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Heng J, Heng HH. Karyotype as code of codes: An inheritance platform to shape the pattern and scale of evolution. Biosystems 2023; 233:105016. [PMID: 37659678 DOI: 10.1016/j.biosystems.2023.105016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/27/2023] [Accepted: 08/28/2023] [Indexed: 09/04/2023]
Abstract
Organismal evolution displays complex dynamics in phase and scale which seem to trend towards increasing biocomplexity and diversity. For over a century, such amazing dynamics have been cleverly explained by the apparently straightforward mechanism of natural selection: all diversification, including speciation, results from the gradual accumulation of small beneficial or near-neutral alterations over long timescales. However, although this has been widely accepted, natural selection makes a crucial assumption that has not yet been validated. Specifically, the informational relationship between small microevolutionary alterations and large macroevolutionary changes in natural selection is unclear. To address the macroevolution-microevolution relationship, it is crucial to incorporate the concept of organic codes and particularly the "karyotype code" which defines macroevolutionary changes. This concept piece examines the karyotype from the perspective of two-phased evolution and four key components of information management. It offers insight into how the karyotype creates and preserves information that defines the scale and phase of macroevolution and, by extension, microevolution. We briefly describe the relationship between the karyotype code, the genetic code, and other organic codes in the context of generating evolutionary novelties in macroevolution and imposing constraints on them as biological routines in microevolution. Our analyses suggest that karyotype coding preserves many organic codes by providing system-level inheritance, and similar analyses are needed to classify and prioritize a large number of different organic codes based on the phases and scales of evolution. Finally, the importance of natural information self-creation is briefly discussed, leading to a call to integrate information and time into the relationship between matter and energy.
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Affiliation(s)
- Julie Heng
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Henry H Heng
- Molecular Medicine and Genomics, 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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2
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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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3
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Yıldız Bölükbaşı E, Karolak JA, Szafranski P, Gambin T, Willard N, Abman SH, Galambos C, Kinsella JP, Stankiewicz P. High-level gonosomal mosaicism for a pathogenic non-coding CNV deletion of the lung-specific FOXF1 enhancer in an unaffected mother of an infant with ACDMPV. Mol Genet Genomic Med 2022; 10:e2062. [PMID: 36124617 PMCID: PMC9651602 DOI: 10.1002/mgg3.2062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/22/2022] [Accepted: 09/08/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) results from haploinsufficiency of the mesenchymal transcription factor FOXF1 gene. To date, only one case of an ACDMPV-causative CNV deletion inherited from a very-low level somatic mosaic mother has been reported. METHODS Clinical, histopathological, and molecular studies, including whole genome sequencing, chromosomal microarray analysis, qPCR, and Sanger sequencing, followed by in vitro fertilization (IVF) with preimplantation genetic testing (PGT) were used to study a family with a deceased neonate with ACDMPV. RESULTS A pathogenic CNV deletion of the lung-specific FOXF1 enhancer in the proband was found to be inherited from an unaffected mother, 36% mosaic for this deletion in her peripheral blood cells. The qPCR analyses of saliva, buccal cells, urine, nail, and hair samples revealed 19%, 18%, 15%, 19%, and 27% variant allele fraction, respectively, indicating a high recurrence risk. Grandparental studies revealed that the deletion arose on the mother's paternal chromosome 16. PGT studies revealed 44% embryos with the deletion, reflecting high-level germline mosaicism. CONCLUSION Our data further demonstrate the importance of parental testing in ACDMPV families and reproductive usefulness of IVF with PGT in families with high-level parental gonosomal mosaicism.
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Affiliation(s)
| | - Justyna A. Karolak
- Chair and Department of Genetics and Pharmaceutical MicrobiologyPoznan University of Medical SciencesPoznanPoland
| | | | - Tomasz Gambin
- Institute of Computer ScienceWarsaw University of TechnologyWarsawPoland
| | - Nicholas Willard
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Steven H. Abman
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Csaba Galambos
- Department of Pathology and Laboratory MedicineUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA,Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - John P. Kinsella
- Department of PediatricsUniversity of Colorado Anschutz Medical CampusAuroraColoradoUSA
| | - Paweł Stankiewicz
- Department of Molecular & Human GeneticsBaylor College of MedicineHoustonTexasUSA
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4
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Vihinen M. Individual Genetic Heterogeneity. Genes (Basel) 2022; 13:genes13091626. [PMID: 36140794 PMCID: PMC9498725 DOI: 10.3390/genes13091626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/25/2022] [Accepted: 09/08/2022] [Indexed: 11/28/2022] Open
Abstract
Genetic variation has been widely covered in literature, however, not from the perspective of an individual in any species. Here, a synthesis of genetic concepts and variations relevant for individual genetic constitution is provided. All the different levels of genetic information and variation are covered, ranging from whether an organism is unmixed or hybrid, has variations in genome, chromosomes, and more locally in DNA regions, to epigenetic variants or alterations in selfish genetic elements. Genetic constitution and heterogeneity of microbiota are highly relevant for health and wellbeing of an individual. Mutation rates vary widely for variation types, e.g., due to the sequence context. Genetic information guides numerous aspects in organisms. Types of inheritance, whether Mendelian or non-Mendelian, zygosity, sexual reproduction, and sex determination are covered. Functions of DNA and functional effects of variations are introduced, along with mechanism that reduce and modulate functional effects, including TARAR countermeasures and intraindividual genetic conflict. TARAR countermeasures for tolerance, avoidance, repair, attenuation, and resistance are essential for life, integrity of genetic information, and gene expression. The genetic composition, effects of variations, and their expression are considered also in diseases and personalized medicine. The text synthesizes knowledge and insight on individual genetic heterogeneity and organizes and systematizes the central concepts.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, BMC B13, Lund University, SE-22184 Lund, Sweden
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5
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6
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Hu B, Gong Y, Wang Y, Xie J, Cheng J, Huang Q. Comprehensive Atlas of Circulating Rare Cells Detected by SE-iFISH and Image Scanning Platform in Patients With Various Diseases. Front Oncol 2022; 12:821454. [PMID: 35311070 PMCID: PMC8924462 DOI: 10.3389/fonc.2022.821454] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/23/2022] Open
Abstract
Objective Circulating rare cells (CRCs) are known as a crucial nucleated cellular response to pathological conditions, yet the landscape of cell types across a wide variety of diseases lacks comprehensive understanding. This study aimed at detecting and presenting a full spectrum of highly heterogeneous CRCs in clinical practice and further explored the characterization of CRC subtypes in distinct biomarker combinations and aneuploid chromosomes among various disease groups. Methods Peripheral blood was obtained from 2,360 patients with different cancers and non-neoplastic diseases. CRC capture and identification were accomplished using a novel platform integrating subtraction enrichment and immunostaining-fluorescence in situ hybridization (SE-iFISH) strategy with a high-throughput automated image scanning system, on which hemocyte, tumor, epithelial, endothelial, mesenchymal, and stemness biomarkers were immunostained and displayed simultaneously. Double chromosome enumeration probe (CEP8 and CEP12) co-detection was performed on isolated CRCs from an extended trial for two chromosome ploidy patterns. Results A comprehensive atlas categorizing the diverse CRCs into 71 subtypes outlining was mapped out. The presence of epithelial-mesenchymal transition (EMT) or endothelial-mesenchymal transition (EndoMT), the cells with progenitor property, hematologic CRCs expressing multiple biomarkers, CRCs at "naked nuclei" status, and the rarely reported aneuploid mesenchymal epithelial-endothelial fusion cluster were described. Circulating tumor cells (CTCs) were detected in 2,157 (91.4%) patients; the total numbers of CTCs and circulating tumor-derived endothelial cells (CTECs) were relatively higher in several digestive system cancer types and non-neoplastic infectious diseases (p < 0.05). Co-detection combining CEP8 and CEP12 showed a higher diagnostic specificity on account of 57.27% false negativity of CRC detection through a single probe of CEP8. Conclusions The alternative biomarkers and chromosomes to be targeted by SE-iFISH and the image scanning platform, along with the comprehensive atlas, offer insight into the heterogeneity of CRCs and reveal potential contributions to specific disease diagnosis and therapeutic target cell discovery.
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Affiliation(s)
- Binjie Hu
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanping Gong
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yulan Wang
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianzhu Xie
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Cheng
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qian Huang
- Molecular Diagnostics Laboratory of Cancer Center, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Heng E, Moy A, Liu G, Heng HH, Zhang K. ER Stress and Micronuclei Cluster: Stress Response Contributes to Genome Chaos in Cancer. Front Cell Dev Biol 2021; 9:673188. [PMID: 34422803 PMCID: PMC8371933 DOI: 10.3389/fcell.2021.673188] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/12/2021] [Indexed: 12/31/2022] Open
Affiliation(s)
- Eric Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Amanda Moy
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Henry H Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, United States
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8
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Liu Q, Grochowski CM, Bi W, Lupski JR, Stankiewicz P. Quantitative Assessment of Parental Somatic Mosaicism for Copy-Number Variant (CNV) Deletions. ACTA ACUST UNITED AC 2021; 106:e99. [PMID: 32176465 DOI: 10.1002/cphg.99] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
As genome sequencing methodologies have become more sensitive in detecting low-frequency rare-variant events, the link between post-zygotic mutagenesis and somatic mosaicism in the etiology of several human genetic conditions other than cancers has become more clear. Given that current clinical-genomics diagnostic methods have limited detection sensitivity for mosaic events, a copy-number variant (CNV) deletion inherited from a parent with low-level (<10%) mosaicism can be erroneously interpreted in the proband to represent a de novo germline event. Here, we describe three sensitive, precise, and cost-efficient methods that can quantitatively assess the potential degree of parental somatic mosaicism levels for CNV deletions: droplet digital PCR (ddPCR), PCR amplicon-based next-generation sequencing (NGS), and quantitative PCR. ddPCR using the EvaGreen fluorescent dye protocol can specifically quantify the deleted or non-deleted alleles by analyzing the number of droplets positive for a fluorescent signal for each event. PCR amplicon-based NGS assesses the allele frequencies of a heterozygous single-nucleotide polymorphism within a deletion region. The difference in number of reads between the two genotypes indicates the level of somatic mosaicism for the CNV deletion. Quantitative PCR can be applied where the relative quantity of the deletion junction-specific product represents the level of mosaicism. Clinical implementation of these quantitative variant-detection methods enables potentially more accurate assessment of disease recurrence risk in family-based genetic counseling, allowing couples to engage in more informed family planning. © 2020 by John Wiley & Sons, Inc. Basic Protocol: Droplet digital PCR (ddPCR) Alternate Protocol 1: PCR amplicon-based next-generation sequencing Alternate Protocol 2: Quantitative real-time PCR (qPCR).
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | | | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Baylor Genetics, Houston, Texas
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
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Charvet B, Pierquin J, Brunel J, Gorter R, Quétard C, Horvat B, Amor S, Portoukalian J, Perron H. Human Endogenous Retrovirus Type W Envelope from Multiple Sclerosis Demyelinating Lesions Shows Unique Solubility and Antigenic Characteristics. Virol Sin 2021; 36:1006-1026. [PMID: 33770381 PMCID: PMC8558138 DOI: 10.1007/s12250-021-00372-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 02/08/2021] [Indexed: 12/15/2022] Open
Abstract
In multiple sclerosis (MS), human endogenous retrovirus W family (HERV-W) envelope protein, pHERV-W ENV, limits remyelination and induces microglia-mediated neurodegeneration. To better understand its role, we examined the soluble pHERV-W antigen from MS brain lesions detected by specific antibodies. Physico-chemical and antigenic characteristics confirmed differences between pHERV-W ENV and syncytin-1. pHERV-W ENV monomers and trimers remained associated with membranes, while hexamers self-assembled from monomers into a soluble macrostructure involving sulfatides in MS brain. Extracellular hexamers are stabilized by internal hydrophobic bonds and external hydrophilic moieties. HERV-W studies in MS also suggest that this diffusible antigen may correspond to a previously described high-molecular-weight neurotoxic factor secreted by MS B-cells and thus represents a major agonist in MS pathogenesis. Adapted methods are now needed to identify encoding HERV provirus(es) in affected cells DNA. The properties and origin of MS brain pHERV-W ENV soluble antigen will allow a better understanding of the role of HERVs in MS pathogenesis. The present results anyhow pave the way to an accurate detection of the different forms of pHERV-W ENV antigen with appropriate conditions that remained unseen until now.
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Affiliation(s)
- Benjamin Charvet
- GeNeuro Innovation, Lyon, 69008, France. .,CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, University of Lyon, ENS Lyon, France. .,Université Claude Bernard Lyon 1, Lyon, 69000, France.
| | | | - Joanna Brunel
- GeNeuro Innovation, Lyon, 69008, France.,CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, University of Lyon, ENS Lyon, France.,Université Claude Bernard Lyon 1, Lyon, 69000, France
| | - Rianne Gorter
- Department of Pathology, Amsterdam UMC, Location VUMC, 1007 MB, Amsterdam, The Netherlands
| | | | - Branka Horvat
- CIRI, International Center for Infectiology Research, INSERM U1111, CNRS UMR5308, University of Lyon, ENS Lyon, France.,Université Claude Bernard Lyon 1, Lyon, 69000, France
| | - Sandra Amor
- Department of Pathology, Amsterdam UMC, Location VUMC, 1007 MB, Amsterdam, The Netherlands.,Centre for Neuroscience and Trauma, Blizard Institute, Barts and London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | | | - Hervé Perron
- GeNeuro Innovation, Lyon, 69008, France. .,Université Claude Bernard Lyon 1, Lyon, 69000, France.
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10
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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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Transcriptome-wide high-throughput mapping of protein-RNA occupancy profiles using POP-seq. Sci Rep 2021; 11:1175. [PMID: 33441968 PMCID: PMC7806670 DOI: 10.1038/s41598-020-80846-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 12/28/2020] [Indexed: 11/13/2022] Open
Abstract
Interaction between proteins and RNA is critical for post-transcriptional regulatory processes. Existing high throughput methods based on crosslinking of the protein–RNA complexes and poly-A pull down are reported to contribute to biases and are not readily amenable for identifying interaction sites on non poly-A RNAs. We present Protein Occupancy Profile-Sequencing (POP-seq), a phase separation based method in three versions, one of which does not require crosslinking, thus providing unbiased protein occupancy profiles on whole cell transcriptome without the requirement of poly-A pulldown. Our study demonstrates that ~ 68% of the total POP-seq peaks exhibited an overlap with publicly available protein–RNA interaction profiles of 97 RNA binding proteins (RBPs) in K562 cells. We show that POP-seq variants consistently capture protein–RNA interaction sites across a broad range of genes including on transcripts encoding for transcription factors (TFs), RNA-Binding Proteins (RBPs) and long non-coding RNAs (lncRNAs). POP-seq identified peaks exhibited a significant enrichment (p value < 2.2e−16) for GWAS SNPs, phenotypic, clinically relevant germline as well as somatic variants reported in cancer genomes, suggesting the prevalence of uncharacterized genomic variation in protein occupied sites on RNA. We demonstrate that the abundance of POP-seq peaks increases with an increase in expression of lncRNAs, suggesting that highly expressed lncRNA are likely to act as sponges for RBPs, contributing to the rewiring of protein–RNA interaction network in cancer cells. Overall, our data supports POP-seq as a robust and cost-effective method that could be applied to primary tissues for mapping global protein occupancies.
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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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13
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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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14
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Liu Q, Karolak JA, Grochowski CM, Wilson TA, Rosenfeld JA, Bacino CA, Lalani SR, Patel A, Breman A, Smith JL, Cheung SW, Lupski JR, Bi W, Stankiewicz P. Parental somatic mosaicism for CNV deletions - A need for more sensitive and precise detection methods in clinical diagnostics settings. Genomics 2020; 112:2937-2941. [PMID: 32387503 DOI: 10.1016/j.ygeno.2020.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/22/2020] [Accepted: 05/04/2020] [Indexed: 10/25/2022]
Abstract
To further assess the scale and level of parental somatic mosaicism, we queried the CMA database at Baylor Genetics. We selected 50 unrelated families where clinically relevant apparent de novo CNV-deletions were found in the affected probands. Parental blood samples screening using deletion junction-specific PCR revealed four parents with somatic mosaicism. Droplet digital PCR (ddPCR), qPCR, and amplicon-based next-generation sequencing (NGS) were applied to validate these findings. Using ddPCR levels of mosaicism ranged from undetectable to 18.5%. Amplicon-based NGS and qPCR for the father with undetectable mosaicism was able to detect mosaicism at 0.39%. In one mother, ddPCR analysis revealed 15.6%, 10.6%, 8.2%, and undetectable levels of mosaicism in her blood, buccal cells, saliva, and urine samples, respectively. Our data suggest that more sensitive and precise methods, e.g. CNV junction-specific LR-PCR, ddPCR, or qPCR may allow for a more refined assessment of the potential disease recurrence risk for an identified variant.
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Affiliation(s)
- Qian Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justyna A Karolak
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Chair and Department of Genetics and Pharmaceutical Microbiology, Poznan University of Medical Sciences, 60-781 Poznan, Poland
| | | | - Theresa A Wilson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA; Texas Children's Hospital, Houston, TX 77030, USA
| | - Seema R Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Amy Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Texas Children's Hospital, Houston, TX 77030, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weimin Bi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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15
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Ye CJ, Chen J, Liu G, Heng HH. Somatic Genomic Mosaicism in Multiple Myeloma. Front Genet 2020; 11:388. [PMID: 32391059 PMCID: PMC7189895 DOI: 10.3389/fgene.2020.00388] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 03/27/2020] [Indexed: 02/06/2023] Open
Affiliation(s)
- Christine J Ye
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Jason Chen
- The Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, 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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16
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Watson CJ, Monstad-Rios AT, Bhimani RM, Gistelinck C, Willaert A, Coucke P, Hsu YH, Kwon RY. Phenomics-Based Quantification of CRISPR-Induced Mosaicism in Zebrafish. Cell Syst 2020; 10:275-286.e5. [PMID: 32191876 DOI: 10.1016/j.cels.2020.02.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 11/04/2019] [Accepted: 02/27/2020] [Indexed: 12/26/2022]
Abstract
Genetic mosaicism can manifest as spatially variable phenotypes that vary from site to site within an organism. Here, we use imaging-based phenomics to quantitate phenotypes at many sites within the axial skeleton of CRISPR-edited G0 zebrafish. Through characterization of loss-of-function cell clusters in the developing skeleton, we identify a distinctive size distribution shown to arise from clonal fragmentation and merger events. We quantitate the phenotypic mosaicism produced by somatic mutations of two genes, plod2 and bmp1a, implicated in human osteogenesis imperfecta. Comparison of somatic, CRISPR-generated G0 mutants to homozygous germline mutants reveals phenotypic convergence, suggesting that CRISPR screens of G0 animals can faithfully recapitulate the biology of inbred disease models. We describe statistical frameworks for phenomic analysis of spatial phenotypic variation present in somatic G0 mutants. In sum, this study defines an approach for decoding spatially variable phenotypes generated during CRISPR-based screens.
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Affiliation(s)
- Claire J Watson
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
| | - Adrian T Monstad-Rios
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Rehaan M Bhimani
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
| | - Charlotte Gistelinck
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Andy Willaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Paul Coucke
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Yi-Hsiang Hsu
- Hebrew SeniorLife Institute for Aging Research, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ronald Y Kwon
- Department of Orthopaedics and Sports Medicine, University of Washington, Seattle, WA, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA; Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
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17
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Bajic VP, Essack M, Zivkovic L, Stewart A, Zafirovic S, Bajic VB, Gojobori T, Isenovic E, Spremo-Potparevic B. The X Files: "The Mystery of X Chromosome Instability in Alzheimer's Disease". Front Genet 2020; 10:1368. [PMID: 32047510 PMCID: PMC6997486 DOI: 10.3389/fgene.2019.01368] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 12/13/2019] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease that affects millions of individuals worldwide and can occur relatively early or later in life. It is well known that genetic components, such as the amyloid precursor protein gene on chromosome 21, are fundamental in early-onset AD (EOAD). To date, however, only the apolipoprotein E4 (ApoE4) gene has been proved to be a genetic risk factor for late-onset AD (LOAD). In recent years, despite the hypothesis that many additional unidentified genes are likely to play a role in AD development, it is surprising that additional gene polymorphisms associated with LOAD have failed to come to light. In this review, we examine the role of X chromosome epigenetics and, based upon GWAS studies, the PCDHX11 gene. Furthermore, we explore other genetic risk factors of AD that involve X-chromosome epigenetics.
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Affiliation(s)
- Vladan P Bajic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Lada Zivkovic
- Department of Physiology, Faculty of Pharmacy, University of Belgrade, Belgrade, Serbia
| | - Alan Stewart
- School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Sonja Zafirovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
| | - Vladimir B Bajic
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Esma Isenovic
- Laboratory for Radiobiology and Molecular Genetics, Vinca Institute of Nuclear Sciences, University of Belgrade, Belgrade, Serbia
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18
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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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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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20
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Komkov AY, Minervina AA, Nugmanov GA, Saliutina MV, Khodosevich KV, Lebedev YB, Mamedov IZ. An advanced enrichment method for rare somatic retroelement insertions sequencing. Mob DNA 2018; 9:31. [PMID: 30450130 PMCID: PMC6208084 DOI: 10.1186/s13100-018-0136-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 10/15/2018] [Indexed: 12/18/2022] Open
Abstract
Background There is increasing evidence that the transpositional activity of retroelements (REs) is not limited to germ line cells, but often occurs in tumor and normal somatic cells. Somatic transpositions were found in several human tissues and are especially typical for the brain. Several computational and experimental approaches for detection of somatic retroelement insertions was developed in the past few years. These approaches were successfully applied to detect somatic insertions in clonally expanded tumor cells. At the same time, identification of somatic insertions presented in small proportion of cells, such as neurons, remains a considerable challenge. Results In this study, we developed a normalization procedure for library enrichment by DNA sequences corresponding to rare somatic RE insertions. Two rounds of normalization increased the number of fragments adjacent to somatic REs in the sequenced sample by more than 26-fold, and the number of identified somatic REs was increased by 8-fold. Conclusions The developed technique can be used in combination with vast majority of modern RE identification approaches and can dramatically increase their capacity to detect rare somatic RE insertions in different types of cells. Electronic supplementary material The online version of this article (10.1186/s13100-018-0136-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alexander Y Komkov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia.,Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Samory Mashela str. 1, Moscow, 117997 Russia
| | - Anastasia A Minervina
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Gaiaz A Nugmanov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Mariia V Saliutina
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Konstantin V Khodosevich
- 3Biotech Research and Innovation Centre, Copenhagen University, Ole Maaløes Vej 5, Copenhagen, 2200 Denmark
| | - Yuri B Lebedev
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia
| | - Ilgar Z Mamedov
- 1Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS, Miklukho-Maklaya str. 16/10, Moscow, 117997 Russia.,4Pirogov Russian National Research Medical University, Ostrovitianov str. 1, Moscow, 117997 Russia
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21
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Ouwens KG, Jansen R, Tolhuis B, Slagboom PE, Penninx BW, Boomsma DI. A characterization of postzygotic mutations identified in monozygotic twins. Hum Mutat 2018; 39:1393-1401. [PMID: 29980163 PMCID: PMC6175188 DOI: 10.1002/humu.23586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 01/09/2023]
Abstract
Postzygotic mutations are DNA changes acquired from the zygote stage onwards throughout the lifespan. These changes lead to differences in DNA sequence among cells of an individual, potentially contributing to the etiology of complex disorders. Here we compared whole genome DNA sequence data of two monozygotic twin pairs, 40 and 100 years old, to detect somatic mosaicism. DNA samples were sequenced twice on two Illumina platforms (13X and 40X read depth) for increased specificity. Using differences in allelic ratios resulted in sets of 1,720 and 1,739 putative postzygotic mutations in the 40-year-old twin pair and 100-year-old twin pair, respectively, for subsequent enrichment analysis. This set of putative mutations was strongly (p < 4.37e-91) enriched in both twin pairs for regulatory elements. The corresponding genes were significantly enriched for genes that are alternatively spliced, and for genes involved in GTPase activity. This research shows that somatic mosaicism can be detected in monozygotic twin pairs by using allelic ratios calculated from DNA sequence data and that the mutations which are found by this approach are not randomly distributed throughout the genome.
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Affiliation(s)
- Klaasjan G. Ouwens
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
- Genalice Core BVNijkerkThe Netherlands
| | - Rick Jansen
- Department of PsychiatryVU University Medical CenterAmsterdamThe Netherlands
| | | | - P. Eline Slagboom
- Department of Molecular EpidemiologyLeids Universitair Medisch CentrumLeidenThe Netherlands
| | | | - Dorret I. Boomsma
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
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22
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23
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Starr S. How to talk about genome editing. Br Med Bull 2018; 126:5-12. [PMID: 29697749 PMCID: PMC5998984 DOI: 10.1093/bmb/ldy015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 04/15/2018] [Indexed: 11/13/2022]
Abstract
Background Human genome editing is an area of growing prominence, with many potential therapeutic applications. Sources of data A project by two UK charities, whose participants included fertility sector patients and practitioners and also people affected by genetic disease and rare disease. Scientific research into, and wider discussion of, genomics and genome editing. Areas of agreement There is a need for improved public and professional understanding of genome editing. Areas of controversy The way genome editing is discussed is often inconsistent and confusing. Simply defining and explaining the term 'genome' can present challenges. Growing points There are approaches that lend themselves to achieving greater clarity and coherence in discussion of genome editing. Areas timely for developing research People's understanding should ideally be able to withstand and evolve alongside current developments in genome editing, rather than being tied firmly to specific aspects of genome editing (which may in future be supplanted).
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Affiliation(s)
- Sandy Starr
- Progress Educational Trust, 140 Grays Inn Road, London, UK
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24
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Rajpathak SN, Deobagkar DD. Aneuploidy: an important model system to understand salient aspects of functional genomics. Brief Funct Genomics 2018; 17:181-190. [PMID: 29228117 DOI: 10.1093/bfgp/elx041] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Maintaining a balance in gene dosage and protein activity is essential to sustain normal cellular functions. Males and females have a wide range of genetic as well as epigenetic differences, where X-linked gene dosage is an essential regulatory factor. Basic understanding of gene dosage maintenance has emerged from the studies carried out using mouse models with FCG (four core genotype) and chromosomal aneuploidy as well as from mono-chromosomal hybrid cells. In mammals, aneuploidy often leads to embryonic lethality particularly in early development with major developmental and structural abnormalities. Thus, in-depth analysis of the causes and consequences of gene dosage alterations is needed to unravel its effects on basic cellular and developmental functions as well as in understanding its medical implications. Cells isolated from individuals with naturally occurring chromosomal aneuploidy can be considered as true representatives, as these cells have stable chromosomal alterations/gene dosage imbalance, which have occurred by modulation of the basic molecular machinery. Therefore, innovative use of these natural aneuploidy cells/organisms with recent molecular and high-throughput techniques will provide an understanding of the basic mechanisms involved in gene dosage balance and the related consequences for functional genomics.
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25
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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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26
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Yusefi AR, Bagheri Lankarani K, Bastani P, Radinmanesh M, Kavosi Z. Risk Factors for Gastric Cancer: A Systematic Review. Asian Pac J Cancer Prev 2018; 19:591-603. [PMID: 29579788 PMCID: PMC5980829 DOI: 10.22034/apjcp.2018.19.3.591] [Citation(s) in RCA: 123] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2017] [Indexed: 02/06/2023] Open
Abstract
Objective: Gastric cancer is one of the leading causes of death worldwide, with many influences contributing to the disease. The aim of this study was to identify the most important risk factors. Methods: This study was conducted in 2017 with a structured overview in the Science Directe, Scopus, PubMed, Cochrane, Web of Science (ISI) databases. In the first step, articles were extracted based on their titles and abstracts; the quality of 43 articles was evaluated using the STORBE tool. Inclusion criteria were studies carried out on human, English language (first step), year of the study and the study type (second step). Results: Finally, 1,381 articles were found, of which 1,269 were excluded in primary and secondary screening. In reviewing the references of the remaining 44 papers, 4 studies were added. Finally, 43 articles were selected for the quality assessment process. A total of 52 risk factors for gastric cancer were identified and classified into nine important categories: diet, lifestyle, genetic predisposition, family history, treatment and medical conditions, infections, demographic characteristics, occupational exposures and ionizing radiation’. Conclusion: Several environmental and genetic factors are involved in the development of gastric cancer. Regarding the role of changes in ‘diet and lifestyle’, considering appropriate nutrition and improving the level of education and awareness of people is vital for early diagnosis and timely treatment of this disease, especially in people with a family history and genetic predisposition.
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Affiliation(s)
- Ali Reza Yusefi
- Student Research Committee, School of Management and Medical Informatics, Hazrat-e Aliasghar Hospital, Shiraz University of Medical Sciences, Shiraz, Iran
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27
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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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Genomic mosaicism in paternal sperm and multiple parental tissues in a Dravet syndrome cohort. Sci Rep 2017; 7:15677. [PMID: 29142202 PMCID: PMC5688122 DOI: 10.1038/s41598-017-15814-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 11/02/2017] [Indexed: 12/21/2022] Open
Abstract
Genomic mosaicism in parental gametes and peripheral tissues is an important consideration for genetic counseling. We studied a Chinese cohort affected by a severe epileptic disorder, Dravet syndrome (DS). There were 56 fathers who donated semen and 15 parents who donated multiple peripheral tissue samples. We used an ultra-sensitive quantification method, micro-droplet digital PCR (mDDPCR), to detect parental mosaicism of the proband’s pathogenic mutation in SCN1A, the causal gene of DS in 112 families. Ten of the 56 paternal sperm samples were found to exhibit mosaicism of the proband’s mutations, with mutant allelic fractions (MAFs) ranging from 0.03% to 39.04%. MAFs in the mosaic fathers’ sperm were significantly higher than those in their blood (p = 0.00098), even after conditional probability correction (p’ = 0.033). In three mosaic fathers, ultra-low fractions of mosaicism (MAF < 1%) were detected in the sperm samples. In 44 of 45 cases, mosaicism was also observed in other parental peripheral tissues. Hierarchical clustering showed that MAFs measured in the paternal sperm, hair follicles and urine samples were clustered closest together. Milder epileptic phenotypes were more likely to be observed in mosaic parents (p = 3.006e-06). Our study provides new insights for genetic counseling.
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Hoya S, Watanabe Y, Hishimoto A, Nunokawa A, Inoue E, Igeta H, Otsuka I, Shibuya M, Egawa J, Sora I, Someya T. Rare FBXO18 variations and risk of schizophrenia: Whole-exome sequencing in two parent-affected offspring trios followed by resequencing and case-control studies. Psychiatry Clin Neurosci 2017; 71:562-568. [PMID: 28317220 DOI: 10.1111/pcn.12526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/07/2017] [Accepted: 03/14/2017] [Indexed: 11/27/2022]
Abstract
AIM Rare variations are suggested to play a role in the genetic etiology of schizophrenia; to further investigate their role, we performed a three-stage study in a Japanese population. METHODS In the first stage, we performed whole-exome sequencing (WES) of two parent-affected offspring trios. In the second stage, we resequenced the FBXO18 coding region in 96 patients. In the third stage, we tested rare non-synonymous FBXO18 variations for association with schizophrenia in two independent populations comprising a total of 1376 patients and 1496 controls. RESULTS A rare frameshift variation (L116fsX) in the FBXO18 gene was recurrently identified by WES in both trios. Resequencing FBXO18 coding regions, we detected three rare non-synonymous variations (V15L, L116fsX, and V1006I). However, there were no significant associations between these rare FBXO18 variations and schizophrenia in the case-control study. CONCLUSION Our present study does not provide evidence for the contribution of rare non-synonymous FBXO18 variations to the genetic etiology of schizophrenia in the Japanese population. However, to draw a definitive conclusion, further studies should be performed using sufficiently large sample sizes.
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Affiliation(s)
- Satoshi Hoya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Department of Psychiatry, Uonuma Institute of Community Medicine, Niigata University Medical and Dental Hospital, Minamiuonuma, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ayako Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Oojima Hospital, Sanjo, Japan
| | - Emiko Inoue
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hirofumi Igeta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Masako Shibuya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.,Division of Medical Education, Comprehensive Medical Education Center, School of Medicine, Faculty of Medicine, Niigata University, Niigata, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiro Sora
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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30
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Saini N, Roberts SA, Klimczak LJ, Chan K, Grimm SA, Dai S, Fargo DC, Boyer JC, Kaufmann WK, Taylor JA, Lee E, Cortes-Ciriano I, Park PJ, Schurman SH, Malc EP, Mieczkowski PA, Gordenin DA. The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts. PLoS Genet 2016; 12:e1006385. [PMID: 27788131 PMCID: PMC5082821 DOI: 10.1371/journal.pgen.1006385] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/23/2016] [Indexed: 12/24/2022] Open
Abstract
Accumulation of somatic changes, due to environmental and endogenous lesions, in the human genome is associated with aging and cancer. Understanding the impacts of these processes on mutagenesis is fundamental to understanding the etiology, and improving the prognosis and prevention of cancers and other genetic diseases. Previous methods relying on either the generation of induced pluripotent stem cells, or sequencing of single-cell genomes were inherently error-prone and did not allow independent validation of the mutations. In the current study we eliminated these potential sources of error by high coverage genome sequencing of single-cell derived clonal fibroblast lineages, obtained after minimal propagation in culture, prepared from skin biopsies of two healthy adult humans. We report here accurate measurement of genome-wide magnitude and spectra of mutations accrued in skin fibroblasts of healthy adult humans. We found that every cell contains at least one chromosomal rearrangement and 600–13,000 base substitutions. The spectra and correlation of base substitutions with epigenomic features resemble many cancers. Moreover, because biopsies were taken from body parts differing by sun exposure, we can delineate the precise contributions of environmental and endogenous factors to the accrual of genetic changes within the same individual. We show here that UV-induced and endogenous DNA damage can have a comparable impact on the somatic mutation loads in skin fibroblasts. Somatic genomes are constantly accumulating changes caused by endogenous lesions, errors in DNA replication and repair, as well as environmental insults. Despite the importance of somatic genome instability in aging and age-related pathologies, including cancers, accurate measurements of mutation loads in healthy cells is still missing. In this study, we developed an experimental approach to accurately determine the somatic genome changes accrued in cell lineages over the lifetime of healthy humans. We show that the amounts and types of mutations in skin cells resemble many cancers, thus indicating that the mechanisms that lead to carcinogenesis are also functional in healthy cells. Moreover, sun-exposed skin cells have a higher mutation load attributable to ultraviolet radiation (UV) unlike cells from hips that were protected by clothing. Our work provides precise measurements of the mutation loads in single cells in human skin. Furthermore our data allowed defining the mutagenic impacts of environmental and endogenous processes within the same individual and led to conclusion that these processes have a comparable impact on the somatic mutation load.
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Affiliation(s)
- Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Steven A. Roberts
- School of Molecular Biosciences, Washington State University, Pullman, Washington, United States Of America
| | - Leszek J. Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Kin Chan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Sara A. Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Shuangshuang Dai
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - David C. Fargo
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Jayne C. Boyer
- Department of Environmental Science and Engineering, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - William K. Kaufmann
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Jack A. Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Eunjung Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Isidro Cortes-Ciriano
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, United States Of America
- Division of Genetics, Brigham and Women’s Hospital, Boston, Massachusetts, United States Of America
| | - Shepherd H. Schurman
- Clinical Research Unit, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
| | - Ewa P. Malc
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Piotr A. Mieczkowski
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina, United States Of America
| | - Dmitry A. Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America
- * E-mail:
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31
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Iourov IY, Vorsanova SG, Korostelev SA, Vasin KS, Zelenova MA, Kurinnaia OS, Yurov YB. [Structural variations of the genome in autistic spectrum disorders with intellectual disability]. Zh Nevrol Psikhiatr Im S S Korsakova 2016; 116:50-54. [PMID: 27500877 DOI: 10.17116/jnevro20161167150-54] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM To analyze structural variations in the genome in children with autism and intellectual disability. MATERIAL AND METHODS Using high-resolution karyotyping (AffymetrixCytoScan HD Array) and original bioinformatic technology, 200 children with autism and intellectual disability were studied. RESULTS AND CONCLUSION Data on structural variations in the genome in children with autism and intellectual disability are provided. Causative genomic pathology (chromosome abnormalities and copy number variations - CNV) was determined in 97 cases (48.5%). Based on these RESULTS 24 candidate genes for autism with intellectual disability were selected. In 16 cases (8%), the chromosome mosaicism manifested as aneuploidy of whole autosomes and sex chromosomes (gonosomes) was identified. In 87 children (43.5%), there were genomic variations, which are characteristic of the so-called «grey zone» of genetic pathology in mental illnesses. Bioinformatic analysis showed that these genomic variations had a pleiotropic effect on the phenotype.
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Affiliation(s)
- I Yu Iourov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Russian Medical Academy of Postgraduate Education, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | | | - K S Vasin
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - M A Zelenova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - O S Kurinnaia
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - Yu B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
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32
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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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33
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Bajic V, Spremo-Potparevic B, Zivkovic L, Isenovic ER, Arendt T. Cohesion and the aneuploid phenotype in Alzheimer's disease: A tale of genome instability. Neurosci Biobehav Rev 2015; 55:365-74. [PMID: 26003528 DOI: 10.1016/j.neubiorev.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 03/26/2015] [Accepted: 05/12/2015] [Indexed: 12/20/2022]
Abstract
Neurons are postmitotic cells that are in permanent cell cycle arrest. However, components of the cell cycle machinery that are expressed in Alzheimer's disease (AD) neurons are showing features of a cycling cell and those attributed to a postmitotic cell as well. Furthermore, the unique physiological operations taking place in neurons, ascribed to "core cell cycle regulators" are also key regulators in cell division. Functions of these cell cycle regulators include neuronal migration, axonal elongation, axon pruning, dendrite morphogenesis and synaptic maturation and plasticity. In this review, we focus on cohesion and cohesion related proteins in reference to their neuronal functions and how impaired centromere/cohesion dynamics may connect cell cycle dysfunction to aneuploidy in AD.
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Affiliation(s)
- Vladan Bajic
- Institute for Nuclear Research "Vinca", Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, P.O. 522, 11001 Belgrade, Serbia.
| | - Biljana Spremo-Potparevic
- Faculty of Pharmacy, Institute of Physiology, Department of Biology and Human Genetics, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Lada Zivkovic
- Faculty of Pharmacy, Institute of Physiology, Department of Biology and Human Genetics, University of Belgrade, Vojvode Stepe 450, 11000 Belgrade, Serbia.
| | - Esma R Isenovic
- Institute for Nuclear Research "Vinca", Laboratory for Radiobiology and Molecular Genetics, University of Belgrade, P.O. 522, 11001 Belgrade, Serbia.
| | - Thomas Arendt
- Paul-Flechsig-Institute for Brain Research, University of Leipzig, School of Medicine, Leipzig, Germany.
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34
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Somatic mosaicism: implications for disease and transmission genetics. Trends Genet 2015; 31:382-92. [PMID: 25910407 DOI: 10.1016/j.tig.2015.03.013] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 03/17/2015] [Accepted: 03/18/2015] [Indexed: 11/21/2022]
Abstract
Nearly all of the genetic material among cells within an organism is identical. However, single-nucleotide variants (SNVs), small insertions/deletions (indels), copy-number variants (CNVs), and other structural variants (SVs) continually accumulate as cells divide during development. This process results in an organism composed of countless cells, each with its own unique personal genome. Thus, every human is undoubtedly mosaic. Mosaic mutations can go unnoticed, underlie genetic disease or normal human variation, and may be transmitted to the next generation as constitutional variants. We review the influence of the developmental timing of mutations, the mechanisms by which they arise, methods for detecting mosaic variants, and the risk of passing these mutations on to the next generation.
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35
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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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36
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Parental somatic mosaicism is underrecognized and influences recurrence risk of genomic disorders. Am J Hum Genet 2014; 95:173-82. [PMID: 25087610 DOI: 10.1016/j.ajhg.2014.07.003] [Citation(s) in RCA: 187] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/08/2014] [Indexed: 11/20/2022] Open
Abstract
New human mutations are thought to originate in germ cells, thus making a recurrence of the same mutation in a sibling exceedingly rare. However, increasing sensitivity of genomic technologies has anecdotally revealed mosaicism for mutations in somatic tissues of apparently healthy parents. Such somatically mosaic parents might also have germline mosaicism that can potentially cause unexpected intergenerational recurrences. Here, we show that somatic mosaicism for transmitted mutations among parents of children with simplex genetic disease is more common than currently appreciated. Using the sensitivity of individual-specific breakpoint PCR, we prospectively screened 100 families with children affected by genomic disorders due to rare deletion copy-number variants (CNVs) determined to be de novo by clinical analysis of parental DNA. Surprisingly, we identified four cases of low-level somatic mosaicism for the transmitted CNV in DNA isolated from parental blood. Integrated probabilistic modeling of gametogenesis developed in response to our observations predicts that mutations in parental blood increase recurrence risk substantially more than parental mutations confined to the germline. Moreover, despite the fact that maternally transmitted mutations are the minority of alleles, our model suggests that sexual dimorphisms in gametogenesis result in a greater proportion of somatically mosaic transmitting mothers who are thus at increased risk of recurrence. Therefore, somatic mosaicism together with sexual differences in gametogenesis might explain a considerable fraction of unexpected recurrences of X-linked recessive disease. Overall, our results underscore an important role for somatic mosaicism and mitotic replicative mutational mechanisms in transmission genetics.
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Bennett RJ, Forche A, Berman J. Rapid mechanisms for generating genome diversity: whole ploidy shifts, aneuploidy, and loss of heterozygosity. Cold Spring Harb Perspect Med 2014; 4:cshperspect.a019604. [PMID: 25081629 DOI: 10.1101/cshperspect.a019604] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Human fungal pathogens can exist in a variety of ploidy states, including euploid and aneuploid forms. Ploidy change has a major impact on phenotypic properties, including the regulation of interactions with the human host. In addition, the rapid emergence of drug-resistant isolates is often associated with the formation of specific supernumerary chromosomes. Pathogens such as Candida albicans and Cryptococcus neoformans appear particularly well adapted for propagation in multiple ploidy states with novel pathways driving ploidy variation. In both species, heterozygous cells also readily undergo loss of heterozygosity (LOH), leading to additional phenotypic changes such as altered drug resistance. Here, we examine the sexual and parasexual cycles that drive ploidy variation in human fungal pathogens and discuss ploidy and LOH events with respect to their far-reaching roles in fungal adaptation and pathogenesis.
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Affiliation(s)
- Richard J Bennett
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island 02912
| | - Anja Forche
- Department of Biology, Bowdoin College, Brunswick, Maine 04011
| | - Judith Berman
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55455 Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
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Pinto IP, Minasi LB, da Cruz AS, de Melo AV, da Cruz e Cunha DM, Pereira RR, Ribeiro CL, da Silva CC, de Melo e Silva D, da Cruz AD. A non-syndromic intellectual disability associated with a de novo microdeletion at 7q and 18p, microduplication at Xp, and 18q partial trisomy detected using chromosomal microarray analysis approach. Mol Cytogenet 2014; 7:44. [PMID: 25028595 PMCID: PMC4099144 DOI: 10.1186/1755-8166-7-44] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome abnormalities that segregate with a disease phenotype can facilitate the identification of disease loci and genes. The relationship between chromosome 18 anomalies with severe intellectual disability has attracted the attention of cytogeneticists worldwide. Duplications of the X chromosome can cause intellectual disability in females with variable phenotypic effects, due in part to variations in X-inactivation patterns. Additionally, deletions of the 7qter region are associated with a range of phenotypes. RESULTS We report the first case of de novo microdeletion at 7q and 18p, 18q partial trisomy, microduplication at Xp associated to intellectual disability in a Brazilian child, presenting a normal karyotype. Karyotyping showed any chromosome alteration. Chromosomal microarray analysis detected a de novo microdeletion at 18p11.32 and 18q partial trisomy, an inherited microdeletion at 7q31.1 and a de novo microduplication at Xp22.33p21.3. CONCLUSIONS Our report illustrates a case that presents complex genomic imbalances which may contribute to a severe clinical phenotypes. The rare and complex phenotypes have to be investigated to define the subsets and allow the phenotypes classification.
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Affiliation(s)
- Irene Plaza Pinto
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Mestrado em Genética, Programa de Pós Graduação Mestrado em Genética, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Mestrado em Genética, Programa de Pós Graduação Mestrado em Genética, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Programa de Pós Graduação em Biologia, Campus Samambaia, Goiânia, GO, Brazil
| | - Aldaires Vieira de Melo
- Universidade Federal de Goiás, Programa de Pós Graduação em Biotecnologia e Biodiversidade, Rede Centro Oeste de Pós Graduação, Pesquisa e Inovação, Campus Samambaia, Goiânia, GO, Brazil
| | - Damiana Míriam da Cruz e Cunha
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Mestrado em Genética, Programa de Pós Graduação Mestrado em Genética, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
| | - Rodrigo Roncato Pereira
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Programa de Pós Graduação em Biologia, Campus Samambaia, Goiânia, GO, Brazil
| | - Cristiano Luiz Ribeiro
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
| | - Claudio Carlos da Silva
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Mestrado em Genética, Programa de Pós Graduação Mestrado em Genética, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
| | - Daniela de Melo e Silva
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Programa de Pós-Graduação em Genética e Biologia Molecular, Laboratório de Genética e Biodiversidade, Universidade Federal de Goiás, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Núcleo de Pesquisas Replicon, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Programa de Pós Graduação em Biologia, Campus Samambaia, Goiânia, GO, Brazil
- Departamento de Biologia, Pontifícia Universidade Católica de Goiás, Mestrado em Genética, Programa de Pós Graduação Mestrado em Genética, Rua 235, n. 40, Bloco L, Área IV Setor Universitário, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós Graduação em Biotecnologia e Biodiversidade, Rede Centro Oeste de Pós Graduação, Pesquisa e Inovação, Campus Samambaia, Goiânia, GO, Brazil
- Laboratório de Citogenética Humana e Genética Molecular, Secretaria do Estado da Saúde de Goiás (LACEN/SESGO), Goiânia, GO, Brazil
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Jacobs K, Mertzanidou A, Geens M, Thi Nguyen H, Staessen C, Spits C. Low-grade chromosomal mosaicism in human somatic and embryonic stem cell populations. Nat Commun 2014; 5:4227. [DOI: 10.1038/ncomms5227] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 05/23/2014] [Indexed: 12/14/2022] Open
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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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Forsberg LA, Absher D, Dumanski JP. Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime. Postgrad Med J 2014; 89:417-26. [PMID: 23781115 PMCID: PMC3711362 DOI: 10.1136/postgradmedj-2012-101322rep] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The heritability of most common, multifactorial diseases is rather modest and known genetic effects account for a small part of it. The remaining portion of disease aetiology has been conventionally ascribed to environmental effects, with an unknown part being stochastic. This review focuses on recent studies highlighting stochastic events of potentially great importance in human disease—the accumulation of post-zygotic structural aberrations with age in phenotypically normal humans. These findings are in agreement with a substantial mutational load predicted to occur during lifetime within the human soma. A major consequence of these results is that the genetic profile of a single tissue collected at one time point should be used with caution as a faithful portrait of other tissues from the same subject or the same tissue throughout life. Thus, the design of studies in human genetics interrogating a single sample per subject or applying lymphoblastoid cell lines may come into question. Sporadic disorders are common in medicine. We wish to stress the non-heritable genetic variation as a potentially important factor behind the development of sporadic diseases. Moreover, associations between post-zygotic mutations, clonal cell expansions and their relation to cancer predisposition are central in this context. Post-zygotic mutations are amenable to robust examination and are likely to explain a sizable part of non-heritable disease causality, which has routinely been thought of as synonymous with environmental factors. In view of the widespread accumulation of genetic aberrations with age and strong predictions of disease risk from such analyses, studies of post-zygotic mutations may be a fruitful approach for delineation of variants that are causative for common human disorders.
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Affiliation(s)
- Lars Anders Forsberg
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Dag Hammarskjölds väg 20, Uppsala, Sweden
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Kim J, Shin JY, Kim JI, Seo JS, Webster MJ, Lee D, Kim S. Somatic deletions implicated in functional diversity of brain cells of individuals with schizophrenia and unaffected controls. Sci Rep 2014; 4:3807. [PMID: 24448323 PMCID: PMC3897957 DOI: 10.1038/srep03807] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 12/27/2013] [Indexed: 12/19/2022] Open
Abstract
While somatic DNA copy number variations (CNVs) have been identified in multiple tissues from normal people, they have not been well studied in brain tissues from individuals with psychiatric disorders. With ultrahigh depth sequencing data, we developed an integrated pipeline for calling somatic deletions using data from multiple tissues of the same individual or a single tissue type taken from multiple individuals. Using the pipelines, we identified 106 somatic deletions in DNA from prefrontal cortex (PFC) and/or cerebellum of two normal controls subjects and/or three individuals with schizophrenia. We then validated somatic deletions in 18 genic and in 1 intergenic region. Somatic deletions in BOD1 and CBX3 were reconfirmed using DNA isolated from non-pyramidal neurons and from cells in white matter using laser capture microdissection (LCM). Our results suggest that somatic deletions may affect metabolic processes and brain development in a region specific manner.
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Affiliation(s)
- Junho Kim
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Jong-Yeon Shin
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea
| | - Jong-Il Kim
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea [4] Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul 110-799, Korea
| | - Jeong-Sun Seo
- 1] Genomic Medicine Institute (GMI), Medical Research Center, Seoul National, University, Seoul 110-799, Korea [2] Psoma Therapeutics Inc., Seoul, 153-781, Korea [3] Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 110-799, Korea [4] Department of Biochemistry and Molecular Biology, Seoul National University, College of Medicine, Seoul 110-799, Korea [5] Macrogen Inc., Seoul 153-781, Korea
| | - Maree J Webster
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD 20850
| | - Doheon Lee
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Sanghyeon Kim
- Stanley Brain Research Laboratory, Stanley Medical Research Institute, 9800 Medical Center Drive, Rockville, MD 20850
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Ramos L, del Rey J, Daina G, Martinez-Passarell O, Rius M, Tuñón D, Campillo M, Benet J, Navarro J. Does the S phase have an impact on the accuracy of comparative genomic hybridization profiles in single fibroblasts and human blastomeres? Fertil Steril 2013; 101:488-95. [PMID: 24314925 DOI: 10.1016/j.fertnstert.2013.10.031] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 10/16/2013] [Accepted: 10/22/2013] [Indexed: 11/26/2022]
Abstract
OBJECTIVE To investigate if there is an association between single-cell replicative stage and the segmental chromosome imbalances detected by comparative genomic hybridization (CGH). DESIGN First, 135 fibroblasts from cell-line GM03184 (Coriell) at three cell stages (G0/G1, S, and G2/M) were amplified by degenerate oligonucleotide-primed polymerase chain reaction (DOP-PCR) or Sureplex and blindly analyzed by CGH. Second, 85 human blastomeres at the interphase and the metaphase stages, from 30 donated human cryopreserved embryos, were amplified by Sureplex and analyzed by CGH. SETTING Academic center for reproductive medicine. PATIENT(S) None. INTERVENTION(S) None. MAIN OUTCOME MEASURE(S) Incidence of aneuploidy and segmental imbalances detected at the different cell stages. RESULT(S) In DOP-PCR amplifications of fibroblasts, an increased incidence of segmental abnormalities was detected in the S phase. In Sureplex amplifications of fibroblasts and blastomeres, no differences were detected between the different cell stages. A significantly increased incidence of structural abnormalities was seen in the aneuploid blastomeres. CONCLUSION(S) The segmental imbalances detected after Sureplex amplification in 73.3% of the cryopreserved embryos analyzed are mainly nontransitory. They correspond to segmental imbalances present in the cells due to chromosome instability, rather than to replicative DNA segments.
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Affiliation(s)
- Laia Ramos
- Unitat de Biologia Cel·lular i Genètica Mèdica. Facultat de Medicina, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Javier del Rey
- Unitat de Biologia Cel·lular i Genètica Mèdica. Facultat de Medicina, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Gemma Daina
- Unitat de Biologia Cel·lular i Genètica Mèdica. Facultat de Medicina, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | | | | | | | - Mercedes Campillo
- Àrea de Medicina Preventiva i de Salut Pública. Facultat de Medicina. Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jordi Benet
- Unitat de Biologia Cel·lular i Genètica Mèdica. Facultat de Medicina, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Joaquima Navarro
- Unitat de Biologia Cel·lular i Genètica Mèdica. Facultat de Medicina, Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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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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Aneuploidy-driven non-heritable genomic variations demonstrate area-specific distribution in the Alzheimer’s disease brain. Mol Neurodegener 2013. [PMCID: PMC3846755 DOI: 10.1186/1750-1326-8-s1-p52] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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46
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Baugher JD, Baugher BD, Shirley MD, Pevsner J. Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent-of-Origin-based Detection (POD) method. BMC Genomics 2013; 14:367. [PMID: 23724825 PMCID: PMC3680018 DOI: 10.1186/1471-2164-14-367] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 05/14/2013] [Indexed: 11/25/2022] Open
Abstract
Background Mosaic somatic alterations are present in all multi-cellular organisms, but the physiological effects of low-level mosaicism are largely unknown. Most mosaic alterations remain undetectable with current analytical approaches, although the presence of such alterations is increasingly implicated as causative for disease. Results Here, we present the Parent-of-Origin-based Detection (POD) method for chromosomal abnormality detection in trio-based SNP microarray data. Our software implementation, triPOD, was benchmarked using a simulated dataset, outperformed comparable software for sensitivity of abnormality detection, and displayed substantial improvement in the detection of low-level mosaicism while maintaining comparable specificity. Examples of low-level mosaic abnormalities from a large autism dataset demonstrate the benefits of the increased sensitivity provided by triPOD. The triPOD analyses showed robustness across multiple types of Illumina microarray chips. Two large, clinically-relevant datasets were characterized and compared. Conclusions Our method and software provide a significant advancement in the ability to detect low-level mosaic abnormalities, thereby opening new avenues for research into the implications of mosaicism in pathogenic and non-pathogenic processes.
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Affiliation(s)
- Joseph D Baugher
- Program in Biochemistry, Cellular and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
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Iourov IY, Vorsanova SG, Yurov YB. Somatic cell genomics of brain disorders: a new opportunity to clarify genetic-environmental interactions. Cytogenet Genome Res 2013; 139:181-8. [PMID: 23428498 DOI: 10.1159/000347053] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Recent genomic advances have exacerbated the problem of interpreting genome-wide association studies aimed at uncovering genetic basis of brain disorders. Despite of a plethora of data on candidate genes determining the susceptibility to neuropsychiatric diseases, no consensus is reached on their intrinsic contribution to the pathogenesis, and the influence of the environment on these genes is incompletely understood. Alternatively, single-cell analyses of the normal and diseased human brain have shown that somatic genome/epigenome variations (somatic mosaicism) do affect neuronal cell populations and are likely to mediate pathogenic processes associated with brain dysfunctions. Such (epi-)genomic changes are likely to arise from disturbances in genome maintenance and cell cycle regulation pathways as well as from environmental exposures. Therefore, one can suggest that, at least in a proportion of cases, inter- and intragenic variations (copy number variations (CNVs) or single nucleotide polymorphisms (SNPs)) associated with major brain disorders (i.e. schizophrenia, Alzheimer's disease, autism) lead to genetic dysregulation resulting in somatic genetic and epigenetic mosaicism. In addition, environmental influences on malfunctioning cellular machinery could trigger a cascade of abnormal processes producing genomic/chromosomal instability (i.e. brain-specific aneuploidy). Here, a brief analysis of a genome-wide association database has allowed us to support these speculations. Accordingly, an ontogenetic 2-/multiple-hit mechanism of brain diseases was hypothesized. Finally, we speculate that somatic cell genomics approach considering both genome-wide associations and somatic (epi-)genomic variations is likely to have bright perspectives for disease-oriented genome research.
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Affiliation(s)
- I Y Iourov
- Research Center of Mental Health, Russian Academy of Medical Sciences, RU–119152 Moscow, Russia.
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An interstitial 20q11.21 microdeletion causing mild intellectual disability and facial dysmorphisms. Case Rep Genet 2013; 2013:353028. [PMID: 23476833 PMCID: PMC3586477 DOI: 10.1155/2013/353028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 01/09/2013] [Indexed: 12/28/2022] Open
Abstract
We report a case of an interstitial chromosome 20q11.21 microdeletion in a 7-year-old male child presenting with mild intellectual disability and facial dysmorphisms. Array comparative genomic hybridization (CGH) has shown that the deletion resulted in the loss of 68 genes, among which 5 genes (COX4I2, MYLK2, ASXL1, DNMT3B, and SNTA1) are disease causing. The size of the deletion was estimated to span 2.6 Mb. Only three cases of deletions encompassing this chromosomal region have been reported. The phenotype of the index patient was found to resemble the mildest cases of Bohring-Opitz syndrome that is caused by ASXL1 mutations. An in silico evaluation of the deleted genomic region has shown that benign genomic variations have never been observed to affect the ASXL1 gene, in contrast to the other disease-causing genes. As a result, it was suggested that ASXL1 loss is likely to be the main cause of the phenotypic manifestations. The present case report indicates that a loss of the disease-causing gene can produce a milder phenotype of a single gene condition.
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Multi-Color Spectral Transcript Analysis (SPECTRA) for Phenotypic Characterization of Tumor Cells. Biomolecules 2013; 3:180-97. [PMID: 24970164 PMCID: PMC4030878 DOI: 10.3390/biom3010180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/31/2013] [Accepted: 02/04/2013] [Indexed: 11/16/2022] Open
Abstract
Many human tumors show significant changes in their signal transduction pathways and, thus, the way the cells interact with their environment. Often caused by chromosomal rearrangements, including gene amplifications, translocations or deletions, the altered levels of gene expression may provide a tumor-specific signature that can be exploited for diagnostic or therapeutic purposes. We investigated the utility of multiplexed fluorescence in situ hybridization (FISH) using non-isotopically labeled cDNA probes detected by Spectral Imaging as a sensitive and rapid procedure to measure tumor-specific gene expression signatures. We used a commercially available system to acquire and analyze multicolor FISH images. Initial investigations used panels of fluorescent calibration standards to evaluate the system. These experiments were followed by hybridization of five-to-six differently labeled cDNA probes, which target the transcripts of tyrosine kinase genes known to be differently expressed in normal cells and tumors of the breast or thyroid gland. The relatively simple, yet efficient, molecular cytogenetic method presented here may find many applications in characterization of solid tumors or disseminated tumor cells. Addressing tumor heterogeneity by means of multi-parameter single cell analyses is expected to enable a wide range of investigations in the areas of tumor stem cells, tumor clonality and disease progression.
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50
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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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