dup-α7-nAChR has been shown to form hetero-pentamer with α7-nAChR and dominant-negatively regulates the channel functions of α7-nAChR. However, the contribution of CHRFAM7A gene to the biology of α7-nAChR in the brain in vivo remains largely a matter of conjecture. CHRFAM7A transgenic mouse was created and differentially expressed proteins were profiled from the whole brain using iTRAQ-2D-LC-MS/MS proteomic technology. Proteins with a fold change of ≥1.2 or ≤0.83 and p < 0.05 were considered to be significant. Bioinformatics analysis showed that over-expression of the CHRFAM7A gene significantly modulated the proteins commonly involved in the signaling pathways of α7-nAChR-mediated neuropsychiatric disorders including Parkinson's disease, Alzheimer's disease, Huntington's disease, and alcoholism, suggesting that the CHRFAM7A gene contributes to the pathogenesis of neuropsychiatric disorders mostly likely through fine-tuning the functions of α7-nAChR in the brain.
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Affiliation(s)
- Yu Jiang
- The Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Lab of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000,China
| | - Haiyang Yuan
- The Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Lab of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000,China
| | - Li Huang
- The Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Lab of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000,China
| | - Xiaojie Hou
- Division of Vascular Surgery, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Rui Zhou
- The Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Lab of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000,China
| | - Xitong Dang
- The Key Laboratory of Medical Electrophysiology, Ministry of Education & Medical Electrophysiological Key Lab of Sichuan Province, Collaborative Innovation Center for Prevention and Treatment of Cardiovascular Disease of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, Sichuan 646000,China; Division of Vascular Surgery, The Affiliated Hospital of Southwest Medical University, Southwest Medical University, Luzhou, Sichuan 646000, China.
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24
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Maroli A, Di Lascio S, Drufuca L, Cardani S, Setten E, Locati M, Fornasari D, Benfante R. Effect of donepezil on the expression and responsiveness to LPS of CHRNA7 and CHRFAM7A in macrophages: A possible link to the cholinergic anti-inflammatory pathway. J Neuroimmunol 2019; 332:155-166. [PMID: 31048268 DOI: 10.1016/j.jneuroim.2019.04.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 04/05/2019] [Accepted: 04/23/2019] [Indexed: 01/17/2023]
Abstract
The α7 nicotinic acetylcholine receptor (CHRNA7) modulates the inflammatory response by activating the cholinergic anti-inflammatory pathway. CHRFAM7A, the human-restricted duplicated form of CHRNA7, has a negative effect on the functioning of α7 receptors, suggesting that CHRFAM7A expression regulation may be a key step in the modulation of inflammation in the human setting. The analysis of the CHRFAM7A gene's regulatory region reveals some of the mechanisms driving its expression and responsiveness to LPS in human immune cell models. Moreover, given the immunomodulatory potential of donepezil we show that it differently modulates CHRFAM7A and CHRNA7 responsiveness to LPS, thus contributing to its therapeutic potential.
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Affiliation(s)
- Annalisa Maroli
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy
| | - Simona Di Lascio
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy
| | - Lorenzo Drufuca
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy; Humanitas Clinical and Research Centre, Rozzano, Italy
| | - Silvia Cardani
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy
| | - Elisa Setten
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy; Humanitas Clinical and Research Centre, Rozzano, Italy
| | - Massimo Locati
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy; Humanitas Clinical and Research Centre, Rozzano, Italy
| | - Diego Fornasari
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy; CNR -Neuroscience Institute, via Vanvitelli 32, 20129 Milan, Italy
| | - Roberta Benfante
- Dept. of Medical Biotechnology and Translational Medicine (BIOMETRA), Università degli Studi di Milano, via Vanvitelli, 20129 Milan, Italy; CNR -Neuroscience Institute, via Vanvitelli 32, 20129 Milan, Italy.
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25
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Kun-Rodrigues C, Orme T, Carmona S, Hernandez DG, Ross OA, Eicher JD, Shepherd C, Parkkinen L, Darwent L, Heckman MG, Scholz SW, Troncoso JC, Pletnikova O, Dawson T, Rosenthal L, Ansorge O, Clarimon J, Lleo A, Morenas-Rodriguez E, Clark L, Honig LS, Marder K, Lemstra A, Rogaeva E, St George-Hyslop P, Londos E, Zetterberg H, Barber I, Braae A, Brown K, Morgan K, Troakes C, Al-Sarraj S, Lashley T, Holton J, Compta Y, Van Deerlin V, Serrano GE, Beach TG, Lesage S, Galasko D, Masliah E, Santana I, Pastor P, Diez-Fairen M, Aguilar M, Tienari PJ, Myllykangas L, Oinas M, Revesz T, Lees A, Boeve BF, Petersen RC, Ferman TJ, Escott-Price V, Graff-Radford N, Cairns NJ, Morris JC, Pickering-Brown S, Mann D, Halliday GM, Hardy J, Trojanowski JQ, Dickson DW, Singleton A, Stone DJ, Guerreiro R, Bras J. A comprehensive screening of copy number variability in dementia with Lewy bodies. Neurobiol Aging 2019; 75:223.e1-223.e10. [PMID: 30448004 PMCID: PMC6541211 DOI: 10.1016/j.neurobiolaging.2018.10.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 10/15/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022]
Abstract
The role of genetic variability in dementia with Lewy bodies (DLB) is now indisputable; however, data regarding copy number variation (CNV) in this disease has been lacking. Here, we used whole-genome genotyping of 1454 DLB cases and 1525 controls to assess copy number variability. We used 2 algorithms to confidently detect CNVs, performed a case-control association analysis, screened for candidate CNVs previously associated with DLB-related diseases, and performed a candidate gene approach to fully explore the data. We identified 5 CNV regions with a significant genome-wide association to DLB; 2 of these were only present in cases and absent from publicly available databases: one of the regions overlapped LAPTM4B, a known lysosomal protein, whereas the other overlapped the NME1 locus and SPAG9. We also identified DLB cases presenting rare CNVs in genes previously associated with DLB or related neurodegenerative diseases, such as SNCA, APP, and MAPT. To our knowledge, this is the first study reporting genome-wide CNVs in a large DLB cohort. These results provide preliminary evidence for the contribution of CNVs in DLB risk.
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Affiliation(s)
- Celia Kun-Rodrigues
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Tatiana Orme
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute (UK DRI) at UCL, London, UK
| | - Susana Carmona
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute (UK DRI) at UCL, London, UK
| | - Dena G Hernandez
- Laboratory of Neurogenetics, National Institutes on Aging, NIH, Bethesda, MD, USA; German Center for Neurodegenerative Diseases (DZNE), Tubingen, Germany
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA
| | - John D Eicher
- Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, MA, USA
| | - Claire Shepherd
- Neuroscience Research Australia, Sydney, Australia and School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia
| | - Laura Parkkinen
- Nuffield Department of Clinical Neurosciences, Oxford Parkinsons Disease Centre, University of Oxford, Oxford, UK
| | - Lee Darwent
- UK Dementia Research Institute (UK DRI) at UCL, London, UK; Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - Michael G Heckman
- Division of Biomedical Statistics and Informatics, Mayo Clinic, Jacksonville, FL, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA; Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Juan C Troncoso
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Olga Pletnikova
- Department of Pathology (Neuropathology), Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ted Dawson
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Liana Rosenthal
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Olaf Ansorge
- Nuffield Department of Clinical Neurosciences, Oxford Parkinsons Disease Centre, University of Oxford, Oxford, UK
| | - Jordi Clarimon
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Alberto Lleo
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Estrella Morenas-Rodriguez
- Memory Unit, Department of Neurology, IIB Sant Pau, Hospital de la Santa Creu i Sant Pau, Universitat Autonoma de Barcelona, Barcelona, Spain; Centro de Investigacion Biomedica en Red en Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Lorraine Clark
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Lawrence S Honig
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Karen Marder
- Taub Institute for Alzheimer Disease and the Aging Brain and Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Afina Lemstra
- Department of Neurology and Alzheimer Center, Neuroscience Campus Amsterdam, VU University Medical Center, Amsterdam, The Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine, University of Toronto, Ontario, Canada
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Diseases and Department of Medicine, University of Toronto, Ontario, Canada; Department of Clinical Neurosciences, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Elisabet Londos
- Clinical Memory Research Unit, Institution of Clinical Sciences Malmo, Lund University, Lund, Sweden
| | - Henrik Zetterberg
- UK Dementia Research Institute at UCL, London UK, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK and Clinical Neurochemistry Laboratory, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Molndal, Sweden
| | - Imelda Barber
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Anne Braae
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kristelle Brown
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - Claire Troakes
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Safa Al-Sarraj
- Department of Basic and Clinical Neuroscience and Institute of Psychiatry, Psychology and Neuroscience, Kings College London, London, UK
| | - Tammaryn Lashley
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Janice Holton
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Yaroslau Compta
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK; Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK and Movement Disorders Unit, Neurology Service, Clinical Neuroscience Institute (ICN), Hospital Clinic, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Vivianna Van Deerlin
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | | | | | - Suzanne Lesage
- Inserm U1127, CNRS UMR7225, Sorbonne Universites, Institut du Cerveau et de la Moelle epiniere, Paris, France
| | - Douglas Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Veterans Affairs San Diego Healthcare System, La Jolla, CA, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Isabel Santana
- Neurology Service, University of Coimbra Hospital, Coimbra, Portugal
| | - Pau Pastor
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, and Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain. Centro de Investigacion Biomedica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain
| | - Monica Diez-Fairen
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, and Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain. Centro de Investigacion Biomedica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain
| | - Miquel Aguilar
- Memory Unit, Department of Neurology, University Hospital Mutua de Terrassa, University of Barcelona, and Fundacio de Docencia I Recerca Mutua de Terrassa, Terrassa, Barcelona, Spain. Centro de Investigacion Biomedica en Red Enfermedades Neurdegenerativas (CIBERNED), Madrid, Spain
| | - Pentti J Tienari
- Molecular Neurology, Research Programs Unit, University of Helsinki, Department of Neurology, Helsinki University Hospital, Helsinki, Finland
| | - Liisa Myllykangas
- Department of Pathology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Minna Oinas
- Department of Neuropathology and Neurosurgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Tamas Revesz
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Andrew Lees
- Queen Square Brain Bank, Department of Molecular Neuroscience, UCL Institute of Neurology, London, UK
| | - Brad F Boeve
- Neurology Department, Mayo Clinic, Rochester, MN, USA
| | | | - Tanis J Ferman
- Department of Psychiatry and Department of Psychology, Mayo Clinic, Jacksonville, FL, USA
| | - Valentina Escott-Price
- MRC Centre for Neuropsychiatric Genetics and Genomics, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Nigel J Cairns
- Knight Alzheimers Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - John C Morris
- Knight Alzheimers Disease Research Center, Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart Pickering-Brown
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - David Mann
- Institute of Brain, Behaviour and Mental Health, Faculty of Medical and Human Sciences, University of Manchester, Manchester, UK
| | - Glenda M Halliday
- Neuroscience Research Australia, Sydney, Australia and School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, Australia; Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - John Hardy
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Disease Research, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, USA
| | | | - Andrew Singleton
- Laboratory of Neurogenetics, National Institutes on Aging, NIH, Bethesda, MD, USA
| | - David J Stone
- Genetics and Pharmacogenomics, Merck and Co, West Point, PA, USA
| | - Rita Guerreiro
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute (UK DRI) at UCL, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal
| | - Jose Bras
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London, UK; UK Dementia Research Institute (UK DRI) at UCL, London, UK; Department of Medical Sciences and Institute of Biomedicine, iBiMED, University of Aveiro, Aveiro, Portugal.
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26
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La Cognata V, Morello G, Gentile G, Cavalcanti F, Cittadella R, Conforti FL, De Marco EV, Magariello A, Muglia M, Patitucci A, Spadafora P, D’Agata V, Ruggieri M, Cavallaro S. NeuroArray: A Customized aCGH for the Analysis of Copy Number Variations in Neurological Disorders. Curr Genomics 2018; 19:431-443. [PMID: 30258275 PMCID: PMC6128384 DOI: 10.2174/1389202919666180404105451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 02/02/2018] [Accepted: 03/13/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Neurological disorders are a highly heterogeneous group of pathological conditions that affect both the peripheral and the central nervous system. These pathologies are characterized by a complex and multifactorial etiology involving numerous environmental agents and genetic susceptibility factors. For this reason, the investigation of their pathogenetic basis by means of traditional methodological approaches is rather arduous. High-throughput genotyping technologies, including the microarray-based comparative genomic hybridization (aCGH), are currently replacing classical detection methods, providing powerful molecular tools to identify genomic unbalanced structural rearrangements and explore their role in the pathogenesis of many complex human diseases. METHODS In this report, we comprehensively describe the design method, the procedures, validation, and implementation of an exon-centric customized aCGH (NeuroArray 1.0), tailored to detect both single and multi-exon deletions or duplications in a large set of multi- and monogenic neurological diseases. This focused platform enables a targeted measurement of structural imbalances across the human genome, targeting the clinically relevant genes at exon-level resolution. CONCLUSION An increasing use of the NeuroArray platform may offer new insights in investigating potential overlapping gene signatures among neurological conditions and defining genotype-phenotype relationships.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | - Sebastiano Cavallaro
- Address correspondence to this author at the Institute of Neurological Sciences, National Research Council, Via Paolo Gaifami 18, 95125, Catania, Italy; Tel: +39-095-7338111; E-mail:
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27
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Lew AR, Kellermayer TR, Sule BP, Szigeti K. Copy Number Variations in Adult-onset Neuropsychiatric Diseases. Curr Genomics 2018; 19:420-430. [PMID: 30258274 PMCID: PMC6128389 DOI: 10.2174/1389202919666180330153842] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 03/01/2017] [Accepted: 03/13/2018] [Indexed: 11/22/2022] Open
Abstract
Adult-onset neuropsychiatric diseases are one of the most challenging areas of medicine. While symptomatic treatments are available, for most of these diseases the exact pathomechanism is not known, thus, disease-modifying therapies are difficult to conceptualize and find. The two most common and best studied neuropsychiatric diseases affecting higher cortical functions in humans are schizophrenia and Alzheimer's disease; both diseases have high heritability, however, the genetic architecture is not fully elucidated. Robust Single Nucleotide Variant (SNV) studies have identified several loci with modest effect sizes. While Copy Number Variants (CNV) make an important contribution to genetic variation, CNV GWAS suffer from dependence on mainly SNP arrays with underperforming genotyping accuracy. We evaluated dynamic range of the assays for three types of CNV loci, including biallelic deletion, high copy gain, and fusion gene, to assess the depth of exploration of the contribution of CNVs to disease susceptibility. Despite the suboptimal genotyping, novel mechanisms are emerging and further large-scale studies with genotyping assays optimized for CNV detection are needed. Furthermore, the CHRFAM7A human-specific fusion gene association warrants large scale locus specific association studies in AD, schizophrenia, bipolar disorder and ADHD.
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Affiliation(s)
- Alexandra R Lew
- Department of Neurology, University at Buffalo, SUNY, Buffalo, NY14203, USA
| | | | - Balint P Sule
- Department of Neurology, University at Buffalo, SUNY, Buffalo, NY14203, USA
| | - Kinga Szigeti
- Department of Neurology, University at Buffalo, SUNY, Buffalo, NY14203, USA
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28
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Viñas-Jornet M, Esteba-Castillo S, Baena N, Ribas-Vidal N, Ruiz A, Torrents-Rodas D, Gabau E, Vilella E, Martorell L, Armengol L, Novell R, Guitart M. High Incidence of Copy Number Variants in Adults with Intellectual Disability and Co-morbid Psychiatric Disorders. Behav Genet 2018; 48:323-336. [PMID: 29882083 PMCID: PMC6028865 DOI: 10.1007/s10519-018-9902-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 05/10/2018] [Indexed: 01/04/2023]
Abstract
A genetic analysis of unexplained mild-moderate intellectual disability and co-morbid psychiatric or behavioural disorders is not systematically conducted in adults. A cohort of 100 adult patients affected by both phenotypes were analysed in order to identify the presence of copy number variants (CNVs) responsible for their condition identifying a yield of 12.8% of pathogenic CNVs (19% when including clinically recognizable microdeletion syndromes). Moreover, there is a detailed clinical description of an additional 11% of the patients harbouring possible pathogenic CNVs—including a 7q31 deletion (IMMP2L) in two unrelated patients and duplications in 3q29, 9p24.2p24.1 and 15q14q15.1—providing new evidence of its contribution to the phenotype. This study adds further proof of including chromosomal microarray analysis (CMA) as a mandatory test to improve the diagnosis in the adult patients in psychiatric services.
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Affiliation(s)
- Marina Viñas-Jornet
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain.,Cellular Biology, Physiology and Immunology Department, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Susanna Esteba-Castillo
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Neus Baena
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain
| | - Núria Ribas-Vidal
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Anna Ruiz
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain
| | - David Torrents-Rodas
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Elisabeth Gabau
- Pediatry-Clinical Genetics Service, Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, Reus, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, CIBERSAM, Reus, Spain
| | - Lluís Armengol
- Research and Development Department, qGenomics Laboratory, Barcelona, Spain
| | - Ramon Novell
- Mental Health and Intellectual Disability Specialized Service, Institut Assistència Sanitària (IAS), Parc Hospitalari Martí i Julià, Girona, Spain
| | - Míriam Guitart
- Genetics lab, UDIAT-centre diagnostic. Parc Taulí Hospital Universitari. Institut d'Investigació i Innovació Parc Taulí I3PT. Universitat Autònoma de Barcelona, C/Parc Tauli,1, 08208, Sabadell, Barcelona, Spain.
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29
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Misra MK, Damotte V, Hollenbach JA. The immunogenetics of neurological disease. Immunology 2018; 153:399-414. [PMID: 29159928 PMCID: PMC5838423 DOI: 10.1111/imm.12869] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 11/09/2017] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
Genes encoding antigen-presenting molecules within the human major histocompatibility complex (MHC) account for the highest component of genetic risk for many neurological diseases, such as multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. Myriad genetic, immunological and environmental factors may contribute to an individual's susceptibility to neurological disease. Here, we review and discuss the decades long research on the influence of genetic variation at the MHC locus and the role of immunogenetic killer cell immunoglobulin-like receptor (KIR) loci in neurological diseases, including multiple sclerosis, neuromyelitis optica, Parkinson's disease, Alzheimer's disease, schizophrenia, myasthenia gravis and amyotrophic lateral sclerosis. The findings of immunogenetic association studies are consistent with a polygenic model of inheritance in the heterogeneous and multifactorial nature of complex traits in various neurological diseases. Future investigation is highly recommended to evaluate both coding and non-coding variation in immunogenetic loci using high-throughput high-resolution next-generation sequencing technologies in diverse ethnic groups to fully appreciate their role in neurological diseases.
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Affiliation(s)
- Maneesh K. Misra
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Vincent Damotte
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
| | - Jill A. Hollenbach
- Department of NeurologySan Francisco School of MedicineUniversity of CaliforniaSan FranciscoCAUSA
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30
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Zhang Y, Liu Y, Zarrei M, Tong W, Dong R, Wang Y, Zhang H, Yang X, MacDonald JR, Uddin M, Scherer SW, Gai Z. Association of IMMP2L deletions with autism spectrum disorder: A trio family study and meta-analysis. Am J Med Genet B Neuropsychiatr Genet 2018; 177:93-100. [PMID: 29152845 DOI: 10.1002/ajmg.b.32608] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 08/28/2017] [Accepted: 10/02/2017] [Indexed: 11/10/2022]
Abstract
IMMP2L, the gene encoding the inner mitochondrial membrane peptidase subunit 2-like protein, has been reported as a candidate gene for Tourette syndrome, autism spectrum disorder (ASD) and additional neurodevelopmental disorders. Here we genotyped 100 trio families with an index proband with autism spectrum disorder in Han Chinese population and found three cases with rare exonic IMMP2L deletions. We have conducted a comprehensive meta-analysis to quantify the association of IMMP2L deletions with ASD using 5,568 cases and 10,279 controls. While the IMMP2L deletions carried non-recurrent breakpoints, in contrast to previous reports, our meta-analysis found no evidence of association (P > 0.05) between IMMP2L deletions and ASD. We also observed common exonic deletions impacting IMMP2L in a separate control (5,971 samples) cohort where subjects were screened for psychiatric conditions. This is the first systematic review and meta-analysis regarding the effect of IMMP2L deletions on ASD, but further investigations in different populations, especially Chinese population may be still needed to confirm our results.
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Affiliation(s)
- Yanqing Zhang
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Yi Liu
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Winnie Tong
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Rui Dong
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Ying Wang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Haiyan Zhang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Xiaomeng Yang
- Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada
| | - Mohammed Uddin
- Mohammed Bin Rashid University of Medicine and Health Sciences, College of Medicine, Dubai, UAE
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Zhongtao Gai
- Pediatric Health Care Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China.,Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Ji'nan, China
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31
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Sekine M, Makino T. Inference of Causative Genes for Alzheimer's Disease Due to Dosage Imbalance. Mol Biol Evol 2017; 34:2396-2407. [PMID: 28666362 DOI: 10.1093/molbev/msx183] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Copy number variations (CNVs) have recently drawn attention as an important genetic factor for diseases, especially common neuropsychiatric disorders including Alzheimer's disease (AD). Because most of the pathogenic CNV regions overlap with multiple genes, it has been challenging to identify the true disease-causing genes amongst them. Notably, a recent study reported that CNV regions containing ohnologs, which are dosage-sensitive genes, are likely to be deleterious. Utilizing the unique feature of ohnologs could be useful for identifying causative genes with pathogenic CNVs, however its effectiveness is still unclear. Although it has been reported that AD is strongly affected by CNVs, most of AD-causing genes with pathogenic CNVs have not been identified yet. Here, we show that dosage-sensitive ohnologs within CNV regions reported in patients with AD are related to the nervous system and are highly expressed in the brain, similar to other known susceptible genes for AD. We found that CNV regions in patients with AD contained dosage-sensitive genes, which are ohnologs not overlapping with control CNV regions, frequently. Furthermore, these dosage-sensitive genes in pathogenic CNV regions had a strong enrichment in the nervous system for mouse knockout phenotype and high expression in the brain similar to the known susceptible genes for AD. Our results demonstrated that selecting dosage-sensitive ohnologs out of multiple genes with pathogenic CNVs is effective in identifying the causative genes for AD. This methodology can be applied to other diseases caused by dosage imbalance and might help to establish the medical diagnosis by analysis of CNVs.
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Affiliation(s)
- Mizuka Sekine
- Department of Biology, Faculty of Science, Tohoku University, Sendai, Japan
| | - Takashi Makino
- Department of Ecology and Evolutionary Biology, Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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32
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Le Guennec K, Quenez O, Nicolas G, Wallon D, Rousseau S, Richard AC, Alexander J, Paschou P, Charbonnier C, Bellenguez C, Grenier-Boley B, Lechner D, Bihoreau MT, Olaso R, Boland A, Meyer V, Deleuze JF, Amouyel P, Munter HM, Bourque G, Lathrop M, Frebourg T, Redon R, Letenneur L, Dartigues JF, Martinaud O, Kalev O, Mehrabian S, Traykov L, Ströbel T, Le Ber I, Caroppo P, Epelbaum S, Jonveaux T, Pasquier F, Rollin-Sillaire A, Génin E, Guyant-Maréchal L, Kovacs GG, Lambert JC, Hannequin D, Campion D, Rovelet-Lecrux A, Rovelet-Lecrux A. 17q21.31 duplication causes prominent tau-related dementia with increased MAPT expression. Mol Psychiatry 2017; 22:1119-1125. [PMID: 27956742 DOI: 10.1038/mp.2016.226] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/26/2016] [Accepted: 10/27/2016] [Indexed: 01/07/2023]
Abstract
To assess the role of rare copy number variations in Alzheimer's disease (AD), we conducted a case-control study using whole-exome sequencing data from 522 early-onset cases and 584 controls. The most recurrent rearrangement was a 17q21.31 microduplication, overlapping the CRHR1, MAPT, STH and KANSL1 genes that was found in four cases, including one de novo rearrangement, and was absent in controls. The increased MAPT gene dosage led to a 1.6-1.9-fold expression of the MAPT messenger RNA. Clinical signs, neuroimaging and cerebrospinal fluid biomarker profiles were consistent with an AD diagnosis in MAPT duplication carriers. However, amyloid positon emission tomography (PET) imaging, performed in three patients, was negative. Analysis of an additional case with neuropathological examination confirmed that the MAPT duplication causes a complex tauopathy, including prominent neurofibrillary tangle pathology in the medial temporal lobe without amyloid-β deposits. 17q21.31 duplication is the genetic basis of a novel entity marked by prominent tauopathy, leading to early-onset dementia with an AD clinical phenotype. This entity could account for a proportion of probable AD cases with negative amyloid PET imaging recently identified in large clinical series.
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Affiliation(s)
- K Le Guennec
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France
| | - O Quenez
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - G Nicolas
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - D Wallon
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - S Rousseau
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - A-C Richard
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - J Alexander
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - P Paschou
- Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece
| | - C Charbonnier
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - C Bellenguez
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - B Grenier-Boley
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Lechner
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - M-T Bihoreau
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - R Olaso
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - A Boland
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - V Meyer
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France
| | - J-F Deleuze
- Centre National de Génotypage, Institut de Génomique, CEA, Evry, France.,Fondation Jean Dausset, Centre d'études du Polymorphisme Humain, Paris, France
| | - P Amouyel
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - H M Munter
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - G Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - M Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, QC, Canada
| | - T Frebourg
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France
| | - R Redon
- Inserm, UMR 1087, l'institut du thorax, CHU Nantes, Nantes, France.,CNRS, UMR 6291, Université de Nantes, Nantes, France
| | - L Letenneur
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - J-F Dartigues
- INSERM, U1219, Bordeaux, France.,Université de Bordeaux, Bordeaux, France
| | - O Martinaud
- CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - O Kalev
- Institute of Pathology and Neuropathology, Kepler University Hospital, Linz, Austria
| | - S Mehrabian
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - L Traykov
- Department of Neurology, Alexandrovska University Hospital, Medical University-Sofia, Sofia, Bulgaria
| | - T Ströbel
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - I Le Ber
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - P Caroppo
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - S Epelbaum
- Sorbonne Universités, Inserm, CNRS, UPMC Univ Paris 06, UMR S 1127, Paris, France.,CNR-MAJ, IMMA, département des maladies du système nerveux, Hôpital Pitié-Salpêtrière, Paris, France
| | - T Jonveaux
- Centre Mémoire de Ressources et de Recherche de Lorraine, CHRU Nancy Service de Gériatrie, Hôpital de Brabois, Vandoeuvre les Nancy, France.,Laboratoire INTERPSY, EA 4432, Groupe de recherche sur les Communications (GRC), Université de Lorraine, Psychologie, Nancy, France
| | - F Pasquier
- CNR-MAJ Inserm U1171, Univ Lille, CHU, Lille, France
| | | | - E Génin
- Inserm, UMR1078, CHU Brest, Université Bretagne Occidentale, Brest, France
| | - L Guyant-Maréchal
- Department of Neurology, Rouen University Hospital, Rouen, France.,Department of Neurophysiology, Rouen University Hospital, Rouen, France
| | - G G Kovacs
- Institute of Neurology, Medical University Vienna, Vienna, Austria
| | - J-C Lambert
- Inserm, U1167, Lille, France.,Institut Pasteur de Lille, Lille, France.,Université Lille-Nord de France, Lille, France
| | - D Hannequin
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Genetics, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - D Campion
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
| | - A Rovelet-Lecrux
- Inserm, U1079, faculté de médecine, Rouen University, IRIB, Normandy University, Rouen, France.,Normandy Centre for Genomic Medicine and Personalized Medicine, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
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Abstract
Ever since initial suggestions that instability at common fragile sites (CFSs) could be responsible for chromosome rearrangements in cancers, CFSs and associated genes have been the subject of numerous studies, leading to questions and controversies about their role and importance in cancer. It is now clear that CFSs are not frequently involved in translocations or other cancer-associated recurrent gross chromosome rearrangements. However, recent studies have provided new insights into the mechanisms of CFS instability, their effect on genome instability, and their role in generating focal copy number alterations that affect the genomic landscape of many cancers.
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Affiliation(s)
- Thomas W Glover
- Department of Human Genetics; the Department of Pathology; and the Department of Pediatrics and Communicable Diseases, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Thomas E Wilson
- Department of Human Genetics; and the Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
| | - Martin F Arlt
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan 48109, USA
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Shah C, DeMichele-Sweet MAA, Sweet RA. Genetics of psychosis of Alzheimer disease. Am J Med Genet B Neuropsychiatr Genet 2017; 174:27-35. [PMID: 26756273 PMCID: PMC5154859 DOI: 10.1002/ajmg.b.32413] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 12/21/2015] [Indexed: 02/06/2023]
Abstract
Psychotic symptoms, comprised of delusions and hallucinations, occur in about half of individuals with Alzheimer disease (AD with psychosis, AD+P). These individuals have greater agitation, aggression, depression, functional impairment, and mortality than individuals without psychosis (AD-P). Although the exact etiopathogenesis of AD+P is unclear, the rapidly developing field of genomics continues to expand our understanding of this disease. Several independent studies have demonstrated familial aggregation and heritability of AD+P. Linkage studies have been suggestive of loci on several chromosomes associated with AD+P. Association studies examining apolipoprotein E gene, the best established genetic risk factor for late-onset AD, did not find any significant association of this gene with AD+P. Other candidate gene studies focusing on monoamine neurotransmitter systems have yielded equivocal results. A genome-wide association study and studies examining copy number variations recently have detected suggestive associations, but have been underpowered. Approaches to increase sizes of AD+P samples for genome wide association studies are discussed. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Chintan Shah
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Robert A. Sweet
- Department of Psychiatry and Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania
- VISN 4 Mental Health Illness Research, Education and Clinical Center (MIRECC), VA Pittsburgh Healthcare System, Pittsburgh, Pennsylvania
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35
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Cuccaro D, De Marco EV, Cittadella R, Cavallaro S. Copy Number Variants in Alzheimer's Disease. J Alzheimers Dis 2017; 55:37-52. [PMID: 27662298 PMCID: PMC5115612 DOI: 10.3233/jad-160469] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/14/2016] [Indexed: 12/18/2022]
Abstract
Alzheimer's disease (AD) is a devastating disease mainly afflicting elderly people, characterized by decreased cognition, loss of memory, and eventually death. Although risk and deterministic genes are known, major genetics research programs are underway to gain further insights into the inheritance of AD. In the last years, in particular, new developments in genome-wide scanning methodologies have enabled the association of a number of previously uncharacterized copy number variants (CNVs, gain or loss of DNA) in AD. Because of the exceedingly large number of studies performed, it has become difficult for geneticists as well as clinicians to systematically follow, evaluate, and interpret the growing number of (sometime conflicting) CNVs implicated in AD. In this review, after a brief introduction of this type of structural variation, and a description of available databases, computational analyses, and technologies involved, we provide a systematic review of all published data showing statistical and scientific significance of pathogenic CNVs and discuss the role they might play in AD.
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Affiliation(s)
- Denis Cuccaro
- Institute of Neurological Sciences, National Research Council, Section of Catania, Italy
| | | | - Rita Cittadella
- Institute of Neurological Sciences, National Research Council, Section of Mangone, Italy
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, National Research Council, Section of Catania, Italy
- Institute of Neurological Sciences, National Research Council, Section of Mangone, Italy
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36
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Zai G, Robbins TW, Sahakian BJ, Kennedy JL. A review of molecular genetic studies of neurocognitive deficits in schizophrenia. Neurosci Biobehav Rev 2017; 72:50-67. [DOI: 10.1016/j.neubiorev.2016.10.024] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 10/17/2016] [Accepted: 10/27/2016] [Indexed: 02/08/2023]
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37
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Lowther C, Speevak M, Armour CM, Goh ES, Graham GE, Li C, Zeesman S, Nowaczyk MJM, Schultz LA, Morra A, Nicolson R, Bikangaga P, Samdup D, Zaazou M, Boyd K, Jung JH, Siu V, Rajguru M, Goobie S, Tarnopolsky MA, Prasad C, Dick PT, Hussain AS, Walinga M, Reijenga RG, Gazzellone M, Lionel AC, Marshall CR, Scherer SW, Stavropoulos DJ, McCready E, Bassett AS. Molecular characterization of NRXN1 deletions from 19,263 clinical microarray cases identifies exons important for neurodevelopmental disease expression. Genet Med 2016; 19:53-61. [PMID: 27195815 PMCID: PMC4980119 DOI: 10.1038/gim.2016.54] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/16/2016] [Indexed: 01/31/2023] Open
Abstract
Purpose The purpose of the current study was to assess the penetrance of NRXN1 deletions. Methods We compared the prevalence and genomic extent of NRXN1 deletions identified among 19,263 clinically referred cases to that of 15,264 controls. The burden of additional clinically relevant CNVs was used as a proxy to estimate the relative penetrance of NRXN1 deletions. Results We identified 41 (0.21%) previously unreported exonic NRXN1 deletions ascertained for developmental delay/intellectual disability, significantly greater than in controls [OR=8.14 (95% CI 2.91–22.72), p< 0.0001)]. Ten (22.7%) of these had a second clinically relevant CNV. Subjects with a deletion near the 3′ end of NRXN1 were significantly more likely to have a second rare CNV than subjects with a 5′ NRXN1 deletion [OR=7.47 (95% CI 2.36–23.61), p=0.0006]. The prevalence of intronic NRXN1 deletions was not statistically different between cases and controls (p=0.618). The majority (63.2%) of intronic NRXN1 deletion cases had a second rare CNV, a two-fold greater prevalence than for exonic NRXN1 deletion cases (p=0.0035). Conclusions The results support the importance of exons near the 5′ end of NRXN1 in the expression of neurodevelopmental disorders. Intronic NRXN1 deletions do not appear to substantially increase the risk for clinical phenotypes.
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Affiliation(s)
- Chelsea Lowther
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Marsha Speevak
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Christine M Armour
- Regional Genetics Program, Children's Hospital of Eastern Ontario, Toronto, ON, Canada
| | - Elaine S Goh
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Gail E Graham
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Chumei Li
- Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada.,McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Susan Zeesman
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Malgorzata J M Nowaczyk
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada.,Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Lee-Anne Schultz
- McMaster Children's Hospital, Department of Pediatrics and Clinical Genetics Program, Hamilton, Ontario, Canada
| | - Antonella Morra
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Rob Nicolson
- Department of Psychiatry, Western University, London, Ontario, Canada
| | | | - Dawa Samdup
- Hotel Dieu Hospital, Child Development Centre, Kingston, Ontario, Canada
| | - Mostafa Zaazou
- Trillium Health Partners Credit Valley Site, Toronto, Ontario, Canada
| | - Kerry Boyd
- Department of Psychiatry, McMaster University, Hamilton, Ontario, Canada
| | - Jack H Jung
- London Health Sciences Centre, Children's Hospital of Western Ontario, London, Ontario, Canada
| | - Victoria Siu
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | | | - Sharan Goobie
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | - Mark A Tarnopolsky
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Chitra Prasad
- Department of Pediatrics, Schulich School of Medicine and Dentistry, London, Ontario, Canada
| | - Paul T Dick
- Grey Bruce Health Services, Owen Sound, Ontario, Canada
| | - Asmaa S Hussain
- London Health Sciences Centre, Children's Hospital of Western Ontario, London, Ontario, Canada
| | | | | | - Matthew Gazzellone
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anath C Lionel
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christian R Marshall
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, the Hospital for Sick Children, Toronto, Ontario, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Dimitri J Stavropoulos
- Cytogenetics Laboratory, Department of Pediatric Laboratory Medicine, the Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elizabeth McCready
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario, Canada
| | - Anne S Bassett
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.,Department of Psychiatry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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38
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Abstract
Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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39
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Szigeti K. New Genome-Wide Methods for Elucidation of Candidate Copy Number Variations (CNVs) Contributing to Alzheimer's Disease Heritability. Methods Mol Biol 2016; 1303:315-26. [PMID: 26235076 DOI: 10.1007/978-1-4939-2627-5_19] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The complexity of human genetic variation has been extended by the observation of abundant and widespread variation in the copy number of submicroscopic DNA segments. The discovery of this novel level of genome organization opened new possibilities concerning the genetic variation that may confer susceptibility to or cause disease. Copy number variants (CNVs) influence gene expression, phenotypic variation and adaptation by altering gene dosage and genome organization. Concordant with the common disease common variant hypothesis these structural variants are now subject to interrogation for disease association. Alzheimer's disease (AD) is a progressive neurodegenerative disease with an estimated heritability of 60-80 %. Large scale genome-wide association studies (GWAS) using high frequency single nucleotide polymorphism (SNP) variants identified ten loci which do not account for the measured heritability. To find the missing heritability systematic assessment of all mutational mechanisms needs to be performed. Between the powerful SNP-GWAS studies and the planned Whole Genome Sequencing projects the contribution of copy number variation (CNV) to the genetic architecture of AD needs to be studied fully.
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Affiliation(s)
- Kinga Szigeti
- Department of Neurology, School of Medicine and Biomedical Sciences, University at Buffalo SUNY, D-2 Buffalo General Hospital, 100 High Street, Buffalo, NY, 14203, USA,
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40
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Bertrand D, Lee CHL, Flood D, Marger F, Donnelly-Roberts D. Therapeutic Potential of α7 Nicotinic Acetylcholine Receptors. Pharmacol Rev 2015; 67:1025-73. [DOI: 10.1124/pr.113.008581] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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41
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Wiseman FK, Al-Janabi T, Hardy J, Karmiloff-Smith A, Nizetic D, Tybulewicz VLJ, Fisher EMC, Strydom A. A genetic cause of Alzheimer disease: mechanistic insights from Down syndrome. Nat Rev Neurosci 2015; 16:564-74. [PMID: 26243569 PMCID: PMC4678594 DOI: 10.1038/nrn3983] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Down syndrome, which arises in individuals carrying an extra copy of chromosome 21, is associated with a greatly increased risk of early-onset Alzheimer disease. It is thought that this risk is conferred by the presence of three copies of the gene encoding amyloid precursor protein (APP)--an Alzheimer disease risk factor--although the possession of extra copies of other chromosome 21 genes may also play a part. Further study of the mechanisms underlying the development of Alzheimer disease in people with Down syndrome could provide insights into the mechanisms that cause dementia in the general population.
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Affiliation(s)
- Frances K Wiseman
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK
| | - Tamara Al-Janabi
- Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF, UK
| | - John Hardy
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK
| | - Annette Karmiloff-Smith
- Centre for Brain and Cognitive Development, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Dean Nizetic
- Lee Kong Chian School of Medicine, Nanyang Technological University, Novena Campus, 11 Mandalay Road, Singapore 308232; and the Blizard Institute, Barts and the London School of Medicine, Queen Mary University of London, 4 Newark Street, London E1 2AT, UK
| | | | - Elizabeth M C Fisher
- Department of Neurodegenerative Disease, Institute of Neurology, University College London, Queen Square, London WC1N 3BG, UK
| | - André Strydom
- Division of Psychiatry, University College London, Maple House, 149 Tottenham Court Road, London W1T 7NF, UK
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42
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Zhao LN, Zheng J, Chew LY, Mu Y. An Investigation on the Fundamental Interaction between Abeta Peptides and the AT-Rich DNA. J Phys Chem B 2015; 119:8247-59. [PMID: 26086541 DOI: 10.1021/acs.jpcb.5b00957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
DNA damage is ubiquitous in all mammalian cells with the occurrence of more than 60,000 times per day per cell. In particular, DNA damage in neurons is found to accumulate with age and has been suggested to interfere with the synthesis of functional proteins. Moreover, recent studies have found through transgenic mice that human amyloid precursor protein causes an increase in DNA double-strand breaks (DSBs) with the effect of a prolongation in DNA repair. It is surmised that amyloid β (Aβ) exacerbates the DNA DSBs in neurons, possibly engendering neuronal dysfunction as a result. However, a good understanding on the holistic interaction mechanisms and the manner in which Aβ intertwines with DNA damage is still in its infancy. In our study, we found that DNA with an AT-rich sequence has a very low binding affinity toward Aβ by means of molecular dynamics simulation. While we have pursued a particular sequence of DNA in this study, other DNA sequences are expected to affect the interaction and binding affinity between DNA and Aβ, and will be pursued in our further research. Nonetheless, we have uncovered favorable interaction between the positively charged side chain of Aβ and the two ends of DNA. The latest experiment reveals that many of the double-stranded breaks in neurons can be fixed via DNA repair mechanisms but not in the case that Aβs are present. It is found that the increased numbers of DSBs prevail in active neurons. Here, on the basis of the favorable interaction between Aβ and the two ends of DNA, we propose the possibility that Aβ prevents DNA repair via binding directly to the break ends of the DNA, which further exacerbates DNA damage. Moreover, we have found that the base pair oxygen of the DNA has a greater preference to form hydrogen bonds than the backbone oxygen with Aβ at the two ends. Thus, we postulate that Aβ could serve to prevent the repair of AT-rich DNA, and it is unlikely to cause its breakage or affect its binding toward histone. Another important observation from our study is that AT-rich DNA has very little or no influence on Aβ oligomerization. Finally, even though we do not observe any dramatic DNA conformational change in the presence of Aβ, we do observe an increase in diversity of the DNA structural parameters such as groove width, local base step, and torsional angles in lieu of Aβ interactions.
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Affiliation(s)
- Li Na Zhao
- †School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore.,‡School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore.,§Bioinformatics Institute, 30 Biopolis Street, Singapore 138671
| | - Jie Zheng
- ‡School of Computer Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore.,∥Genome Institute of Singapore, A* STAR, 60 Biopolis Street, Singapore 138672
| | - Lock Yue Chew
- †School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore.,⊥Complexity Institute, Nanyang Technological University, 18 Nanyang Drive, Singapore
| | - Yuguang Mu
- #School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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43
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Weiner MW, Veitch DP, Aisen PS, Beckett LA, Cairns NJ, Cedarbaum J, Green RC, Harvey D, Jack CR, Jagust W, Luthman J, Morris JC, Petersen RC, Saykin AJ, Shaw L, Shen L, Schwarz A, Toga AW, Trojanowski JQ. 2014 Update of the Alzheimer's Disease Neuroimaging Initiative: A review of papers published since its inception. Alzheimers Dement 2015; 11:e1-120. [PMID: 26073027 PMCID: PMC5469297 DOI: 10.1016/j.jalz.2014.11.001] [Citation(s) in RCA: 203] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 04/18/2013] [Indexed: 01/18/2023]
Abstract
The Alzheimer's Disease Neuroimaging Initiative (ADNI) is an ongoing, longitudinal, multicenter study designed to develop clinical, imaging, genetic, and biochemical biomarkers for the early detection and tracking of Alzheimer's disease (AD). The initial study, ADNI-1, enrolled 400 subjects with early mild cognitive impairment (MCI), 200 with early AD, and 200 cognitively normal elderly controls. ADNI-1 was extended by a 2-year Grand Opportunities grant in 2009 and by a competitive renewal, ADNI-2, which enrolled an additional 550 participants and will run until 2015. This article reviews all papers published since the inception of the initiative and summarizes the results to the end of 2013. The major accomplishments of ADNI have been as follows: (1) the development of standardized methods for clinical tests, magnetic resonance imaging (MRI), positron emission tomography (PET), and cerebrospinal fluid (CSF) biomarkers in a multicenter setting; (2) elucidation of the patterns and rates of change of imaging and CSF biomarker measurements in control subjects, MCI patients, and AD patients. CSF biomarkers are largely consistent with disease trajectories predicted by β-amyloid cascade (Hardy, J Alzheimer's Dis 2006;9(Suppl 3):151-3) and tau-mediated neurodegeneration hypotheses for AD, whereas brain atrophy and hypometabolism levels show predicted patterns but exhibit differing rates of change depending on region and disease severity; (3) the assessment of alternative methods of diagnostic categorization. Currently, the best classifiers select and combine optimum features from multiple modalities, including MRI, [(18)F]-fluorodeoxyglucose-PET, amyloid PET, CSF biomarkers, and clinical tests; (4) the development of blood biomarkers for AD as potentially noninvasive and low-cost alternatives to CSF biomarkers for AD diagnosis and the assessment of α-syn as an additional biomarker; (5) the development of methods for the early detection of AD. CSF biomarkers, β-amyloid 42 and tau, as well as amyloid PET may reflect the earliest steps in AD pathology in mildly symptomatic or even nonsymptomatic subjects and are leading candidates for the detection of AD in its preclinical stages; (6) the improvement of clinical trial efficiency through the identification of subjects most likely to undergo imminent future clinical decline and the use of more sensitive outcome measures to reduce sample sizes. Multimodal methods incorporating APOE status and longitudinal MRI proved most highly predictive of future decline. Refinements of clinical tests used as outcome measures such as clinical dementia rating-sum of boxes further reduced sample sizes; (7) the pioneering of genome-wide association studies that leverage quantitative imaging and biomarker phenotypes, including longitudinal data, to confirm recently identified loci, CR1, CLU, and PICALM and to identify novel AD risk loci; (8) worldwide impact through the establishment of ADNI-like programs in Japan, Australia, Argentina, Taiwan, China, Korea, Europe, and Italy; (9) understanding the biology and pathobiology of normal aging, MCI, and AD through integration of ADNI biomarker and clinical data to stimulate research that will resolve controversies about competing hypotheses on the etiopathogenesis of AD, thereby advancing efforts to find disease-modifying drugs for AD; and (10) the establishment of infrastructure to allow sharing of all raw and processed data without embargo to interested scientific investigators throughout the world.
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Affiliation(s)
- Michael W Weiner
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA; Department of Radiology, University of California, San Francisco, CA, USA; Department of Medicine, University of California, San Francisco, CA, USA; Department of Psychiatry, University of California, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, CA, USA.
| | - Dallas P Veitch
- Department of Veterans Affairs Medical Center, Center for Imaging of Neurodegenerative Diseases, San Francisco, CA, USA
| | - Paul S Aisen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Laurel A Beckett
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | - Nigel J Cairns
- Knight Alzheimer's Disease Research Center, Washington University School of Medicine, Saint Louis, MO, USA; Department of Neurology, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jesse Cedarbaum
- Neurology Early Clinical Development, Biogen Idec, Cambridge, MA, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Danielle Harvey
- Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, USA
| | | | - William Jagust
- Helen Wills Neuroscience Institute, University of California Berkeley, Berkeley, CA, USA
| | - Johan Luthman
- Neuroscience Clinical Development, Neuroscience & General Medicine Product Creation Unit, Eisai Inc., Philadelphia, PA, USA
| | - John C Morris
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | | | - Andrew J Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Leslie Shaw
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Li Shen
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adam Schwarz
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN, USA
| | - Arthur W Toga
- Laboratory of Neuroimaging, Institute of Neuroimaging and Informatics, Keck School of Medicine of University of Southern California, Los Angeles, CA, USA
| | - John Q Trojanowski
- Institute on Aging, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Alzheimer's Disease Core Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Udall Parkinson's Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Pathology and Laboratory Medicine, Center for Neurodegenerative Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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44
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Zheng X, Demirci FY, Barmada MM, Richardson GA, Lopez OL, Sweet RA, Kamboh MI, Feingold E. Genome-wide copy-number variation study of psychosis in Alzheimer's disease. Transl Psychiatry 2015; 5:e574. [PMID: 26035058 PMCID: PMC4490277 DOI: 10.1038/tp.2015.64] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Revised: 01/23/2015] [Accepted: 02/08/2015] [Indexed: 01/17/2023] Open
Abstract
About 40-60% of patients with late-onset Alzheimer's disease (AD) develop psychosis, which represents a distinct phenotype of more severe cognitive and functional deficits. The estimated heritability of AD+P is ~61%, which makes it a good target for genetic mapping. We performed a genome-wide copy-number variation (CNV) study on 496 AD cases with psychosis (AD+P), 639 AD subjects with intermediate psychosis (AD intermediate P) and 156 AD subjects without psychosis (AD-P) who were recruited at the University of Pittsburgh Alzheimer's Disease Research Center using over 1 million single-nucleotide polymorphisms (SNPs) and CNV markers. CNV load analysis found no significant difference in total and average CNV length and CNV number in the AD+P or AD intermediate P groups compared with the AD-P group. Our analysis revealed a marginally significant lower number of duplication events in AD+P cases compared with AD-P controls (P=0.059) using multivariable regression model. The most interesting finding was the presence of a genome-wide significant duplication in the APC2 gene on chromosome 19, which was protective against developing AD+P (odds ratio=0.42; P=7.2E-10). We also observed suggestive associations of duplications with AD+P in the SET (P=1.95E-06), JAG2 (P=5.01E-07) and ZFPM1 (P=2.13E-07) genes and marginal association of a deletion in CNTLN (P=8.87E-04). We have identified potential novel loci for psychosis in Alzheimer's disease that warrant follow-up in large-scale independent studies.
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Affiliation(s)
- X Zheng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA,Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC 27514, USA. E-mail:
| | - F Y Demirci
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - M M Barmada
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - G A Richardson
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - O L Lopez
- Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,VISN 4 Mental Illness Research, Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - R A Sweet
- Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Department of Neurology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,VISN 4 Mental Illness Research, Education and Clinical Center, VA Pittsburgh Healthcare System, Pittsburgh, PA, USA
| | - M I Kamboh
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - E Feingold
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
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45
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Wang M, Li Y, Lin L, Song G, Deng T. GSTM1 Null Genotype and GSTP1 Ile105Val Polymorphism Are Associated with Alzheimer's Disease: a Meta-Analysis. Mol Neurobiol 2015; 53:1355-1364. [PMID: 25633095 DOI: 10.1007/s12035-015-9092-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/12/2015] [Indexed: 01/09/2023]
Abstract
Published studies on the associations between glutathione S-transferase (GST) polymorphisms and Alzheimer's disease reported controversial findings. A meta-analysis of published studies was performed to assess the associations between polymorphisms of GSTM1, GSTT1 and GSTP1, and Alzheimer's disease. PubMed, Embase, and other databases were searched for case-control on the associations between polymorphisms of GSTM1, GSTT1 and GSTP1, and Alzheimer's disease. The odds ratio (OR) and 95% confidence interval (95% CI) were used to assess the associations. Eleven articles were finally included into the meta-analysis, including eight studies on GSTM1 null genotype, six studies on GSTT1 null genotype, and six studies on GSTP1 Ile105Val polymorphism. Overall, GSTM1 null genotype was associated with increased risk of Alzheimer's disease (fixed effect OR = 1.34, 95% CI 1.10-1.64, P = 0.004). GSTT1 null genotype was not associated with risk of Alzheimer's disease (random effect OR = 1.15, 95% CI 0.68-1.92, P = 0.60). Besides, GSTP1 Ile105Val polymorphism was significantly associated with increased risk of Alzheimer's disease (Val vs Ile: OR = 1.45, 95% CI 1.05-1.99, P = 0.023; ValVal vs IleIle: OR = 1.87, 95% CI 1.30-2.69, P = 0.001; ValVal vs IleIle + IleVal: OR = 1.76, 95% CI 1.24-2.51, P = 0.002). No obvious risk of publication bias was observed in the meta-analysis. GSTM1 null genotype and GSTP1 Ile105Val polymorphism are associated with increased risk of Alzheimer's disease. More studies with large sample size are needed to validate the findings in the meta-analysis.
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Affiliation(s)
- Mo Wang
- Neurology Department No.1, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Yu Li
- Neurology Department No.1, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Lulu Lin
- Neurology Department No.1, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China
| | - Guijun Song
- Neurology Department No.1, The Second Affiliated Hospital of Dalian Medical University, Dalian, 116023, China.
| | - Teng Deng
- Capital Medical University, Beijing, 100068, China
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46
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Costantini TW, Dang X, Coimbra R, Eliceiri BP, Baird A. CHRFAM7A, a human-specific and partially duplicated α7-nicotinic acetylcholine receptor gene with the potential to specify a human-specific inflammatory response to injury. J Leukoc Biol 2014; 97:247-57. [PMID: 25473097 DOI: 10.1189/jlb.4ru0814-381r] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conventional wisdom presumes that the α7nAChR product of CHRNA7 expression mediates the ability of the vagus nerve to regulate the inflammatory response to injury and infection. Yet, 15 years ago, a 2nd structurally distinct and human-specific α7nAChR gene was discovered that has largely escaped attention of the inflammation research community. The gene, originally called dupα7nAChR but now known as CHRFAM7A, has been studied exhaustively in psychiatric research because of its association with mental illness. However, dupα7nAChR/CHRFAM7A expression is relatively low in human brain but elevated in human leukocytes. Furthermore, α7nAChR research in human tissues has been confounded by cross-reacting antibodies and nonspecific oligonucleotide primers that crossreact in immunoblotting, immunohistochemistry, and RT-PCR. Yet, 3 independent reports show the human-specific CHRFAM7A changes cell responsiveness to the canonical α7nAChR/CHRNA7 ion-gated channel. Because of its potential for the injury research community, its possible significance to human leukocyte biology, and its relevance to human inflammation, we review the discovery and structure of the dupα7nAChR/CHRFAM7A gene, the distribution of its mRNA, and its biologic activities and then discuss its possible role(s) in specifying human inflammation and injury. In light of emerging concepts that point to a role for human-specific genes in complex human disease, the existence of a human-specific α7nAChR regulating inflammatory responses in injury underscores the need for caution in extrapolating findings in the α7nAChR literature to man. To this end, we discuss the translational implications of a uniquely human α7nAChR-like gene on new drug target discovery and therapeutics development for injury, infection, and inflammation.
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Affiliation(s)
- Todd W Costantini
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Xitong Dang
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Raul Coimbra
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Brian P Eliceiri
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
| | - Andrew Baird
- Division of Trauma, Surgical Critical Care, Burn and Acute Critical Care, Department of Surgery, University of California San Diego Health Sciences, San Diego, California, USA
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47
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Jenkins A, Apud JA, Zhang F, Decot H, Weinberger DR, Law AJ. Identification of candidate single-nucleotide polymorphisms in NRXN1 related to antipsychotic treatment response in patients with schizophrenia. Neuropsychopharmacology 2014; 39:2170-8. [PMID: 24633560 PMCID: PMC4104334 DOI: 10.1038/npp.2014.65] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Revised: 02/20/2014] [Accepted: 03/09/2014] [Indexed: 12/22/2022]
Abstract
Neurexins are presynaptic neuronal adhesion molecules that interact with postsynaptic neuroligins to form an inter-synaptic complex required for synaptic specification and efficient neurotransmission. Deletions and point mutations in the neurexin 1 (NRXN1) gene are associated with a broad spectrum of neuropsychiatric and neurodevelopmental disorders, including autism, intellectual disability, epilepsy, developmental delay, and schizophrenia. Recently, small nucleotide polymorphisms in NRXN1 have been associated with antipsychotic drug response in patients with schizophrenia. Based on previous suggestive evidence of an impact on clozapine response in patients with schizophrenia, we conducted an association study of NRXN1 polymorphisms (rs12467557 and rs10490162) with antipsychotic treatment response in 54 patients with schizophrenia in a double blind, placebo-controlled NIMH inpatient crossover trial and examined for association with risk for schizophrenia in independent case-control and family-based clinical cohorts. Pharmacogenetic analysis in the placebo controlled trial revealed significant association of rs12467557and rs10490162 with drug response, whereby individuals homozygous for the A allele, at either SNP, showed significant improvement in positive symptoms, general psychopathology, thought disturbance, and negative symptoms, whereas patients carrying the G allele showed no overall response. Although we did not find evidence of the same NRXN1 SNPs being associated with results of the NIMH sponsored CATIE trial, other SNPs showed weakly positive signals. The family and case-control analyses for schizophrenia risk were negative. Our results provide confirmatory evidence of genetically determined differences in drug response in patients with schizophrenia related to NRXN1 variation. Furthermore, these findings potentially implicate NRXN1 in the therapeutic actions of antipsychotic drugs.
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Affiliation(s)
- Aaron Jenkins
- Clinical Brain Disorders Branch, Genes, Cognition and Psychosis Program, National Institute of Mental Health, National Institute of Health, National Institutes of Health, Bethesda, MD, USA,University of Kentucky College of Medicine, Lexington, KY, USA
| | - José A Apud
- Clinical Brain Disorders Branch, Genes, Cognition and Psychosis Program, National Institute of Mental Health, National Institute of Health, National Institutes of Health, Bethesda, MD, USA
| | - Fengyu Zhang
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA
| | - Heather Decot
- Clinical Brain Disorders Branch, Genes, Cognition and Psychosis Program, National Institute of Mental Health, National Institute of Health, National Institutes of Health, Bethesda, MD, USA
| | - Daniel R Weinberger
- Lieber Institute for Brain Development, Johns Hopkins University Medical Campus, Baltimore, MD, USA,Departments of Psychiatry, Neurology, Neuroscience and the McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Amanda J Law
- Departments of Psychiatry and Cell and Developmental Biology, University of Colorado, School of Medicine, Aurora, CO, USA,Departments of Psychiatry and Cell and Developmental Biology, University of Colorado, School of Medicine, Mailstop 8344, RC1 North, RM. 8101, Aurora, CO 80045, USA, Tel: +1 303 724 4418, Fax: +1 303 724 4425, E-mail:
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48
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Alzheimer's disease--a panorama glimpse. Int J Mol Sci 2014; 15:12631-50. [PMID: 25032844 PMCID: PMC4139864 DOI: 10.3390/ijms150712631] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Revised: 06/26/2014] [Accepted: 07/10/2014] [Indexed: 01/05/2023] Open
Abstract
The single-mutation of genes associated with Alzheimer's disease (AD) increases the production of Aβ peptides. An elevated concentration of Aβ peptides is prone to aggregation into oligomers and further deposition as plaque. Aβ plaques and neurofibrillary tangles are two hallmarks of AD. In this review, we provide a broad overview of the diverses sources that could lead to AD, which include genetic origins, Aβ peptides and tau protein. We shall discuss on tau protein and tau accumulation, which result in neurofibrillary tangles. We detail the mechanisms of Aβ aggregation, fibril formation and its polymorphism. We then show the possible links between Aβ and tau pathology. Furthermore, we summarize the structural data of Aβ and its precursor protein obtained via Nuclear Magnetic Resonance (NMR) or X-ray crystallography. At the end, we go through the C-terminal and N-terminal truncated Aβ variants. We wish to draw reader's attention to two predominant and toxic Aβ species, namely Aβ4-42 and pyroglutamate amyloid-beta peptides, which have been neglected for more than a decade and may be crucial in Aβ pathogenesis due to their dominant presence in the AD brain.
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49
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Shen L, Thompson PM, Potkin SG, Bertram L, Farrer LA, Foroud TM, Green RC, Hu X, Huentelman MJ, Kim S, Kauwe JSK, Li Q, Liu E, Macciardi F, Moore JH, Munsie L, Nho K, Ramanan VK, Risacher SL, Stone DJ, Swaminathan S, Toga AW, Weiner MW, Saykin AJ. Genetic analysis of quantitative phenotypes in AD and MCI: imaging, cognition and biomarkers. Brain Imaging Behav 2014; 8:183-207. [PMID: 24092460 PMCID: PMC3976843 DOI: 10.1007/s11682-013-9262-z] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The Genetics Core of the Alzheimer's Disease Neuroimaging Initiative (ADNI), formally established in 2009, aims to provide resources and facilitate research related to genetic predictors of multidimensional Alzheimer's disease (AD)-related phenotypes. Here, we provide a systematic review of genetic studies published between 2009 and 2012 where either ADNI APOE genotype or genome-wide association study (GWAS) data were used. We review and synthesize ADNI genetic associations with disease status or quantitative disease endophenotypes including structural and functional neuroimaging, fluid biomarker assays, and cognitive performance. We also discuss the diverse analytical strategies used in these studies, including univariate and multivariate analysis, meta-analysis, pathway analysis, and interaction and network analysis. Finally, we perform pathway and network enrichment analyses of these ADNI genetic associations to highlight key mechanisms that may drive disease onset and trajectory. Major ADNI findings included all the top 10 AD genes and several of these (e.g., APOE, BIN1, CLU, CR1, and PICALM) were corroborated by ADNI imaging, fluid and cognitive phenotypes. ADNI imaging genetics studies discovered novel findings (e.g., FRMD6) that were later replicated on different data sets. Several other genes (e.g., APOC1, FTO, GRIN2B, MAGI2, and TOMM40) were associated with multiple ADNI phenotypes, warranting further investigation on other data sets. The broad availability and wide scope of ADNI genetic and phenotypic data has advanced our understanding of the genetic basis of AD and has nominated novel targets for future studies employing next-generation sequencing and convergent multi-omics approaches, and for clinical drug and biomarker development.
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Affiliation(s)
- Li Shen
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Paul M. Thompson
- Imaging Genetics Center, Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
| | - Steven G. Potkin
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
| | - Lars Bertram
- Neuropsychiatric Genetics Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany
| | - Lindsay A. Farrer
- Biomedical Genetics L320, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 USA
| | - Tatiana M. Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Robert C. Green
- Division of Genetics and Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
| | - Xiaolan Hu
- Clinical Genetics, Exploratory Clinical & Translational Research, Bristol-Myers Squibbs, Pennington, NJ 08534 USA
| | - Matthew J. Huentelman
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004 USA
| | - Sungeun Kim
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - John S. K. Kauwe
- Departments of Biology, Neuroscience, Brigham Young University, 675 WIDB, Provo, UT 84602 USA
| | - Qingqin Li
- Department of Neuroscience Biomarkers, Janssen Research and Development, LLC, Raritan, NJ 08869 USA
| | - Enchi Liu
- Biomarker Discovery, Janssen Alzheimer Immunotherapy Research and Development, LLC, South San Francisco, CA 94080 USA
| | - Fabio Macciardi
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
- Department of Sciences and Biomedical Technologies, University of Milan, Segrate, MI Italy
| | - Jason H. Moore
- Department of Genetics, Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, NH 03756 USA
| | - Leanne Munsie
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN 46285 USA
| | - Kwangsik Nho
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Vijay K. Ramanan
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - Shannon L. Risacher
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - David J. Stone
- Merck Research Laboratories, 770 Sumneytown Pike, WP53B-120, West Point, PA 19486 USA
| | - Shanker Swaminathan
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
| | - Arthur W. Toga
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
| | - Michael W. Weiner
- Departments of Radiology, Medicine and Psychiatry, UC San Francisco, San Francisco, CA 94143 USA
| | - Andrew J. Saykin
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Center for Neuroimaging and Indiana Alzheimer’s Disease Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, 355 W 16th Street, Suite 4100, Indianapolis, IN 46202 USA
- Imaging Genetics Center, Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
- Department of Psychiatry and Human Behavior, University of California Irvine, Irvine, CA 92617 USA
- Neuropsychiatric Genetics Group, Max-Planck Institute for Molecular Genetics, Berlin, Germany
- Biomedical Genetics L320, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118 USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202 USA
- Division of Genetics and Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115 USA
- Clinical Genetics, Exploratory Clinical & Translational Research, Bristol-Myers Squibbs, Pennington, NJ 08534 USA
- Neurogenomics Division, The Translational Genomics Research Institute, Phoenix, AZ 85004 USA
- Departments of Biology, Neuroscience, Brigham Young University, 675 WIDB, Provo, UT 84602 USA
- Department of Neuroscience Biomarkers, Janssen Research and Development, LLC, Raritan, NJ 08869 USA
- Biomarker Discovery, Janssen Alzheimer Immunotherapy Research and Development, LLC, South San Francisco, CA 94080 USA
- Department of Sciences and Biomedical Technologies, University of Milan, Segrate, MI Italy
- Department of Genetics, Computational Genetics Laboratory, Dartmouth Medical School, Lebanon, NH 03756 USA
- Tailored Therapeutics, Eli Lilly and Company, Indianapolis, IN 46285 USA
- Merck Research Laboratories, 770 Sumneytown Pike, WP53B-120, West Point, PA 19486 USA
- Laboratory of Neuro Imaging, Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095 USA
- Departments of Radiology, Medicine and Psychiatry, UC San Francisco, San Francisco, CA 94143 USA
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50
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Persengiev S, Kondova I, Bontrop R. Insights on the functional interactions between miRNAs and copy number variations in the aging brain. Front Mol Neurosci 2013; 6:32. [PMID: 24106459 PMCID: PMC3788589 DOI: 10.3389/fnmol.2013.00032] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Accepted: 09/11/2013] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are regulatory genetic elements that coordinate the expression of thousands of genes and play important roles in brain aging and neurodegeneration. DNA polymorphisms affecting miRNA biogenesis, dosage, and gene targeting may represent potentially functional variants. The consequences of single nucleotide polymorphisms affecting miRNA function were previously demonstrated by both experimental and computational methods. However, little is known about how copy number variations (CNVs) influence miRNA metabolism and regulatory networks. We discuss potential mechanisms of CNVs-mediated effects on miRNA function and regulation that might have consequences for brain aging. We argue that CNVs, which potentially can alter miRNA expression, regulation or target gene recognition, are possible functional variants and should be considered high priority candidates in genotype–phenotype mapping studies of brain-related disorders.
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