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Lu Y, Hatzipantelis CJ, Langmead CJ, Stewart GD. Molecular insights into orphan G protein-coupled receptors relevant to schizophrenia. Br J Pharmacol 2024; 181:2095-2113. [PMID: 37605621 DOI: 10.1111/bph.16221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/25/2023] [Accepted: 07/23/2023] [Indexed: 08/23/2023] Open
Abstract
Schizophrenia remains a sizable socio-economic burden that continues to be treated with therapeutics based on 70-year old science. All currently approved therapeutics primarily target the dopamine D2 receptor to achieve their efficacy. Whilst dopaminergic dysregulation is a key feature in this disorder, the targeting of dopaminergic machinery has yielded limited efficacy and an appreciable side effect burden. Over the recent decades, numerous drugs that engage non-dopaminergic G protein-coupled receptors (GPCRs) have yielded a promise of efficacy without the deleterious side effect profile, yet none have successfully completed clinical studies and progressed to the market. More recently, there has been increased attention around non-dopaminergic GPCR-targeting drugs, which demonstrated efficacy in some schizophrenia symptom domains. This provides renewed hope that effective schizophrenia treatment may lie outside of the dopaminergic space. Despite the potential for muscarinic receptor- (and other well-characterised GPCR families) targeting drugs to treat schizophrenia, they are often plagued with complications such as lack of receptor subtype selectivity and peripheral on-target side effects. Orphan GPCR studies have opened a new avenue of exploration with many demonstrating schizophrenia-relevant mechanisms and a favourable expression profile, thus offering potential for novel drug development. This review discusses centrally expressed orphan GPCRs: GPR3, GPR6, GPR12, GPR52, GPR85, GPR88 and GPR139 and their relationship to schizophrenia. We review their expression, signalling mechanisms and cellular function, in conjunction with small molecule development and structural insights. We seek to provide a snapshot of the growing evidence and development potential of new classes of schizophrenia therapeutics. LINKED ARTICLES: This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
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Affiliation(s)
- Yao Lu
- Drug Discovery Biology and Neuroscience & Mental Health Therapeutic Program Area, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
| | | | - Christopher J Langmead
- Drug Discovery Biology and Neuroscience & Mental Health Therapeutic Program Area, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
- Phrenix Therapeutics, Parkville, Australia
| | - Gregory D Stewart
- Drug Discovery Biology and Neuroscience & Mental Health Therapeutic Program Area, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Australia
- Neuromedicines Discovery Centre, Monash University, Parkville, Australia
- Phrenix Therapeutics, Parkville, Australia
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2
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Primak A, Bozov K, Rubina K, Dzhauari S, Neyfeld E, Illarionova M, Semina E, Sheleg D, Tkachuk V, Karagyaur M. Morphogenetic theory of mental and cognitive disorders: the role of neurotrophic and guidance molecules. Front Mol Neurosci 2024; 17:1361764. [PMID: 38646100 PMCID: PMC11027769 DOI: 10.3389/fnmol.2024.1361764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/04/2024] [Indexed: 04/23/2024] Open
Abstract
Mental illness and cognitive disorders represent a serious problem for the modern society. Many studies indicate that mental disorders are polygenic and that impaired brain development may lay the ground for their manifestation. Neural tissue development is a complex and multistage process that involves a large number of distant and contact molecules. In this review, we have considered the key steps of brain morphogenesis, and the major molecule families involved in these process. The review provides many indications of the important contribution of the brain development process and correct functioning of certain genes to human mental health. To our knowledge, this comprehensive review is one of the first in this field. We suppose that this review may be useful to novice researchers and clinicians wishing to navigate the field.
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Affiliation(s)
- Alexandra Primak
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Kirill Bozov
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Kseniya Rubina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Stalik Dzhauari
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Elena Neyfeld
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Federal State Budgetary Educational Institution of the Higher Education “A.I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Maria Illarionova
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Ekaterina Semina
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
| | - Dmitriy Sheleg
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Federal State Budgetary Educational Institution of the Higher Education “A.I. Yevdokimov Moscow State University of Medicine and Dentistry” of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Vsevolod Tkachuk
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
| | - Maxim Karagyaur
- Faculty of Medicine, Lomonosov Moscow State University, Moscow, Russia
- Institute for Regenerative Medicine, Medical Research and Education Center, Lomonosov Moscow State University, Moscow, Russia
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3
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Zhang R, Chen J. Research progress on the role of orphan receptor GPR139 in neuropsychiatric behaviours. Eur J Pharmacol 2023; 960:176150. [PMID: 38059447 DOI: 10.1016/j.ejphar.2023.176150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/09/2023] [Accepted: 10/20/2023] [Indexed: 12/08/2023]
Abstract
The study of orphan G protein-coupled receptors (GPCRs) holds much promise for increasing our understanding of neuropsychiatric diseases and for the development of new therapeutic strategies for these diseases. GPR139 is an orphan GPCR expressed in the central nervous system, especially in areas of the brain that control movement, motivation, and reward, and those that regulate neuropsychiatric behaviour. This review provides information about the discovery, tissue expression, signal transduction pathways, and physiological functions of GPR139, as well as how GPR139 interacts with other GPCRs, which form heteromeric complexes that affect their pharmacology and function. We also discuss the utility and therapeutic potential of ligands that target GPR139, including the pharmacological properties of reported agonists and antagonists. Finally, we highlight the pathologic role of GPR139 in neuropsychiatric behaviour and its potential as a therapeutic target in neuropsychiatric disorders.
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Affiliation(s)
- Rumin Zhang
- Neurobiology Key Laboratory of Jining Medical University, Jining, 272067, China; School of Mental Health, Jining Medical University, Jining, 272067, China
| | - Jing Chen
- Neurobiology Key Laboratory of Jining Medical University, Jining, 272067, China; School of Mental Health, Jining Medical University, Jining, 272067, China; Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV47AL, UK.
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4
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Zhan N, Sham PC, So HC, Lui SSY. The genetic basis of onset age in schizophrenia: evidence and models. Front Genet 2023; 14:1163361. [PMID: 37441552 PMCID: PMC10333597 DOI: 10.3389/fgene.2023.1163361] [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: 02/10/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Schizophrenia is a heritable neurocognitive disorder affecting about 1% of the population, and usually has an onset age at around 21-25 in males and 25-30 in females. Recent advances in genetics have helped to identify many common and rare variants for the liability to schizophrenia. Earlier evidence appeared to suggest that younger onset age is associated with higher genetic liability to schizophrenia. Clinical longitudinal research also found that early and very-early onset schizophrenia are associated with poor clinical, neurocognitive, and functional profiles. A recent study reported a heritability of 0.33 for schizophrenia onset age, but the genetic basis of this trait in schizophrenia remains elusive. In the pre-Genome-Wide Association Study (GWAS) era, genetic loci found to be associated with onset age were seldom replicated. In the post-Genome-Wide Association Study era, new conceptual frameworks are needed to clarify the role of onset age in genetic research in schizophrenia, and to identify its genetic basis. In this review, we first discussed the potential of onset age as a characterizing/subtyping feature for psychosis, and as an important phenotypic dimension of schizophrenia. Second, we reviewed the methods, samples, findings and limitations of previous genetic research on onset age in schizophrenia. Third, we discussed a potential conceptual framework for studying the genetic basis of onset age, as well as the concepts of susceptibility, modifier, and "mixed" genes. Fourth, we discussed the limitations of this review. Lastly, we discussed the potential clinical implications for genetic research of onset age of schizophrenia, and how future research can unveil the potential mechanisms for this trait.
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Affiliation(s)
- Na Zhan
- Department of Psychiatry, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Pak C. Sham
- Department of Psychiatry, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- Centre of PanorOmic Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
- State Key Laboratory of Brain and Cognitive Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Hon-Cheong So
- School of Biomedical Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research of Common Diseases, Kunming Institute of Zoology and the Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Department of Psychiatry, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- CUHK Shenzhen Research Institute, Shenzhen, China
- Margaret K. L. Cheung Research Centre for Management of Parkinsonism, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Brain and Mind Institute, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
- Hong Kong Branch of the Chinese Academy of Sciences Center for Excellence in Animal Evolution and Genetics, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| | - Simon S. Y. Lui
- Department of Psychiatry, School of Clinical Medicine, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
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5
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Caniceiro AB, Bueschbell B, Schiedel AC, Moreira IS. Class A and C GPCR Dimers in Neurodegenerative Diseases. Curr Neuropharmacol 2022; 20:2081-2141. [PMID: 35339177 PMCID: PMC9886835 DOI: 10.2174/1570159x20666220327221830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/21/2022] [Accepted: 03/23/2022] [Indexed: 11/22/2022] Open
Abstract
Neurodegenerative diseases affect over 30 million people worldwide with an ascending trend. Most individuals suffering from these irreversible brain damages belong to the elderly population, with onset between 50 and 60 years. Although the pathophysiology of such diseases is partially known, it remains unclear upon which point a disease turns degenerative. Moreover, current therapeutics can treat some of the symptoms but often have severe side effects and become less effective in long-term treatment. For many neurodegenerative diseases, the involvement of G proteincoupled receptors (GPCRs), which are key players of neuronal transmission and plasticity, has become clearer and holds great promise in elucidating their biological mechanism. With this review, we introduce and summarize class A and class C GPCRs, known to form heterodimers or oligomers to increase their signalling repertoire. Additionally, the examples discussed here were shown to display relevant alterations in brain signalling and had already been associated with the pathophysiology of certain neurodegenerative diseases. Lastly, we classified the heterodimers into two categories of crosstalk, positive or negative, for which there is known evidence.
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Affiliation(s)
- Ana B. Caniceiro
- Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Beatriz Bueschbell
- PhD Programme in Experimental Biology and Biomedicine, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Casa Costa Alemão, 3030-789 Coimbra, Portugal; ,These authors contributed equally to this work.
| | - Anke C. Schiedel
- Department of Pharmaceutical & Medicinal Chemistry, Pharmaceutical Institute, University of Bonn, D-53121 Bonn, Germany;
| | - Irina S. Moreira
- University of Coimbra, Department of Life Sciences, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; ,Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal,Address correspondence to this author at the Center for Neuroscience and Cell Biology, Center for Innovative Biomedicine and Biotechnology, 3004-504 Coimbra, Portugal; E-mail:
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6
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The role of orphan receptor GPR139 in neuropsychiatric behavior. Neuropsychopharmacology 2022; 47:902-913. [PMID: 33479510 PMCID: PMC8882194 DOI: 10.1038/s41386-021-00962-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/05/2021] [Indexed: 01/30/2023]
Abstract
Orphan G protein Coupled Receptors (GPCRs) present attractive targets both for understanding neuropsychiatric diseases and for development of novel therapeutics. GPR139 is an orphan GPCR expressed in select brain circuits involved in controlling movement, motivation and reward. It has been linked to the opioid and dopamine neuromodulatory systems; however, its role in animal behavior and neuropsychiatric processes is poorly understood. Here we present a comprehensive behavioral characterization of a mouse model with a GPR139 null mutation. We show that loss of GPR139 in mice results in delayed onset hyperactivity and prominent neuropsychiatric manifestations including elevated stereotypy, increased anxiety-related traits, delayed acquisition of operant responsiveness, disruption of cued fear conditioning and social interaction deficits. Furthermore, mice lacking GPR139 exhibited complete loss of pre-pulse inhibition and developed spontaneous 'hallucinogenic' head-twitches, altogether suggesting schizophrenia-like symptomatology. Remarkably, a number of these behavioral deficits could be rescued by the administration of μ-opioid and D2 dopamine receptor (D2R) antagonists: naltrexone and haloperidol, respectively, suggesting that loss of neuropsychiatric manifestations in mice lacking GPR139 are driven by opioidergic and dopaminergic hyper-functionality. The inhibitory influence of GPR139 on D2R signaling was confirmed in cell-based functional assays. These observations define the role of GPR139 in controlling behavior and implicate in vivo actions of this receptor in the neuropsychiatric process with schizophrenia-like pathology.
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7
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Reichard HA, Schiffer HH, Monenschein H, Atienza JM, Corbett G, Skaggs AW, Collia DR, Ray WJ, Serrats J, Bliesath J, Kaushal N, Lam BP, Amador-Arjona A, Rahbaek L, McConn DJ, Mulligan VJ, Brice N, Gaskin PLR, Cilia J, Hitchcock S. Discovery of TAK-041: a Potent and Selective GPR139 Agonist Explored for the Treatment of Negative Symptoms Associated with Schizophrenia. J Med Chem 2021; 64:11527-11542. [PMID: 34260228 DOI: 10.1021/acs.jmedchem.1c00820] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The orphan G-protein-coupled receptor GPR139 is highly expressed in the habenula, a small brain nucleus that has been linked to depression, schizophrenia (SCZ), and substance-use disorder. High-throughput screening and a medicinal chemistry structure-activity relationship strategy identified a novel series of potent and selective benzotriazinone-based GPR139 agonists. Herein, we describe the chemistry optimization that led to the discovery and validation of multiple potent and selective in vivo GPR139 agonist tool compounds, including our clinical candidate TAK-041, also known as NBI-1065846 (compound 56). The pharmacological characterization of these GPR139 agonists in vivo demonstrated GPR139-agonist-dependent modulation of habenula cell activity and revealed consistent in vivo efficacy to rescue social interaction deficits in the BALB/c mouse strain. The clinical GPR139 agonist TAK-041 is being explored as a novel drug to treat negative symptoms in SCZ.
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Affiliation(s)
- Holly A Reichard
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Hans H Schiffer
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Holger Monenschein
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Josephine M Atienza
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Gerard Corbett
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Cambridge, Cambridgeshire CB4 0PZ, U.K
| | - Alton W Skaggs
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Deanna R Collia
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - William J Ray
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Jordi Serrats
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Joshua Bliesath
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Nidhi Kaushal
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Betty P Lam
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Alejandro Amador-Arjona
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Lisa Rahbaek
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Donavon J McConn
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
| | - Victoria J Mulligan
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Cambridge, Cambridgeshire CB4 0PZ, U.K
| | - Nicola Brice
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Cambridge, Cambridgeshire CB4 0PZ, U.K
| | - Philip L R Gaskin
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Cambridge, Cambridgeshire CB4 0PZ, U.K
| | - Jackie Cilia
- Takeda Cambridge Ltd., 418 Cambridge Science Park, Cambridge, Cambridgeshire CB4 0PZ, U.K
| | - Stephen Hitchcock
- Takeda California, Inc., 9625 Towne Centre Drive, San Diego, California 92121, United States
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8
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Qin F, Luo X, Cai G, Xiao F. Shall genomic correlation structure be considered in copy number variants detection? Brief Bioinform 2021; 22:6295811. [PMID: 34114005 DOI: 10.1093/bib/bbab215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/16/2021] [Accepted: 05/17/2021] [Indexed: 11/14/2022] Open
Abstract
Copy number variation has been identified as a major source of genomic variation associated with disease susceptibility. With the advent of whole-exome sequencing (WES) technology, massive WES data have been generated, allowing for the identification of copy number variants (CNVs) in the protein-coding regions with direct functional interpretation. We have previously shown evidence of the genomic correlation structure in array data and developed a novel chromosomal breakpoint detection algorithm, LDcnv, which showed significantly improved detection power through integrating the correlation structure in a systematic modeling manner. However, it remains unexplored whether the genomic correlation exists in WES data and how such correlation structure integration can improve the CNV detection accuracy. In this study, we first explored the correlation structure of the WES data using the 1000 Genomes Project data. Both real raw read depth and median-normalized data showed strong evidence of the correlation structure. Motivated by this fact, we proposed a correlation-based method, CORRseq, as a novel release of the LDcnv algorithm in profiling WES data. The performance of CORRseq was evaluated in extensive simulation studies and real data analysis from the 1000 Genomes Project. CORRseq outperformed the existing methods in detecting medium and large CNVs. In conclusion, it would be more advantageous to model genomic correlation structure in detecting relatively long CNVs. This study provides great insights for methodology development of CNV detection with NGS data.
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Affiliation(s)
- Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina (USC), Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, USC, Discovery 449, 915 Greene St, Columbia, SC 29208, USA
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9
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Luo X, Qin F, Cai G, Xiao F. Integrating genomic correlation structure improves copy number variations detection. Bioinformatics 2021; 37:312-317. [PMID: 32805016 DOI: 10.1093/bioinformatics/btaa737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/23/2020] [Accepted: 08/12/2020] [Indexed: 12/16/2022] Open
Abstract
MOTIVATION Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD). RESULTS We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms. AVAILABILITY AND IMPLEMENTATION https://github.com/FeifeiXiaoUSC/LDcnv. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xizhi Luo
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Fei Qin
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Guoshuai Cai
- Department of Environmental Health Science, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC 29208, USA
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10
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Hao N, Niu YS, Xiao F, Zhang H. A super scalable algorithm for short segment detection. STATISTICS IN BIOSCIENCES 2021; 13:18-33. [PMID: 33737983 DOI: 10.1007/s12561-020-09278-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
In many applications such as copy number variant (CNV) detection, the goal is to identify short segments on which the observations have different means or medians from the background. Those segments are usually short and hidden in a long sequence, and hence are very challenging to find. We study a super scalable short segment (4S) detection algorithm in this paper. This nonparametric method clusters the locations where the observations exceed a threshold for segment detection. It is computationally efficient and does not rely on Gaussian noise assumption. Moreover, we develop a framework to assign significance levels for detected segments. We demonstrate the advantages of our proposed method by theoretical, simulation, and real data studies.
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Affiliation(s)
- Ning Hao
- Department of Mathematics, University of Arizona, Tucson, AZ 85721
| | - Yue Selena Niu
- Department of Mathematics, University of Arizona, Tucson, AZ 85721
| | - Feifei Xiao
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia, SC 29201
| | - Heping Zhang
- Department of Biostatistics, Yale School of Public Health, New Haven, CT 06510
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11
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Habenula GPR139 is associated with fear learning in the zebrafish. Sci Rep 2021; 11:5549. [PMID: 33692406 PMCID: PMC7946892 DOI: 10.1038/s41598-021-85002-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/23/2021] [Indexed: 01/09/2023] Open
Abstract
G-protein coupled receptor 139 (GPR139) is an evolutionarily conserved orphan receptor, predominantly expressing in the habenula of vertebrate species. The habenula has recently been implicated in aversive response and its associated learning. Here, we tested the hypothesis that GPR139 signalling in the habenula may play a role in fear learning in the zebrafish. We examined the effect of intraperitoneal injections of a human GPR139-selective agonist (JNJ-63533054) on alarm substance-induced fear learning using conditioned place avoidance paradigm, where an aversive stimulus is paired with one compartment, while its absence is associated with the other compartment of the apparatus. The results indicate that fish treated with 1 µg/g body weight of GPR139 agonist displayed no difference in locomotor activity and alarm substance-induced fear response. However, avoidance to fear-conditioned compartment was diminished, which suggests that the agonist blocks the consolidation of contextual fear memory. On the other hand, fish treated with 0.1 µg/g body weight of GPR139 agonist spent a significantly longer time in the unconditioned neutral compartment as compared to the conditioned (punished and unpunished) compartments. These results suggest that activation of GPR139 signalling in the habenula may be involved in fear learning and the decision-making process in the zebrafish.
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12
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Imamura A, Morimoto Y, Ono S, Kurotaki N, Kanegae S, Yamamoto N, Kinoshita H, Tsujita T, Okazaki Y, Ozawa H. Genetic and environmental factors of schizophrenia and autism spectrum disorder: insights from twin studies. J Neural Transm (Vienna) 2020; 127:1501-1515. [PMID: 32285255 PMCID: PMC7578126 DOI: 10.1007/s00702-020-02188-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023]
Abstract
Twin studies of psychiatric disorders such as schizophrenia and autism spectrum disorder have employed epidemiological approaches that determine heritability by comparing the concordance rate between monozygotic twins (MZs) and dizygotic twins. The basis for these studies is that MZs share 100% of their genetic information. Recently, biological studies based on molecular methods are now being increasingly applied to examine the differences between MZs discordance for psychiatric disorders to unravel their possible causes. Although recent advances in next-generation sequencing have increased the accuracy of this line of research, there has been greater emphasis placed on epigenetic changes versus DNA sequence changes as the probable cause of discordant psychiatric disorders in MZs. Since the epigenetic status differs in each tissue type, in addition to the DNA from the peripheral blood, studies using DNA from nerve cells induced from postmortem brains or induced pluripotent stem cells are being carried out. Although it was originally thought that epigenetic changes occurred as a result of environmental factors, and thus were not transmittable, it is now known that such changes might possibly be transmitted between generations. Therefore, the potential possible effects of intestinal flora inside the body are currently being investigated as a cause of discordance in MZs. As a result, twin studies of psychiatric disorders are greatly contributing to the elucidation of genetic and environmental factors in the etiology of psychiatric conditions.
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Affiliation(s)
- Akira Imamura
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan.
| | - Yoshiro Morimoto
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Ono
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Kurotaki
- Department of Clinical Psychiatry, Graduate School of Medicine, Kagawa University, Kita-gun, Japan
| | - Shinji Kanegae
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
| | - Naoki Yamamoto
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hirohisa Kinoshita
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Yuji Okazaki
- Koseikai Michinoo Hospital, Nagasaki, Japan
- Tokyo Metropolitan Matsuzawa Hospital, Tokyo, Japan
| | - Hiroki Ozawa
- Child and Adolescent Psychiatry Community Partnership Unit, Nagasaki University Hospital, Nagasaki, Japan
- Unit of Translation Medicine, Department of Neuropsychiatry, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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Falker-Gieske C, Iffland H, Preuß S, Bessei W, Drögemüller C, Bennewitz J, Tetens J. Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes. BMC Genet 2020; 21:114. [PMID: 33004014 PMCID: PMC7528462 DOI: 10.1186/s12863-020-00920-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/22/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic variants and affected genes that lead to FP behavior. To achieve that we imputed low-density genotypes from two different populations of layers divergently selected for FP to sequence level by performing whole genome sequencing on founder and half-sib individuals. In order to decipher the genetic structure of FP, genome wide association studies and meta-analyses of two resource populations were carried out by focusing on the traits 'feather pecks delivered' (FPD) and the 'posterior probability of a hen to belong to the extreme feather pecking subgroup' (pEFP). RESULTS In this meta-analysis, we discovered numerous genes that are affected by polymorphisms significantly associated with the trait FPD. Among them SPATS2L, ZEB2, KCHN8, and MRPL13 which have been previously connected to psychiatric disorders with the latter two being responsive to nicotine treatment. Gene set enrichment analysis revealed that phosphatidylinositol signaling is affected by genes identified in the GWAS and that the Golgi apparatus as well as brain structure may be involved in the development of a FP phenotype. Further, we were able to validate a previously discovered QTL for the trait pEFP on GGA1, which contains variants affecting NIPA1, KIAA1211L, AFF3, and TSGA10. CONCLUSIONS We provide evidence for the involvement of numerous genes in the propensity to exhibit FP behavior that could aid in the selection against this unwanted trait. Furthermore, we identified variants that are involved in phosphatidylinositol signaling, Golgi metabolism and cell structure and therefore propose changes in brain structure to be an influential factor in FP, as already described in human neuropsychiatric disorders.
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Affiliation(s)
- Clemens Falker-Gieske
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany.
| | - Hanna Iffland
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Siegfried Preuß
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Werner Bessei
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bremgartenstr. 109a, 3001, Bern, Switzerland
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, Garbenstr. 17, 70599, Stuttgart, Germany
| | - Jens Tetens
- Department of Animal Sciences, Georg-August-University, Burckhardtweg 2, 37077, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August-University, Albrecht-Thaer-Weg 3, 37075, Göttingen, Germany
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Alblooshi H, Al Safar H, El Kashef A, Al Ghaferi H, Shawky M, Hulse GK, Tay GK. Stratified analyses of genome wide association study data reveal haplotypes for a candidate gene on chromosome 2 (KIAA1211L) is associated with opioid use in patients of Arabian descent. BMC Psychiatry 2020; 20:41. [PMID: 32005204 PMCID: PMC6995052 DOI: 10.1186/s12888-019-2425-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 12/30/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Genome Wide Association Studies (GWAS) have been conducted to identify genes and pathways involved in development of opioid use disorder. This study extends the first GWAS of substance use disorder (SUD) patients from the United Arab Emirates (UAE) by stratifying the study group based on opioid use, which is the most common substance of use in this cohort. METHODS The GWAS cohort consisted of 512 (262 case, 250 controls) male participants from the UAE. The samples were genotyped using the Illumina Omni5 Exome system. Data was stratified according to opioid use using PLINK. Haplotype analysis was conducted using Haploview 4.2. RESULTS Two main associations were identified in this study. Firstly, two SNPs on chromosome 7 were associated with opioid use disorder, rs118129027 (p-value = 1.23 × 10 - 8) and rs74477937 (p-value = 1.48 × 10 - 8). This has been reported in Alblooshi et al. (Am J Med Genet B Neuropsychiatr Genet 180(1):68-79, 2019). Secondly, haplotypes on chromosome 2 which mapped to the KIAA1211L locus were identified in association with opioid use. Five SNPs in high linkage disequilibrium (LD) (rs2280142, rs6542837, rs12712037, rs10175560, rs11900524) were arranged into haplotypes. Two haplotypes GAGCG and AGTTA were associated with opioid use disorders (p-value 3.26 × 10- 8 and 7.16 × 10- 7, respectively). CONCLUSION This is the first GWAS to identify candidate genes associated with opioid use disorder in participants from the UAE. The lack of other genetic data of Arabian descent opioid use patients has hindered replication of the findings. Nevertheless, the outcomes implicate new pathways in opioid use disorder that requires further research to assess the role of the identified genes in the development of opioid use disorder.
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Affiliation(s)
- Hiba Alblooshi
- 0000 0004 1936 7910grid.1012.2Division of Psychiatry, the University of Western Australia, Crawley, Western Australia Australia ,0000 0004 1936 7910grid.1012.2School of Human Science, The University of Western Australia, Crawley, Western Australia Australia ,0000 0001 2193 6666grid.43519.3aCollege of Medicine and Health Science, The United Arab Emirates University, Al Ain, United Arab Emirates
| | - Habiba Al Safar
- 0000 0004 1762 9729grid.440568.bCenter of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates ,0000 0004 1762 9729grid.440568.bDepartment of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates
| | - Ahmed El Kashef
- National Rehabilitation Center, Abu Dhabi, United Arab Emirates
| | | | - Mansour Shawky
- National Rehabilitation Center, Abu Dhabi, United Arab Emirates
| | - Gary K. Hulse
- 0000 0004 1936 7910grid.1012.2Division of Psychiatry, the University of Western Australia, Crawley, Western Australia Australia ,0000 0004 0389 4302grid.1038.aSchool of Health and Medical Science, Edith Cowan University, Joondalup, Western Australia Australia
| | - Guan K. Tay
- 0000 0004 1936 7910grid.1012.2Division of Psychiatry, the University of Western Australia, Crawley, Western Australia Australia ,0000 0004 1762 9729grid.440568.bCenter of Biotechnology, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates ,0000 0004 1762 9729grid.440568.bDepartment of Biomedical Engineering, Khalifa University of Science and Technology, Abu Dhabi, United Arab Emirates ,0000 0004 0389 4302grid.1038.aSchool of Health and Medical Science, Edith Cowan University, Joondalup, Western Australia Australia
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Vedel L, Nøhr AC, Gloriam DE, Bräuner-Osborne H. Pharmacology and function of the orphan GPR139 G protein-coupled receptor. Basic Clin Pharmacol Toxicol 2019; 126 Suppl 6:35-46. [PMID: 31132229 PMCID: PMC7318219 DOI: 10.1111/bcpt.13263] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 05/21/2019] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) constitute the largest family of receptors and membrane proteins in the human genome with ~800 members of which half are olfactory. GPCRs are activated by a very broad range of endogenous signalling molecules and are involved in a plethora of physiological functions. All GPCRs contain a transmembrane domain, consisting of a bundle of seven α-helices spanning the cell membrane, and forming the majority of the known ortho- or allosteric ligand binding sites. Due to their many physiological functions and the accessible and druggable transmembrane pocket, GPCRs constitute the largest family of drug targets mediating the actions of 34% of currently marketed drugs. GPCRs activate one or more of the four G protein families (Gq/11 , Gi/o , Gs and G12/13 ) and/or ß-arrestin. About a third of the non-olfactory GPCRs are referred to as orphan receptors which means that their endogenous agonist(s) have not yet been found or firmly established. In this MiniReview, we focus on the orphan GPR139 receptor, for which the aromatic amino acids L-Trp and L-Phe as well as ACTH/α-MSH-related peptides have been proposed as endogenous agonists. GPR139 has been reported to activate several G protein pathways of which Gq/11 is the primary one. The receptor shows the highest expression in the striatum, thalamus, hypothalamus, pituitary and habenula of the human, rat and mouse CNS. We review the surrogate agonists and antagonists that have been published as well as the agonist pharmacophore and binding site. Finally, the putative physiological functions and therapeutic potential are outlined.
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Affiliation(s)
- Line Vedel
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Anne Cathrine Nøhr
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - David E Gloriam
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Hans Bräuner-Osborne
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
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16
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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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17
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Chen YC, Sudre G, Sharp W, Donovan F, Chandrasekharappa SC, Hansen N, Elnitski L, Shaw P. Neuroanatomic, epigenetic and genetic differences in monozygotic twins discordant for attention deficit hyperactivity disorder. Mol Psychiatry 2018; 23:683-690. [PMID: 28322272 PMCID: PMC5914518 DOI: 10.1038/mp.2017.45] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 01/10/2017] [Accepted: 01/17/2017] [Indexed: 12/18/2022]
Abstract
The study of monozygotic twins discordant for attention deficit hyperactivity disorder can elucidate mechanisms that contribute to the disorder, which affects ~7% of children. First, using in vivo neuroanatomic imaging on 14 pairs of monozygotic twins (mean age 9.7, s.d. 1.9 years), we found that discordance for the disorder is mirrored by differing dimensions of deep brain structures (the striatum and cerebellum), but not the cerebral cortex. Next, using whole-blood DNA from the same twins, we found a significant enrichment of epigenetic differences in genes expressed in these 'discordant' brain structures. Specifically, there is differential methylation of probes lying in the shore and shelf and enhancer regions of striatal and cerebellar genes. Notably, gene sets pertaining to the cerebral cortex (which did not differ in volume between affected and unaffected twins) were not enriched by differentially methylated probes. Genotypic differences between the twin pairs-such as copy number and rare, single-nucleotide variants-did not contribute to phenotypic discordance. Pathway analyses of the genes implicated by the most differentially methylated probes implicated γ-aminobutyric acid (GABA), dopamine and serotonin neurotransmitter systems. The study illustrates how neuroimaging can help guide the search for epigenomic mechanisms in neurodevelopmental disorders.
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Affiliation(s)
- Yun-Ching Chen
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, NHGRI/NIH, Bethesda
| | - Gustavo Sudre
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, NHGRI/NIH, Bethesda
| | - Wendy Sharp
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, NHGRI/NIH, Bethesda
| | - Frank Donovan
- Genomics Core and Cancer Genomics Unit, Cancer Genetics and Comparative Genomics Branch, NHGRI/NIH, Bethesda
| | | | | | - Laura Elnitski
- Genomic Functional Analysis Section, Translational and Functional Genomics Branch, NHGRI/NIH, Bethesda
| | - Philip Shaw
- Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, NHGRI/NIH, Bethesda
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18
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Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders. Twin Res Hum Genet 2018; 21:1-11. [DOI: 10.1017/thg.2017.69] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Hundreds of penetrant risk loci have been identified across different neurodevelopmental disorders (NDDs), and these often involve rare (<1% frequency) copy number variations (CNVs), which can involve one or more genes. Monozygotic (MZ) twin pairs are long thought to share 100% of their genomic information. However, genetic differences in the form of postzygotic somatic variants have been reported recently both in typically developing (TD) and in clinically discordant MZ pairs. We sought to investigate the contribution of rare CNVs in 100 twin pairs enriched for NDD phenotypes with a particular focus on postzygotic CNVs in MZ pairs discordant for autism spectrum disorder (ASD) using the Illumina Infinium PsychArray. In our sample, no postzygotic de novo CNVs were found in 55 MZ twin pairs, including the 13 pairs discordant for ASD. We did detect a higher rate of CNVs overlapping genes involved in disorders of the nervous system, such as a rare deletion affecting HNRNPU, in MZ pairs discordant and concordant for ASD in comparison with TD pairs (p = .02). Our results are in concordance with earlier findings that postzygotic de novo CNV events are typically rare in genomic DNA derived from saliva or blood, and suggests that the discordance of NDDs in our sample of twins is not explained by discordant CNVs. Still, studies investigating postzygotic variation in MZ discordant twins using DNA from different tissues and single cells and higher resolution genomics are needed in the future.
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Alavi MS, Shamsizadeh A, Azhdari-Zarmehri H, Roohbakhsh A. Orphan G protein-coupled receptors: The role in CNS disorders. Biomed Pharmacother 2017; 98:222-232. [PMID: 29268243 DOI: 10.1016/j.biopha.2017.12.056] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 12/12/2017] [Accepted: 12/14/2017] [Indexed: 12/20/2022] Open
Abstract
There are various types of receptors in the central nervous system (CNS). G protein-coupled receptors (GPCRs) have the highest expression with a wide range of physiological functions. A newer sub group of these receptors namely orphan GPCRs have been discovered. GPR3, GPR6, GPR17, GPR26, GPR37, GPR39, GPR40, GPR50, GPR52, GPR54, GPR55, GPR85, GPR88, GPR103, and GPR139 are the selected orphan GPCRs for this article. Their roles in the central nervous system have not been understood well so far. However, recent studies show that they may have very important functions in the CNS. Hence, in the present study, we reviewed most recent findings regarding the physiological roles of the selected orphan GPCRs in the CNS. After a brief presentation of each receptor, considering the results from genetic and pharmacological manipulation of the receptors, their roles in the pathophysiology of different diseases and disorders including anxiety, depression, schizophrenia, epilepsy, Alzheimer's disease, Parkinson's disease, and substance abuse will be discussed. At present, our knowledge regarding the role of GPCRs in the brain is very limited. However, previous limited studies show that orphan GPCRs have an important place in psychopharmacology and these receptors are potential new targets for the treatment of major CNS diseases.
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Affiliation(s)
- Mohaddeseh Sadat Alavi
- Division of Neurocognitive Sciences, Psychiatry and Behavioral Sciences Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ali Shamsizadeh
- Physiology-Pharmacology Research Center, Rafsanjan University of Medical Sciences, Rafsanjan, Iran
| | - Hassan Azhdari-Zarmehri
- Department of Basic Medical Sciences and Neuroscience Research Center, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Ali Roohbakhsh
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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20
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Castellani CA, Melka MG, Gui JL, Gallo AJ, O'Reilly RL, Singh SM. Post-zygotic genomic changes in glutamate and dopamine pathway genes may explain discordance of monozygotic twins for schizophrenia. Clin Transl Med 2017; 6:43. [PMID: 29181591 PMCID: PMC5704032 DOI: 10.1186/s40169-017-0174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/05/2017] [Indexed: 01/06/2023] Open
Abstract
Background Monozygotic twins are valuable in assessing the genetic vs environmental contribution to diseases. In the era of complete genome sequences, they allow identification of mutational mechanisms and specific genes and pathways that offer predisposition to the development of complex diseases including schizophrenia. Methods We sequenced the complete genomes of two pairs of monozygotic twins discordant for schizophrenia (MZD), including one representing a family tetrad. The family specific complete sequences have allowed identification of post zygotic mutations between MZD genomes. It allows identification of affected genes including relevant network and pathways that may account for the diseased state in pair specific patient. Results We found multiple twin specific sequence differences between co-twins that included small nucleotides [single nucleotide variants (SNV), small indels and block substitutions], copy number variations (CNVs) and structural variations. The genes affected by these changes belonged to a number of canonical pathways, the most prominent ones are implicated in schizophrenia and related disorders. Although these changes were found in both twins, they were more frequent in the affected twin in both pairs. Two specific pathway defects, glutamate receptor signaling and dopamine feedback in cAMP signaling pathways, were uniquely affected in the two patients representing two unrelated families. Conclusions We have identified genome-wide post zygotic mutations in two MZD pairs affected with schizophrenia. It has allowed us to use the threshold model and propose the most likely cause of this disease in the two patients studied. The results support the proposition that each schizophrenia patient may be unique and heterogeneous somatic de novo events may contribute to schizophrenia threshold and discordance of the disease in monozygotic twins. Electronic supplementary material The online version of this article (10.1186/s40169-017-0174-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- C A Castellani
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada. .,McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - M G Melka
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - J L Gui
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - A J Gallo
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - R L O'Reilly
- Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - S M Singh
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada.,Department of Psychiatry, The University of Western Ontario, London, ON, N6A 5B7, Canada
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21
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Bustamante ML, Herrera L, Gaspar PA, Nieto R, Maturana A, Villar MJ, Salinas V, Silva H. Shifting the focus toward rare variants in schizophrenia to close the gap from genotype to phenotype. Am J Med Genet B Neuropsychiatr Genet 2017; 174:663-670. [PMID: 28901686 DOI: 10.1002/ajmg.b.32550] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 04/25/2017] [Indexed: 01/16/2023]
Abstract
Schizophrenia (SZ) is a disorder with a high heritability and a complex architecture. Several dozen genetic variants have been identified as risk factors through genome-wide association studies including large population-based samples. However, the bulk of the risk cannot be accounted for by the genes associated to date. Rare mutations have been historically seen as relevant only for some infrequent, Mendelian forms of psychosis. Recent findings, however, show that the subset of patients that present a mutation with major effect is larger than expected. We discuss some of the molecular findings of these studies. SZ is clinically and genetically heterogeneous. To identify the genetic variation underlying the disorder, research should be focused on features that are more likely a product of genetic heterogeneity. Based on the phenotypical correlations with rare variants, cognition emerges as a relevant domain to study. Cognitive disturbances could be useful in selecting cases that have a higher probability of carrying deleterious mutations, as well as on the correct ascertainment of sporadic cases for the identification of de novo variants.
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Affiliation(s)
- M Leonor Bustamante
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile.,Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - Luisa Herrera
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Pablo A Gaspar
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile.,Biomedical Neurosciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Rodrigo Nieto
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile
| | - Alejandro Maturana
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - María José Villar
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile
| | - Valeria Salinas
- Faculty of Medicine, Program of Human Genetics, Biomedical Sciences Institute, Universidad de Chile, Santiago de Chile, Chile
| | - Hernán Silva
- Clínica Psiquiátrica Universitaria, Universidad de Chile, Santiago de Chile, Chile.,Faculty of Medicine, Department of Neurosciences, Universidad de Chile, Santiago de Chile, Chile.,Biomedical Neurosciences Institute, Universidad de Chile, Santiago de Chile, Chile
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22
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VarScan2 analysis of de novo variants in monozygotic twins discordant for schizophrenia. Psychiatr Genet 2017; 27:62-70. [DOI: 10.1097/ypg.0000000000000162] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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23
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Peng R, Zhou Y, Xie HN, Zheng J, Xie YJ, Yang JB. MCDA twins with discordant malformations: submicroscopic chromosomal anomalies detected by chromosomal microarray analysis and clinical outcomes. Prenat Diagn 2016; 36:766-74. [PMID: 27315788 DOI: 10.1002/pd.4859] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/03/2016] [Accepted: 06/10/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Ruan Peng
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Yi Zhou
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Hong-Ning Xie
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Ju Zheng
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Ying-Jun Xie
- Department of Ultrasonic Medicine; Fetal Medical Center, The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
| | - Jian-Bo Yang
- Department of Obstetrics and Gynecology; The First Affiliated Hospital of Sun Yat-sen University; Guangzhou China
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Bayer Andersen K, Leander Johansen J, Hentzer M, Smith GP, Dietz GPH. Protection of Primary Dopaminergic Midbrain Neurons by GPR139 Agonists Supports Different Mechanisms of MPP(+) and Rotenone Toxicity. Front Cell Neurosci 2016; 10:164. [PMID: 27445691 PMCID: PMC4923153 DOI: 10.3389/fncel.2016.00164] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Accepted: 06/03/2016] [Indexed: 12/21/2022] Open
Abstract
The G-protein coupled receptor 139 (GPR139) is expressed specifically in the brain in areas of relevance for motor control. GPR139 function and signal transduction pathways are elusive, and results in the literature are even contradictory. Here, we examined the potential neuroprotective effect of GPR139 agonism in primary culture models of dopaminergic (DA) neuronal degeneration. We find that in vitro GPR139 agonists protected primary mesencephalic DA neurons against 1-methyl-4-phenylpyridinium (MPP(+))-mediated degeneration. Protection was concentration-dependent and could be blocked by a GPR139 antagonist. However, the protection of DA neurons was not found against rotenone or 6-hydroxydopamine (6-OHDA) mediated degeneration. Our results support differential mechanisms of toxicity for those substances commonly used in Parkinson's disease (PD) models and potential for GPR139 agonists in neuroprotection.
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Affiliation(s)
| | | | - Morten Hentzer
- Department of Molecular Screening, H. Lundbeck A/S Valby, Denmark
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Lyu N, Guan LL, Ma H, Wang XJ, Wu BM, Shang FH, Wang D, Wen H, Yu X. Failure to Identify Somatic Mutations in Monozygotic Twins Discordant for Schizophrenia by Whole Exome Sequencing. Chin Med J (Engl) 2016; 129:690-5. [PMID: 26960372 PMCID: PMC4804415 DOI: 10.4103/0366-6999.178009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Schizophrenia (SCZ) is a severe, debilitating, and complex psychiatric disorder with multiple causative factors. An increasing number of studies have determined that rare variations play an important role in its etiology. A somatic mutation is a rare form of genetic variation that occurs at an early stage of embryonic development and is thought to contribute substantially to the development of SCZ. The aim of the study was to explore the novel pathogenic somatic single nucleotide variations (SNVs) and somatic insertions and deletions (indels) of SCZ. Methods: One Chinese family with a monozygotic (MZ) twin pair discordant for SCZ was included. Whole exome sequencing was performed in the co-twin and their parents. Rigorous filtering processes were conducted to prioritize pathogenic somatic variations, and all identified SNVs and indels were further confirmed by Sanger sequencing. Results: One somatic SNV and two somatic indels were identified after rigorous selection processes. However, none was validated by Sanger sequencing. Conclusions: This study is not alone in the failure to identify pathogenic somatic variations in MZ twins, suggesting that exonic somatic variations are extremely rare. Further efforts are warranted to explore the potential genetic mechanism of SCZ.
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Affiliation(s)
| | - Li-Li Guan
- Peking University Sixth Hospital, Peking University Institute of Mental Health, Key Laboratory of Mental Health, Ministry of Health (Peking University), Beijing 100191, China
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Castellani CA, Melka MG, Diehl EJ, Laufer BI, O'Reilly RL, Singh SM. DNA methylation in psychosis: insights into etiology and treatment. Epigenomics 2015; 7:67-74. [PMID: 25687467 DOI: 10.2217/epi.14.66] [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] [Indexed: 12/12/2022] Open
Abstract
Evidence for involvement of DNA methylation in psychosis forms the focus of this perspective. Of interest are results from two independent sets of experiments including rats treated with antipsychotic drugs and monozygotic twins discordant for schizophrenia. The results show that DNA methylation is increased in rats treated with antipsychotic drugs, reflecting the global effect of the drugs. Some of these changes are also seen in affected schizophrenic twins that were treated with antipsychotics. The genes and pathways identified in the unrelated experiments are relevant to neurodevelopment and psychiatric disorders. The common cause is hypothesized to be aberrations resulting from medication use. However, this needs to be established by future studies that address the origin of methylation changes in psychosis.
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Abstract
Since Tysk et al's pioneering analysis of the Swedish twin registry, twin and family studies continue to support a strong genetic basis of the inflammatory bowel diseases. The coefficient of heritability for siblings of inflammatory bowel disease probands is 25 to 42 for Crohn's disease and 4 to 15 for ulcerative colitis. Heritability estimates for Crohn's disease and ulcerative colitis from pooled twin studies are 0.75 and 0.67, respectively. However, this is at odds with the much lower heritability estimates from Genome-Wide Association Studies (GWAS). This "missing heritability" is likely due to shortfalls in both family studies and GWAS. The coefficient of heritability fails to account for familial shared environment. Heritability calculations from twin data are based on Falconer's method, with premises that are increasingly understood to be flawed. GWAS based heritability estimates may underestimate heritability due to incomplete linkage disequilibrium, and because some single nucleotide polypeptides (SNPs) do not reach a level of significance to allow detection. SNPs missed by GWAS include common SNPs with low penetrance and rare SNPs with high penetrance. All methods of heritability estimation regard genetic and environmental variance as separate entities, although it is now understood that there is a complex multidirectional interplay between genetic are environmental factors mediated by the microbiota, the epigenome, and the innate and acquired immune systems. Due to the limitations of heritability estimates, it is unlikely that a true value for heritability will be reached. Further work aimed at quantifying the variance explained across GWAS, epigenome-wide, and microbiota-wide association studies will help to define factors leading to inflammatory bowel disease.
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28
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Pirooznia M, Goes FS, Zandi PP. Whole-genome CNV analysis: advances in computational approaches. Front Genet 2015; 6:138. [PMID: 25918519 PMCID: PMC4394692 DOI: 10.3389/fgene.2015.00138] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Accepted: 03/23/2015] [Indexed: 01/04/2023] Open
Abstract
Accumulating evidence indicates that DNA copy number variation (CNV) is likely to make a significant contribution to human diversity and also play an important role in disease susceptibility. Recent advances in genome sequencing technologies have enabled the characterization of a variety of genomic features, including CNVs. This has led to the development of several bioinformatics approaches to detect CNVs from next-generation sequencing data. Here, we review recent advances in CNV detection from whole genome sequencing. We discuss the informatics approaches and current computational tools that have been developed as well as their strengths and limitations. This review will assist researchers and analysts in choosing the most suitable tools for CNV analysis as well as provide suggestions for new directions in future development.
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Affiliation(s)
- Mehdi Pirooznia
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Fernando S Goes
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA
| | - Peter P Zandi
- Mood Disorders Center, Department of Psychiatry and Behavioral Sciences, School of Medicine, Johns Hopkins University Baltimore, MD, USA ; Department of Mental Health, Johns Hopkins Bloomberg School of Public Health Baltimore, MD, USA USA
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Abstract
Eph receptor tyrosine kinases control cell-cell interactions during normal and oncogenic development, and are implicated in a range of processes including angiogenesis, stem cell maintenance and metastasis. They are thus of great interest as targets for cancer therapy. EphA3, originally isolated from leukemic and melanoma cells, is presently one of the most promising therapeutic targets, with multiple tumor-promoting roles in a variety of cancer types. This review focuses on EphA3, its functions in controlling cellular behavior, both in normal and pathological development, and most particularly in cancer.
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Affiliation(s)
- Peter W Janes
- Department of Biochemistry and Molecular Biology, Monash University , Victoria , Australia and
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