1
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Jeong M, Choi JH, Jang H, Sohn DH, Wang Q, Lee J, Yao L, Lee EJ, Fan J, Pratelli M, Wang EH, Snyder CN, Wang XY, Shin S, Gittis AH, Sung TC, Spitzer NC, Lim BK. Viral vector-mediated transgene delivery with novel recombinase systems for targeting neuronal populations defined by multiple features. Neuron 2024; 112:56-72.e4. [PMID: 37909037 PMCID: PMC10916502 DOI: 10.1016/j.neuron.2023.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 05/21/2023] [Accepted: 09/26/2023] [Indexed: 11/02/2023]
Abstract
A comprehensive understanding of neuronal diversity and connectivity is essential for understanding the anatomical and cellular mechanisms that underlie functional contributions. With the advent of single-cell analysis, growing information regarding molecular profiles leads to the identification of more heterogeneous cell types. Therefore, the need for additional orthogonal recombinase systems is increasingly apparent, as heterogeneous tissues can be further partitioned into increasing numbers of specific cell types defined by multiple features. Critically, new recombinase systems should work together with pre-existing systems without cross-reactivity in vivo. Here, we introduce novel site-specific recombinase systems based on ΦC31 bacteriophage recombinase for labeling multiple cell types simultaneously and a novel viral strategy for versatile and robust intersectional expression of any transgene. Together, our system will help researchers specifically target different cell types with multiple features in the same animal.
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Affiliation(s)
- Minju Jeong
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jun-Hyeok Choi
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Hyeonseok Jang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dong Hyun Sohn
- Department of Microbiology and Immunology, Pusan National University School of Medicine, Yangsan 50612, Republic of Korea
| | - Qingdi Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Joann Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Li Yao
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eun Ji Lee
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jiachen Fan
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marta Pratelli
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric H Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Christen N Snyder
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Xiao-Yun Wang
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sora Shin
- Center for Neurobiology Research, Fralin Biomedical Research Institute at Virginia Tech Carilion, Virginia Tech, Roanoke, VA, USA; Department of Human Nutrition, Foods, and Exercise, Virginia Tech, Blacksburg, VA, USA
| | - Aryn H Gittis
- Department of Biological Sciences and Center for the Neural Basis of Cognition, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Tsung-Chang Sung
- Transgenic Core, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Nicholas C Spitzer
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Byung Kook Lim
- Neurobiology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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2
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Lee H, Ciabatti E, González-Rueda A, Williams E, Nugent F, Mookerjee S, Morgese F, Tripodi M. Combining long-term circuit mapping and network transcriptomics with SiR-N2c. Nat Methods 2023; 20:580-589. [PMID: 36864202 PMCID: PMC7614628 DOI: 10.1038/s41592-023-01787-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 01/23/2023] [Indexed: 03/04/2023]
Abstract
An exciting frontier in circuit neuroscience lies at the intersection between neural network mapping and single-cell genomics. Monosynaptic rabies viruses provide a promising platform for the merger of circuit mapping methods with -omics approaches. However, three key limitations have hindered the extraction of physiologically meaningful gene expression profiles from rabies-mapped circuits: inherent viral cytotoxicity, high viral immunogenicity and virus-induced alteration of cellular transcriptional regulation. These factors alter the transcriptional and translational profiles of infected neurons and their neighboring cells. To overcome these limitations we applied a self-inactivating genomic modification to the less immunogenic rabies strain, CVS-N2c, to generate a self-inactivating CVS-N2c rabies virus (SiR-N2c). SiR-N2c not only eliminates undesired cytotoxic effects but also substantially reduces gene expression alterations in infected neurons and dampens the recruitment of innate and acquired immune responses, thus enabling open-ended interventions on neural networks and their genetic characterization using single-cell genomic approaches.
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Affiliation(s)
- Hassal Lee
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Ernesto Ciabatti
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | | | - Elena Williams
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Fiona Nugent
- IMAXT Laboratory, Cancer Research UK Cambridge Institute, Cambridge, UK
| | | | - Fabio Morgese
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marco Tripodi
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
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3
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Heng E, Thanedar S, Heng HH. Challenges and Opportunities for Clinical Cytogenetics in the 21st Century. Genes (Basel) 2023; 14:493. [PMID: 36833419 PMCID: PMC9956237 DOI: 10.3390/genes14020493] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The powerful utilities of current DNA sequencing technology question the value of developing clinical cytogenetics any further. By briefly reviewing the historical and current challenges of cytogenetics, the new conceptual and technological platform of the 21st century clinical cytogenetics is presented. Particularly, the genome architecture theory (GAT) has been used as a new framework to emphasize the importance of clinical cytogenetics in the genomic era, as karyotype dynamics play a central role in information-based genomics and genome-based macroevolution. Furthermore, many diseases can be linked to elevated levels of genomic variations within a given environment. With karyotype coding in mind, new opportunities for clinical cytogenetics are discussed to integrate genomics back into cytogenetics, as karyotypic context represents a new type of genomic information that organizes gene interactions. The proposed research frontiers include: 1. focusing on karyotypic heterogeneity (e.g., classifying non-clonal chromosome aberrations (NCCAs), studying mosaicism, heteromorphism, and nuclear architecture alteration-mediated diseases), 2. monitoring the process of somatic evolution by characterizing genome instability and illustrating the relationship between stress, karyotype dynamics, and diseases, and 3. developing methods to integrate genomic data and cytogenomics. We hope that these perspectives can trigger further discussion beyond traditional chromosomal analyses. Future clinical cytogenetics should profile chromosome instability-mediated somatic evolution, as well as the degree of non-clonal chromosomal aberrations that monitor the genomic system's stress response. Using this platform, many common and complex disease conditions, including the aging process, can be effectively and tangibly monitored for health benefits.
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Affiliation(s)
- Eric Heng
- Stanford University, 450 Jane Stanford Way, Stanford, CA 94305, USA
| | - Sanjana Thanedar
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Henry H. Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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4
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Ji Z, Song Q, Su J. Editorial: Advanced computational systems biology approaches for accelerating comprehensive research of the human brain. Front Genet 2023; 14:1143789. [PMID: 36845385 PMCID: PMC9948396 DOI: 10.3389/fgene.2023.1143789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Affiliation(s)
- Zhiwei Ji
- College of Artificial Intelligence, Nanjing Agricultural University, Nanjing, China,*Correspondence: Zhiwei Ji,
| | - Qianqian Song
- School of Medicine, Wake Forest University, Winston-Salem, NC, United States
| | - Jing Su
- School of Medicine, Indiana University Bloomington, Bloomington, IN, United States
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5
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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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Yurov YB, Vorsanova SG, Iourov IY. FISHing for Chromosome Instability and Aneuploidy in the Alzheimer's Disease Brain. Methods Mol Biol 2022; 2561:191-204. [PMID: 36399271 DOI: 10.1007/978-1-0716-2655-9_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is the method of choice for visualizing chromosomal DNA in post-mitotic cells. The availability of chromosome-enumeration (centromeric), site-specific, and multicolor-banding DNA probes offers opportunities to uncover genomic changes, at the chromosomal level, in single interphase nuclei. Alzheimer's disease (AD) has been associated repeatedly with (sub)chromosome instability and aneuploidy, likely affecting the brain. Although the types and rates of chromosome instability in the AD brain remain a matter of debate, molecular cytogenetic analysis of brain cells appears to be important for uncovering mechanisms of neurodegeneration. Here, we describe a FISH protocol for studying chromosome instability and aneuploidy in the AD brain.
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Affiliation(s)
- Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia
| | - Ivan Y Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia. .,Vorsanova's Laboratory of Molecular Cytogenetics of Neuropsychiatric Diseases, Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Moscow, Russia.
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Iourov IY, Vorsanova SG, Kurinnaia OS, Kutsev SI, Yurov YB. Somatic mosaicism in the diseased brain. Mol Cytogenet 2022; 15:45. [PMID: 36266706 PMCID: PMC9585840 DOI: 10.1186/s13039-022-00624-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/10/2022] Open
Abstract
It is hard to believe that all the cells of a human brain share identical genomes. Indeed, single cell genetic studies have demonstrated intercellular genomic variability in the normal and diseased brain. Moreover, there is a growing amount of evidence on the contribution of somatic mosaicism (the presence of genetically different cell populations in the same individual/tissue) to the etiology of brain diseases. However, brain-specific genomic variations are generally overlooked during the research of genetic defects associated with a brain disease. Accordingly, a review of brain-specific somatic mosaicism in disease context seems to be required. Here, we overview gene mutations, copy number variations and chromosome abnormalities (aneuploidy, deletions, duplications and supernumerary rearranged chromosomes) detected in the neural/neuronal cells of the diseased brain. Additionally, chromosome instability in non-cancerous brain diseases is addressed. Finally, theoretical analysis of possible mechanisms for neurodevelopmental and neurodegenerative disorders indicates that a genetic background for formation of somatic (chromosomal) mosaicism in the brain is likely to exist. In total, somatic mosaicism affecting the central nervous system seems to be a mechanism of brain 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, Moscow, Russia. .,Vorsanova'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. .,Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia.
| | - Svetlana G Vorsanova
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova'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
| | - Oxana S Kurinnaia
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova'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
| | | | - Yuri B Yurov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia.,Vorsanova'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
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8
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Iourov IY, Heng HH. Editorial: Somatic genomic mosaicism & human disease. Front Genet 2022; 13:1045559. [PMID: 36276972 PMCID: PMC9585291 DOI: 10.3389/fgene.2022.1045559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ivan Y. Iourov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia
- Vorsanova’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
- Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia
- *Correspondence: Ivan Y. Iourov,
| | - Henry H. Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, United States
- Department of Pathology, Wayne State University School of Medicine, Detroit, United States
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10
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Vorsanova SG, Demidova IA, Kolotii AD, Kurinnaia OS, Kravets VS, Soloviev IV, Yurov YB, Iourov IY. Klinefelter syndrome mosaicism in boys with neurodevelopmental disorders: a cohort study and an extension of the hypothesis. Mol Cytogenet 2022; 15:8. [PMID: 35248137 PMCID: PMC8897849 DOI: 10.1186/s13039-022-00588-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 02/21/2022] [Indexed: 01/14/2023] Open
Abstract
Abstract
Background
Klinefelter syndrome is a common chromosomal (aneuploidy) disorder associated with an extra X chromosome in males. Regardless of numerous studies dedicated to somatic gonosomal mosaicism, Klinefelter syndrome mosaicism (KSM) has not been systematically addressed in clinical cohorts. Here, we report on the evaluation of KSM in a large cohort of boys with neurodevelopmental disorders. Furthermore, these data have been used for an extension of the hypothesis, which we have recently proposed in a report on Turner’s syndrome mosaicism in girls with neurodevelopmental disorders.
Results
Klinefelter syndrome-associated karyotypes were revealed in 49 (1.1%) of 4535 boys. Twenty one boys (0.5%) were non-mosaic 47,XXY individuals. KSM was found in 28 cases (0.6%) and manifested as mosaic aneuploidy (50,XXXXXY; 49,XXXXY; 48,XXXY; 48,XXYY; 47,XXY; and 45,X were detected in addition to 47,XXY/46,XY) and mosaic supernumerary marker chromosomes derived from chromosome X (ring chromosomes X and rearranged chromosomes X). It is noteworthy that KSM was concomitant with Rett-syndrome-like phenotypes caused by MECP2 mutations in 5 boys (0.1%).
Conclusion
Our study provides data on the occurrence of KSM in neurodevelopmental disorders among males. Accordingly, it is proposed that KSM may be a possible element of pathogenic cascades in psychiatric and neurodegenerative diseases. These observations allowed us to extend the hypothesis proposed in our previous report on the contribution of somatic gonosomal mosaicism (Turner’s syndrome mosaicism) to the etiology of neurodevelopmental disorders. Thus, it seems to be important to monitor KSM (a possible risk factor or a biomarker for adult-onset multifactorial brain diseases) and analysis of neuromarkers for aging in individuals with Klinefelter syndrome. Cases of two or more supernumerary chromosomes X were all associated with KSM. Finally, Rett syndrome-like phenotypes associated with KSM appear to be more common in males with neurodevelopmental disorders than previously recognized.
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Iourov IY, Yurov YB, Vorsanova SG, Kutsev SI. Chromosome Instability, Aging and Brain Diseases. Cells 2021; 10:cells10051256. [PMID: 34069648 PMCID: PMC8161106 DOI: 10.3390/cells10051256] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/16/2021] [Accepted: 05/18/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability (CIN) has been repeatedly associated with aging and progeroid phenotypes. Moreover, brain-specific CIN seems to be an important element of pathogenic cascades leading to neurodegeneration in late adulthood. Alternatively, CIN and aneuploidy (chromosomal loss/gain) syndromes exhibit accelerated aging phenotypes. Molecularly, cellular senescence, which seems to be mediated by CIN and aneuploidy, is likely to contribute to brain aging in health and disease. However, there is no consensus about the occurrence of CIN in the aging brain. As a result, the role of CIN/somatic aneuploidy in normal and pathological brain aging is a matter of debate. Still, taking into account the effects of CIN on cellular homeostasis, the possibility of involvement in brain aging is highly likely. More importantly, the CIN contribution to neuronal cell death may be responsible for neurodegeneration and the aging-related deterioration of the brain. The loss of CIN-affected neurons probably underlies the contradiction between reports addressing ontogenetic changes of karyotypes within the aged brain. In future studies, the combination of single-cell visualization and whole-genome techniques with systems biology methods would certainly define the intrinsic role of CIN in the aging of the normal and diseased brain.
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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; (Y.B.Y.); (S.G.V.)
- 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
- Department of Medical Biological Disciplines, Belgorod State University, 308015 Belgorod, Russia
- Correspondence: ; Tel.: +7-495-109-03-93 (ext. 3500)
| | - Yuri B. Yurov
- Yurov’s Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, 117152 Moscow, Russia; (Y.B.Y.); (S.G.V.)
- 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; (Y.B.Y.); (S.G.V.)
- 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
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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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13
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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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14
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Vorsanova SG, Kolotii AD, Kurinnaia OS, Kravets VS, Demidova IA, Soloviev IV, Yurov YB, Iourov IY. Turner's syndrome mosaicism in girls with neurodevelopmental disorders: a cohort study and hypothesis. Mol Cytogenet 2021; 14:9. [PMID: 33573679 PMCID: PMC7879607 DOI: 10.1186/s13039-021-00529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 01/14/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Turner's syndrome is associated with either monosomy or a wide spectrum of structural rearrangements of chromosome X. Despite the interest in studying (somatic) chromosomal mosaicism, Turner's syndrome mosaicism (TSM) remains to be fully described. This is especially true for the analysis of TSM in clinical cohorts (e.g. cohorts of individuals with neurodevelopmental disorders). Here, we present the results of studying TSM in a large cohort of girls with neurodevelopmental disorders and a hypothesis highlighting the diagnostic and prognostic value. RESULTS Turner's syndrome-associated karyotypes were revealed in 111 (2.8%) of 4021 girls. Regular Turner's syndrome-associated karyotypes were detected in 35 girls (0.9%). TSM was uncovered in 76 girls (1.9%). TSM manifested as mosaic aneuploidy (45,X/46,XX; 45,X/47,XXX/46,XX; 45,X/47,XXX) affected 47 girls (1.2%). Supernumerary marker chromosomes derived from chromosome X have been identified in 11 girls with TSM (0.3%). Isochromosomes iX(q) was found in 12 cases (0.3%); one case was non-mosaic. TSM associated with ring chromosomes was revealed in 5 girls (0.1%). CONCLUSION The present cohort study provides data on the involvement of TSM in neurodevelopmental disorders among females. Thus, TSM may be an element of pathogenic cascades in brain diseases (i.e. neurodegenerative and psychiatric disorders). Our data allowed us to propose a hypothesis concerning ontogenetic variability of TSM levels. Accordingly, it appears that molecular cytogenetic monitoring of TSM, which is a likely risk factor/biomarker for adult-onset multifactorial diseases, is required.
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Affiliation(s)
- Svetlana G Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Alexey D Kolotii
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Oksana S Kurinnaia
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Victor S Kravets
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Irina A Demidova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Ilya V Soloviev
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Yuri B Yurov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412.,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522
| | - Ivan Y Iourov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, Moscow, Russia, 125412. .,Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow, Russia, 115522. .,Department of Medical Biological Disciplines, Belgorod State University, Belgorod, Russia, 308015.
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The Cytogenomic "Theory of Everything": Chromohelkosis May Underlie Chromosomal Instability and Mosaicism in Disease and Aging. Int J Mol Sci 2020; 21:ijms21218328. [PMID: 33171981 PMCID: PMC7664247 DOI: 10.3390/ijms21218328] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/28/2023] Open
Abstract
Mechanisms for somatic chromosomal mosaicism (SCM) and chromosomal instability (CIN) are not completely understood. During molecular karyotyping and bioinformatic analyses of children with neurodevelopmental disorders and congenital malformations (n = 612), we observed colocalization of regular chromosomal imbalances or copy number variations (CNV) with mosaic ones (n = 47 or 7.7%). Analyzing molecular karyotyping data and pathways affected by CNV burdens, we proposed a mechanism for SCM/CIN, which had been designated as “chromohelkosis” (from the Greek words chromosome ulceration/open wound). Briefly, structural chromosomal imbalances are likely to cause local instability (“wreckage”) at the breakpoints, which results either in partial/whole chromosome loss (e.g., aneuploidy) or elongation of duplicated regions. Accordingly, a function for classical/alpha satellite DNA (protection from the wreckage towards the centromere) has been hypothesized. Since SCM and CIN are ubiquitously involved in development, homeostasis and disease (e.g., prenatal development, cancer, brain diseases, aging), we have metaphorically (ironically) designate the system explaining chromohelkosis contribution to SCM/CIN as the cytogenomic “theory of everything”, similar to the homonymous theory in physics inasmuch as it might explain numerous phenomena in chromosome biology. Recognizing possible empirical and theoretical weaknesses of this “theory”, we nevertheless believe that studies of chromohelkosis-like processes are required to understand structural variability and flexibility of the genome.
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Gupta P, Balasubramaniam N, Chang HY, Tseng FG, Santra TS. A Single-Neuron: Current Trends and Future Prospects. Cells 2020; 9:E1528. [PMID: 32585883 PMCID: PMC7349798 DOI: 10.3390/cells9061528] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/15/2020] [Accepted: 06/19/2020] [Indexed: 12/11/2022] Open
Abstract
The brain is an intricate network with complex organizational principles facilitating a concerted communication between single-neurons, distinct neuron populations, and remote brain areas. The communication, technically referred to as connectivity, between single-neurons, is the center of many investigations aimed at elucidating pathophysiology, anatomical differences, and structural and functional features. In comparison with bulk analysis, single-neuron analysis can provide precise information about neurons or even sub-neuron level electrophysiology, anatomical differences, pathophysiology, structural and functional features, in addition to their communications with other neurons, and can promote essential information to understand the brain and its activity. This review highlights various single-neuron models and their behaviors, followed by different analysis methods. Again, to elucidate cellular dynamics in terms of electrophysiology at the single-neuron level, we emphasize in detail the role of single-neuron mapping and electrophysiological recording. We also elaborate on the recent development of single-neuron isolation, manipulation, and therapeutic progress using advanced micro/nanofluidic devices, as well as microinjection, electroporation, microelectrode array, optical transfection, optogenetic techniques. Further, the development in the field of artificial intelligence in relation to single-neurons is highlighted. The review concludes with between limitations and future prospects of single-neuron analyses.
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Affiliation(s)
- Pallavi Gupta
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
| | - Nandhini Balasubramaniam
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
| | - Hwan-You Chang
- Department of Medical Science, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Fan-Gang Tseng
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Tamil Nadu 600036, India; (P.G.); (N.B.)
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Vorsanova SG, Yurov YB, Iourov IY. Dynamic nature of somatic chromosomal mosaicism, genetic-environmental interactions and therapeutic opportunities in disease and aging. Mol Cytogenet 2020; 13:16. [PMID: 32411302 PMCID: PMC7206664 DOI: 10.1186/s13039-020-00488-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 04/24/2020] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Somatic chromosomal mosaicism is the presence of cell populations differing with respect to the chromosome complements (e.g. normal and abnormal) in an individual. Chromosomal mosaicism is associated with a wide spectrum of disease conditions and aging. Studying somatic genome variations has indicated that amounts of chromosomally abnormal cells are likely to be unstable. As a result, dynamic changes of mosaicism rates occur through ontogeny. Additionally, a correlation between disease severity and mosaicism rates appears to exist. High mosaicism rates are usually associated with severe disease phenotypes, whereas low-level mosaicism is generally observed in milder disease phenotypes or in presumably unaffected individuals. Here, we hypothesize that dynamic nature of somatic chromosomal mosaicism may result from genetic-environmental interactions creating therapeutic opportunities in the associated diseases and aging. CONCLUSION Genetic-environmental interactions seem to contribute to the dynamic nature of somatic mosaicism. Accordingly, an external influence on cellular populations may shift the ratio of karyotypically normal and abnormal cells in favor of an increase in the amount of cells without chromosome rearrangements. Taking into account the role of somatic chromosomal mosaicism in health and disease, we have hypothesized that artificial changing of somatic mosaicism rates may be beneficial in individuals suffering from the associated diseases and/or behavioral or reproductive problems. In addition, such therapeutic procedures might be useful for anti-aging strategies (i.e. possible rejuvenation through a decrease in levels of chromosomal mosaicism) increasing the lifespan. Finally, the hypothesis appears to be applicable to any type of somatic mosacism.
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Affiliation(s)
- Svetlana G. Vorsanova
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
- Mental Health Research Center, 117152 Moscow, Russia
| | - Yuri B. Yurov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
- Mental Health Research Center, 117152 Moscow, Russia
| | - Ivan Y. Iourov
- Veltischev Research and Clinical Institute for Pediatrics of the Pirogov Russian National Research Medical University, Ministry of Health of Russian Federation, 125412 Moscow, Russia
- Mental Health Research Center, 117152 Moscow, Russia
- Department of Medical Biological Disciplines, Belgorod State University, 308015 Belgorod, Russia
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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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19
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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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20
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Lui A, Wang J, Chio L, Landry MP. Synthetic probe development for measuring single or few-cell activity and efflux. Methods Enzymol 2019; 628:19-41. [PMID: 31668229 PMCID: PMC10461879 DOI: 10.1016/bs.mie.2019.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Studying the single cell protein secretome offers the opportunity to understand how a phenotypically heterogeneous population of individual cells contribute to ensemble physiology and signaling. Polarized secretion events such as neurotransmitter release and cytokine signaling necessitates spatiotemporal information to elucidate structure-function relationships. Polymer functionalized single-walled carbon nanotube protein sensor arrays allow microscopic imaging of secreted protein footprints and enable the study of the spatiotemporal heterogeneity of protein secretion at the single-cell level. The protocols for carbon nanotube sensor creation, sensor array preparation, and imaging secreted proteins in both prokaryotic and mammalian cells are presented in this chapter. Secreted RAP1 and HIV-1 integrase proteins were used as proof-of-concept examples. Additionally, we discuss potential variety of protein and non-protein analyte effluxes that can be imaged using this platform, as well as current and future perspectives related to sensor development and deployment.
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Affiliation(s)
- Alison Lui
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Jeffrey Wang
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Linda Chio
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States
| | - Markita P Landry
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, CA, United States; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States; California Institute for Quantitative Biosciences (QB3), Berkeley, CA, United States; Chan-Zuckerberg Biohub, San Francisco, CA, United States.
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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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Abstract
Background:
The recently developed single-cell RNA sequencing (scRNA-seq) has
attracted a great amount of attention due to its capability to interrogate expression of individual
cells, which is superior to traditional bulk cell sequencing that can only measure mean gene
expression of a population of cells. scRNA-seq has been successfully applied in finding new cell
subtypes. New computational challenges exist in the analysis of scRNA-seq data.
Objective:
We provide an overview of the features of different similarity calculation and clustering
methods, in order to facilitate users to select methods that are suitable for their scRNA-seq. We
would also like to show that feature selection methods are important to improve clustering
performance.
Results:
We first described similarity measurement methods, followed by reviewing some new
clustering methods, as well as their algorithmic details. This analysis revealed several new
questions, including how to automatically estimate the number of clustering categories, how to
discover novel subpopulation, and how to search for new marker genes by using feature selection
methods.
Conclusion:
Without prior knowledge about the number of cell types, clustering or semisupervised
learning methods are important tools for exploratory analysis of scRNA-seq data.</P>
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Affiliation(s)
- Xiaoshu Zhu
- School of Computer Science and Engineering, Central South University, 410083, Changsha, Hunan, China
| | - Hong-Dong Li
- School of Computer Science and Engineering, Central South University, 410083, Changsha, Hunan, China
| | - Lilu Guo
- School of Computer Science and Engineering, Yulin Normal University, 537000, Yulin, Guangxi, China
| | - Fang-Xiang Wu
- Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SKS7N5A9, Canada
| | - Jianxin Wang
- School of Computer Science and Engineering, Central South University, 410083, Changsha, Hunan, China
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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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Yu M, Hou Y, Song R, Xu X, Yao S. Tunable Confinement for Bridging Single-Cell Manipulation and Single-Molecule DNA Linearization. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800229. [PMID: 29575689 DOI: 10.1002/smll.201800229] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/07/2018] [Indexed: 06/08/2023]
Abstract
DNA linearization by nanoconfinement has offered a new avenue toward large-scale genome mapping. The ability to smoothly interface the widely different length scales from cell manipulation to DNA linearization is critical to the development of single-cell genomic mapping or sequencing technologies. Conventional nanochannel technologies for DNA analysis suffer from complex fabrication procedures, DNA stacking at the nanochannel entrance, and inefficient solution exchange. In this work, a dynamic and tunable confinement strategy is developed to manipulate and linearize genomic-length DNA molecules from a single cell. By leveraging pneumatic microvalve control and elastomeric collapse, an array of nanochannels with confining dimension down to 20 nm and length up to sub-millimeter is created and can be dynamically tuned in size. The curved edges of the microvalve form gradual transitions from microscale to nanoscale confinement, smoothly facilitating DNA entry into the nanochannels. A unified micro/nanofluidic device that integrates single-cell trapping and lysis, DNA extraction, purification, labeling, and linearization is developed based on dynamically controllable nanochannels. Mbp-long DNA molecules are extracted directly from a single cell and in situ linearized in the nanochannels. The device provides a facile and promising platform to achieve the ultimate goal of single-cell, single-genome analysis.
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Affiliation(s)
- Miao Yu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Youmin Hou
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Ruyuan Song
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Xiaonan Xu
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
| | - Shuhuai Yao
- Department of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, China
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Kowloon, 999077, Hong Kong, 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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29
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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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30
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Shepherd CE, Yang Y, Halliday GM. Region- and Cell-specific Aneuploidy in Brain Aging and Neurodegeneration. Neuroscience 2018; 374:326-334. [PMID: 29432756 DOI: 10.1016/j.neuroscience.2018.01.050] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 01/02/2018] [Accepted: 01/23/2018] [Indexed: 12/13/2022]
Abstract
Variations in genomic DNA content, or aneuploidy, are a well-recognized feature of normal human brain development. Whether changes in the levels of aneuploidy are a factor in Alzheimer's disease (AD) is less clear, as the data reported to date vary substantially in the levels of aneuploidy detected (0.7-11.5%), possibly due to methodological limitations, but also influenced by individual, regional and cellular heterogeneity as well as variations in cell subtypes. These issues have not been adequately addressed to date. While it is known that the DNA damage response increases with age, the limited human studies investigating aneuploidy in normal aging also show variable results, potentially due to susceptibility to age-related neurodegenerative processes. Neuronal aneuploidy has recently been reported in multiple brain regions in Lewy body disease, but similar genomic changes are not a feature of all synucleinopathies and aneuploidy does not appear to be related to alpha-synuclein aggregation. Rather, aneuploidy was associated with Alzheimer's pathology in the hippocampus and anterior cingulate cortex and neuronal degeneration in the substantia nigra. The association between Alzheimer's pathology and aneuploidy in regions with limited neurodegeneration is supported by a growing body of in vitro and in vivo data on aneuploidy and beta-amyloid and tau abnormalities. Large-scale studies using high-resolution techniques alongside other sensitive and specific methodologies are now required to assess the true extent of cell- and region-specific aneuploidy in aging and neurodegeneration, and to determine any associations with pathologies.
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Affiliation(s)
- C E Shepherd
- Neuroscience Research Australia, Margarete Ainsworth Building, Barker Street, Randwick, Sydney 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney 2031, Australia.
| | - Y Yang
- Neuroscience Research Australia, Margarete Ainsworth Building, Barker Street, Randwick, Sydney 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney 2031, Australia; Brain and Mind Centre, Sydney Medical School, The University of Sydney, Australia.
| | - G M Halliday
- Neuroscience Research Australia, Margarete Ainsworth Building, Barker Street, Randwick, Sydney 2031, Australia; School of Medical Sciences, University of New South Wales, Sydney 2031, Australia; Brain and Mind Centre, Sydney Medical School, The University of Sydney, Australia.
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31
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Vu TQ, de Castro RMB, Qin L. Bridging the gap: microfluidic devices for short and long distance cell-cell communication. LAB ON A CHIP 2017; 17:1009-1023. [PMID: 28205652 PMCID: PMC5473339 DOI: 10.1039/c6lc01367h] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cell-cell communication is a crucial component of many biological functions. For example, understanding how immune cells and cancer cells interact, both at the immunological synapse and through cytokine secretion, can help us understand and improve cancer immunotherapy. The study of how cells communicate and form synaptic connections is important in neuroscience, ophthalmology, and cancer research. But in order to increase our understanding of these cellular phenomena, better tools need to be developed that allow us to study cell-cell communication in a highly controlled manner. Some technical requirements for better communication studies include manipulating cells spatiotemporally, high resolution imaging, and integrating sensors. Microfluidics is a powerful platform that has the ability to address these requirements and other current limitations. In this review, we describe some new advances in microfluidic technologies that have provided researchers with novel methods to study intercellular communication. The advantages of microfluidics have allowed for new capabilities in both single cell-cell communication and population-based communication. This review highlights microfluidic communication devices categorized as "short distance", or primarily at the single cell level, and "long distance", which mostly encompasses population level studies. Future directions and translation/commercialization will also be discussed.
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Affiliation(s)
- Timothy Quang Vu
- Department of Bioengineering, Rice University, Houston, TX 77030, USA and Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Ricardo Miguel Bessa de Castro
- College of Engineering, Swansea University Singleton Park, Swansea, UK and Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Lidong Qin
- Department of Nanomedicine, Houston Methodist Research Institute, Houston, TX 77030, USA. and Department of Cell and Developmental Biology, Weill Cornell Medical College, New York, NY 10065, USA
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32
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Dunaway KW, Islam MS, Coulson RL, Lopez SJ, Vogel Ciernia A, Chu RG, Yasui DH, Pessah IN, Lott P, Mordaunt C, Meguro-Horike M, Horike SI, Korf I, LaSalle JM. Cumulative Impact of Polychlorinated Biphenyl and Large Chromosomal Duplications on DNA Methylation, Chromatin, and Expression of Autism Candidate Genes. Cell Rep 2016; 17:3035-3048. [PMID: 27974215 PMCID: PMC5206988 DOI: 10.1016/j.celrep.2016.11.058] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/14/2016] [Accepted: 11/20/2016] [Indexed: 12/17/2022] Open
Abstract
Rare variants enriched for functions in chromatin regulation and neuronal synapses have been linked to autism. How chromatin and DNA methylation interact with environmental exposures at synaptic genes in autism etiologies is currently unclear. Using whole-genome bisulfite sequencing in brain tissue and a neuronal cell culture model carrying a 15q11.2-q13.3 maternal duplication, we find that significant global DNA hypomethylation is enriched over autism candidate genes and affects gene expression. The cumulative effect of multiple chromosomal duplications and exposure to the pervasive persistent organic pollutant PCB 95 altered methylation of more than 1,000 genes. Hypomethylated genes were enriched for H2A.Z, increased maternal UBE3A in Dup15q corresponded to reduced levels of RING1B, and bivalently modified H2A.Z was altered by PCB 95 and duplication. These results demonstrate the compounding effects of genetic and environmental insults on the neuronal methylome that converge upon dysregulation of chromatin and synaptic genes.
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Affiliation(s)
- Keith W Dunaway
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - M Saharul Islam
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Rochelle L Coulson
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - S Jesse Lopez
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Annie Vogel Ciernia
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Roy G Chu
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Dag H Yasui
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Isaac N Pessah
- Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA; Veterinary Molecular Biosciences, UC Davis, Davis, CA 95616, USA
| | - Paul Lott
- Genome Center, UC Davis, Davis, CA 95616, USA
| | - Charles Mordaunt
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA
| | - Makiko Meguro-Horike
- Advanced Science Research Center, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Japan
| | - Shin-Ichi Horike
- Advanced Science Research Center, Kanazawa University, 13-1 Takaramachi, Kanazawa 920-8640, Japan
| | - Ian Korf
- Genome Center, UC Davis, Davis, CA 95616, USA
| | - Janine M LaSalle
- Medical Microbiology and Immunology, UC Davis, Davis, CA 95616, USA; Genome Center, UC Davis, Davis, CA 95616, USA; MIND Institute, UC Davis, Davis, CA 95616, USA; Center for Children's Environmental Health, UC Davis, Davis, CA 95616, USA.
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Increased neuronal death and disturbed axonal growth in the Polμ-deficient mouse embryonic retina. Sci Rep 2016; 6:25928. [PMID: 27172884 PMCID: PMC4865816 DOI: 10.1038/srep25928] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/25/2016] [Indexed: 01/04/2023] Open
Abstract
Programmed cell death occurs naturally at different stages of neural development, including neurogenesis. The functional role of this early phase of neural cell death, which affects recently differentiated neurons among other cell types, remains undefined. Some mouse models defective in DNA double-strand break (DSB) repair present massive cell death during neural development, occasionally provoking embryonic lethality, while other organs and tissues remain unaffected. This suggests that DSBs occur frequently and selectively in the developing nervous system. We analyzed the embryonic retina of a mouse model deficient in the error-prone DNA polymerase μ (Polμ), a key component of the non-homologous end-joining (NHEJ) repair system. DNA DSBs were increased in the mutant mouse at embryonic day 13.5 (E13.5), as well as the incidence of cell death that affected young neurons, including retinal ganglion cells (RGCs). Polμ(-/-) mice also showed disturbed RGC axonal growth and navigation, and altered distribution of the axonal guidance molecules L1-CAM and Bravo (also known as Nr-CAM). These findings demonstrate that Polμ is necessary for proper retinal development, and support that the generation of DSBs and their repair via the NHEJ pathway are genuine processes involved in neural development.
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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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Genomic Copy Number Variation Affecting Genes Involved in the Cell Cycle Pathway: Implications for Somatic Mosaicism. Int J Genomics 2015; 2015:757680. [PMID: 26421275 PMCID: PMC4569762 DOI: 10.1155/2015/757680] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 07/27/2015] [Indexed: 12/20/2022] Open
Abstract
Somatic genome variations (mosaicism) seem to represent a common mechanism for human intercellular/interindividual diversity in health and disease. However, origins and mechanisms of somatic mosaicism remain a matter of conjecture. Recently, it has been hypothesized that zygotic genomic variation naturally occurring in humans is likely to predispose to nonheritable genetic changes (aneuploidy) acquired during the lifetime through affecting cell cycle regulation, genome stability maintenance, and related pathways. Here, we have evaluated genomic copy number variation (CNV) in genes implicated in the cell cycle pathway (according to Kyoto Encyclopedia of Genes and Genomes/KEGG) within a cohort of patients with intellectual disability, autism, and/or epilepsy, in which the phenotype was not associated with genomic rearrangements altering this pathway. Benign CNVs affecting 20 genes of the cell cycle pathway were detected in 161 out of 255 patients (71.6%). Among them, 62 individuals exhibited >2 CNVs affecting the cell cycle pathway. Taking into account the number of individuals demonstrating CNV of these genes, a support for this hypothesis appears to be presented. Accordingly, we speculate that further studies of CNV burden across the genes implicated in related pathways might clarify whether zygotic genomic variation generates somatic mosaicism in health and disease.
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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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Satterlee JS, Beckel-Mitchener A, Little R, Procaccini D, Rutter JL, Lossie AC. Neuroepigenomics: Resources, Obstacles, and Opportunities. NEUROEPIGENETICS 2015; 1:2-13. [PMID: 25722961 PMCID: PMC4337407 DOI: 10.1016/j.nepig.2014.10.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Long-lived post-mitotic cells, such as the majority of human neurons, must respond effectively to ongoing changes in neuronal stimulation or microenvironmental cues through transcriptional and epigenomic regulation of gene expression. The role of epigenomic regulation in neuronal function is of fundamental interest to the neuroscience community, as these types of studies have transformed our understanding of gene regulation in post-mitotic cells. This perspective article highlights many of the resources available to researchers interested in neuroepigenomic investigations and discusses some of the current obstacles and opportunities in neuroepigenomics.
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Affiliation(s)
- John S. Satterlee
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Andrea Beckel-Mitchener
- National Institute on Mental Health (NIMH), Division of Neuroscience and Basic Behavioral Science, 6001 Executive Boulevard Bethesda, MD 20892-9641, USA
| | - Roger Little
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Dena Procaccini
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Joni L. Rutter
- National Institute on Drug Abuse (NIDA), Division of Basic Neurobiology and Behavioral Research, 6001 Executive Boulevard, Bethesda, MD 20850, USA
| | - Amy C. Lossie
- Office of Behavioral and Social Sciences Research (OBSSR), Division of Program Coordination, Planning, and Strategic Initiatives, Office of the Director/National Institutes of Health (NIH), 31 Center Drive, Bethesda, MD 20892, USA
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Yang Y, Shepherd C, Halliday G. Aneuploidy in Lewy body diseases. Neurobiol Aging 2014; 36:1253-60. [PMID: 25595497 DOI: 10.1016/j.neurobiolaging.2014.12.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 12/13/2014] [Accepted: 12/13/2014] [Indexed: 12/13/2022]
Abstract
An increase in DNA content is associated with neuronal degeneration in Alzheimer's disease but has not been evaluated in Lewy body diseases. Using stereological principles, flow cytometry, and standard histopathologic methods, we evaluated the number and DNA content of neurons and all cells and the severity of Lewy and Alzheimer pathologies, in brain regions affected at different stages in Lewy body diseases compared with controls. An increase in neuronal DNA content was observed in all the affected brain regions examined, although this change was related to different pathologies. In the substantia nigra, increased neuronal DNA content related to neuronal loss, whereas in the cortex and hippocampus, increased neuronal DNA content related to Alzheimer pathologies. Of note, increased neuronal DNA content did not relate to the deposition of Lewy bodies in any region examined. These data support the concept that increased DNA content increases neuronal susceptibility to degeneration and Alzheimer pathologies.
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Affiliation(s)
- Yue Yang
- Neuroscience Research Australia, Randwick, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
| | - Claire Shepherd
- Neuroscience Research Australia, Randwick, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia
| | - Glenda Halliday
- Neuroscience Research Australia, Randwick, New South Wales, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Kensington, New South Wales, Australia.
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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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41
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Abstract
Zusammenfassung
Das gesunde menschliche Gehirn weist ein bemerkenswert hohes Maß an somatischen Zellmosaiken auf. Zum einen ist dies altersassoziiert, und darüber hinaus wurde nachgewiesen, dass stärker ausgeprägte Zellmosaike im Gehirn Grundlage für neurologische und/oder psychiatrische Störungen (z. B. Alzheimer-Krankheit oder Schizophrenie) sind bzw. damit im Zusammenhang stehen. Möglicherweise eröffnen diese neueren Erkenntnisse künftig Anwendungsmöglichkeiten für die klinische Diagnostik, z. B. in Kombination mit neuen Biomarkern. In diesem Zusammenhang könnte eine vielversprechende Perspektive die Erforschung molekularer Signalwege sein, die die Zellen vor Genom- und/oder Chromosomeninstabilität schützen könnten.
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Affiliation(s)
- Ivan Y. Iourov
- Aff1 grid.466123.4 National Research Center for Mental Health Russian Academy of Medical Sciences Zgorodnoe sh. 2 117152 Moscow Russische Föderation
- Aff2 grid.415738.c 0000000092162496 Institute of Pediatrics and Children Surgery Russian Federation Ministry of Health Moscow Russische Föderation
- Aff3 grid.465497.d Department of Medical Genetics Russian Medical Academy of Postgraduate Education Moscow Russische Föderation
| | - Svetlana G. Vorsanova
- Aff1 grid.466123.4 National Research Center for Mental Health Russian Academy of Medical Sciences Zgorodnoe sh. 2 117152 Moscow Russische Föderation
- Aff2 grid.415738.c 0000000092162496 Institute of Pediatrics and Children Surgery Russian Federation Ministry of Health Moscow Russische Föderation
- Aff4 grid.466944.d Moscow City University of Psychology and Education Moscow Russische Föderation
| | - Thomas Liehr
- Aff5 grid.10388.32 0000000122403300 Jena University Hospital, Friedrich Schiller University Institute of Human Genetics Kollegiengasse 10 07743 Jena Deutschland
| | - Yuri B. Yurov
- Aff1 grid.466123.4 National Research Center for Mental Health Russian Academy of Medical Sciences Zgorodnoe sh. 2 117152 Moscow Russische Föderation
- Aff2 grid.415738.c 0000000092162496 Institute of Pediatrics and Children Surgery Russian Federation Ministry of Health Moscow Russische Föderation
- Aff4 grid.466944.d Moscow City University of Psychology and Education Moscow Russische Föderation
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Horne SD, Chowdhury SK, Heng HHQ. Stress, genomic adaptation, and the evolutionary trade-off. Front Genet 2014; 5:92. [PMID: 24795754 PMCID: PMC4005935 DOI: 10.3389/fgene.2014.00092] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 04/03/2014] [Indexed: 12/27/2022] Open
Abstract
Cells are constantly exposed to various internal and external stresses. The importance of cellular stress and its implication to disease conditions have become popular research topics. Many ongoing investigations focus on the sources of stress, their specific molecular mechanisms and interactions, especially regarding their contributions to many common and complex diseases through defined molecular pathways. Numerous molecular mechanisms have been linked to endoplasmic reticulum stress along with many unexpected findings, drastically increasing the complexity of our molecular understanding and challenging how to apply individual mechanism-based knowledge in the clinic. A newly emergent genome theory searches for the synthesis of a general evolutionary mechanism that unifies different types of stress and functional relationships from a genome-defined system point of view. Herein, we discuss the evolutionary relationship between stress and somatic cell adaptation under physiological, pathological, and somatic cell survival conditions, the multiple meanings to achieve adaptation and its potential trade-off. In particular, we purposely defocus from specific stresses and mechanisms by redirecting attention toward studying underlying general mechanisms.
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Affiliation(s)
- Steven D Horne
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University Detroit, MI, USA
| | | | - Henry H Q Heng
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University Detroit, MI, USA ; Department of Pathology, School of Medicine, Wayne State University Detroit, MI, USA
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43
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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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Brain somatic mutations: the dark matter of psychiatric genetics? Mol Psychiatry 2014; 19:156-8. [PMID: 24342990 DOI: 10.1038/mp.2013.168] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 10/10/2013] [Accepted: 10/21/2013] [Indexed: 02/02/2023]
Abstract
Although inherited DNA sequences have a well-demonstrated role in psychiatric disease risk, for even the most heritable mental disorders, monozygotic twins are discordant at a significant rate. The genetic variation associated with mental disorders has heretofore been based on the search for rare or common variation in blood cells. This search is based on the premise that every somatic cell shares an identical DNA sequence, so that variation found in lymphocytes should reflect variation present in brain cells. Evidence from the study of cancer cells, stem cells and now neurons demonstrate that this premise is false. Somatic mutation is common in human cells and has been implicated in a range of diseases beyond cancer. The exuberant proliferation of cortical precursors during fetal development provides a likely environment for somatic mutation in neuronal and glial lineages. Studies of rare neurodevelopmental disorders, such as hemimegencephaly, demonstrate somatic mutations in affected cortical cells that cannot be detected in unaffected parts of the brain or in peripheral cells. This perspective argues for the need to investigate somatic variation in the brain as an explanation of the discordance in monozygotic twins, a proximate cause of mental disorders in individuals with inherited risk, and a potential guide to novel treatment targets.
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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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46
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Genetic, epigenetic and stem cell alterations in endometriosis: new insights and potential therapeutic perspectives. Clin Sci (Lond) 2013; 126:123-38. [PMID: 24059589 DOI: 10.1042/cs20130099] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Human endometrium is a highly dynamic tissue, undergoing periodic growth and regression at each menstrual cycle. Endometriosis is a frequent chronic pathological status characterized by endometrial tissue with an ectopic localization, causing pelvic pain and infertility and a variable clinical presentation. In addition, there is well-established evidence that, although endometriosis is considered benign, it is associated with an increased risk of malignant transformation in approximately 1.0% of affected women, with the involvement of multiple pathways of development. Increasing evidence supports a key contribution of different stem/progenitor cell populations not only in the cyclic regeneration of eutopic endometrium, but also in the pathogenesis of at least some types of endometriosis. Evidence has arisen from experiments in animal models of disease through different kinds of assays (including clonogenicity, the label-retaining cell approach, the analysis of undifferentiation markers), as well as from descriptive studies on ectopic and eutopic tissue samples harvested from affected women. Changes in stem cell populations in endometriotic lesions are associated with genetic and epigenetic alterations, including imbalance of miRNA expression, histone and DNA modifications and chromosomal aberrations. The present short review mainly summarizes the latest observations contributing to the current knowledge regarding the presence and the potential contribution of stem/progenitor cells in eutopic endometrium and the aetiology of endometriosis, together with a report of the most recently identified genetic and epigenetic alterations in endometriosis. We also describe the potential advantages of single cell molecular profiling in endometrium and in endometriotic lesions. All these data can have clinical implications and provide a basis for new potential therapeutic applications.
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47
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Tan SJ, Kee MZL, Mathuru AS, Burkholder WF, Jesuthasan SJ. A microfluidic device to sort cells based on dynamic response to a stimulus. PLoS One 2013; 8:e78261. [PMID: 24250795 PMCID: PMC3826715 DOI: 10.1371/journal.pone.0078261] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 09/09/2013] [Indexed: 11/25/2022] Open
Abstract
Single cell techniques permit the analysis of cellular properties that are obscured by studying the average behavior of cell populations. One way to determine how gene expression contributes to phenotypic differences among cells is to combine functional analysis with transcriptional profiling of single cells. Here we describe a microfluidic device for monitoring the responses of single cells to a ligand and then collecting cells of interest for transcriptional profiling or other assays. As a test, cells from the olfactory epithelium of zebrafish were screened by calcium imaging to identify sensory neurons that were responsive to the odorant L-lysine. Single cells were subsequently recovered for transcriptional profiling by qRT-PCR. Responsive cells all expressed TRPC2 but not OMP, consistent with known properties of amino-acid sensitive olfactory neurons. The device can be adapted for other areas in biology where there is a need to sort and analyze cells based on their signaling responses.
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Affiliation(s)
- Swee Jin Tan
- Microfluidics Systems Biology Lab, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Michelle Z. L. Kee
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
| | - Ajay Sriram Mathuru
- Neural Circuitry and Behavior Lab, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - William F. Burkholder
- Microfluidics Systems Biology Lab, Institute of Molecular and Cell Biology, Singapore, Singapore
| | - Suresh J. Jesuthasan
- Neuroscience and Behavioral Disorders Program, Duke-National University of Singapore Graduate Medical School, Singapore, Singapore
- Neural Circuitry and Behavior Lab, Institute of Molecular and Cell Biology, Singapore, Singapore
- Department of Physiology, National University of Singapore, Singapore, Singapore
- * E-mail:
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Johnson BR, Atallah J, Plachetzki DC. The importance of tissue specificity for RNA-seq: highlighting the errors of composite structure extractions. BMC Genomics 2013; 14:586. [PMID: 23985010 PMCID: PMC3765781 DOI: 10.1186/1471-2164-14-586] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Accepted: 08/17/2013] [Indexed: 11/10/2022] Open
Abstract
Background A composite biological structure, such as an insect head or abdomen, contains many internal structures with distinct functions. Composite structures are often used in RNA-seq studies, though it is unclear how expression of the same gene in different tissues and structures within the same structure affects the measurement (or even utility) of the resulting patterns of gene expression. Here we determine how complex composite tissue structure affects measures of gene expression using RNA-seq. Results We focus on two structures in the honey bee (the sting gland and digestive tract) both contained within one larger structure, the whole abdomen. For each of the three structures, we used RNA-seq to identify differentially expressed genes between two developmental stages, nurse bees and foragers. Based on RNA-seq for each structure-specific extraction, we found that RNA-seq with composite structures leads to many false negatives (genes strongly differentially expressed in particular structures which are not found to be differentially expressed within the composite structure). We also found a significant number of genes with one pattern of differential expression in the tissue-specific extraction, and the opposite in the composite extraction, suggesting multiple signals from such genes within the composite structure. We found these patterns for different classes of genes including transcription factors. Conclusions Many RNA-seq studies currently use composite extractions, and even whole insect extractions, when tissue and structure specific extractions are possible. This is due to the logistical difficultly of micro-dissection and unawareness of the potential errors associated with composite extractions. The present study suggests that RNA-seq studies of composite structures are prone to false negatives and difficult to interpret positive signals for genes with variable patterns of local expression. In general, our results suggest that RNA-seq on large composite structures should be avoided unless it is possible to demonstrate that the effects shown here do not exist for the genes of interest.
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Affiliation(s)
- Brian R Johnson
- Department of Entomology, University of California, Davis, 1 Shields Ave, Davis, CA 95616, USA.
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Hultén MA, Jonasson J, Iwarsson E, Uppal P, Vorsanova SG, Yurov YB, Iourov IY. Trisomy 21 mosaicism: we may all have a touch of Down syndrome. Cytogenet Genome Res 2013; 139:189-92. [PMID: 23306383 DOI: 10.1159/000346028] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Ever increasing sophistication in the application of new analytical technology has revealed that our genomes are much more fluid than was contemplated only a few years ago. More specifically, this concerns interindividual variation in copy number (CNV) of structural chromosome aberrations, i.e. microdeletions and microduplications. It is important to recognize that in this context, we still lack basic knowledge on the impact of the CNV in normal cells from individual tissues, including that of whole chromosomes (aneuploidy). Here, we highlight this challenge by the example of the very first chromosome aberration identified in the human genome, i.e. an extra chromosome 21 (trisomy 21, T21), which is causative of Down syndrome (DS). We consider it likely that most, if not all, of us are T21 mosaics, i.e. everyone carries some cells with an extra chromosome 21, in some tissues. In other words, we may all have a touch of DS. We further propose that the occurrence of such tissue-specific T21 mosaicism may have important ramifications for the understanding of the pathogenesis, prognosis and treatment of medical problems shared between people with DS and those in the general non-DS population.
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Affiliation(s)
- M A Hultén
- Warwick Medical School, University of Warwick, Warwick, UK.
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