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Iourov IY, Gerasimov AP, Zelenova MA, Ivanova NE, Kurinnaia OS, Zabrodskaya YM, Demidova IA, Barantsevich ER, Vasin KS, Kolotii AD, Ushanov VV, Sitovskaya DA, Lobzhanidze TBA, Iuditskaia ME, Iakushev NS, Zhumatov MM, Vorsanova SG, Samochernyh KA. Cytogenomic epileptology. Mol Cytogenet 2023; 16:1. [PMID: 36600272 PMCID: PMC9814426 DOI: 10.1186/s13039-022-00634-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Molecular cytogenetic and cytogenomic studies have made a contribution to genetics of epilepsy. However, current genomic research of this devastative condition is generally focused on the molecular genetic aspects (i.e. gene hunting, detecting mutations in known epilepsy-associated genes, searching monogenic causes of epilepsy). Nonetheless, chromosomal abnormalities and copy number variants (CNVs) represent an important part of genetic defects causing epilepsy. Moreover, somatic chromosomal mosaicism and genome/chromosome instability seem to be a possible mechanism for a wide spectrum of epileptic conditions. This idea becomes even more attracting taking into account the potential of molecular neurocytogenetic (neurocytogenomic) studies of the epileptic brain. Unfortunately, analyses of chromosome numbers and structure in the affected brain or epileptogenic brain foci are rarely performed. Therefore, one may conclude that cytogenomic area of genomic epileptology is poorly researched. Accordingly, molecular cytogenetic and cytogenomic studies of the clinical cohorts and molecular neurocytogenetic analyses of the epileptic brain appear to be required. Here, we have performed a theoretical analysis to define the targets of the aforementioned studies and to highlight future directions for molecular cytogenetic and cytogenomic research of epileptic disorders in the widest sense. To succeed, we have formed a consortium, which is planned to perform at least a part of suggested research. Taking into account the nature of the communication, "cytogenomic epileptology" has been introduced to cover the research efforts in this field of medical genomics and epileptology. Additionally, initial results of studying cytogenomic variations in the Russian neurodevelopmental cohort are reviewed with special attention to epilepsy. In total, we have concluded that (i) epilepsy-associated cytogenomic variations require more profound research; (ii) ontological analyses of epilepsy genes affected by chromosomal rearrangements and/or CNVs with unraveling pathways implicating epilepsy-associated genes are beneficial for epileptology; (iii) molecular neurocytogenetic (neurocytogenomic) analysis of postoperative samples are warranted in patients suffering from epileptic disorders.
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Affiliation(s)
- Ivan Y. Iourov
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia ,grid.445984.00000 0001 2224 0652Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
| | - Alexandr P. Gerasimov
- grid.452417.1Research Laboratory of Pediatric Neurosurgery, Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Maria A. Zelenova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Natalya E. Ivanova
- grid.452417.1Scientific Department of Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Oksana S. Kurinnaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Yulia M. Zabrodskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Irina A. Demidova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Evgeny R. Barantsevich
- grid.412460.5Postgraduate Neurology and Manual Medicine Department, Pavlov First Saint-Petersburg State Medical University, Saint Petersburg, Russia
| | - Kirill S. Vasin
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Alexey D. Kolotii
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Vseslav V. Ushanov
- grid.452417.1Department of Neurosurgery, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Darya A. Sitovskaya
- grid.452417.1Research Laboratory of Pathomorphology of the Nervous System, Almazov National Medical Research Centre, Saint Petersburg, Russia
| | - Timur B.-A. Lobzhanidze
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Maria E. Iuditskaia
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Nikita S. Iakushev
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Muslim M. Zhumatov
- grid.445931.e0000 0004 0471 4078Saint Petersburg State Pediatric Medical University, Saint Petersburg, Russia
| | - Svetlana G. Vorsanova
- grid.466467.10000 0004 0627 319XYurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia ,grid.78028.350000 0000 9559 0613Vorsanova’s Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics and Pediatric Surgery of the Pirogov Russian National Research Medical University of the Russian Ministry of Health, Moscow, Russia
| | - Konstantin A. Samochernyh
- grid.452417.1Polenov Neurosurgical Institute, Almazov National Medical Research Centre, Saint Petersburg, Russia
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Medvedeva AV, Tokmatcheva EV, Kaminskaya AN, Vasileva SA, Nikitina EA, Zhuravlev SA, Zakharov GA, Zatsepina OG, Savvateeva-Popova EV. Parent-of-origin effects on nuclear chromatin organization and behavior in a Drosophila model for Williams-Beuren Syndrome. Vavilovskii Zhurnal Genet Selektsii 2021; 25:472-485. [PMID: 34595370 PMCID: PMC8460428 DOI: 10.18699/vj21.054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/31/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Prognosis of neuropsychiatric disorders in progeny requires consideration of individual (1) parent-of-origin effects (POEs) relying on (2) the nerve cell nuclear 3D chromatin architecture and (3) impact of parent-specific miRNAs. Additionally, the shaping of cognitive phenotypes in parents depends on both learning acquisition and forgetting, or memory erasure. These processes are independent and controlled by different signal cascades: the first is cAMPdependent, the second relies on actin remodeling by small GTPase Rac1 - LIMK1 (LIM-kinase 1). Simple experimental model systems such as Drosophila help probe the causes and consequences leading to human neurocognitive pathologies. Recently, we have developed a Drosophila model for Williams-Beuren Syndrome (WBS): a mutant agnts3 of the agnostic locus (X:11AB) harboring the dlimk1 gene. The agnts3 mutation drastically increases the frequency of ectopic contacts (FEC) in specific regions of intercalary heterochromatin, suppresses learning/memory and affects locomotion. As is shown in this study, the polytene X chromosome bands in reciprocal hybrids between agnts3 and the wild type strain Berlin are heterogeneous in modes of FEC regulation depending either on maternal or paternal gene origin. Bioinformatic analysis reveals that FEC between X:11AB and the other X chromosome bands correlates with the occurrence of short (~30 bp) identical DNA fragments partly homologous to Drosophila 372-bp satellite DNA repeat. Although learning acquisition in a conditioned courtship suppression paradigm is similar in hybrids, the middle-term memory formation shows patroclinic inheritance. Seemingly, this depends on changes in miR-974 expression. Several parameters of locomotion demonstrate heterosis. Our data indicate that the agnts3 locus is capable of trans-regulating gene activity via POEs on the chromatin nuclear organization, thereby affecting behavior.
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Affiliation(s)
- A V Medvedeva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E V Tokmatcheva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - A N Kaminskaya
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia
| | - S A Vasileva
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - E A Nikitina
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia Herzen State Pedagogical University of Russia, St. Petersburg, Russia
| | - S A Zhuravlev
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - G A Zakharov
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
| | - O G Zatsepina
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Moscow, Russia
| | - E V Savvateeva-Popova
- Pavlov Institute of Physiology of the Russian Academy of Sciences, St. Petersburg, Russia
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McGowan-Jordan J, Hastings R, Moore S. Re: International System for Human Cytogenetic or Cytogenomic Nomenclature (ISCN): Some Thoughts, by T. Liehr. Cytogenet Genome Res 2021; 161:225-226. [PMID: 34407535 DOI: 10.1159/000516655] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 04/20/2021] [Indexed: 11/19/2022] Open
Affiliation(s)
| | - Ros Hastings
- John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Sarah Moore
- Genetics and Molecular Pathology, SA Pathology, SA Genomics Health Alliance, Adelaide, South Australia, Australia
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Iourov IY, Vorsanova SG, Kurinnaia OS, Zelenova MA, Vasin KS, Yurov YB. Causes and Consequences of Genome Instability in Psychiatric and Neurodegenerative Diseases. Mol Biol 2021. [DOI: 10.1134/s0026893321010155] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Iourov IY, Vorsanova SG, Yurov YB. Systems Cytogenomics: Are We Ready Yet? Curr Genomics 2021; 22:75-78. [PMID: 34220294 PMCID: PMC8188578 DOI: 10.2174/1389202922666210219112419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 11/26/2022] Open
Abstract
With the introduction of systems theory to genetics, numerous opportunities for genomic research have been identified. Consequences of DNA sequence variations are systematically evaluated using the network- or pathway-based analysis, a technological basis of systems biology or, more precisely, systems genomics. Despite comprehensive descriptions of advantages offered by systems genomic approaches, pathway-based analysis is uncommon in cytogenetic (cytogenomic) studies, i.e. genome analysis at the chromosomal level. Here, we would like to express our opinion that current cytogenomics benefits from the application of systems biology methodology. Accordingly, systems cytogenomics appears to be a biomedical area requiring more attention than it actually receives.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia.,Department of Medical Biological Disciplines, Belgorod State University, 308015, Belgorod, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia
| | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, 117152, Russia.,Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, 125412, Russia
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Bajic VP, Essack M, Zivkovic L, Stewart A, Zafirovic S, Bajic VB, Gojobori T, Isenovic E, Spremo-Potparevic B. The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease". Front Genet 2020; 10:1368. [PMID: 32047510 PMCID: PMC6997486 DOI: 10.3389/fgene.2019.01368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics.
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Affiliation(s)
- Vladan P Bajic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lada Zivkovic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Alan Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Sonja Zafirovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma Isenovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
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Iourov IY, Vorsanova SG, Yurov YB. The variome concept: focus on CNVariome. Mol Cytogenet 2019; 12:52. [PMID: 31890032 PMCID: PMC6924070 DOI: 10.1186/s13039-019-0467-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 12/13/2019] [Indexed: 02/07/2023] Open
Abstract
Background Variome may be used for designating complex system of interplay between genomic variations specific for an individual or a disease. Despite the recognized complexity of genomic basis for phenotypic traits and diseases, studies of genetic causes of a disease are usually dedicated to the identification of single causative genomic changes (mutations). When such an artificially simplified model is employed, genomic basis of phenotypic outcomes remains elusive in the overwhelming majority of human diseases. Moreover, it is repeatedly demonstrated that multiple genomic changes within an individual genome are likely to underlie the phenome. Probably the best example of cumulative effect of variome on the phenotype is CNV (copy number variation) burden. Accordingly, we have proposed a variome concept based on CNV studies providing the evidence for the existence of a CNVariome (the set of CNV affecting an individual genome), a target for genomic analyses useful for unraveling genetic mechanisms of diseases and phenotypic traits. Conclusion Variome (CNVariome) concept suggests that a genomic milieu is determined by the whole set of genomic variations (CNV) within an individual genome. The genomic milieu is likely to result from interplay between these variations. Furthermore, such kind of variome may be either individual or disease-specific. Additionally, such variome may be pathway-specific. The latter is able to affect molecular/cellular pathways of genome stability maintenance leading to occurrence of genomic/chromosome instability and/or somatic mosaicism resulting in somatic variome. This variome type seems to be important for unraveling disease mechanisms, as well. Finally, it appears that bioinformatic analysis of both individual and somatic variomes in the context of diseases- and pathway-specific variomes is the most promising way to determine genomic basis of the phenome and to unravel disease mechanisms for the management and treatment of currently incurable diseases.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
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Ye CJ, Stilgenbauer L, Moy A, Liu G, Heng HH. What Is Karyotype Coding and Why Is Genomic Topology Important for Cancer and Evolution? Front Genet 2019; 10:1082. [PMID: 31737054 PMCID: PMC6838208 DOI: 10.3389/fgene.2019.01082] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 10/09/2019] [Indexed: 12/14/2022] Open
Abstract
While the importance of chromosomal/nuclear variations vs. gene mutations in diseases is becoming more appreciated, less is known about its genomic basis. Traditionally, chromosomes are considered the carriers of genes, and genes define bio-inheritance. In recent years, the gene-centric concept has been challenged by the surprising data of various sequencing projects. The genome system theory has been introduced to offer an alternative framework. One of the key concepts of the genome system theory is karyotype or chromosomal coding: chromosome sets function as gene organizers, and the genomic topologies provide a context for regulating gene expression and function. In other words, the interaction of individual genes, defined by genomic topology, is part of the full informational system. The genes define the “parts inheritance,” while the karyotype and genomic topology (the physical relationship of genes within a three-dimensional nucleus) plus the gene content defines “system inheritance.” In this mini-review, the concept of karyotype or chromosomal coding will be briefly discussed, including: 1) the rationale for searching for new genomic inheritance, 2) chromosomal or karyotype coding (hypothesis, model, and its predictions), and 3) the significance and evidence of chromosomal coding (maintaining and changing the system inheritance-defined bio-systems). This mini-review aims to provide a new conceptual framework for appreciating the genome organization-based information package and its ultimate importance for future genomic and evolutionary studies.
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Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Lukas Stilgenbauer
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Amanda Moy
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Guo Liu
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Henry H Heng
- Center for Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States.,Department of Pathology, Wayne State University School of Medicine, Detroit, MI, United States
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Affiliation(s)
- Ivan Y. Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow 117152, Russian Federation
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Affiliation(s)
- Ivan Y. Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow 117152, Russian Federation
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Iourov IY, Vorsanova SG, Yurov YB, Kutsev SI. Ontogenetic and Pathogenetic Views on Somatic Chromosomal Mosaicism. Genes (Basel) 2019; 10:E379. [PMID: 31109140 PMCID: PMC6562967 DOI: 10.3390/genes10050379] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/27/2022] Open
Abstract
Intercellular karyotypic variability has been a focus of genetic research for more than 50 years. It has been repeatedly shown that chromosome heterogeneity manifesting as chromosomal mosaicism is associated with a variety of human diseases. Due to the ability of changing dynamically throughout the ontogeny, chromosomal mosaicism may mediate genome/chromosome instability and intercellular diversity in health and disease in a bottleneck fashion. However, the ubiquity of negligibly small populations of cells with abnormal karyotypes results in difficulties of the interpretation and detection, which may be nonetheless solved by post-genomic cytogenomic technologies. In the post-genomic era, it has become possible to uncover molecular and cellular pathways to genome/chromosome instability (chromosomal mosaicism or heterogeneity) using advanced whole-genome scanning technologies and bioinformatic tools. Furthermore, the opportunities to determine the effect of chromosomal abnormalities on the cellular phenotype seem to be useful for uncovering the intrinsic consequences of chromosomal mosaicism. Accordingly, a post-genomic review of chromosomal mosaicism in the ontogenetic and pathogenetic contexts appears to be required. Here, we review chromosomal mosaicism in its widest sense and discuss further directions of cyto(post)genomic research dedicated to chromosomal heterogeneity.
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Affiliation(s)
- Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia.
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, 125412 Moscow, Russia.
| | - Sergei I Kutsev
- Research Centre for Medical Genetics, 115522 Moscow, Russia.
- Molecular & Cell Genetics Department, Pirogov Russian National Research Medical University, 117997 Moscow, Russia.
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Iourov IY, Vorsanova SG, Yurov YB. Pathway-based classification of genetic diseases. Mol Cytogenet 2019; 12:4. [PMID: 30766616 PMCID: PMC6362588 DOI: 10.1186/s13039-019-0418-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 01/22/2019] [Indexed: 02/07/2023] Open
Abstract
Background In medical genetics, diseases are classified according to the nature (hypothetical nature) of the underlying genetic defect. The classification is “gene-centric” and “factor-centric”; a disease may be, thereby, designated as monogenic, oligogenic or polygenic/multifactorial. Chromosomal diseases/syndromes and abnormalities are generally considered apart from these designations due to distinctly different formation mechanisms and simultaneous encompassing from several to several hundreds of co-localized genes. These definitions are ubiquitously used and are perfectly suitable for human genetics issues in historical and academic perspective. However, recent achievements in systems biology have offered a possibility to explore the consequences of a genetic defect from genomic variations to molecular/cellular pathway alterations unique to a disease. Since pathogenetic mechanisms (pathways) are more influential on our understating of disease presentation and progression than genetic defects per se, a need for a disease classification reflecting both genetic causes and molecular/cellular mechanisms appears to exist. Here, we propose an extension to the common disease classification based on the underlying genetic defects, which focuses on disease-specific molecular pathways. Conclusion The basic idea of our classification is to propose pathways as parameters for designating a genetic disease. To proceed, we have followed the tradition of using ancient Greek words and prefixes to create the terms for the pathway-based classification of genetic diseases. We have chosen the word “griphos” (γρῖφος), which simultaneously means “net” and “puzzle”, accurately symbolizing the term “pathway” currently used in molecular biology and medicine. Thus, diseases may be classified as monogryphic (single pathway is altered to result in a phenotype), digryphic (two pathways are altered to result in a phenotype), etc.; additionally, diseases may be designated as oligogryphic (several pathways are altered to result in a phenotype), polygryphic (numerous pathways or cascades of pathways are altered to result in a phenotype) and homeogryphic in cases of comorbid diseases resulted from shared pathway alterations. We suppose that classifying illness this way using both “gene-centric” and “pathway-centric” concepts is able to revolutionize current views on genetic diseases.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia.,Department of Medical Genetics, Russian Medical Academy of Continuous Professional Education, Moscow, 125993 Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, 117152 Moscow, Russia.,2Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
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Iourov IY. Cytopostgenomics: What is it and how does it work? Curr Genomics 2019; 20:77-78. [PMID: 31555057 PMCID: PMC6728900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Affiliation(s)
- Ivan Y. Iourov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow 117152, Russia
- Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow 125412, Russia
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Yurov YB, Vorsanova SG, Demidova IA, Kravets VS, Vostrikov VM, Soloviev IV, Uranova NA, Iourov IY. [Genomic instability in the brain: chromosomal mosaicism in schizophrenia]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 116:86-91. [PMID: 28091506 DOI: 10.17116/jnevro201611611186-91] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM Experimental verification of the hypothesis about the possible involvement of the mosaic genome variations (mosaic aneuploidy) in the pathogenesis of a number of mental illnesses, including schizophrenia and autism: a genetic study of the level of mosaic genome variations in cells of the brain autopsy tissues in healthy controls and schizophrenia. MATERIAL AND METHODS Autopsy brain tissues of 15 unaffected controls and 15 patients with schizophrenia were analyzed by molecular cytogenetic methods to determine the frequency of chromosomal mutations (the mosaic aneuploidy) in neural human cells. The original collection of chromosome-enumeration DNA probes to autosomes 1, 9, 15, 16, 18 and the sex chromosomes X and Y was used for the interphase cytogenetic analysis of chromosomes in the cells of the brain. RESULTS AND CONCLUSION The frequency of low-level aneuploidy per individual chromosome was 0.54% (median - 0.53%; 95% confidence interval (CI) CI - 0.41-1.13%) in controls and 1.66% (median - 1.55%; 95% CI -1.32-2.12%) in schizophrenia (p=0.000013). Thus, the three-fold increase in aneuploidy frequency in the brain in schizophrenia was detected. It is suggested that mosaic aneuploidy, as a significant biological marker of genomic instability, may lead to genеtic imbalance and abnormal functional activity of neural cells and neural networks in schizophrenia.
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Affiliation(s)
- Y B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishev Clinical Research Institute of Pediatrics, Moscow, Russia; Pirogov Russian National Research Medical University, Minzdrav RF, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishev Clinical Research Institute of Pediatrics, Moscow, Russia; Pirogov Russian National Research Medical University, Minzdrav RF, Moscow, Russia
| | - I A Demidova
- Mental Health Research Center, Moscow, Russia; Veltishev Clinical Research Institute of Pediatrics, Moscow, Russia; Pirogov Russian National Research Medical University, Minzdrav RF, Moscow, Russia
| | - V S Kravets
- Mental Health Research Center, Moscow, Russia; Veltishev Clinical Research Institute of Pediatrics, Moscow, Russia; Pirogov Russian National Research Medical University, Minzdrav RF, Moscow, Russia
| | | | | | - N A Uranova
- Mental Health Research Center, Moscow, Russia
| | - I Y Iourov
- Mental Health Research Center, Moscow, Russia; Veltishev Clinical Research Institute of Pediatrics, Moscow, Russia; Pirogov Russian National Research Medical University, Minzdrav RF, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
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Yang Y, Xia C, Zhou Z, Wei D, Xu K, Jia J, Xu W, Zhang H. A multiplex ligation‑dependent probe amplification‑based next‑generation sequencing approach for the detection of copy number variations in the human genome. Mol Med Rep 2018; 18:5823-5833. [PMID: 30365071 DOI: 10.3892/mmr.2018.9581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 09/28/2018] [Indexed: 11/05/2022] Open
Abstract
The aim of the present study was to describe a multiplex ligation‑dependent probe amplification (MLPA)‑based next‑generation sequencing (NGS) assay that exhibited a significantly higher efficiency in detecting copy number variations (CNVs) and known single‑nucleotide variants, compared with traditional MLPA. MLPA polymerase chain reaction products were used to construct a library with indexed adapters, which was subsequently tested on an NGS platform, and the resulting data were analyzed by a series of analytical software. The reads from each probe reflected genetic variations in the target regions, and fragment differentiation was based on the specific base composition of the sequences, rather than fragment length, which was determined by capillary electrophoresis. The results of this approach were not only consistent with the MLPA results following capillary electrophoresis, but also coincided with the CNV results from the single‑nucleotide polymorphism array chip. This method allowed high‑throughput screening for the number of fragments and samples by integrating additional indices for detection. Furthermore, this technology precisely and accurately performed large‑scale detection and quantification of DNA variations, thereby serving as an effective and sensitive method for diagnosing genetic disorders caused by CNVs and known single‑nucleotide variations. Notably, MLPA‑NGS circumvents the problems associated with the inaccuracies of NGS in CNV detection due to the use of target sequence capture.
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Affiliation(s)
- Yongchen Yang
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Chaoran Xia
- Shanghai Institute of Medical Genetics, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Zaiwei Zhou
- Product Department, WuXi Health Net Co., Ltd., Shanghai 200131, P.R. China
| | - Dongkai Wei
- BasePair Biotechnology Co., Ltd., Suzhou, Jiangsu 215028, P.R. China
| | - Kangping Xu
- BasePair Biotechnology Co., Ltd., Suzhou, Jiangsu 215028, P.R. China
| | - Jia Jia
- Shanghai Center for Bioinformation Technology, Shanghai Institutes of Biomedicine, Shanghai Academy of Science and Technology, Shanghai 201203, P.R. China
| | - Wuhen Xu
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
| | - Hong Zhang
- Department of Laboratory Medicine, Children's Hospital of Shanghai, Shanghai Jiao Tong University, Shanghai 200040, P.R. China
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Yurov YB, Vorsanova SG, Demidova IA, Kolotii AD, Soloviev IV, Iourov IY. Mosaic Brain Aneuploidy in Mental Illnesses: An Association of Low-level Post-zygotic Aneuploidy with Schizophrenia and Comorbid Psychiatric Disorders. Curr Genomics 2018; 19:163-172. [PMID: 29606903 PMCID: PMC5850504 DOI: 10.2174/1389202918666170717154340] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Revised: 11/18/2016] [Accepted: 01/16/2017] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Postzygotic chromosomal variation in neuronal cells is hypothesized to make a substantial contribution to the etiology and pathogenesis of neuropsychiatric disorders. However, the role of somatic genome instability and mosaic genome variations in common mental illnesses is a matter of conjecture. MATERIALS AND METHODS To estimate the pathogenic burden of somatic chromosomal mutations, we determined the frequency of mosaic aneuploidy in autopsy brain tissues of subjects with schizophrenia and other psychiatric disorders (intellectual disability comorbid with autism spectrum disorders). Recently, post-mortem brain tissues of subjects with schizophrenia, intellectual disability and unaffected controls were analyzed by Interphase Multicolor FISH (MFISH), Quantitative Fluorescent in situ Hybridization (QFISH) specially designed to register rare mosaic chromosomal mutations such as lowlevel aneuploidy (whole chromosome mosaic deletion/duplication). The low-level mosaic aneuploidy in the diseased brain demonstrated significant 2-3-fold frequency increase in schizophrenia (p=0.0028) and 4-fold increase in intellectual disability comorbid with autism (p=0.0037) compared to unaffected controls. Strong associations of low-level autosomal/sex chromosome aneuploidy (p=0.001, OR=19.0) and sex chromosome-specific mosaic aneuploidy (p=0.006, OR=9.6) with schizophrenia were revealed. CONCLUSION Reviewing these data and literature supports the hypothesis suggesting that an association of low-level mosaic aneuploidy with common and, probably, overlapping psychiatric disorders does exist. Accordingly, we propose a pathway for common neuropsychiatric disorders involving increased burden of rare de novo somatic chromosomal mutations manifesting as low-level mosaic aneuploidy mediating local and general brain dysfunction.
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Affiliation(s)
- Yuri B. Yurov
- Mental Health Research Center, Moscow, Russian Federation
- Separated Structural Unit “Clinical Research Institute of Pediatrics named after Y.E Veltishev”, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Svetlana G. Vorsanova
- Mental Health Research Center, Moscow, Russian Federation
- Separated Structural Unit “Clinical Research Institute of Pediatrics named after Y.E Veltishev”, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Irina A. Demidova
- Mental Health Research Center, Moscow, Russian Federation
- Separated Structural Unit “Clinical Research Institute of Pediatrics named after Y.E Veltishev”, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Alexei D. Kolotii
- Mental Health Research Center, Moscow, Russian Federation
- Separated Structural Unit “Clinical Research Institute of Pediatrics named after Y.E Veltishev”, Pirogov Russian National Research Medical University, Moscow, Russian Federation
| | | | - Ivan Y. Iourov
- Mental Health Research Center, Moscow, Russian Federation
- Separated Structural Unit “Clinical Research Institute of Pediatrics named after Y.E Veltishev”, Pirogov Russian National Research Medical University, Moscow, Russian Federation
- Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Ministry of Health, Moscow, Russian Federation
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Vorsanova SG, Zelenova MA, Yurov YB, Iourov IY. Behavioral Variability and Somatic Mosaicism: A Cytogenomic Hypothesis. Curr Genomics 2018; 19:158-162. [PMID: 29606902 PMCID: PMC5850503 DOI: 10.2174/1389202918666170719165339] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/11/2016] [Accepted: 01/01/2017] [Indexed: 02/06/2023] Open
Abstract
Behavioral sciences are inseparably related to genetics. A variety of neurobehavioral phenotypes are suggested to result from genomic variations. However, the contribution of genetic factors to common behavioral disorders (i.e. autism, schizophrenia, intellectual disability) remains to be understood when an attempt to link behavioral variability to a specific genomic change is made. Probably, the least appreciated genetic mechanism of debilitating neurobehavioral disorders is somatic mosaicism or the occurrence of genetically diverse (neuronal) cells in an individual’s brain. Somatic mosaicism is assumed to affect directly the brain being associated with specific behavioral patterns. As shown in studies of chromosome abnormalities (syndromes), genetic mosaicism is able to change dynamically the phenotype due to inconsistency of abnormal cell proportions. Here, we hypothesize that brain-specific postzygotic changes of mosaicism levels are able to modulate variability of behavioral phenotypes. More precisely, behavioral phenotype variability in individuals exhibiting somatic mosaicism might correlate with changes in the amount of genetically abnormal cells throughout the lifespan. If proven, the hypothesis can be used as a basis for therapeutic interventions through regulating levels of somatic mosaicism to increase functioning and to improve overall condition of individuals with behavioral problems.
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Affiliation(s)
- Svetlana G Vorsanova
- Separated Structural Unit "Clinical Research Institute of Pediatrics at Pirogov Russian National Research Medical University named after Y.E Veltishev", Ministry of Health of Russian Federation, Moscow125412, Russian Federation.,Mental Health Research Center, Moscow117152, Russian Federation.,Moscow State University of Psychology and Education, Moscow127051, Russian Federation
| | - Maria A Zelenova
- Separated Structural Unit "Clinical Research Institute of Pediatrics at Pirogov Russian National Research Medical University named after Y.E Veltishev", Ministry of Health of Russian Federation, Moscow125412, Russian Federation.,Mental Health Research Center, Moscow117152, Russian Federation.,Moscow State University of Psychology and Education, Moscow127051, Russian Federation
| | - Yuri B Yurov
- Separated Structural Unit "Clinical Research Institute of Pediatrics at Pirogov Russian National Research Medical University named after Y.E Veltishev", Ministry of Health of Russian Federation, Moscow125412, Russian Federation.,Mental Health Research Center, Moscow117152, Russian Federation.,Moscow State University of Psychology and Education, Moscow127051, Russian Federation
| | - Ivan Y Iourov
- Separated Structural Unit "Clinical Research Institute of Pediatrics at Pirogov Russian National Research Medical University named after Y.E Veltishev", Ministry of Health of Russian Federation, Moscow125412, Russian Federation.,Mental Health Research Center, Moscow117152, Russian Federation.,Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Moscow123995, Russian Federation
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Iourov IY, Zelenova MA, Vorsanova SG, Voinova VV, Yurov YB. 4q21.2q21.3 Duplication: Molecular and Neuropsychological Aspects. Curr Genomics 2018; 19:173-178. [PMID: 29606904 PMCID: PMC5850505 DOI: 10.2174/1389202918666170717161426] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/20/2016] [Accepted: 01/20/2017] [Indexed: 12/15/2022] Open
Abstract
During the last decades, a large amount of newly described microduplications and microdeletions associated with intellectual disability (ID) and related neuropsychiatric diseases have been discovered. However, due to natural limitations, a significant part of them has not been the focus of multidisciplinary approaches. Here, we address previously undescribed chromosome 4q21.2q21.3 microduplication for gene prioritization, evaluation of cognitive abilities and estimation of genomic mechanisms for brain dysfunction by molecular cytogenetic (cytogenomic) and gene expression (meta-) analyses as well as for neuropsychological assessment. We showed that duplication at 4q21.2q21.3 is associated with moderate ID, cognitive deficits, developmental delay, language impairment, memory and attention problems, facial dysmorphisms, congenital heart defect and dentinogenesis imperfecta. Gene-expression meta-analysis prioritized the following genes: ENOPH1, AFF1, DSPP, SPARCL1, and SPP1. Furthermore, genotype/phenotype correlations allowed the attribution of each gene gain to each phenotypic feature. Neuropsychological testing showed visual-perceptual and fine motor skill deficits, reduced attention span, deficits of the nominative function and problems in processing both visual and aural information. Finally, emerging approaches including molecular cytogenetic, bioinformatic (genome/epigenome meta-analysis) and neuropsychological methods are concluded to be required for comprehensive neurological, genetic and neuropsychological descriptions of new genomic rearrangements/diseases associated with ID.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Ministry of Health, Moscow, Russian Federation
| | - Maria A Zelenova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Svetlana G Vorsanova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Victoria V Voinova
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
| | - Yuri B Yurov
- Mental Health Research Center, Moscow, Russian Federation.,Separated Structural Unit "Clinical Research Institute of Pediatrics named after Y.E Veltishev", Pirogov Russian National Research Medical University, Ministry of Health, Moscow, Russian Federation.,Moscow State University of Psychology and Education, Moscow, Russian Federation
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Poot M. Retrotransposing Gremlins May Disrupt Our Brain's Genomes. Mol Syndromol 2016; 8:55-57. [PMID: 28611545 DOI: 10.1159/000453247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2016] [Indexed: 11/19/2022] Open
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Abstract
This review focuses at the problem of the genetic basis of comorbidity. We discuss the concepts and terms relating to combinations of diseases. The guidelines of the study of comorbidity using modern high throughput methods and approaches of genetics, molecular biology and bioinformatics are designated. In this review we present results of studies showing genetic specificity for the combined phenotypes dif-ferent from the isolated disease, we considergene-gene and gene-environment interactions in comorbidity. We also discuss the role of single nucleotide polymorphisms and structural genome variations in the development of comorbidity. Own results of researching shared genes of inversely comorbid diseases like as bronchial asthma and tuberculosis are presented.
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Affiliation(s)
- Ye. Yu. Bragina
- Research Institute for Medical Genetics, Tomsk, Russian Federation
| | - M. B. Freidin
- Research Institute for Medical Genetics, Tomsk, Russian Federation
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3p22.1p21.31 microdeletion identifies CCK as Asperger syndrome candidate gene and shows the way for therapeutic strategies in chromosome imbalances. Mol Cytogenet 2015; 8:82. [PMID: 26523151 PMCID: PMC4628252 DOI: 10.1186/s13039-015-0185-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 09/10/2015] [Indexed: 01/25/2023] Open
Abstract
Background In contrast to other autism spectrum disorders, chromosome abnormalities are rare in Asperger syndrome (AS) or high-functioning autism. Consequently, AS was occasionally subjected to classical positional cloning. Here, we report on a case of AS associated with a deletion of the short arm of chromosome 3. Further in silico analysis has identified a candidate gene for AS and has suggested a therapeutic strategy for manifestations of the chromosome rearrangement. Results Using array comparative genomic hybridization, an interstitial deletion of 3p22.1p21.31 (~2.5 Mb in size) in a child with Asperger’s syndrome, seborrheic dermatitis and chronic pancreatitis was detected. Original bioinformatic approach to the prioritization of candidate genes/processes identified CCK (cholecystokinin) as a candidate gene for AS. In addition to processes associated with deleted genes, bioinformatic analysis of CCK gene interactome indicated that zinc deficiency might be a pathogenic mechanism in this case. This suggestion was supported by plasma zinc concentration measurements. The increase of zinc intake produced a rise in zinc plasma concentration and the improvement in the patient’s condition. Conclusions Our study supported previous linkage findings and had suggested a new candidate gene in AS. Moreover, bioinformatic analysis identified the pathogenic mechanism, which was used to propose a therapeutic strategy for manifestations of the deletion. The relative success of this strategy allows speculating that therapeutic or dietary normalization of metabolic processes altered by a chromosome imbalance or genomic copy number variations may be a way for treating at least a small proportion of cases of these presumably incurable genetic conditions.
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Iourov IY, Vorsanova SG, Korostelev SA, Zelenova MA, Yurov YB. Long contiguous stretches of homozygosity spanning shortly the imprinted loci are associated with intellectual disability, autism and/or epilepsy. Mol Cytogenet 2015; 8:77. [PMID: 26478745 PMCID: PMC4608298 DOI: 10.1186/s13039-015-0182-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 09/27/2015] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Long contiguous stretches of homozygosity (LCSH) (regions/runs of homozygosity) are repeatedly detected by single-nucleotide polymorphism (SNP) chromosomal microarrays. Providing important clues regarding parental relatedness (consanguinity), uniparental disomy, chromosomal recombination or rearrangements, LCSH are rarely considered as a possible epigenetic cause of neurodevelopmental disorders. Additionally, despite being relevant to imprinting, LCSH at imprinted loci have not been truly addressed in terms of pathogenicity. In this study, we examined LCSH in children with unexplained intellectual disability, autism, congenital malformations and/or epilepsy focusing on chromosomal regions which harbor imprinted disease genes. RESULTS Out of 267 cases, 14 (5.2 %) were found to have LCSH at imprinted loci associated with a clinical outcome. There were 5 cases of LCSH at 15p11.2, 4 cases of LCSH at 7q31.2, 3 cases of LCSH at 11p15.5, and 2 cases of LCSH at 7q21.3. Apart from a case of LCSH at 7q31.33q32.3 (~4 Mb in size), all causative LCSH were 1-1.5 Mb in size. Clinically, these cases were characterized by a weak resemblance to corresponding imprinting diseases (i.e., Silver-Russell, Beckwith-Wiedemann, and Prader-Willi/Angelman syndromes), exhibiting distinctive intellectual disability, autistic behavior, developmental delay, seizures and/or facial dysmorphisms. Parental consanguinity was detected in 8 cases (3 %), and these cases did not exhibit LCSH at imprinted loci. CONCLUSIONS This study demonstrates that shorter LCSH at chromosomes 7q21.3, 7q31.2, 11p15.5, and 15p11.2 occur with a frequency of about 5 % in the children with intellectual disability, autism, congenital malformations and/or epilepsy. Consequently, this type of epigenetic mutations appears to be the most common one among children with neurodevelopmental diseases. Finally, since LCSH less than 2.5-10 Mb in size are generally ignored in diagnostic SNP microarray studies, one can conclude that an important epigenetic cause of intellectual disability, autism or epilepsy is actually overlooked.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, 123995 Moscow, Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | | | - Maria A Zelenova
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, 117152 Moscow, Russia ; Separated Structural Unit "Clinical Research Institute of Pediatrics", Russian National Research Medical University named after N.I. Pirogov, Ministry of Health of Russian Federation, 125412 Moscow, Russia
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Bajic V, Spremo-Potparevic B, Zivkovic L, Isenovic ER, Arendt T. Cohesion and the aneuploid phenotype in Alzheimer's disease: A tale of genome instability. Neurosci Biobehav Rev 2015; 55:365-74. [PMID: 26003528 DOI: 10.1016/j.neubiorev.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 03/26/2015] [Accepted: 05/12/2015] [Indexed: 12/20/2022]
Abstract
Neurons are postmitotic cells that are in permanent cell cycle arrest. However, components of the cell cycle machinery that are expressed in Alzheimer's disease (AD) neurons are showing features of a cycling cell and those attributed to a postmitotic cell as well. Furthermore, the unique physiological operations taking place in neurons, ascribed to "core cell cycle regulators" are also key regulators in cell division. Functions of these cell cycle regulators include neuronal migration, axonal elongation, axon pruning, dendrite morphogenesis and synaptic maturation and plasticity. In this review, we focus on cohesion and cohesion related proteins in reference to their neuronal functions and how impaired centromere/cohesion dynamics may connect cell cycle dysfunction to aneuploidy in AD.
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Affiliation(s)
- Vladan Bajic
- Institute for Nuclear Research "Vinca", Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, P.O. 522, 11001 Belgrade, Serbia.
| | - Biljana Spremo-Potparevic
- Faculty of Pharmacy, Institute of Physiology, Department of Biology and Human Genetics, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Lada Zivkovic
- Faculty of Pharmacy, Institute of Physiology, Department of Biology and Human Genetics, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Esma R Isenovic
- Institute for Nuclear Research "Vinca", Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, P.O. 522, 11001 Belgrade, Serbia.
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany.
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Sakai M, Watanabe Y, Someya T, Araki K, Shibuya M, Niizato K, Oshima K, Kunii Y, Yabe H, Matsumoto J, Wada A, Hino M, Hashimoto T, Hishimoto A, Kitamura N, Iritani S, Shirakawa O, Maeda K, Miyashita A, Niwa SI, Takahashi H, Kakita A, Kuwano R, Nawa H. Assessment of copy number variations in the brain genome of schizophrenia patients. Mol Cytogenet 2015; 8:46. [PMID: 26136833 PMCID: PMC4487564 DOI: 10.1186/s13039-015-0144-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/12/2015] [Indexed: 11/28/2022] Open
Abstract
Background Cytogenomic mutations and chromosomal abnormality are implicated in the neuropathology of several brain diseases. Cell heterogeneity of brain tissues makes their detection and validation difficult, however. In the present study, we analyzed gene dosage alterations in brain DNA of schizophrenia patients and compared those with the copy number variations (CNVs) identified in schizophrenia patients as well as with those in Asian lymphocyte DNA and attempted to obtain hints at the pathological contribution of cytogenomic instability to schizophrenia. Results Brain DNA was extracted from postmortem striatum of schizophrenia patients and control subjects (n = 48 each) and subjected to the direct two color microarray analysis that limits technical data variations. Disease-associated biases of relative DNA doses were statistically analyzed with Bonferroni’s compensation on the premise of brain cell mosaicism. We found that the relative gene dosage of 85 regions significantly varied among a million of probe sites. In the candidate CNV regions, 26 regions had no overlaps with the common CNVs found in Asian populations and included the genes (i.e., ANTXRL, CHST9, DNM3, NDST3, SDK1, STRC, SKY) that are associated with schizophrenia and/or other psychiatric diseases. The majority of these candidate CNVs exhibited high statistical probabilities but their signal differences in gene dosage were less than 1.5-fold. For test evaluation, we rather selected the 10 candidate CNV regions that exhibited higher aberration scores or larger global effects and were thus confirmable by PCR. Quantitative PCR verified the loss of gene dosage at two loci (1p36.21 and 1p13.3) and confirmed the global variation of the copy number distributions at two loci (11p15.4 and 13q21.1), both indicating the utility of the present strategy. These test loci, however, exhibited the same somatic CNV patterns in the other brain region. Conclusions The present study lists the candidate regions potentially representing cytogenomic CNVs in the brain of schizophrenia patients, although the significant but modest alterations in their brain genome doses largely remain to be characterized further. Electronic supplementary material The online version of this article (doi:10.1186/s13039-015-0144-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miwako Sakai
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan ; Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | - Kazuaki Araki
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan
| | - Masako Shibuya
- Department of Psychiatry, Graduate School of Medical and Dental Sciences, Niigata University, 1-757, Asahimachi-dori, 951-8510 Niigata, Japan
| | | | | | - Yasuto Kunii
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Hirooki Yabe
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Junya Matsumoto
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Akira Wada
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Mizuki Hino
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Takeshi Hashimoto
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Akitoyo Hishimoto
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Noboru Kitamura
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan
| | - Shuji Iritani
- Matsuzawa Hospital, Setagaya-ku, 156-0057 Tokyo, Japan ; Department of Mental Health, Nagoya University Graduate School of Medicine, 466-8550 Nagoya, Aichi Japan
| | - Osamu Shirakawa
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan ; Department of Neuropsychiatry, Kinki University Faculty of Medicine, 589-8511 Osaka-Sayama, Osaka Japan
| | - Kiyoshi Maeda
- Division of Psychiatry and Neurology, Kobe University Graduate School of Medicine, 650-0017 Kobe, Hyogo Japan ; Department of Social Rehabilitation, Kobe University School of Medicine, 654-0142 Hyogo, Japan
| | - Akinori Miyashita
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Shin-Ichi Niwa
- Departments of Neuropsychiatry, Fukushima Medical University School of Medicine, 960-1295 Fukushima, Japan
| | - Hitoshi Takahashi
- Pathology and Brain Disease Research Center, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Akiyoshi Kakita
- Pathology and Brain Disease Research Center, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Ryozo Kuwano
- Department of Molecular Genetics, Brain Research Institute, Niigata University, 951-8585 Niigata, Japan
| | - Hiroyuki Nawa
- Department of Molecular Neurobiology, Brain Research Institute, Niigata University, 1-757, Asahimachi-dori, 951-8585 Niigata, Japan
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Iourov IY, Vorsanova SG, Yurov YB. In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research. Mol Cytogenet 2014; 7:98. [PMID: 25525469 PMCID: PMC4269961 DOI: 10.1186/s13039-014-0098-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023] Open
Abstract
Background The availability of multiple in silico tools for prioritizing genetic variants widens the possibilities for converting genomic data into biological knowledge. However, in molecular cytogenetics, bioinformatic analyses are generally limited to result visualization or database mining for finding similar cytogenetic data. Obviously, the potential of bioinformatics might go beyond these applications. On the other hand, the requirements for performing successful in silico analyses (i.e. deep knowledge of computer science, statistics etc.) can hinder the implementation of bioinformatics in clinical and basic molecular cytogenetic research. Here, we propose a bioinformatic approach to prioritization of genomic variations that is able to solve these problems. Results Selecting gene expression as an initial criterion, we have proposed a bioinformatic approach combining filtering and ranking prioritization strategies, which includes analyzing metabolome and interactome data on proteins encoded by candidate genes. To finalize the prioritization of genetic variants, genomic, epigenomic, interactomic and metabolomic data fusion has been made. Structural abnormalities and aneuploidy revealed by array CGH and FISH have been evaluated to test the approach through determining genotype-phenotype correlations, which have been found similar to those of previous studies. Additionally, we have been able to prioritize copy number variations (CNV) (i.e. differentiate between benign CNV and CNV with phenotypic outcome). Finally, the approach has been applied to prioritize genetic variants in cases of somatic mosaicism (including tissue-specific mosaicism). Conclusions In order to provide for an in silico evaluation of molecular cytogenetic data, we have proposed a bioinformatic approach to prioritization of candidate genes and CNV. While having the disadvantage of possible unavailability of gene expression data or lack of expression variability between genes of interest, the approach provides several advantages. These are (i) the versatility due to independence from specific databases/tools or software, (ii) relative algorithm simplicity (possibility to avoid sophisticated computational/statistical methodology) and (iii) applicability to molecular cytogenetic data because of the chromosome-centric nature. In conclusion, the approach is able to become useful for increasing the yield of molecular cytogenetic techniques.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Moscow, 123995 Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
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Yurov YB, Vorsanova SG, Liehr T, Kolotii AD, Iourov IY. X chromosome aneuploidy in the Alzheimer's disease brain. Mol Cytogenet 2014; 7:20. [PMID: 24602248 PMCID: PMC3995993 DOI: 10.1186/1755-8166-7-20] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Accepted: 02/11/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although the link between brain aging and Alzheimer's disease (AD) is a matter of debate, processes hallmarking cellular and tissue senescence have been repeatedly associated with its pathogenesis. Here, we have studied X chromosome aneuploidy (a recognized feature of aged cell populations) in the AD brain. RESULTS Extended molecular neurocytogenetic analyses of X chromosome aneuploidy in 10 female AD as well as 10 age and sex matched female control postmortem brain samples was performed by multiprobe/quantitative FISH. Additionally, aneuploidy rate in the brain samples of 5 AD and as 5 age and sex matched control subjects were analyzed by interphase chromosome-specific multicolor banding (ICS-MCB). Totally, 182,500 cells in the AD brain and 182,500 cells in the unaffected brain were analyzed. The mean rate of X chromosome aneuploidy in AD samples was approximately two times higher than in control (control: mean - 1.32%, 95% CI 0.92- 1.71%; AD: mean - 2.79%, 95% CI 1.88-3.69; P = 0.013). One AD sample demonstrated mosaic aneuploidy of chromosome X confined to the hippocampus affecting about 10% of cells. ICS-MCB confirmed the presence of X chromosome aneuploidy in the hippocampal tissues of AD brain (control: mean - 1.74%, 95% CI 1.38- 2.10%; AD: mean - 4.92%, 95% CI 1.14-8.71; P < 0.001). CONCLUSIONS Addressing X chromosome number variation in the brain, we observed that somatically acquired (post-zygotic) aneuploidy causes large-scale genomic alterations in neural cells of AD patients and, therefore, can be involved in pathogenesis of this common neurodegenerative disorder. In the context of debates about possible interplay between brain aging and AD neurodegeneration, our findings suggest that X chromosome aneuploidy can contribute to both processes. To this end we conclude that mosaic aneuploidy in the brain is a new non-heritable genetic factor predisposing to AD.
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Affiliation(s)
| | | | - Thomas Liehr
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia.
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An interstitial deletion at 10q26.2q26.3. Case Rep Genet 2014; 2014:505832. [PMID: 24649379 PMCID: PMC3932651 DOI: 10.1155/2014/505832] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2013] [Accepted: 01/01/2014] [Indexed: 12/08/2022] Open
Abstract
We present a case of an interstitial subtelomeric 10q26 deletion in a male child with moderate developmental delay and minor dysmorphic features. Using array comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), we have detected an interstitial deletion at 10q26.2q26.3 encompassing a 5.8 Mb region and spanning 24 genes. Interestingly, losses of this chromosome 10 region have not been previously associated with a phenotype outcome. According to an in silico evaluation, we have suggested that PPP2R2D and BNIP3 losses are likely a cause of developmental delay in the index patient. Our data allow to speculating that haploinsufficiency of these two genes in 10q26.3, which is usually ignored in the context of chromosome 10q deletions, has a phenotypic effect.
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Xq28 (MECP2) microdeletions are common in mutation-negative females with Rett syndrome and cause mild subtypes of the disease. Mol Cytogenet 2013; 6:53. [PMID: 24283533 PMCID: PMC4176196 DOI: 10.1186/1755-8166-6-53] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 01/13/2023] Open
Abstract
Background Rett syndrome (RTT) is an X-linked neurodevelopmental disease affecting predominantly females caused by MECP2 mutations. Although RTT is classically considered a monogenic disease, a stable proportion of patients, who do not exhibit MECP2 sequence variations, does exist. Here, we have attempted at uncovering genetic causes underlying the disorder in mutation-negative cases by whole genome analysis using array comparative genomic hybridization (CGH) and a bioinformatic approach. Results Using BAC and oligonucleotide array CGH, 39 patients from RTT Russian cohort (in total, 354 RTT patients), who did not bear intragenic MECP2 mutations, were studied. Among the individuals studied, 12 patients were those with classic RTT and 27 were those with atypical RTT. We have detected five 99.4 kb deletions in chromosome Xq28 affecting MECP2 associated with mild manifestations of classic RTT and five deletions encompassing MECP2 spanning 502.428 kb (three cases), 539.545 kb (one case) and 877.444 kb (one case) associated with mild atypical RTT. A case has demonstrated somatic mosaicism. Regardless of RTT type and deletion size, all the cases exhibited mild phenotypes. Conclusions Our data indicate for the first time that no fewer than 25% of RTT cases without detectable MECP2 mutations are caused by Xq28 microdeletions. Furthermore, Xq28 (MECP2) deletions are likely to cause mild subtypes of the disease, which can manifest as both classical and atypical RTT.
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Lyon D, Elmore L, Aboalela N, Merrill-Schools J, McCain N, Starkweather A, Elswick RK, Jackson-Cook C. Potential epigenetic mechanism(s) associated with the persistence of psychoneurological symptoms in women receiving chemotherapy for breast cancer: a hypothesis. Biol Res Nurs 2013; 16:160-74. [PMID: 23585573 DOI: 10.1177/1099800413483545] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Due to recent treatment advances, there have been improvements in the proportion of women surviving a diagnosis of breast cancer (BC). However, many of these survivors report persistent adverse side effects following treatment, such as cognitive dysfunction, depressive symptoms, anxiety, fatigue, sleep disturbances, and pain. Investigators have examined circulating levels of inflammatory markers, particularly serum cytokines, for a potential causal relationship to the development/persistence of these psychoneurological symptoms (PNS). While inflammatory activation, resulting from perceived stress or other factors, may directly contribute to the development of PNS, we offer an alternative hypothesis, suggesting that these symptoms are an early step in a cascade of biological changes leading to epigenetic alterations at the level of deoxyribonucleic acid (DNA) methylation, histone modifications, and/or chromatin structure/chromosomal instability. Given that epigenetic patterns have plasticity, if this conjectured relationship between epigenomic/acquired genomic alterations and the development/persistence of PNS is confirmed, it could provide foundational knowledge for future research leading to the recognition of predictive markers and/or treatments to alleviate PNS in women with BC. In this article, we discuss an evolving theory of the biological basis of PNS, integrating knowledge related to inflammation and DNA repair in the context of genetic and epigenetic science to expand the paradigm for understanding symptom acquisition/persistence following chemotherapy.
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Affiliation(s)
- Debra Lyon
- 1Department of Family and Community Health Nursing, Virginia Commonwealth University School of Nursing, Richmond, VA, USA
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Iourov IY, Vorsanova SG, Yurov YB. Somatic cell genomics of brain disorders: a new opportunity to clarify genetic-environmental interactions. Cytogenet Genome Res 2013; 139:181-8. [PMID: 23428498 DOI: 10.1159/000347053] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent genomic advances have exacerbated the problem of interpreting genome-wide association studies aimed at uncovering genetic basis of brain disorders. Despite of a plethora of data on candidate genes determining the susceptibility to neuropsychiatric diseases, no consensus is reached on their intrinsic contribution to the pathogenesis, and the influence of the environment on these genes is incompletely understood. Alternatively, single-cell analyses of the normal and diseased human brain have shown that somatic genome/epigenome variations (somatic mosaicism) do affect neuronal cell populations and are likely to mediate pathogenic processes associated with brain dysfunctions. Such (epi-)genomic changes are likely to arise from disturbances in genome maintenance and cell cycle regulation pathways as well as from environmental exposures. Therefore, one can suggest that, at least in a proportion of cases, inter- and intragenic variations (copy number variations (CNVs) or single nucleotide polymorphisms (SNPs)) associated with major brain disorders (i.e. schizophrenia, Alzheimer's disease, autism) lead to genetic dysregulation resulting in somatic genetic and epigenetic mosaicism. In addition, environmental influences on malfunctioning cellular machinery could trigger a cascade of abnormal processes producing genomic/chromosomal instability (i.e. brain-specific aneuploidy). Here, a brief analysis of a genome-wide association database has allowed us to support these speculations. Accordingly, an ontogenetic 2-/multiple-hit mechanism of brain diseases was hypothesized. Finally, we speculate that somatic cell genomics approach considering both genome-wide associations and somatic (epi-)genomic variations is likely to have bright perspectives for disease-oriented genome research.
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Affiliation(s)
- I Y Iourov
- Research Center of Mental Health, Russian Academy of Medical Sciences, RU–119152 Moscow, Russia.
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An interstitial 20q11.21 microdeletion causing mild intellectual disability and facial dysmorphisms. Case Rep Genet 2013; 2013:353028. [PMID: 23476833 PMCID: PMC3586477 DOI: 10.1155/2013/353028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/09/2013] [Indexed: 12/28/2022] Open
Abstract
We report a case of an interstitial chromosome 20q11.21 microdeletion in a 7-year-old male child presenting with mild intellectual disability and facial dysmorphisms. Array comparative genomic hybridization (CGH) has shown that the deletion resulted in the loss of 68 genes, among which 5 genes (COX4I2, MYLK2, ASXL1, DNMT3B, and SNTA1) are disease causing. The size of the deletion was estimated to span 2.6 Mb. Only three cases of deletions encompassing this chromosomal region have been reported. The phenotype of the index patient was found to resemble the mildest cases of Bohring-Opitz syndrome that is caused by ASXL1 mutations. An in silico evaluation of the deleted genomic region has shown that benign genomic variations have never been observed to affect the ASXL1 gene, in contrast to the other disease-causing genes. As a result, it was suggested that ASXL1 loss is likely to be the main cause of the phenotypic manifestations. The present case report indicates that a loss of the disease-causing gene can produce a milder phenotype of a single gene condition.
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York TP, Brumelle J, Juusola J, Kendler KS, Eaves LJ, Amstadter AB, Aggen SH, Jones KH, Ferreira-Gonzalez A, Jackson-Cook C. Increased frequency of micronuclei in adults with a history of childhood sexual abuse: a discordant monozygotic twin study. PLoS One 2013; 8:e55337. [PMID: 23383158 PMCID: PMC3559336 DOI: 10.1371/journal.pone.0055337] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 11/23/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Childhood sexual abuse (CSA) is a traumatic life event associated with an increased lifetime risk for psychopathology/morbidity. The long-term biological consequences of CSA-elicited stress on chromosomal stability in adults are unknown. The primary aim of this study was to determine if the rate of acquired chromosomal changes, measured using the cytokinesis-block micronucleus assay on stimulated peripheral blood lymphocytes, differs in adult female monozygotic twins discordant for CSA. METHODS Monozygotic twin pairs discordant for CSA were identified from a larger population-based sample of female adult twins for whom the experience of CSA was assessed by self-report (51 individuals including a reference sample). Micronuclei (MN) contain chromatin from structurally normal or abnormal chromosomes that are excluded from the daughter nuclei during cell division and serve as a biomarker to assess acquired chromosomal instability. RESULTS Female twins exposed to CSA exhibited a 1.63-fold average increase in their frequency of MN compared to their nonexposed genetically identical cotwins (Paired t-test, t₁₆ = 2.65, P = 0.017). No additional effects of familial factors were detected after controlling for the effect of CSA exposure. A significant interaction between CSA history and age was observed, suggesting that the biological effects of CSA on MN formation may be cumulative. CONCLUSIONS These data support a direct link between CSA exposure and MN formation measured in adults that is not attributable to genetic or environmental factors shared by siblings. Further research is warranted to understand the biological basis for the observed increase in acquired chromosomal findings in people exposed to CSA and to determine if acquired somatic chromosomal abnormalities/somatic clonal mosaicism might mediate the adult pathology associated with CSA.
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Affiliation(s)
- Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University, Richmond, Virginia, United States of America.
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Iourov IY, Vorsanova SG, Kurinnaia OS, Zelenova MA, Silvanovich AP, Yurov YB. Molecular karyotyping by array CGH in a Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies. Mol Cytogenet 2012; 5:46. [PMID: 23272938 PMCID: PMC3547809 DOI: 10.1186/1755-8166-5-46] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 01/28/2023] Open
Abstract
Background Array comparative genomic hybridization (CGH) has been repeatedly shown to be a successful tool for the identification of genomic variations in a clinical population. During the last decade, the implementation of array CGH has resulted in the identification of new causative submicroscopic chromosome imbalances and copy number variations (CNVs) in neuropsychiatric (neurobehavioral) diseases. Currently, array-CGH-based technologies have become an integral part of molecular diagnosis and research in individuals with neuropsychiatric disorders and children with intellectual disability (mental retardation) and congenital anomalies. Here, we introduce the Russian cohort of children with intellectual disability, autism, epilepsy and congenital anomalies analyzed by BAC array CGH and a novel bioinformatic strategy. Results Among 54 individuals highly selected according to clinical criteria and molecular and cytogenetic data (from 2426 patients evaluated cytogenetically and molecularly between November 2007 and May 2012), chromosomal imbalances were detected in 26 individuals (48%). In two patients (4%), a previously undescribed condition was observed. The latter has been designated as meiotic (constitutional) genomic instability resulted in multiple submicroscopic rearrangements (including CNVs). Using bioinformatic strategy, we were able to identify clinically relevant CNVs in 15 individuals (28%). Selected cases were confirmed by molecular cytogenetic and molecular genetic methods. Eight out of 26 chromosomal imbalances (31%) have not been previously reported. Among them, three cases were co-occurrence of subtle chromosome 9 and 21 deletions. Conclusions We conducted an array CGH study of Russian patients suffering from intellectual disability, autism, epilepsy and congenital anomalies. In total, phenotypic manifestations of clinically relevant genomic variations were found to result from genomic rearrangements affecting 1247 disease-causing and pathway-involved genes. Obviously, a significantly lesser part of them are true candidates for intellectual disability, autism or epilepsy. The success of our preliminary array CGH and bioinformatic study allows us to expand the cohort. According to the available literature, this is the first comprehensive array CGH evaluation of a Russian cohort of children with neuropsychiatric disorders and congenital anomalies.
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Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Russian Academy of Medical Sciences, 119152, Moscow, Russia.
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Iourov IY, Vorsanova SG, Yurov YB. Single cell genomics of the brain: focus on neuronal diversity and neuropsychiatric diseases. Curr Genomics 2012; 13:477-88. [PMID: 23449087 PMCID: PMC3426782 DOI: 10.2174/138920212802510439] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2011] [Revised: 01/30/2012] [Accepted: 06/12/2012] [Indexed: 12/21/2022] Open
Abstract
Single cell genomics has made increasingly significant contributions to our understanding of the role that somatic genome variations play in human neuronal diversity and brain diseases. Studying intercellular genome and epigenome variations has provided new clues to the delineation of molecular mechanisms that regulate development, function and plasticity of the human central nervous system (CNS). It has been shown that changes of genomic content and epigenetic profiling at single cell level are involved in the pathogenesis of neuropsychiatric diseases (schizophrenia, mental retardation (intellectual/leaning disability), autism, Alzheimer's disease etc.). Additionally, several brain diseases were found to be associated with genome and chromosome instability (copy number variations, aneuploidy) variably affecting cell populations of the human CNS. The present review focuses on the latest advances of single cell genomics, which have led to a better understanding of molecular mechanisms of neuronal diversity and neuropsychiatric diseases, in the light of dynamically developing fields of systems biology and "omics".
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Affiliation(s)
- Ivan Y Iourov
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
| | - Svetlana G Vorsanova
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
- Center for Neurobiological Diagnosis of Genetic Psychiatric Disorders, Moscow City University of Psychology and Education, Russia
| | - Yuri B Yurov
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow, Russia
- Institute of Pediatrics and Children Surgery, Minzdravsotsrazvitia, Moscow, Russia
- Center for Neurobiological Diagnosis of Genetic Psychiatric Disorders, Moscow City University of Psychology and Education, Russia
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Marzuki NS, Anggaratri HW, Suciati LP, Ambarwati DD, Paramayuda C, Kartapradja H, Pulungan AB, Harahap A. Diversity of sex chromosome abnormalities in a cohort of 95 Indonesian patients with monosomy X. Mol Cytogenet 2011; 4:23. [PMID: 21992692 PMCID: PMC3216851 DOI: 10.1186/1755-8166-4-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 10/12/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Monosomy × or 45,X is a cytogenetic characteristic for Turner syndrome. This chromosome anomaly is encountered in around 50% of cases, but wide variations of other anomalies have been found. This report is to describe the cytogenetic characteristics of 45,X individuals. To the best of our knowledge, there were no large series of 45,X cases has been reported from Indonesia. RESULTS Ninety five cases with 45,X cell line found, of which 60 were detected by karyotyping, 4 by FISH for sex chromosomes, and 31 by both karyotyping and FISH. Using karyotyping 37 out of 91 cases(40.6%) were identified as 45,X individuals, while cases who underwent FISH only 4 out of 35 cases (11.4%) showed 45,X result, resulting in total of 39 45,X cases (41.1%), and the rest 56 (58.9%) cases are mosaic. Among these cases, 21 out of 95 (22.1%) have Y or part of Y as the second or third sex chromosome in their additional cell lines. Result discrepancies revealed in 22 out of 31 cases who underwent both FISH and karyotyping, of which 7 showed normal 46,XX or 46,XY karyotypes, but by FISH, additional monosomy × cell line was found. Most of the cases were referred at the age of puberty (8-13 years old) or after that (14-18 years old), 31 and 21 cases respectively, and there were 14 cases were sent in adulthood. CONCLUSION Wide variations of sex chromosome aberrations have been detected using the combination of conventional cytogenetic and FISH, including detection of low level of mosaicism and Y-chromosome fragments. Result discrepancies using both techniques were found in 22/31 cases, and in order to obtain a more details of sex chromosome constitution of individuals with 45,X cell line both FISH and karyotyping should be carried out simultaneously.
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Affiliation(s)
- Nanis S Marzuki
- Eijkman Institute for Molecular Biology, Jl, Diponegoro 69, Jakarta, 10430, Indonesia.
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Smith CL, Bolton A, Nguyen G. Genomic and epigenomic instability, fragile sites, schizophrenia and autism. Curr Genomics 2011; 11:447-69. [PMID: 21358990 PMCID: PMC3018726 DOI: 10.2174/138920210793176001] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 12/31/2022] Open
Abstract
Increasing evidence links genomic and epigenomic instability, including multiple fragile sites regions to neuropsychiatric diseases including schizophrenia and autism. Cancer is the only other disease associated with multiple fragile site regions, and genome and epigenomic instability is a characteristic of cancer. Research on cancer is far more advanced than research on neuropsychiatric disease; hence, insight into neuropsychiatric disease may be derived from cancer research results. Towards this end, this article will review the evidence linking schizophrenia and other neuropsychiatric diseases (especially autism) to genomic and epigenomic instability, and fragile sites. The results of studies on genetic, epigenetic and environmental components of schizophrenia and autism point to the importance of the folate-methionine-transulfuration metabolic hub that is diseases also perturbed in cancer. The idea that the folate-methionine-transulfuration hub is important in neuropsychiatric is exciting because this hub present novel targets for drug development, suggests some drugs used in cancer may be useful in neuropsychiatric disease, and raises the possibility that nutrition interventions may influence the severity, presentation, or dynamics of disease.
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Affiliation(s)
- Cassandra L Smith
- Molecular Biotechnology Research Laboratory, Departments of Biomedical Engineering, Biology and Pharmacology, Boston University, Boston, MA, USA
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Iourov IY, Vorsanova SG, Yurov YB. Somatic genome variations in health and disease. Curr Genomics 2011; 11:387-96. [PMID: 21358982 PMCID: PMC3018718 DOI: 10.2174/138920210793176065] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 05/24/2010] [Accepted: 05/26/2010] [Indexed: 12/29/2022] Open
Abstract
It is hard to imagine that all the cells of the human organism (about 10(14)) share identical genome. Moreover, the number of mitoses (about 10(16)) required for the organism's development and maturation during ontogeny suggests that at least a proportion of them could be abnormal leading, thereby, to large-scale genomic alterations in somatic cells. Experimental data do demonstrate such genomic variations to exist and to be involved in human development and interindividual genetic variability in health and disease. However, since current genomic technologies are mainly based on methods, which analyze genomes from a large pool of cells, intercellular or somatic genome variations are significantly less appreciated in modern bioscience. Here, a review of somatic genome variations occurring at all levels of genome organization (i.e. DNA sequence, subchromosomal and chromosomal) in health and disease is presented. Looking through the available literature, it was possible to show that the somatic cell genome is extremely variable. Additionally, being mainly associated with chromosome or genome instability (most commonly manifesting as aneuploidy), somatic genome variations are involved in pathogenesis of numerous human diseases. The latter mainly concerns diseases of the brain (i.e. autism, schizophrenia, Alzheimer's disease) and immune system (autoimmune diseases), chromosomal and some monogenic syndromes, cancers, infertility and prenatal mortality. Taking into account data on somatic genome variations and chromosome instability, it becomes possible to show that related processes can underlie non-malignant pathology such as (neuro)degeneration or other local tissue dysfunctions. Together, we suggest that detection and characterization of somatic genome behavior and variations can provide new opportunities for human genome research and genetics.
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Affiliation(s)
- I Y Iourov
- National Research Center of Mental Health, Russian Academy of Medical Sciences
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Vorsanova SG, Yurov YB, Soloviev IV, Iourov IY. Molecular cytogenetic diagnosis and somatic genome variations. Curr Genomics 2011; 11:440-6. [PMID: 21358989 PMCID: PMC3018725 DOI: 10.2174/138920210793176010] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/26/2010] [Accepted: 06/01/2010] [Indexed: 12/22/2022] Open
Abstract
Human molecular cytogenetics integrates the knowledge on chromosome and genome organization at the molecular and cellular levels in health and disease. Molecular cytogenetic diagnosis is an integral part of current genomic medicine and is the standard of care in medical genetics and cytogenetics, reproductive medicine, pediatrics, neuropsychiatry and oncology. Regardless numerous advances in this field made throughout the last two decades, researchers and practitioners who apply molecular cytogenetic techniques may encounter several problems that are extremely difficult to solve. One of them is undoubtedly the occurrence of somatic genome and chromosome variations, leading to genomic and chromosomal mosaicism, which are related but not limited to technological and evaluative limitations as well as multiplicity of interpretations. More dramatically, current biomedical literature almost lacks descriptions, guidelines or solutions of these problems. The present article overviews all these problems and gathers those exclusive data acquired from studies of genome and chromosome instability that is relevant to identification and interpretations of this fairly common cause of somatic genomic variations and chromosomal mosaicism. Although the way to define pathogenic value of all the intercellular variations of the human genome is far from being completely understood, it is possible to propose recommendations on molecular cytogenetic diagnosis and management of somatic genome variations in clinical population.
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Affiliation(s)
- S G Vorsanova
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii
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Weier JF, Ferlatte C, Weier HUG. Somatic genomic variations in extra-embryonic tissues. Curr Genomics 2011; 11:402-8. [PMID: 21358984 PMCID: PMC3018720 DOI: 10.2174/138920210793175994] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Revised: 05/01/2010] [Accepted: 05/07/2010] [Indexed: 12/31/2022] Open
Abstract
In the mature chorion, one of the membranes that exist during pregnancy between the developing fetus and mother, human placental cells form highly specialized tissues composed of mesenchyme and floating or anchoring villi. Using fluorescence in situ hybridization, we found that human invasive cytotrophoblasts isolated from anchoring villi or the uterine wall had gained individual chromosomes; however, chromosome losses were detected infrequently. With chromosomes gained in what appeared to be a chromosome-specific manner, more than half of the invasive cytotrophoblasts in normal pregnancies were found to be hyperdiploid. Interestingly, the rates of hyperdiploid cells depended not only on gestational age, but were strongly associated with the extraembryonic compartment at the fetal-maternal interface from which they were isolated. Since hyperdiploid cells showed drastically reduced DNA replication as measured by bromodeoxyuridine incorporation, we conclude that aneuploidy is a part of the normal process of placentation potentially limiting the proliferative capabilities of invasive cytotrophoblasts. Thus, under the special circumstances of human reproduction, somatic genomic variations may exert a beneficial, anti-neoplastic effect on the organism.
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Yurov YB, Vorsanova SG, Iourov IY. Ontogenetic variation of the human genome. Curr Genomics 2011; 11:420-5. [PMID: 21358986 PMCID: PMC3018722 DOI: 10.2174/138920210793175958] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 05/19/2010] [Accepted: 05/20/2010] [Indexed: 11/22/2022] Open
Abstract
The human genome demonstrates variable levels of instability during ontogeny. Achieving the highest rate during early prenatal development, it decreases significantly throughout following ontogenetic stages. A failure to decrease or a spontaneous increase of genomic instability can promote infertility, pregnancy losses, chromosomal and genomic diseases, cancer, immunodeficiency, or brain diseases depending on developmental stage at which it occurs. Paradoxically, late ontogeny is associated with increase of genomic instability that is considered a probable mechanism for human aging. The latter is even more appreciable in human diseases associated with pathological or accelerated aging (i.e. Alzheimer's disease and ataxia-telangiectasia). These observations resulted in a hypothesis suggesting that somatic genomic variations throughout ontogeny are determinants of cellular vitality in health and disease including intrauterine development, postnatal life and aging. The most devastative effect of somatic genome variations is observed when it manifests as chromosome instability or aneuploidy, which has been repeatedly noted to produce pathologic conditions and to mediate developmental regulatory and aging processes. However, no commonly accepted concepts on the role of chromosome/genome instability in determination of human health span and life span are available. Here, a review of these ontogenetic variations is given to propose a new "dynamic genome" model for pathological and natural genomic changes throughout life that mimic those of phylogenetic diversity.
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Affiliation(s)
- Y B Yurov
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii
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Abstract
Alzheimer?s disease (AD), as the most common form of dementia, has for many
years attracted the attention of researchers around the world, primarily
because of the problems of reliable diagnostic methods that could help in the
early detection of this devastating disease. One of the important aspects of
genetic research related to AD is the analysis of chromosome instability
which includes: aneuploidies of different chromosomes, telomere shortening
and the phenomenon of premature centromere division (PCD). The aim of this
study was to describe specific biomarkers in different types of cells as
potential parameters for the diagnosis of AD in order to promptly recognize
pre-symptomatic stages and prevent the development of disease and/or slow
down its progression.
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45
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Iourov IY, Vorsanova SG, Saprina EA, Yurov YB. Identification of candidate genes of autism on the basis of molecular cytogenetic and in silico studies of the genome organization of chromosomal regions involved in unbalanced rearrangements. RUSS J GENET+ 2010. [DOI: 10.1134/s102279541010011x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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46
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Yurov YB, Vorsanova SG, Solov’ev IV, Iourov IY. Instability of chromosomes in human nerve cells (Normal and with Neuromental Diseases). RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410100121] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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47
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Liehr T, Karamysheva T, Merkas M, Brecevic L, Hamid AB, Ewers E, Mrasek K, Kosyakova N, Weise A. Somatic mosaicism in cases with small supernumerary marker chromosomes. Curr Genomics 2010; 11:432-9. [PMID: 21358988 PMCID: PMC3018724 DOI: 10.2174/138920210793176029] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Revised: 05/30/2010] [Accepted: 06/01/2010] [Indexed: 11/22/2022] Open
Abstract
Somatic mosaicism is something that is observed in everyday lives of cytogeneticists. Chromosome instability is one of the leading causes of large-scale genome variation analyzable since the correct human chromosome number was established in 1956. Somatic mosaicism is also a well-known fact to be present in cases with small supernumerary marker chromosomes (sSMC), i.e. karyotypes of 47,+mar/46. In this study, the data available in the literature were collected concerning the frequency mosaicism in different subgroups of patients with sSMC. Of 3124 cases with sSMC 1626 (52%) present with somatic mosaicism. Some groups like patients with Emanuel-, cat-eye- or i(18p)- syndrome only tend rarely to develop mosaicism, while in Pallister-Killian syndrome every patient is mosaic. In general, acrocentric and non-acrocentric derived sSMCs are differently susceptible to mosaicism; non-acrocentric derived ones are hereby the less stable ones. Even though, in the overwhelming majority of the cases, somatic mosaicism does not have any detectable clinical effects, there are rare cases with altered clinical outcomes due to mosaicism. This is extremely important for prenatal genetic counseling. Overall, as mosaicism is something to be considered in at least every second sSMC case, array-CGH studies cannot be offered as a screening test to reliably detect this kind of chromosomal aberration, as low level mosaic cases and cryptic mosaics are missed by that.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | | | - Martina Merkas
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
- School of Medicine Zagreb University, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Lukrecija Brecevic
- School of Medicine Zagreb University, Croatian Institute for Brain Research, Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Elisabeth Ewers
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | - Anja Weise
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
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48
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Vorsanova SG, Voinova VY, Yurov IY, Kurinnaya OS, Demidova IA, Yurov YB. Cytogenetic, Molecular-Cytogenetic, and Clinical-Genealogical Studies of the Mothers of Children with Autism: A Search for Familial Genetic Markers for Autistic Disorders. ACTA ACUST UNITED AC 2010; 40:745-56. [DOI: 10.1007/s11055-010-9321-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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49
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Hehir-Kwa JY, Wieskamp N, Webber C, Pfundt R, Brunner HG, Gilissen C, de Vries BBA, Ponting CP, Veltman JA. Accurate distinction of pathogenic from benign CNVs in mental retardation. PLoS Comput Biol 2010; 6:e1000752. [PMID: 20421931 PMCID: PMC2858682 DOI: 10.1371/journal.pcbi.1000752] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2009] [Accepted: 03/19/2010] [Indexed: 11/18/2022] Open
Abstract
Copy number variants (CNVs) have recently been recognized as a common form of genomic variation in humans. Hundreds of CNVs can be detected in any individual genome using genomic microarrays or whole genome sequencing technology, but their phenotypic consequences are still poorly understood. Rare CNVs have been reported as a frequent cause of neurological disorders such as mental retardation (MR), schizophrenia and autism, prompting widespread implementation of CNV screening in diagnostics. In previous studies we have shown that, in contrast to benign CNVs, MR-associated CNVs are significantly enriched in genes whose mouse orthologues, when disrupted, result in a nervous system phenotype. In this study we developed and validated a novel computational method for differentiating between benign and MR-associated CNVs using structural and functional genomic features to annotate each CNV. In total 13 genomic features were included in the final version of a Naïve Bayesian Tree classifier, with LINE density and mouse knock-out phenotypes contributing most to the classifier's accuracy. After demonstrating that our method (called GECCO) perfectly classifies CNVs causing known MR-associated syndromes, we show that it achieves high accuracy (94%) and negative predictive value (99%) on a blinded test set of more than 1,200 CNVs from a large cohort of individuals with MR. These results indicate that this classification method will be of value for objectively prioritizing CNVs in clinical research and diagnostics. Rare copy number variants (CNVs) are a frequent cause of neurological disorders such as mental retardation (MR). However CNVs are also commonly identified in healthy individuals. It is therefore crucial for both diagnostic and research applications to be able to distinguish between disease-causing CNVs and “benign” CNVs occurring as normal genomic variation. Separating these two types can take advantage of significant differences in their genomic contents. For example, benign CNVs are enriched in repetitive sequences. By contrast, CNVs associated with MR tend to have high densities of functional elements, including genes whose mouse orthologues, when knocked-out, lead to specific nervous system abnormalities. We have developed a novel objective approach that is effective in distinguishing MR-associated CNVs from benign CNVs based on the presence of 13 genomic attributes. This method is able to achieve high accuracies in a cohort of CNVs known to cause MR and in a cohort of individuals with unexplained MR. The development of this technique promises to substantially improve the methodology for determining the pathogenicity of CNVs.
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Affiliation(s)
- Jayne Y. Hehir-Kwa
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Nienke Wieskamp
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Caleb Webber
- MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Rolph Pfundt
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Han G. Brunner
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Christian Gilissen
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Bert B. A. de Vries
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
| | - Chris P. Ponting
- MRC Functional Genomics Unit, University of Oxford, Department of Physiology, Anatomy and Genetics, Oxford, United Kingdom
| | - Joris A. Veltman
- Radboud University Nijmegen Medical Centre, Department of Human Genetics, Nijmegen, The Netherlands
- * E-mail:
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50
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Vorsanova SG, Yurov YB, Iourov IY. Human interphase chromosomes: a review of available molecular cytogenetic technologies. Mol Cytogenet 2010; 3:1. [PMID: 20180947 PMCID: PMC2830939 DOI: 10.1186/1755-8166-3-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 01/11/2010] [Indexed: 01/05/2023] Open
Abstract
Human karyotype is usually studied by classical cytogenetic (banding) techniques. To perform it, one has to obtain metaphase chromosomes of mitotic cells. This leads to the impossibility of analyzing all the cell types, to moderate cell scoring, and to the extrapolation of cytogenetic data retrieved from a couple of tens of mitotic cells to the whole organism, suggesting that all the remaining cells possess these genomes. However, this is far from being the case inasmuch as chromosome abnormalities can occur in any cell along ontogeny. Since somatic cells of eukaryotes are more likely to be in interphase, the solution of the problem concerning studying postmitotic cells and larger cell populations is interphase cytogenetics, which has become more or less applicable for specific biomedical tasks due to achievements in molecular cytogenetics (i.e. developments of fluorescence in situ hybridization -- FISH, and multicolor banding -- MCB). Numerous interphase molecular cytogenetic approaches are restricted to studying specific genomic loci (regions) being, however, useful for identification of chromosome abnormalities (aneuploidy, polyploidy, deletions, inversions, duplications, translocations). Moreover, these techniques are the unique possibility to establish biological role and patterns of nuclear genome organization at suprachromosomal level in a given cell. Here, it is to note that this issue is incompletely worked out due to technical limitations. Nonetheless, a number of state-of-the-art molecular cytogenetic techniques (i.e multicolor interphase FISH or interpahase chromosome-specific MCB) allow visualization of interphase chromosomes in their integrity at molecular resolutions. Thus, regardless numerous difficulties encountered during studying human interphase chromosomes, molecular cytogenetics does provide for high-resolution single-cell analysis of genome organization, structure and behavior at all stages of cell cycle.
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Affiliation(s)
- Svetlana G Vorsanova
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
| | - Yuri B Yurov
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
| | - Ivan Y Iourov
- Institute of Pediatrics and Children Surgery, Rosmedtechnologii, Moscow, 127412, Russia
- National Research Center of Mental Health, Russian Academy of Medical Sciences, Moscow 119152, Russia
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