1
|
Zlotina A, Maslova A, Pavlova O, Kosyakova N, Al-Rikabi A, Liehr T, Krasikova A. New Insights Into Chromomere Organization Provided by Lampbrush Chromosome Microdissection and High-Throughput Sequencing. Front Genet 2020; 11:57. [PMID: 32127797 PMCID: PMC7038795 DOI: 10.3389/fgene.2020.00057] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/17/2020] [Indexed: 11/13/2022] Open
Abstract
Giant lampbrush chromosomes (LBCs) typical for growing oocytes of various animal species are characterized by a specific chromomere-loop appearance and massive transcription. Chromomeres represent universal units of chromatin packaging at LBC stage. While quite good progress has been made in investigation of LBCs structure and function, chromomere organization still remains poorly understood. To extend our knowledge on chromomere organization, we applied microdissection to chicken LBCs. In particular, 31 and 5 individual chromomeres were dissected one by one along the macrochromosome 4 and one microchromosome, respectively. The data on genomic context of individual chromomeres was obtained by high-throughput sequencing of the corresponding chromomere DNA. Alignment of adjacent chromomeres to chicken genome assembly provided information on chromomeres size and genomic boarders, indicating that prominent marker chromomeres are about 4–5 Mb in size, while common chromomeres of 1.5–3.5 Mb. Analysis of genomic features showed that the majority of chromomere-loop complexes combine gene-dense and gene-poor regions, while massive loopless DAPI-positive chromomeres lack genes and are remarkably enriched with different repetitive elements. Finally, dissected LBC chromomeres were compared with chromatin domains (topologically associated domains [TADs] and A/B-compartments), earlier identified by Hi-C technique in interphase nucleus of chicken embryonic fibroblasts. Generally, the results obtained suggest that chromomeres of LBCs do not correspond unambiguously to any type of well-established spatial domains of interphase nucleus in chicken somatic cells.
Collapse
Affiliation(s)
- Anna Zlotina
- Saint Petersburg State University, Saint Petersburg, Russia
| | | | - Olga Pavlova
- Saint Petersburg State University, Saint Petersburg, Russia
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Alla Krasikova
- Saint Petersburg State University, Saint Petersburg, Russia
| |
Collapse
|
2
|
Gokhman VE, Cioffi MDB, König C, Pollmann M, Gantert C, Krogmann L, Steidle JLM, Kosyakova N, Liehr T, Al-Rikabi A. Microdissection and whole chromosome painting confirm karyotype transformation in cryptic species of the Lariophagus distinguendus (Förster, 1841) complex (Hymenoptera: Pteromalidae). PLoS One 2019; 14:e0225257. [PMID: 31725808 PMCID: PMC6855445 DOI: 10.1371/journal.pone.0225257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/31/2019] [Indexed: 11/18/2022] Open
Abstract
Karyotypes of two cryptic species of parasitoid Hymenoptera with n = 5 and 6 belonging to the Lariophagus distinguendus (Förster, 1841) complex, which includes cosmopolitan parasitoids of coleopteran stored-product pests, were studied using glass-needle based microdissection, reverse and cross-species fluorescence in situ hybridisation (FISH). This experiment strongly indicates that the largest metacentric chromosome in the karyotype with n = 5 originated from a particular fusion between the only acrocentric and a smaller metacentric chromosome of the set with n = 6, therefore confirming our previous hypothesis based on the karyotypic analysis using chromosome morphometrics. This study represents the first successful application of both microdissection and whole chromosome painting for the reconstruction of karyotypic rearrangements in closely related species of parasitoids, as well as in the order Hymenoptera in general.
Collapse
Affiliation(s)
| | - Marcelo de Bello Cioffi
- Department of Genetics and Evolution, Federal University of São Carlos, São Carlos, São Paulo, Brazil
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Christian König
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Marie Pollmann
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Cornelia Gantert
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
| | - Lars Krogmann
- Institute for Zoology, University of Hohenheim, Stuttgart, Germany
- Department of Entomology, State Museum of Natural History Stuttgart, Stuttgart, Germany
| | | | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Ahmed Al-Rikabi
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| |
Collapse
|
3
|
Zlotina A, Maslova A, Kosyakova N, Al-Rikabi ABH, Liehr T, Krasikova A. Heterochromatic regions in Japanese quail chromosomes: comprehensive molecular-cytogenetic characterization and 3D mapping in interphase nucleus. Chromosome Res 2018; 27:253-270. [DOI: 10.1007/s10577-018-9597-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/01/2018] [Accepted: 12/04/2018] [Indexed: 11/29/2022]
|
4
|
Ribeiro IP, Rodrigues JM, Mascarenhas A, Kosyakova N, Caramelo F, Liehr T, Melo JB, Carreira IM. Cytogenetic, genomic, and epigenetic characterization of the HSC-3 tongue cell line with lymph node metastasis. J Oral Sci 2018; 60:70-81. [PMID: 29479029 DOI: 10.2334/josnusd.16-0811] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Oral carcinoma develops from squamous epithelial cells by the acquisition of multiple (epi) genetic alterations that target different genes and molecular pathways. Herein, we performed a comprehensive genomic and epigenetic characterization of the HSC-3 cell line through karyotyping, multicolor fluorescence in situ hybridization, array comparative genomic hybridization, and methylation-specific multiplex ligation-dependent probe amplification. HSC-3 turned out to be a near-triploid cell line with a modal number of 61 chromosomes. Banding and molecular cytogenetic analyses revealed that nonrandom gains of chromosomal segments occurred more frequently than losses. Overall, gains of chromosome 1, 3q, 5p, 7p, 8q, 9q, 10, 11p, 11q13, 12, 13, 14, 17, 18p, 20, Yp, and Xq were observed. The largest region affected by copy number loss was observed at chromosome 18q. Several of the observed genomic imbalances and their mapped genes were already associated with oral carcinoma and/or adverse prognosis, invasion, and metastasis in cancer. The most common rearrangements observed were translocations in the centromeric/near-centromeric regions. RARB, ESR1, and CADM1 genes were methylated and showed copy number losses, whereas TP73 and GATA5 presented with methylation and copy number gains. Thus, the current study presents a comprehensive characterization of the HSC-3 cell line; the use of this cell line may contribute to enriching the resources available for oral cancer research, especially for the testing of therapeutic agents.
Collapse
Affiliation(s)
- Ilda P Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
| | - Joana M Rodrigues
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra
| | | | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University
| | - Francisco Caramelo
- Laboratory of Biostatistics and Medical Informatics, Faculty of Medicine, University of Coimbra
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University
| | - Joana B Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
| | - Isabel M Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra.,Center of Investigation on Environment Genetics and Oncobiology, Faculty of Medicine, University of Coimbra
| |
Collapse
|
5
|
Cioffi MDB, Sánchez A, Marchal JA, Kosyakova N, Liehr T, Trifonov V, Bertollo LAC. Correction to: Whole chromosome painting reveals independent origin of sex chromosomes in closely related forms of a fish species. Genetica 2017; 146:123. [PMID: 29260363 DOI: 10.1007/s10709-017-0001-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
ere, we report that a paragraph from the "Discussion" section of Cioffi et al. (2011; p. 1070, 4th paragraph of column 1) was transcribed (with only minor edits) from an introductory paragraph previously published in Chromosome Research by O'Meally et al.
Collapse
Affiliation(s)
- Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | - Antonio Sánchez
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Juan Alberto Marchal
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales, Universidad de Jaén, Jaén, Spain
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Kollegiengasse 10, 07743, Jena, Germany
| | - Vladimir Trifonov
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | | |
Collapse
|
6
|
Moysés-Oliveira M, Giannuzzi G, Fish RJ, Rosenfeld JA, Petit F, Soares MDF, Kulikowski LD, Di-Battista A, Zamariolli M, Xia F, Liehr T, Kosyakova N, Carvalheira G, Parker M, Seaby EG, Ennis S, Gilbert RD, Hagelstrom RT, Cremona ML, Li WL, Malhotra A, Chandrasekhar A, Perry DL, Taft RJ, McCarrier J, Basel DG, Andrieux J, Stumpp T, Antunes F, Pereira GJ, Neerman-Arbez M, Meloni VA, Drummond-Borg M, Melaragno MI, Reymond A. Inactivation of AMMECR1 is associated with growth, bone, and heart alterations. Hum Mutat 2017; 39:281-291. [PMID: 29193635 DOI: 10.1002/humu.23373] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/18/2017] [Accepted: 11/18/2017] [Indexed: 01/26/2023]
Abstract
We report five individuals with loss-of-function of the X-linked AMMECR1: a girl with a balanced X-autosome translocation and inactivation of the normal X-chromosome; two boys with maternally inherited and de novo nonsense variants; and two half-brothers with maternally inherited microdeletion variants. They present with short stature, cardiac and skeletal abnormalities, and hearing loss. Variants of unknown significance in AMMECR1 in four male patients from two families with partially overlapping phenotypes were previously reported. AMMECR1 is coexpressed with genes implicated in cell cycle regulation, five of which were previously associated with growth and bone alterations. Our knockdown of the zebrafish orthologous gene resulted in phenotypes reminiscent of patients' features. The increased transcript and encoded protein levels of AMMECR1L, an AMMECR1 paralog, in the t(X;9) patient's cells indicate a possible partial compensatory mechanism. AMMECR1 and AMMECR1L proteins dimerize and localize to the nucleus as suggested by their nucleic acid-binding RAGNYA folds. Our results suggest that AMMECR1 is potentially involved in cell cycle control and linked to a new syndrome with growth, bone, heart, and kidney alterations with or without elliptocytosis.
Collapse
Affiliation(s)
- Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.,Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Giuliana Giannuzzi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Richard J Fish
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Florence Petit
- Clinique de Génétique, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | | | - Leslie Domenici Kulikowski
- Department of Pathology, Laboratório de Citogenômica, LIM 03, Hospital das Clínicas, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Adriana Di-Battista
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Malú Zamariolli
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Thomas Liehr
- Universitätsklinikum Jena, Institut für Humangenetik, Jena, Germany
| | | | - Gianna Carvalheira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Michael Parker
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, United Kingdom
| | - Eleanor G Seaby
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Sarah Ennis
- Genomic Informatics Group, University Hospital Southampton, Southampton, United Kingdom
| | - Rodney D Gilbert
- Southampton Children's Hospital, University Hospital Southampton, Southampton, United Kingdom
| | | | - Maria L Cremona
- Illumina Clinical Services Laboratory, San Diego, California
| | - Wenhui L Li
- Illumina Clinical Services Laboratory, San Diego, California
| | - Alka Malhotra
- Illumina Clinical Services Laboratory, San Diego, California
| | | | - Denise L Perry
- Illumina Clinical Services Laboratory, San Diego, California
| | - Ryan J Taft
- Illumina Clinical Services Laboratory, San Diego, California
| | - Julie McCarrier
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Donald G Basel
- Department of Pediatrics, Section of Genetics, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Joris Andrieux
- Institut de Génétique Médicale, CHU Lille - Hôpital Jeanne de Flandre, Lille, France
| | - Taiza Stumpp
- Developmental Biology Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Antunes
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Gustavo José Pereira
- Department of Pharmacology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Marguerite Neerman-Arbez
- Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| |
Collapse
|
7
|
Guja K, Liehr T, Rincic M, Kosyakova N, Hussein Azawi SS. Molecular Cytogenetic Characterization Identified the Murine B-Cell Lymphoma Cell Line A-20 as a Model for Sporadic Burkitt's Lymphoma. J Histochem Cytochem 2017; 65:669-677. [PMID: 28902524 DOI: 10.1369/0022155417731319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Here, we report the first molecular cytogenetic characterization of the BALB/cAnN mouse derived B-cell non-Hodgkin lymphoma (B-cell NHL) cell lines A-20. Even though previously used as a model for testing of, for example, dexametason, up to present, no data in the genetic properties of A-20 were available. The present study closed this gap and provides evidence that A-20 is a model for B-cell NHL subgroup sporadic Burkitt's lymphoma. C-myc oncogene is involved in a translocation and copy number alterations as gain of murine 14q material could be observed. Interestingly, the cell line showed the karyotype 39,X,-X or -Y,t(2;15)(qE5;qD2),del(6)(qB3qC3),del(9)(qA3qA4),dup(14)(qE1qE4) in ~95% of the cells, being exceptionally stable for cell lines being established 38 years ago. Still, ~5% of the cells showed polyploidization followed by chromothripsis. It remains to be determined if this can be observed also in other cell lines, just has not been reported yet, and/or if it is a unique feature of A-20. Overall, finally here, the necessary genetic data to identify A-20 as a model for human sporadic Burkitt's lymphoma are provided.
Collapse
Affiliation(s)
- Karolina Guja
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.,Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Martina Rincic
- Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Zagreb, Croatia
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Shaymaa S Hussein Azawi
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
8
|
Santiago F, Lima S, Pinheiro T, Silvestre RT, Otero UB, Tabalipa MM, Kosyakova N, Ornellas MH, Liehr T, Alves G. Benzene poisoning, clinical and blood abnormalities in two Brazilian female gas station attendants: two case reports. BMC Res Notes 2017; 10:52. [PMID: 28100263 PMCID: PMC5241924 DOI: 10.1186/s13104-016-2369-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/30/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Brazilian gas station workers are chronically exposed to benzene, toluene, xylene (BTX) during their working time. Describe below two cases of latin female gas station workers with benzene poisoning symptoms and miscarriage history. CASE PRESENTATION In both cases were identified complex chromosomal rearrangements (CCR) with fluorescence in situ hybridization, applied to whole chromosome paints by chromosomes 1, 2 and 4. The lower natural killer cell (NK) cells have also been observed in cases correspondents, especially the rare type of NK (NKbright) in their peripheral blood cells. CONCLUSIONS It is known that acquired chromosomal aberrations are positively correlated with cancer and reproductive risk. In concordance, lower NK cytotoxicity increases the risk for cancer, as well. Thus, this is the first study providing hints on a possible causative relation of lower NK cytotoxicity and increase rates of chromosomal rearrangements including CCRs.
Collapse
Affiliation(s)
- Fábio Santiago
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Pós-graduação em Ciências Médicas (PGCM), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Simone Lima
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tayná Pinheiro
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rafaele Tavares Silvestre
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Pós-graduação em Ciências Médicas (PGCM), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Ubirani Barros Otero
- Unidade Técnica de Exposição Ocupacional, Ambiental e Câncer, Coordenação de Prevenção e Vigilância, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Marianne Medeiros Tabalipa
- Unidade Técnica de Exposição Ocupacional, Ambiental e Câncer, Coordenação de Prevenção e Vigilância, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
| | - Maria Helena Ornellas
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil. .,Pós-graduação em Ciências Médicas (PGCM), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil. .,Departamento de Patologia Geral, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Avenida Professor Manuel de Abreu 444, 4° andar, Vila Isabel, Rio de Janeiro, 20551-030, Brazil.
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
| | - Gilda Alves
- Laboratório de Marcadores Circulantes, Departamento de Patologia e Laboratórios, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Pós-graduação em Ciências Médicas (PGCM), Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Coordenação de Pesquisa, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| |
Collapse
|
9
|
Malinverni ACM, Colovati ME, Perez ABA, Caneloi TP, Oliveira HR, Kosyakova N, Liehr T, Hamid AB, Melaragno MI. Unusual Duplication in the Pericentromeric Region of Chromosome 9 in a Patient with Phenotypic Alterations. Cytogenet Genome Res 2017; 150:100-105. [PMID: 28064285 DOI: 10.1159/000453574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2016] [Indexed: 11/19/2022] Open
Abstract
Several alterations involving the pericentromeric region of chromosome 9 are considered as normal population variants. These heterochromatic variants or heteromorphisms can include 9qh+, 9cen+, 9ph+, 9ph-, inv(9)(p11q13), and other patterns which can only be defined by FISH studies. However, some heteromorphisms have been found more frequently in patients with several clinical disorders. Here, we report on a patient with intellectual disability, language and neurodevelopmental delay, as well as facial dysmorphism and an unusual chromosome 9. While the banding karyotype was indicative of a simple pericentric inversion of one chromosome 9 [46,XX,inv(9)(p12q13)], array comparative genomic hybridization showed a 6-Mb duplication, including 22 genes: arr[hg19] 9p13.1p11.2(38,869,901- 44,870,714)×3 dn. Molecular cytogenetics using a panel of probes specific for the pericentromeric region of chromosome 9 showed an unusual, rearranged chromosome 9, der(9)(pter→p11.2::q21.11→q12::p11.2→p13.2::q12→p11.2::q21.11→qter), that has not been described before. The patient's phenotypic alterations are probably due to the de novo 6-Mb 9p duplication, although a review of similar cases showed some reports considering this duplication in the euchromatic region as a benign variant. Interestingly, this is the first report of a possible adverse inversion loop formation due to a known heteromorphic pericentric inversion present in the phenotypically normal father of the patient.
Collapse
Affiliation(s)
- Andréa C M Malinverni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Kubicova E, Trifonov V, Borovecki F, Liehr T, Rincic M, Kosyakova N, Hussein S. First Molecular Cytogenetic Characterization of Murine Malignant Mesothelioma Cell Line AE17 and In Silico Translation to the Human Genome. Curr Bioinform 2017. [DOI: 10.2174/1574893611666160606164459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
11
|
|
12
|
Merlo MA, Iziga R, Portela-Bens S, Cross I, Kosyakova N, Liehr T, Manchado M, Rebordinos L. Analysis of the histone cluster in Senegalese sole (Solea senegalensis): evidence for a divergent evolution of two canonical histone clusters. Genome 2016; 60:441-453. [PMID: 28177835 DOI: 10.1139/gen-2016-0143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The Senegalese sole (Solea senegalensis) is commercially very important and a priority species for aquaculture product diversification. The main histone cluster was identified within two BAC clones. However, two replacement histones (H1.0 and H3.3) were found in another BAC clone. Different types of canonical histones H2A and H2B were found within the same species for the first time. Phylogenetic analysis demonstrated that the different types of H1, H2A, and H2B histones were all more similar to each other than to canonical histones from other species. The canonical histone H3 of S. senegalensis differs from subtypes H3.1 and H3.2 in humans at the site of residue 96, where a serine is found instead of an alanine. This same polymorphism has been found only in Danio rerio. The karyotype of S. senegalensis comprises 21 pairs of chromosomes, distributed in 3 metacentric pairs, 2 submetacentric pairs, 4 subtelocentric pairs, and 12 acrocentric pairs. The two BAC clones that contain the clusters of canonical histones were both mapped on the largest metacentric pair, and mFISH analysis confirmed the co-location with the dmrt1 gene in that pair. Three chromosome markers have been identified which, in addition to those previously described, account for 18 chromosome pairs in S. senegalensis.
Collapse
Affiliation(s)
- Manuel Alejandro Merlo
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Roger Iziga
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Silvia Portela-Bens
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Ismael Cross
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| | - Nadezda Kosyakova
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Thomas Liehr
- b Institut für Humangenetik, Universitätsklinikum Jena, 07743 Jena, Germany
| | - Manuel Manchado
- c Centro IFAPA "El Toruño", 11500 Puerto de Santa María, Cádiz, Spain
| | - Laureana Rebordinos
- a Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510 Cádiz, Spain
| |
Collapse
|
13
|
Kadioglu O, Cao J, Kosyakova N, Mrasek K, Liehr T, Efferth T. Genomic and transcriptomic profiling of resistant CEM/ADR-5000 and sensitive CCRF-CEM leukaemia cells for unravelling the full complexity of multi-factorial multidrug resistance. Sci Rep 2016; 6:36754. [PMID: 27824156 PMCID: PMC5099876 DOI: 10.1038/srep36754] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 10/17/2016] [Indexed: 12/18/2022] Open
Abstract
We systematically characterised multifactorial multidrug resistance (MDR) in CEM/ADR5000 cells, a doxorubicin-resistant sub-line derived from drug-sensitive, parental CCRF-CEM cells developed in vitro. RNA sequencing and network analyses (Ingenuity Pathway Analysis) were performed. Chromosomal aberrations were identified by array-comparative genomic hybridisation (aCGH) and multicolour fluorescence in situ hybridisation (mFISH). Fifteen ATP-binding cassette transporters and numerous new genes were overexpressed in CEM/ADR5000 cells. The basic karyotype in CCRF-CEM cells consisted of 47, XX, der(5)t(5;14) (q35.33;q32.3), del(9) (p14.1), +20. CEM/ADR5000 cells acquired additional aberrations, including X-chromosome loss, 4q and 14q deletion, chromosome 7 inversion, balanced and unbalanced two and three way translocations: t(3;10), der(3)t(3;13), der(5)t(18;5;14), t(10;16), der(18)t(7;18), der(18)t(21;18;5), der(21;21;18;5) and der(22)t(9;22). CCRF-CEM consisted of two and CEM/ADR5000 of five major sub-clones, indicating genetic tumor heterogeneity. Loss of 3q27.1 in CEM/ADR5000 caused down-regulation of ABCC5 and ABCF3 expression, Xq28 loss down-regulated ABCD1 expression. ABCB1, the most well-known MDR gene, was 448-fold up-regulated due to 7q21.12 amplification. In addition to well-known drug resistance genes, numerous novel genes and genomic aberrations were identified. Transcriptomics and genetics in CEM/AD5000 cells unravelled a range of MDR mechanisms, which is much more complex than estimated thus far. This may have important implications for future treatment strategies.
Collapse
Affiliation(s)
- Onat Kadioglu
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Jingming Cao
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| |
Collapse
|
14
|
Weise A, Bhatt S, Piaszinski K, Kosyakova N, Fan X, Altendorf-Hofmann A, Tanomtong A, Chaveerach A, de Cioffi MB, de Oliveira E, Walther JU, Liehr T, Chaudhuri JP. Chromosomes in a genome-wise order: evidence for metaphase architecture. Mol Cytogenet 2016; 9:36. [PMID: 27123045 PMCID: PMC4847357 DOI: 10.1186/s13039-016-0243-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 04/12/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND One fundamental finding of the last decade is that, besides the primary DNA sequence information there are several epigenetic "information-layers" like DNA-and histone modifications, chromatin packaging and, last but not least, the position of genes in the nucleus. RESULTS We postulate that the functional genomic architecture is not restricted to the interphase of the cell cycle but can also be observed in the metaphase stage, when chromosomes are most condensed and microscopically visible. If so, it offers the unique opportunity to directly analyze the functional aspects of genomic architecture in different cells, species and diseases. Another aspect not directly accessible by molecular techniques is the genome merged from two different haploid parental genomes represented by the homologous chromosome sets. Our results show that there is not only a well-known and defined nuclear architecture in interphase but also in metaphase leading to a bilateral organization of the two haploid sets of chromosomes. Moreover, evidence is provided for the parental origin of the haploid grouping. CONCLUSIONS From our findings we postulate an additional epigenetic information layer within the genome including the organization of homologous chromosomes and their parental origin which may now substantially change the landscape of genetics.
Collapse
Affiliation(s)
- Anja Weise
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Samarth Bhatt
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Katja Piaszinski
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Nadezda Kosyakova
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Xiaobo Fan
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Annelore Altendorf-Hofmann
- />Department of General, Visceral und Vascular Surgery, Jena University Hospital, Kochstr. 2, Jena, 07743 Germany
| | - Alongklod Tanomtong
- />Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd, Khon Kaen, Muang District 40002 Thailand
| | - Arunrat Chaveerach
- />Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd, Khon Kaen, Muang District 40002 Thailand
| | - Marcelo Bello de Cioffi
- />Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP Brazil
| | - Edivaldo de Oliveira
- />Instituto Evandro Chagas, Seção de Meio Ambiente, Laboratório de Cultura de Tecidos e Citogenética, Ananindeua, PA Brazil
| | - Joachim-U. Walther
- />Instituto Evandro Chagas, Seção de Meio Ambiente, Laboratório de Cultura de Tecidos e Citogenética, Ananindeua, PA Brazil
| | - Thomas Liehr
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
| | - Jyoti P. Chaudhuri
- />Institute of Human Genetics, Jena University Hospital, Postfach, 07740, Jena, Germany
- />Kinderklinik, Ludwig Maximillians Universität, 80337 Munich, Germany
| |
Collapse
|
15
|
Portela-Bens S, Merlo MA, Rodríguez ME, Cross I, Manchado M, Kosyakova N, Liehr T, Rebordinos L. Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis. Chromosoma 2016; 126:261-277. [PMID: 27080536 DOI: 10.1007/s00412-016-0589-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/31/2016] [Accepted: 04/04/2016] [Indexed: 11/27/2022]
Abstract
The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.
Collapse
Affiliation(s)
- Silvia Portela-Bens
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Alejandro Merlo
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - María Esther Rodríguez
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Ismael Cross
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain
| | - Manuel Manchado
- Centro IFAPA "El Toruño", 11500, Puerto de Santa María, Cádiz, Spain
| | - Nadezda Kosyakova
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Thomas Liehr
- Institut für Humangenetik, Universitätsklinikum Jena, 07743, Jena, Germany
| | - Laureana Rebordinos
- Área de Genética, Facultad de Ciencias del Mar y Ambientales, Universidad de Cádiz, 11510, Cádiz, Spain.
| |
Collapse
|
16
|
Zlotina A, Kulikova T, Kosyakova N, Liehr T, Krasikova A. Microdissection of lampbrush chromosomes as an approach for generation of locus-specific FISH-probes and samples for high-throughput sequencing. BMC Genomics 2016; 17:126. [PMID: 26897606 PMCID: PMC4761191 DOI: 10.1186/s12864-016-2437-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/05/2016] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Over the past two decades, chromosome microdissection has been widely used in diagnostics and research enabling analysis of chromosomes and their regions through probe generation and establishing of chromosome- and chromosome region-specific DNA libraries. However, relatively small physical size of mitotic chromosomes limited the use of the conventional chromosome microdissection for investigation of tiny chromosomal regions. RESULTS In the present study, we developed a workflow for mechanical microdissection of giant transcriptionally active lampbrush chromosomes followed by the preparation of whole-chromosome and locus-specific fluorescent in situ hybridization (FISH)-probes and high-throughput sequencing. In particular, chicken (Gallus g. domesticus) lampbrush chromosome regions as small as single chromomeres, individual lateral loops and marker structures were successfully microdissected. The dissected fragments were mapped with high resolution to target regions of the corresponding lampbrush chromosomes. For investigation of RNA-content of lampbrush chromosome structures, samples retrieved by microdissection were subjected to reverse transcription. Using high-throughput sequencing, the isolated regions were successfully assigned to chicken genome coordinates. As a result, we defined precisely the loci for marker structures formation on chicken lampbrush chromosomes 2 and 3. Additionally, our data suggest that large DAPI-positive chromomeres of chicken lampbrush chromosome arms are characterized by low gene density and high repeat content. CONCLUSIONS The developed technical approach allows to obtain DNA and RNA samples from particular lampbrush chromosome loci, to define precisely the genomic position, extent and sequence content of the dissected regions. The data obtained demonstrate that lampbrush chromosome microdissection provides a unique opportunity to correlate a particular transcriptional domain or a cytological structure with a known DNA sequence. This approach offers great prospects for detailed exploration of functionally significant chromosomal regions.
Collapse
Affiliation(s)
- Anna Zlotina
- Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Tatiana Kulikova
- Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany.
| | - Alla Krasikova
- Department of Cytology and Histology, Saint Petersburg State University, Saint Petersburg, Russia.
| |
Collapse
|
17
|
Moysés-Oliveira M, Guilherme RS, Meloni VA, Di Battista A, de Mello CB, Bragagnolo S, Moretti-Ferreira D, Kosyakova N, Liehr T, Carvalheira GM, Melaragno MI. X-linked intellectual disability related genes disrupted by balanced X-autosome translocations. Am J Med Genet B Neuropsychiatr Genet 2015; 168:669-77. [PMID: 26290131 DOI: 10.1002/ajmg.b.32355] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/10/2015] [Indexed: 11/10/2022]
Abstract
Detailed molecular characterization of chromosomal rearrangements involving X-chromosome has been a key strategy in identifying X-linked intellectual disability-causing genes. We fine-mapped the breakpoints in four women with balanced X-autosome translocations and variable phenotypes, in order to investigate the corresponding genetic contribution to intellectual disability. We addressed the impact of the gene interruptions in transcription and discussed the consequences of their functional impairment in neurodevelopment. Three patients presented with cognitive impairment, reinforcing the association between the disrupted genes (TSPAN7-MRX58, KIAA2022-MRX98, and IL1RAPL1-MRX21/34) and intellectual disability. While gene expression analysis showed absence of TSPAN7 and KIAA2022 expression in the patients, the unexpected expression of IL1RAPL1 suggested a fusion transcript ZNF611-IL1RAPL1 under the control of the ZNF611 promoter, gene disrupted at the autosomal breakpoint. The X-chromosomal breakpoint definition in the fourth patient, a woman with normal intellectual abilities, revealed disruption of the ZDHHC15 gene (MRX91). The expression assays did not detect ZDHHC15 gene expression in the patient, thus questioning its involvement in intellectual disability. Revealing the disruption of an X-linked intellectual disability-related gene in patients with balanced X-autosome translocation is a useful tool for a better characterization of critical genes in neurodevelopment. © 2015 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Mariana Moysés-Oliveira
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roberta Santos Guilherme
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil.,Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Vera Ayres Meloni
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Adriana Di Battista
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | | | - Silvia Bragagnolo
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Danilo Moretti-Ferreira
- Departament of Genetics, Instituto de Biocincias de Botucatu, Universidade Estadual de São Paulo, São Paulo, Brazil
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - Gianna Maria Carvalheira
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Genetics Division, Universidade Federal de São Paulo, São Paulo, Brazil
| |
Collapse
|
18
|
Fan X, Supiwong W, Weise A, Mrasek K, Kosyakova N, Tanomtong A, Pinthong K, Trifonov VA, Cioffi MDB, Grothmann P, Liehr T, Oliveira EH. Comprehensive characterization of evolutionary conserved breakpoints in four New World Monkey karyotypes compared to Chlorocebus aethiops and Homo sapiens. Heliyon 2015; 1:e00042. [PMID: 27441227 PMCID: PMC4945616 DOI: 10.1016/j.heliyon.2015.e00042] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 10/20/2015] [Accepted: 10/23/2015] [Indexed: 11/21/2022] Open
Abstract
Comparative cytogenetic analysis in New World Monkeys (NWMs) using human multicolor banding (MCB) probe sets were not previously done. Here we report on an MCB based FISH-banding study complemented with selected locus-specific and heterochromatin specific probes in four NWMs and one Old World Monkey (OWM) species, i.e. in Alouatta caraya (ACA), Callithrix jacchus (CJA), Cebus apella (CAP), Saimiri sciureus (SSC), and Chlorocebus aethiops (CAE), respectively. 107 individual evolutionary conserved breakpoints (ECBs) among those species were identified and compared with those of other species in previous reports. Especially for chromosomal regions being syntenic to human chromosomes 6, 8, 9, 10, 11, 12 and 16 previously cryptic rearrangements could be observed. 50.4% (54/107) NWM-ECBs were colocalized with those of OWMs, 62.6% (62/99) NWM-ECBs were related with those of Hylobates lar (HLA) and 66.3% (71/107) NWM-ECBs corresponded with those known from other mammalians. Furthermore, human fragile sites were aligned with the ECBs found in the five studied species and interestingly 66.3% ECBs colocalized with those fragile sites (FS). Overall, this study presents detailed chromosomal maps of one OWM and four NWM species. This data will be helpful to further investigation on chromosome evolution in NWM and hominoids in general and is prerequisite for correct interpretation of future sequencing based genomic studies in those species.
Collapse
Key Words
- ACA, Alouatta caraya
- Atelidae
- BACs, bacterial artificial chromosomes
- CAE, Chlorocebus aethiops
- CAP, Cebus apella
- CJA, Callithrix jacchus
- Cebidae
- EC, evolutionary conserved
- ECBs, evolutionary conserved breakpoints
- Evolutionary conserved breakpoints
- Evolutionary genetics
- FISH, fluorescence in situ hybridization
- FS, fragile site
- Fragile sites
- Genetics
- HCM, heterochromatin mix
- HLA, Hylobates lar
- HSA, Homo sapiens
- HSBs, homologous syntenic blocks
- MCB, multicolor banding
- Multicolor banding
- NGS, Next-generation sequencing
- NOR, nucleolus organizer region
- NWMs, New World Monkeys
- New World Monkeys
- OWMs, Old World Monkeys
- Old World Monkeys
- SSC, Saimiri sciureus
- subCTM, sub-centromere/subtelomere-specific multicolor (FISH)
- wcp, whole human chromosome painting
Collapse
Affiliation(s)
- Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Weerayuth Supiwong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Alongkoad Tanomtong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | - Krit Pinthong
- Department of Biology Faculty of Science, KhonKaen University, 123 Moo 16 Mittapap Rd., Muang District, KhonKaen 40002, Thailand
| | | | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Pierre Grothmann
- Serengeti-Park Hodenhagen GmbH, Am Safaripark 1, 29693, Hodenhagen, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Edivaldo H.C.de Oliveira
- Faculdade de Ciências Naturais, ICEN, Universidade Federal do Pará, Campus Universitário do Guamá, 66075-110 Belém-PA, Brazil
| |
Collapse
|
19
|
Weise A, Kosyakova N, Voigt M, Aust N, Mrasek K, Löhmer S, Rubtsov N, Karamysheva TV, Trifonov VA, Hardekopf D, Jančušková T, Pekova S, Wilhelm K, Liehr T, Fan X. Comprehensive Analyses of White-Handed Gibbon Chromosomes Enables Access to 92 Evolutionary Conserved Breakpoints Compared to the Human Genome. Cytogenet Genome Res 2015; 145:42-9. [PMID: 25926034 DOI: 10.1159/000381764] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2015] [Indexed: 11/19/2022] Open
Abstract
Gibbon species (Hylobatidae) impress with an unusually high number of numerical and structural chromosomal changes within the family itself as well as compared to other Hominoidea including humans. In former studies applying molecular cytogenetic methods, 86 evolutionary conserved breakpoints (ECBs) were reported in the white-handed gibbon (Hylobates lar, HLA) with respect to the human genome. To analyze those ECBs in more detail and also to achieve a better understanding of the fast karyotype evolution in Hylobatidae, molecular data for these regions are indispensably necessary. In the present study, we obtained whole chromosome-specific probes by microdissection of all 21 HLA autosomes and prepared them for aCGH. Locus-specific DNA probes were also used for further molecular cytogenetic characterization of selected regions. Thus, we could map 6 yet unreported ECBs in HLA with respect to the human genome. Additionally, in 26 of the 86 previously reported ECBs, the present approach enabled a more precise breakpoint mapping. Interestingly, a preferred localization of ECBs within segmental duplications, copy number variant regions, and fragile sites was observed.
Collapse
Affiliation(s)
- Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
20
|
Moysés-Oliveira M, Guilherme RDS, Dantas AG, Ueta R, Perez AB, Haidar M, Canonaco R, Meloni VA, Kosyakova N, Liehr T, Carvalheira GM, Melaragno MI. Genetic mechanisms leading to primary amenorrhea in balanced X-autosome translocations. Fertil Steril 2015; 103:1289-96.e2. [PMID: 25747126 DOI: 10.1016/j.fertnstert.2015.01.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 01/15/2015] [Accepted: 01/21/2015] [Indexed: 11/19/2022]
Abstract
OBJECTIVE To map the X-chromosome and autosome breakpoints in women with balanced X-autosome translocations and primary amenorrhea, searching candidate genomic loci for female infertility. DESIGN Retrospective and case-control study. SETTING University-based research laboratory. PATIENT(S) Three women with balanced X-autosome translocation and primary amenorrhea. INTERVENTION(S) Conventional cytogenetic methods, genomic array, array painting, fluorescence in situ hybridization, and quantitative reverse transcription-polymerase chain reaction. MAIN OUTCOME MEASURE(S) Karyotype, copy number variation, breakpoint mapping, and gene expression levels. RESULT(S) All patients presented with breakpoints in the Xq13q21 region. In two patients, the X-chromosome breakpoint disrupted coding sequences (KIAA2022 and ZDHHC15 genes). Although both gene disruptions caused absence of transcription in peripheral blood, there is no evidence that supports the involvement of these genes with ovarian function. The ZDHHC15 gene belongs to a conserved syntenic region that encompasses the FGF16 gene, which plays a role in female germ line development. The break in the FGF16 syntenic block may have disrupted the interaction between the FGF16 promoter and its cis-regulatory element. In the third patient, although both breakpoints are intergenic, a gene that plays a role in the DAX1 pathway (FHL2 gene) flanks distally the autosome breakpoint. The FHL2 gene may be subject to position effect due to the attachment of an autosome segment in Xq21 region. CONCLUSION(S) The etiology of primary amenorrhea in balanced X-autosome translocation patients may underlie more complex mechanisms than interruption of specific X-linked candidate genes, such as position effect. The fine mapping of the rearrangement breakpoints may be a tool for identifying genetic pathogenic mechanisms for primary amenorrhea.
Collapse
Affiliation(s)
- Mariana Moysés-Oliveira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Roberta Dos Santos Guilherme
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil; Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Anelisa Gollo Dantas
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Renata Ueta
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Beatriz Perez
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Mauro Haidar
- Departament of Gynecology, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosane Canonaco
- Genetics Division, Hospital do Servidor Público do Estado de São Paulo, São Paulo, Brazil
| | - Vera Ayres Meloni
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Gianna Maria Carvalheira
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Maria Isabel Melaragno
- Genetics Division, Department of Morphology and Genetics, Universidade Federal de São Paulo, São Paulo, Brazil.
| |
Collapse
|
21
|
Brečević L, Rinčić M, Krsnik Ž, Sedmak G, Hamid AB, Kosyakova N, Galić I, Liehr T, Borovečki F. Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci 2015; 6:59-86. [PMID: 28123791 PMCID: PMC4936614 DOI: 10.1515/tnsci-2015-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/29/2014] [Indexed: 12/14/2022] Open
Abstract
We describe an as yet unreported neocentric small supernumerary marker chromosome (sSMC) derived from chromosome 1p21.3p21.2. It was present in 80% of the lymphocytes in a male patient with intellectual disability, severe speech deficit, mild dysmorphic features, and hyperactivity with elements of autism spectrum disorder (ASD). Several important neurodevelopmental genes are affected by the 3.56 Mb copy number gain of 1p21.3p21.2, which may be considered reciprocal in gene content to the recently recognized 1p21.3 microdeletion syndrome. Both 1p21.3 deletions and the presented duplication display overlapping symptoms, fitting the same disorder category. Contribution of coding and non-coding genes to the phenotype is discussed in the light of cellular and intercellular homeostasis disequilibrium. In line with this the presented 1p21.3p21.2 copy number gain correlated to 1p21.3 microdeletion syndrome verifies the hypothesis of a cumulative effect of the number of deregulated genes - homeostasis disequilibrium leading to overlapping phenotypes between microdeletion and microduplication syndromes. Although miR-137 appears to be the major player in the 1p21.3p21.2 region, deregulation of the DPYD (dihydropyrimidine dehydrogenase) gene may potentially affect neighboring genes underlying the overlapping symptoms present in both the copy number loss and copy number gain of 1p21. Namely, the all-in approach revealed that DPYD is a complex gene whose expression is epigenetically regulated by long non-coding RNAs (lncRNAs) within the locus. Furthermore, the long interspersed nuclear element-1 (LINE-1) L1MC1 transposon inserted in DPYD intronic transcript 1 (DPYD-IT1) lncRNA with its parasites, TcMAR-Tigger5b and pair of Alu repeats appears to be the “weakest link” within the DPYD gene liable to break. Identification of the precise mechanism through which DPYD is epigenetically regulated, and underlying reasons why exactly the break (FRA1E) happens, will consequently pave the way toward preventing severe toxicity to the antineoplastic drug 5-fluorouracil (5-FU) and development of the causative therapy for the dihydropyrimidine dehydrogenase deficiency.
Collapse
Affiliation(s)
- Lukrecija Brečević
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- E-mail: ;
| | - Martina Rinčić
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Ivan Galić
- Center for Rehabilitation Stančić, Stančić bb, 10370 Stančić, Croatia
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
| |
Collapse
|
22
|
Supiwong W, Liehr T, Cioffi MB, Chaveerach A, Kosyakova N, Fan X, Tanee T, Tanomtong A. Comparative cytogenetic mapping of rRNA genes among naked catfishes: implications for genomic evolution in the Bagridae family. Genet Mol Res 2014; 13:9533-42. [PMID: 25501163 DOI: 10.4238/2014.november.12.2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In the present study, the karyotype and chromosomal characteristics of 9 species of the Bagridae fish family were investigated using conventional Giemsa staining as well as dual-color fluorescence in situ hybridization to detect the 18S and 5S rDNA sites. In addition to describing the karyotype of several Bagridae catfishes, we established molecular cytogenetic techniques to study this group. The 9 species contained a diploid chromosomal number, varying from 50 (Pseudomystus siamensis) to 62 (Hemibagrus wyckii), while none contained heteromorphic sex chromosomes. 18S rDNA sites were detected in only 1 chromosomal pair among all species evaluated. However, 3 different patterns were observed for the distribution of the 5S rDNA: 2 sites were found in the genus Mystus and in P. siamensis, multiple sites were observed in the genus Hemibagrus, and a syntenic condition for the 18S and 5S rDNA sites was identified in H. wyckii. The extensive variation in the number and chromosomal position of rDNA clusters observed among these Bagridae species may be related to the intense evolutionary dynamics of rDNA-repeated units, which generates divergent chromosomal distribution patterns even among closely related species. In summary, the distribution of repetitive DNA sequences provided novel, useful information regarding the evolutionary relationships between Bagridae fishes.
Collapse
Affiliation(s)
- W Supiwong
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - T Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - M B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brasil
| | - A Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, Muangkhonkaen District, Khon Kaen, Thailand
| | - N Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - X Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany
| | - T Tanee
- Faculty of Environment and Resource Studies, Mahasarakham University, Kantarawichai District, Mahasarakham, Thailand
| | - A Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, Muangkhonkaen District, Khon Kaen, Thailand
| |
Collapse
|
23
|
Karamysheva T, Kosyakova N, Guediche N, Liehr T. Small supernumerary marker chromosomes and the nuclear architecture of sperm – a study in a fertile and an infertile brother. Syst Biol Reprod Med 2014; 61:32-6. [DOI: 10.3109/19396368.2014.979956] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
24
|
Hussein SS, Kreskowski K, Ziegler M, Klein E, Hamid AB, Kosyakova N, Volleth M, Liehr T, Fan X, Piaszinski K. Mitotic stability of small supernumerary marker chromosomes depends on their shape and telomeres - a long term in vitro study. Gene 2014; 552:246-8. [PMID: 25245454 DOI: 10.1016/j.gene.2014.09.041] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/19/2014] [Indexed: 12/23/2022]
Abstract
Mosaicism is present in more than 50% of the cases with small supernumerary marker chromosomes (sSMCs) and karyotype 47,XX,+mar/46,XX or 47,XY,+mar/46,XY. Recently we provided first evidence that the mitotic stability of sSMC is dependent on their structure, i.e. their shape. Thus, here we performed a long term in vitro study on 12 selected cell lines from the Else Kröner-Fresenius-sSMC-cellbank (http://ssmc-tl.com/ekf-cellbank.html) to test mitotic sSMC stability systematically. The obtained results showed that inverted duplicated shaped and also the so-called complex sSMCs (group 1) are by far more stable, than centric-minute- or ring-shaped sSMCs (groups 2). Generally speaking, the percentage of cells with group-1-sSMCs remained stable over 90 days of cell culture, while that of group-2-sSMCs in parts dramatically decreased. In one group-2-cell line the sSMC was even lost completely after 30 days of in vitro culture, in others the sSMC was depleted in up to 40% of the cells. Still the highest rate of sSMC loss was recorded during EBV-transformation. Overall, the major difference between groups 1 and 2 was the number of telomeres per sSMC. In group 1 the sSMCs had "original" telomeres at both of their ends; in group 2 the sSMCs had either no, possibly secondary acquired and/or only one original telomere. This absence of protective telomeric sequences in group 2 seems to make sSMC more susceptible for loss during cell division. Still, also a growth advantage of cells without sSMC cannot be neglected entirely.
Collapse
Affiliation(s)
- Shaymaa Subhi Hussein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Katharina Kreskowski
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Monika Ziegler
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Elisabeth Klein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Ahmed B Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Marianne Volleth
- Institut für Humangenetik, Universitätsklinikum, Leipziger Str. 44, 39120 Magdeburg, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany.
| | - Xiaobo Fan
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Katja Piaszinski
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| |
Collapse
|
25
|
Jancuskova T, Plachy R, Zemankova L, Hardekopf DW, Stika J, Zejskova L, Praulich I, Kreuzer KA, Rothe A, Othman MA, Kosyakova N, Pekova S. Molecular characterization of the rare translocation t(3;10)(q26;q21) in an acute myeloid leukemia patient. Mol Cytogenet 2014; 7:47. [PMID: 25071866 PMCID: PMC4113123 DOI: 10.1186/1755-8166-7-47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 07/02/2014] [Indexed: 01/17/2023] Open
Abstract
Background In acute myeloid leukemia (AML), the MDS1 and EVI1 complex locus - MECOM, also known as the ecotropic virus integration site 1 - EVI1, located in band 3q26, can be rearranged with a variety of partner chromosomes and partner genes. Here we report on a 57-year-old female with AML who presented with the rare translocation t(3;10)(q26;q21) involving the MECOM gene. Our aim was to identify the fusion partner on chromosome 10q21 and to characterize the precise nucleotide sequence of the chromosomal breakpoint. Methods Cytogenetic and molecular-cytogenetic techniques, chromosome microdissection, next generation sequencing, long-range PCR and direct Sanger sequencing were used to map the chromosomal translocation. Results Using a combination of cytogenetic and molecular approaches, we mapped the t(3;10)(q26;q21) to the single nucleotide level, revealing a fusion of the MECOM gene (3q26.2) and C10orf107 (10q21.2). Conclusions The approach described here opens up new possibilities in characterizing acquired as well as congenital chromosomal aberrations. In addition, DNA sequences of chromosomal breakpoints may be a useful tool for unique molecular minimal residual disease target identification in acute leukemia patients.
Collapse
Affiliation(s)
- Tereza Jancuskova
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - Radek Plachy
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - Lucie Zemankova
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - David Warren Hardekopf
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - Jiri Stika
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - Lenka Zejskova
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| | - Inka Praulich
- Department I of Internal Medicine, University at Cologne, Kerpener Str., Cologne, Germany
| | - Karl-Anton Kreuzer
- Department I of Internal Medicine, University at Cologne, Kerpener Str., Cologne, Germany
| | - Achim Rothe
- Oncological Therapy Center, Buchforststr., Cologne, Germany
| | - Moneeb Ak Othman
- Jena University Hospital, Institute of Human Genetics, Kollegiengasse 10, Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Institute of Human Genetics, Kollegiengasse 10, Jena, Germany
| | - Sona Pekova
- Laboratory for Molecular Diagnostics, synlab genetics s.r.o., Evropska 176/16, Prague 6 16000, Czech Republic
| |
Collapse
|
26
|
Supiwong W, Liehr T, Cioffi MB, Chaveerach A, Kosyakova N, Pinthong K, Tanee T, Tanomtong A. Chromosomal evolution in naked catfishes (Bagridae, Siluriformes): A comparative chromosome mapping study. ZOOL ANZ 2014. [DOI: 10.1016/j.jcz.2014.02.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
27
|
Spittel H, Kubek F, Kreskowski K, Ziegler M, Klein E, Hamid AB, Kosyakova N, Radhakrishnan G, Junge A, Kozlowski P, Schulze B, Martin T, Huhle D, Mehnert K, Rodríguez L, Ergun MA, Sarri C, Militaru M, Stipoljev F, Tittelbach H, Vasheghani F, de Bello Cioffi M, Hussein SS, Fan X, Volleth M, Liehr T. Mitotic stability of small supernumerary marker chromosomes: a study based on 93 immortalized cell lines. Cytogenet Genome Res 2014; 142:151-60. [PMID: 24714101 DOI: 10.1159/000360776] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/07/2014] [Indexed: 11/19/2022] Open
Abstract
Small supernumerary marker chromosomes (sSMC) are known for being present in mosaic form as 47,+mar/46 in >50% of the cases with this kind of extra chromosomes. However, no detailed studies have been done for the mitotic stability of sSMC so far, mainly due to the lack of a corresponding in vitro model system. Recently, we established an sSMC-cell bank (Else Kröner-Fresenius-sSMC-cellbank) with >150 cell lines. Therefore, 93 selected sSMC cases were studied here for the presence of the corresponding marker chromosomes before and after Epstein-Barr virus-induced immortalization. The obtained results showed that dicentric inverted duplicated-shaped sSMC are by far more stable in vitro than monocentric centric minute- or ring-shaped sSMC. Simultaneously, a review of the literature revealed that a comparable shape-dependent mitotic stability can be found in vivo in sSMC carriers. Additionally, a possible impact of the age of the sSMC carrier on mitotic stability was found: sSMC cell lines established from patients between 10-20 years of age were predominantly mitotically unstable. The latter finding was independent of the sSMC shape. The present study shows that in vitro models can lead to new and exciting insights into the biology of this genetically and clinically heterogeneous patient group.
Collapse
Affiliation(s)
- Hannes Spittel
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
28
|
Santiago F, Alves G, Otero UB, Tabalipa MM, Scherrer LR, Kosyakova N, Ornellas MH, Liehr T. Monitoring of gas station attendants exposure to benzene, toluene, xylene (BTX) using three-color chromosome painting. Mol Cytogenet 2014; 7:15. [PMID: 24576355 PMCID: PMC3974043 DOI: 10.1186/1755-8166-7-15] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 02/12/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chronic exposure of BTX (benzene, toluene, xylene) may lead to progressive degeneration of bone marrow, aplastic anemia and/or leukemia. In Brazil there is no self-service fuel in gas stations and attendants fill the fuel themselves. Due to this they are chronically exposed to high concentration of BTX. Occupational exposure to benzene has been associated with increased chromosomal aberrations in peripheral blood lymphocytes. Fluorescence in situ hybridization (FISH) using whole chromosome painting (wcp) probes allows the rapid detection of chromosomal aberration. In the present study three-color wcp probes for chromosomes 1, 2 and 4 were used for monitoring 60 gas station attendants. RESULTS Blood tests were done and interviews were conducted for each worker. For searching for possible associations between the clinical characteristics and the frequency of chromosomal aberrations the workers were divided into two groups (≤ 10 chromosomal abnormalities per 1,000 metaphases and > 10 chromosomal abnormalities per 1,000 metaphases).The studied workers had a low median age (36 year), albeit long period of BTX exposure (median was 16 years). Low prevalence of smoking and moderate consumption of alcoholic beverages were found in this population. The cytogenetic analysis showed 16.6% (10/60) of workers with a high frequency of chromosomal abnormalities (>10 chromosomal abnormalities per 1,000 metaphases). Translocations were the most frequently observed chromosome aberration. The statistical analysis revealed highly significant differences in skin color (p = 0.002) and a weak significant differences in gender (p = 0.052) distribution between the two groups. CONCLUSION 16.6% of the studied population showed elevated frequencies of chromosomal abnormalities, which is highly likely to be correlated with their exposure to BTX during their work. Therefore, further studies are needed for better characterize the work associated damage of the genome in gas station workers. It is necessary to better understand the risks that these workers are exposed, so that we can be effective in preventing diseases and maintaining the health of these workers and possibly the offspring.
Collapse
Affiliation(s)
| | - Gilda Alves
- Programa de Pós-Graduação em Ciências Médicas, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brasil.
| | | | | | | | | | | | | |
Collapse
|
29
|
Xiaobo F, Pinthong K, Mkrtchyan H, Siripiyasing P, Kosyakova N, Supiwong W, Tanomtong A, Chaveerach A, Liehr T, de Bello Cioffi M, Weise A. First detailed reconstruction of the karyotype of Trachypithecus cristatus (Mammalia: Cercopithecidae). Mol Cytogenet 2013; 6:58. [PMID: 24341374 PMCID: PMC3914712 DOI: 10.1186/1755-8166-6-58] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 11/21/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The chromosomal homologies of human (Homo sapiens = HSA) and silvered leaf monkey (Trachypithecus cristatus = TCR) have been previously studied by classical chromosome staining and by fluorescence in situ hybridization (FISH) applying chromosome-specific DNA probes of all human chromosomes in the 1980s and 1990s, respectively. RESULTS However, as the resolution of these techniques is limited we used multicolor banding (MCB) at an ~250-band level, and other selected human DNA probes to establish a detailed chromosomal map of TCR. Therefore it was possible to precisely determine evolutionary conserved breakpoints, orientation of segments and distribution of specific regions in TCR compared to HSA. Overall, 69 evolutionary conserved breakpoints including chromosomal segments, which failed to be resolved in previous reports, were exactly identified and characterized. CONCLUSIONS This work also represents the first molecular cytogenetic one characterizing a multiple sex chromosome system with a male karyotype 44,XY1Y2. The obtained results are compared to other available data for old world monkeys and drawbacks in hominoid evolution are discussed.
Collapse
Affiliation(s)
- Fan Xiaobo
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Krit Pinthong
- Faculty of Science and Technology, Surindra Rajabhat University, 186 Moo 1, Surin, Maung District 32000, Thailand
| | - Hasmik Mkrtchyan
- Center of Medical Genetics and Primary Health Care, Abovyan Str 34/3, 001, Yerevan, Armenia
| | - Pornnarong Siripiyasing
- Faculty of Science and Technology, Rajabhat Maha Sarakham University, 80 Nakonsawan Rd, Maha Sarakham, Talad, Maung District 44000, Thailand
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Weerayuth Supiwong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Alongkoad Tanomtong
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Arunrat Chaveerach
- Department of Biology, Faculty of Science, Khon Kaen University, 123 Moo 16 Mittapap Rd., Khon Kaen, Muang District 40002, Thailand
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
| | - Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil
| | - Anja Weise
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Kollegiengasse 10, Jena D-07743, Germany
- Institut für Humangenetik, Postfach, Jena D-07740, Germany
| |
Collapse
|
30
|
Supiwong W, Liehr T, Cioffi MB, Chaveerach A, Kosyakova N, Pinthong K, Tanee T, Tanomtong A. Karyotype and cytogenetic mapping of 9 classes of repetitive DNAs in the genome of the naked catfish Mystus bocourti (Siluriformes, Bagridae). Mol Cytogenet 2013; 6:51. [PMID: 24266901 PMCID: PMC4176197 DOI: 10.1186/1755-8166-6-51] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 09/20/2013] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND In the present study, conventional and molecular cytogenetic studies were performed in the naked catfish Mystus bocourti (Siluriformes, Bagridae). Besides the conventional Giemsa staining, fluorescence in situ hybridization (FISH) using nine classes of repetitive DNAs namely 5S and 18S rDNAs, U2 snRNA, the microsatellites (CA)15 and (GA)15, telomeric repeats, and the retrotransposable elements Rex1, 3 and 6. was also performed. RESULTS M. bocourti had 2n = 56 chromosomes with a karyotype composed by 11 m + 11 sm + 6 st/a and a fundamental number (NF) equal to 100 in both sexes. Heteromorphic sex chromosome cannot be identified. The U2 snRNA, 5S and 18S rDNA were present in only one pair of chromosomes but none of them in a syntenic position. Microsatellites (CA)15 and (GA)15 showed hybridization signals at subtelomeric regions of all chromosomes with a stronger accumulation into one specific chromosomal pair. FISH with the telomeric probe revealed hybridization signals on each telomere of all chromosomes and interstitial telomeric sites (ITS) were not detected. The retrotransposable elements Rex1, 3 and 6 were generally spread throughout the genome. CONCLUSIONS In general, the repetitive sequences were not randomly distributed in the genome, suggesting a pattern of compartmentalization on the heterochromatic region of the chromosomes. Little is known about the structure and organization of bagrid genomes and the knowledge of the chromosomal distribution of repetitive DNA sequences in M. bocourti represents the first step for achieving an integrated view of their genomes.
Collapse
Affiliation(s)
- Weerayuth Supiwong
- Department of Biology Faculty of Science, Khon Kaen University, 123 Mitraphap Highway, Khon Kaen 40002, Muangkhonkaen District, Thailand.
| | | | | | | | | | | | | | | |
Collapse
|
31
|
Liehr T, Cirkovic S, Lalic T, Guc-Scekic M, de Almeida C, Weimer J, Iourov I, Melaragno MI, Guilherme RS, Stefanou EGG, Aktas D, Kreskowski K, Klein E, Ziegler M, Kosyakova N, Volleth M, Hamid AB. Complex small supernumerary marker chromosomes - an update. Mol Cytogenet 2013; 6:46. [PMID: 24171835 PMCID: PMC4129180 DOI: 10.1186/1755-8166-6-46] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 09/26/2013] [Indexed: 11/10/2022] Open
Abstract
Background Complex small supernumerary marker chromosomes (sSMC) constitute one of the smallest subgroups of sSMC in general. Complex sSMC consist of chromosomal material derived from more than one chromosome; the best known representative of this group is the derivative chromosome 22 {der(22)t(11;22)} or Emanuel syndrome. In 2008 we speculated that complex sSMC could be part of an underestimated entity. Results Here, the overall yet reported 412 complex sSMC are summarized. They constitute 8.4% of all yet in detail characterized sSMC cases. The majority of the complex sSMC is contributed by patients suffering from Emanuel syndrome (82%). Besides there are a der(22)t(8;22)(q24.1;q11.1) and a der(13)t(13;18)(q11;p11.21) or der(21)t(18;21)(p11.21;q11.1) = der(13 or 21)t(13 or 21;18) syndrome. The latter two represent another 2.6% and 2.2% of the complex sSMC-cases, respectively. The large majority of complex sSMC has a centric minute shape and derives from an acrocentric chromosome. Nonetheless, complex sSMC can involve material from each chromosomal origin. Most complex sSMC are inherited form a balanced translocation in one parent and are non-mosaic. Interestingly, there are hot spots for the chromosomal breakpoints involved. Conclusions Complex sSMC need to be considered in diagnostics, especially in non-mosaic, centric minute shaped sSMC. As yet three complex-sSMC-associated syndromes are identified. As recurrent breakpoints in the complex sSMC were characterized, it is to be expected that more syndromes are identified in this subgroup of sSMC. Overall, complex sSMC emphasize once more the importance of detailed cytogenetic analyses, especially in patients with idiopathic mental retardation.
Collapse
Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany ; Institut für Humangenetik, Postfach, Jena D-07740, Germany
| | - Sanja Cirkovic
- Laboratory for Medical Genetics, Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Radoje Dakic str. 6-8, Belgrade 11070, Serbia
| | - Tanja Lalic
- Laboratory for Medical Genetics, Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Radoje Dakic str. 6-8, Belgrade 11070, Serbia
| | - Marija Guc-Scekic
- Laboratory for Medical Genetics, Mother and Child Health Care Institute of Serbia "Dr Vukan Cupic", Radoje Dakic str. 6-8, Belgrade 11070, Serbia ; University of Belgrade, Faculty of Biology, Belgrade, Serbia
| | - Cynthia de Almeida
- Military Hospital associated with "Universidad de la República (UDELAR)", Montevideo, Uruguay
| | - Jörg Weimer
- Department of Gynecology and Obstetrics, UKSH Campus Kiel, Arnold-Heller-Str. 3; House 24, Kiel 24105, Germany
| | - Ivan Iourov
- Research Center for Mental Health, RAMS, Moscow, Russia ; Institute of Pediatrics and Children Surgery, RF Ministry of Health, Moscow, Russia
| | - Maria Isabel Melaragno
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo SP, 04023-900, Brazil
| | - Roberta S Guilherme
- Department of Morphology and Genetics, Universidade Federal de São Paulo, Rua Botucatu 740, São Paulo SP, 04023-900, Brazil
| | - Eunice-Georgia G Stefanou
- Department of Pediatrics, Laboratory of Medical Genetics, University General Hospital of Patras, Rion, Patras 26504, Greece
| | - Dilek Aktas
- Hacettepe University School of Medicine, Dept of Medical Genetics, 06100 Sihhiye, Ankara, Turkey
| | - Katharina Kreskowski
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany
| | - Elisabeth Klein
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany
| | - Monika Ziegler
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany
| | - Marianne Volleth
- Institut für Humangenetik, Universitätsklinikum, Leipziger Str. 44, Magdeburg 39120, Germany
| | - Ahmed B Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany
| |
Collapse
|
32
|
Liehr T, Weise A, Hamid AB, Fan X, Klein E, Aust N, Othman MA, Mrasek K, Kosyakova N. Multicolor FISH methods in current clinical diagnostics. Expert Rev Mol Diagn 2013; 13:251-5. [PMID: 23570403 DOI: 10.1586/erm.12.146] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Multicolor FISH (mFISH) assays are currently indispensable for a precise description of derivative chromosomes. Routine application of such techniques on human chromosomes started in 1996 with the simultaneous use of all 24 human whole-chromosome painting probes in multiplex-FISH and spectral karyotyping. Since then, multiple approaches for chromosomal differentiation based on multicolor-FISH (MFISH) assays have been developed. Predominantly, they are applied to characterize marker or derivative chromosomes identified in conventional banding analysis. Since the introduction of array-based comparative genomic hybridization (aCGH), mFISH is also applied to verify and further delineate aCGH-detected aberrations. For the latter, it is important to consider the fact that aCGH cannot detect or characterize balanced rearrangements, which are important to be resolved in detail in infertility diagnostics. In addition, mFISH is necessary to distinguish different imbalanced situations detectable in aCGH; small supernumerary marker chromosomes have to be differentiated from insertions or unbalanced translocations. This review presents an overview on the available mFISH methods and their applications in pre- and post-natal clinical genetics.
Collapse
Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Jancuskova T, Plachy R, Stika J, Zemankova L, Hardekopf DW, Liehr T, Kosyakova N, Cmejla R, Zejskova L, Kozak T, Zak P, Zavrelova A, Havlikova P, Karas M, Junge A, Ramel C, Pekova S. A method to identify new molecular markers for assessing minimal residual disease in acute leukemia patients. Leuk Res 2013; 37:1363-73. [PMID: 23870092 DOI: 10.1016/j.leukres.2013.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 05/20/2013] [Accepted: 06/05/2013] [Indexed: 01/13/2023]
Abstract
Acute leukemias (AL) comprise a heterogeneous group of hematologic malignancies, and individual patient responses to treatment can be difficult to predict. Monitoring of minimal residual disease (MRD) is thus very important and holds great potential for improving treatment strategies. Common MRD targets include recurrent cytogenetic abnormalities and mutations in important hematological genes; unfortunately well-characterized targets are lacking in many AL patients. Here we demonstrate a technical approach for the identification and mapping of novel clone-specific chromosomal abnormalities down to the nucleotide level. We used molecular cytogenetics, chromosome microdissection, amplification of the microdissected material, and next-generation sequencing to develop PCR-based MRD assays based on unique breakpoint sequences.
Collapse
Affiliation(s)
- Tereza Jancuskova
- Chambon, Laboratory for Molecular Diagnostics, Prague, Czech Republic
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Nazaryan L, Stefanou EG, Hansen C, Kosyakova N, Bak M, Sharkey FH, Mantziou T, Papanastasiou AD, Velissariou V, Liehr T, Syrrou M, Tommerup N. The strength of combined cytogenetic and mate-pair sequencing techniques illustrated by a germline chromothripsis rearrangement involving FOXP2. Eur J Hum Genet 2013; 22:338-43. [PMID: 23860044 PMCID: PMC3925275 DOI: 10.1038/ejhg.2013.147] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 05/17/2013] [Accepted: 05/23/2013] [Indexed: 11/13/2022] Open
Abstract
Next-generation mate-pair sequencing (MPS) has revealed that many constitutional complex chromosomal rearrangements (CCRs) are associated with local shattering of chromosomal regions (chromothripsis). Although MPS promises to identify the molecular basis of the abnormal phenotypes associated with many CCRs, none of the reported mate-pair sequenced complex rearrangements have been simultaneously studied with state-of-the art molecular cytogenetic techniques. Here, we studied chromothripsis-associated CCR involving chromosomes 2, 5 and 7, associated with global developmental and psychomotor delay and severe speech disorder. We identified three truncated genes: CDH12, DGKB and FOXP2, confirming the role of FOXP2 in severe speech disorder, and suggestive roles of CDH12 and/or DGKB for the global developmental and psychomotor delay. Our study confirmes the power of MPS for detecting breakpoints and truncated genes at near nucleotide resolution in chromothripsis. However, only by combining MPS data with conventional G-banding and extensive fluorescence in situ hybridizations could we delineate the precise structure of the derivative chromosomes.
Collapse
Affiliation(s)
- Lusine Nazaryan
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Eunice G Stefanou
- Laboratory of Medical Genetics, Cytogenetics Unit, Department of Pediatrics, University General Hospital of Patras, Patras, Greece
| | - Claus Hansen
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Nadezda Kosyakova
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Mads Bak
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| | - Freddie H Sharkey
- Department of Molecular Genetics, Western General Hospital, Edinburgh, UK
| | - Theodora Mantziou
- Laboratory of General Biology, University of Ioannina, Ioannina, Greece
| | | | - Voula Velissariou
- Department of Genetics and Molecular Biology, 'Mitera' General Maternity/Gynecology and Children's Hospital, Hygeia Group, Athens, Greece
| | - Thomas Liehr
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Maria Syrrou
- Laboratory of General Biology, University of Ioannina, Ioannina, Greece
| | - Niels Tommerup
- Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, Faculty of Health Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
35
|
Kosyakova N, Grigorian A, Liehr T, Manvelyan M, Simonyan I, Mkrtchyan H, Aroutiounian R, Polityko AD, Kulpanovich AI, Egorova T, Jaroshevich E, Frolova A, Shorokh N, Naumchik IV, Volleth M, Schreyer I, Nelle H, Stumm M, Wegner RD, Reising-Ackermann G, Merkas M, Brecevic L, Martin T, Rodríguez L, Bhatt S, Ziegler M, Kreskowski K, Weise A, Sazci A, Vorsanova S, Cioffi MDB, Ergul E. Heteromorphic variants of chromosome 9. Mol Cytogenet 2013; 6:14. [PMID: 23547710 PMCID: PMC3626942 DOI: 10.1186/1755-8166-6-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Accepted: 01/30/2013] [Indexed: 12/05/2022] Open
Abstract
Background Heterochromatic variants of pericentromere of chromosome 9 are reported and discussed since decades concerning their detailed structure and clinical meaning. However, detailed studies are scarce. Thus, here we provide the largest ever done molecular cytogenetic research based on >300 chromosome 9 heteromorphism carriers. Results In this study, 334 carriers of heterochromatic variants of chromosome 9 were included, being 192 patients from Western Europe and the remainder from Easter-European origin. A 3-color-fluorescence in situ hybridization (FISH) probe-set directed against for 9p12 to 9q13~21.1 (9het-mix) and 8 different locus-specific probes were applied for their characterization. The 9het-mix enables the characterization of 21 of the yet known 24 chromosome 9 heteromorphic patterns. In this study, 17 different variants were detected including five yet unreported; the most frequent were pericentric inversions (49.4%) followed by 9qh-variants (23.9%), variants of 9ph (11.4%), cenh (8.2%), and dicentric- (3.8%) and duplication-variants (3.3%). For reasons of simplicity, a new short nomenclature for the yet reported 24 heteromorphic patterns of chromosome 9 is suggested. Six breakpoints involved in four of the 24 variants could be narrowed down using locus-specific probes. Conclusions Based on this largest study ever done in carriers of chromosome 9 heteromorphisms, three of the 24 detailed variants were more frequently observed in Western than in Eastern Europe. Besides, there is no clear evidence that infertility is linked to any of the 24 chromosome 9 heteromorphic variants.
Collapse
Affiliation(s)
- Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Kosyakova N, Hamid AB, Chaveerach A, Pinthong K, Siripiyasing P, Supiwong W, Romanenko S, Trifonov V, Fan X. Generation of multicolor banding probes for chromosomes of different species. Mol Cytogenet 2013; 6:6. [PMID: 23374863 PMCID: PMC3575270 DOI: 10.1186/1755-8166-6-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 12/14/2012] [Indexed: 02/04/2023] Open
Abstract
Background The multicolor banding (MCB/mBAND) technique provides a unique opportunity to characterize intrachromosomal rearrangements and to determine chromosomal breakpoints. Until recently, MCB probes have only been available for human and some murine chromosomes. Generation of MCB probes for chromosomes of other species, useful and required in many cytogenetics research fields, was limited by technical difficulties. MCB probes are established by chromosome microdissection followed by whole genomic DNA amplification. However, unambiguous identification of the target chromosome is required for MCB-probe establishment. Previously proposed protocols suggested G-banding staining or preliminary FISH with whole chromosome paints (WCP) as methods to identify the chromosome of interest. Results Here we present a complete workflow for MCB probe generation for those cases and species where chromosome morphology is too challenging to recognize target chromosomes by conventional methods and where WCP probes are not available. The workflow was successfully applied for murine chromosomes that are difficult to identify unambiguously. Additionally, we showed that glass-needle based microdissection enables establishment of a whole set of WCP paints by microdissection of individual chromosomes of a single metaphase Conclusions The present method can be applied for generation of whole or region-specific DNA probes for species, where karyotyping of G-banded chromosomes is challenging due to similar chromosome morphology and/or chromosome banding patterns.
Collapse
Affiliation(s)
- Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena, D-07743, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Leibiger C, Kosyakova N, Mkrtchyan H, Glei M, Trifonov V, Liehr T. First molecular cytogenetic high resolution characterization of the NIH 3T3 cell line by murine multicolor banding. J Histochem Cytochem 2013; 61:306-12. [PMID: 23321776 PMCID: PMC3621507 DOI: 10.1369/0022155413476868] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Since being established in 1963, the murine fibroblast cell line NIH 3T3 has been used in thousands of studies. NIH 3T3 immortalized spontaneously and became tetraploid shortly after its establishment. Here we report the first molecular cytogenetic characterization of NIH 3T3 using fluorescence in situ hybridization based multicolor banding (mcb). Overall, a complex rearranged karyotype presenting 16 breakpoints was characterized. Also it was possible to deduce the resulting gains and losses of copy numbers in NIH 3T3. Overall, only 1.8% of the NIH 3T3 genome is disome, 26.2% tri-, 60% tetra-, 10.8% quinta-, and 1.2% hexasome. Strikingly, the cell line gained only 4 derivative chromosomes since its first cytogenetic description in 1989. An attempt to align the observed imbalances of the studied cell line with their homologous regions in humans gave the following surprising result: NIH 3T3 shows imbalances as typically seen in human solid cancers of ectodermal origin.
Collapse
Affiliation(s)
- Christine Leibiger
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | |
Collapse
|
38
|
Liehr T, Kosyakova N. Small supernumerary marker chromosomes (sSMC) - what about the genotype-phenotype correlation? Tsitologiia 2013; 55:165-166. [PMID: 23795458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Genotype-phenotype correlations in patients with small supernumerary marker chromosomes (sSMC) are still difficult to asses. Here we review the presently known influence of chromosomal imbalance induced by sSMC size and origin, mosaicism of sSMC in different cells of the body and uniparental disomy (UPD) of sSMC's sister chromosomes on the clinical outcome.
Collapse
Affiliation(s)
- Th Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
| | | |
Collapse
|
39
|
Kosyakova N, Trifonov V, Romanenko S, Mkrtchyan H, Graphodatsky A, Liehr T. Murine multicolor banding. Tsitologiia 2013; 55:259-260. [PMID: 23875460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Multicolor banding approach, first introduced for human chromosomes only, was established as an optimal approach for karyotyping of murine chromosomes. Here we present the established mcb probe sets for all murine autosomes and the X-chromosome and review their potential application.
Collapse
Affiliation(s)
- N Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
| | | | | | | | | | | |
Collapse
|
40
|
Liehr T, Klein E, Mrasek K, Kosyakova N, Guilherme R, Aust N, Venner C, Weise A, Hamid A. Clinical Impact of Somatic Mosaicism in Cases with Small Supernumerary Marker Chromosomes. Cytogenet Genome Res 2013; 139:158-63. [DOI: 10.1159/000346026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
41
|
Lopez Corrales NL, Mrasek K, Voigt M, Liehr T, Kosyakova N. Comprehensive characterization of genomic instability in pluripotent stem cells and their derived neuroprogenitor cell lines. Appl Transl Genom 2012; 1:21-24. [PMID: 27896049 PMCID: PMC5121198 DOI: 10.1016/j.atg.2012.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The genomic integrity of two human pluripotent stem cells and their derived neuroprogenitor cell lines was studied, applying a combination of high-resolution genetic methodologies. The usefulness of combining array-comparative genomic hybridization (aCGH) and multiplex fluorescence in situ hybridization (M-FISH) techniques should be delineated to exclude/detect a maximum of possible genomic structural aberrations. Interestingly, in parts different genomic imbalances at chromosomal and subchromosomal levels were detected in pluripotent stem cells and their derivatives. Some of the copy number variations were inherited from the original cell line, whereas other modifications were presumably acquired during the differentiation and manipulation procedures. These results underline the necessity to study both pluripotent stem cells and their differentiated progeny by as many approaches as possible in order to assess their genomic stability before using them in clinical therapies.
Collapse
Affiliation(s)
- Nestor Luis Lopez Corrales
- Visiting Scientist CnPQ Fellowship, Brazil; Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Kristin Mrasek
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Martin Voigt
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743 Jena, Germany
| |
Collapse
|
42
|
Nelle H, Schreyer I, Ewers E, Mrasek K, Kosyakova N, Merkas M, Hamid AB, Fahsold R, Ujfalusi A, Anderson J, Rubtsov N, Küchler A, von Eggeling F, Hentschel J, Weise A, Liehr T. Presence of harmless small supernumerary marker chromosomes hampers molecular genetic diagnosis: a case report. Mol Med Rep 2012; 3:571-4. [PMID: 21472281 DOI: 10.3892/mmr_00000299] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Mental retardation is correlated in approximately 0.4% of cases with the presence of a small supernumerary marker chromosome (sSMC). However, here we report a case of a carrier of a heterochromatic harmless sSMC with fragile X syndrome (Fra X). In approximately 2% of sSMC cases, similar heterochromatic sSMC were observed in a clinically abnormal carriers. In a subset of such cases, uniparental disomy (UPD) of the corresponding sister chromosomes was shown to be the cause of mental retardation. For the remainder of the cases, including the present one, the sSMC was just a random finding not related to the clinical phenotype. Thus, it is proposed to test patients with heterochromatic sSMC and mental retardation of unclear cause as follows: i) exclude UPD, ii) test for Fra X as it is a major cause of inherited mental retardation, and iii) perform chip-based assays or tests for special genetic diseases according to the phenotype. In any case, the diagnosis of a cytogenetic aberration such as an sSMC should not automatically be considered the resolution of a clinical case.
Collapse
Affiliation(s)
- Heike Nelle
- Institute of Human Genetics and Anthropology, Jena University Hospital, 07740 Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Corrales NLL, Mrasek K, Voigt M, Liehr T, Kosyakova N. Copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitors. Gene 2012; 506:377-9. [PMID: 22820389 DOI: 10.1016/j.gene.2012.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2012] [Revised: 07/03/2012] [Accepted: 07/05/2012] [Indexed: 01/22/2023]
Abstract
Results from the analysis of copy number variations (CNVs) in human pluripotent cell-derived neuroprogenitor cell lines (hiPSC and hESC-derived NPC) are presented. Two different types of CNVs were detected: a) CNVs inherited from the original source of pluripotent cells (hESC and hiPSC) and b) CNVs detected either in the original source of pluripotent cells or in the derived NPC cell lines but not in both at the same time. Our data suggest that submicroscopic chromosomal changes happened during culture and manipulation of cells and those differentiation procedures could result in gains and losses of genomic regions in pluripotent cell-derived neuroprogenitors. Overall, the results indicate that even chromosomally stable stem cell lines would need to be analyzed in detail by high resolution methodologies before their clinical use.
Collapse
|
44
|
Papoulidis I, Kontodiou M, Tzimina M, Saitis I, Hamid AB, Klein E, Kosyakova N, Kordass U, Kunz J, Siomou E, Nicolaides P, Orru S, Thomaidis L, Liehr T, Petersen MB, Manolakos E. Tetrasomy 9p mosaicism associated with a normal phenotype in two cases. Cytogenet Genome Res 2012; 136:237-41. [PMID: 22487875 DOI: 10.1159/000337520] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/13/2012] [Indexed: 01/19/2023] Open
Abstract
Tetrasomy 9p is a rare chromosomal syndrome and about 30% of known cases exhibit mosaicism. Approximately 50 of the reported cases with tetrasomy 9p mosaicism show a characteristic facial appearance, growth failure, and developmental delay. However, 3 patients with mosaicism for isochromosome 9p and a normal phenotype have also been reported. We report 2 additional cases of clinically normal young females with tetrasomy 9p mosaicism, one of whom also exhibited X chromosome aneuploidy mosaicism leading to an overall of 6 different cell lines. STR analysis performed on this complex mosaic case indicated that the extra isochromosome was of maternal origin while the X chromosome aneuploidy was of paternal origin, indicating a postzygotic event.
Collapse
Affiliation(s)
- I Papoulidis
- Eurogenetica S.A., Thessaloniki and Athens, Greece
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Weise A, Mrasek K, Klein E, Mulatinho M, Llerena JC, Hardekopf D, Pekova S, Bhatt S, Kosyakova N, Liehr T. Microdeletion and microduplication syndromes. J Histochem Cytochem 2012; 60:346-58. [PMID: 22396478 DOI: 10.1369/0022155412440001] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The widespread use of whole genome analysis based on array comparative genomic hybridization in diagnostics and research has led to a continuously growing number of microdeletion and microduplication syndromes (MMSs) connected to certain phenotypes. These MMSs also include increasing instances in which the critical region can be reciprocally deleted or duplicated. This review catalogues the currently known MMSs and the corresponding critical regions including phenotypic consequences. Besides the pathogenic pathways leading to such rearrangements, the different detection methods and their limitations are discussed. Finally, the databases available for distinguishing between reported benign or pathogenic copy number alterations are highlighted. Overall, a review of MMSs that previously were also denoted "genomic disorders" or "contiguous gene syndromes" is given.
Collapse
Affiliation(s)
- Anja Weise
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Jena, Germany.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Klein E, Rocchi M, Ovens-Raeder A, Kosyakova N, Weise A, Ziegler M, Meins M, Morlot S, Fischer W, Volleth M, Polityko A, Ogilvie CM, Kraus C, Liehr T. Five novel locations of Neocentromeres in human: 18q22.1, Xq27.1∼27.2, Acro p13, Acro p12, and heterochromatin of unknown origin. Cytogenet Genome Res 2012; 136:163-6. [PMID: 22377933 DOI: 10.1159/000336648] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/13/2011] [Indexed: 11/19/2022] Open
Abstract
Since the first report in 1993, an ectopic centromere, i.e. neocentromere formation, has been reported in more than 100 small supernumerary marker chromosomes (sSMC), in 7 instances of centromere repositioning, and in about a dozen cases with more complex chromosomal rearrangements. Here we report 2 new cases with centromere repositioning and 3 neocentric sSMC consisting exclusively of heterochromatic material. Yet, no centromere formation was reported for the regions 18q22.1 and Xq27.1∼27.2 as it was observed in the 2 cases with centromere repositioning here; in both cases, cytogenetically an inversion was suggested. Two of the 3 neocentric sSMC were derived from a short arm of an acrocentric chromosome. The remainder neocentric sSMC case was previously reported and was stainable only by material derived from itself.
Collapse
Affiliation(s)
- E Klein
- Institute of Human Genetics, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
de Bello Cioffi M, Sánchez A, Marchal JA, Kosyakova N, Liehr T, Trifonov V, Bertollo LAC. Whole chromosome painting reveals independent origin of sex chromosomes in closely related forms of a fish species. Genetica 2011; 139:1065-72. [PMID: 21927842 DOI: 10.1007/s10709-011-9610-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/08/2011] [Indexed: 11/29/2022]
Abstract
The wolf fish Hoplias malabaricus includes well differentiated sex systems (XY and X(1)X(2)Y in karyomorphs B and D, respectively), a nascent XY pair (karyomorph C) and not recognized sex chromosomes (karyomorph A). We performed the evolutionary analysis of these sex chromosomes, using two X chromosome-specific probes derived by microdissection from the XY and X(1)X(2)Y sex systems. A putative-sex pair in karyomorph A was identified, from which the differentiated XY system was evolved, as well as the clearly evolutionary relationship between the nascent XY system and the origin of the multiple X(1)X(2)Y chromosomes. The lack of recognizable signals on the sex chromosomes after the reciprocal cross-FISH experiments highlighted that they evolved independently from non-homologous autosomal pairs. It is noteworthy that these distinct pathways occur inside the same nominal species, thus exposing the high plasticity of sex chromosome evolution in lower vertebrates. Possible mechanisms underlying this sex determination liability are also discussed.
Collapse
Affiliation(s)
- Marcelo de Bello Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP, Brazil.
| | | | | | | | | | | | | |
Collapse
|
48
|
Mkrtchyan H, Gross M, Hinreiner S, Polytiko A, Manvelyan M, Mrasek K, Kosyakova N, Ewers E, Nelle H, Liehr T, Bhatt S, Thoma K, Gebhart E, Wilhelm S, Fahsold R, Volleth M, Weise A. The human genome puzzle - the role of copy number variation in somatic mosaicism. Curr Genomics 2011; 11:426-31. [PMID: 21358987 PMCID: PMC3018723 DOI: 10.2174/138920210793176047] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2010] [Revised: 05/01/2010] [Accepted: 05/24/2010] [Indexed: 11/30/2022] Open
Abstract
The discovery of copy number variations (CNV) in the human genome opened new perspectives in the study of the genetic causes of inherited disorders and the etiology of common diseases. Differently patterned instances of somatic mosaicism in CNV regions have been shown to be present in monozygotic twins and throughout different tissues within an individual. A single-cell-level investigation of CNV in different human cell types led us to uncover mitotically derived genomic mosaicism, which is stable in different cell types of one individual. A unique study of immortalized B-lymphoblastoid cell lines obtained with 20 year interval from the same two subjects shows that mitotic changes in CNV regions may happen early during embryonic development and seem to occur only once, as levels of mosaicism remained stable. This finding has the potential to change our concept of dynamic human genome variation. We propose that further genomic studies should focus on the single-cell level, to understand better the etiology and physiology of aging and diseases mediated by somatic variations.
Collapse
Affiliation(s)
- Hasmik Mkrtchyan
- Jena University Hospital, Institute of Human Genetics and Anthropology, Jena, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Cioffi MB, Sánchez A, Marchal JA, Kosyakova N, Liehr T, Trifonov V, Bertollo LA. Cross-species chromosome painting tracks the independent origin of multiple sex chromosomes in two cofamiliar Erythrinidae fishes. BMC Evol Biol 2011; 11:186. [PMID: 21718509 PMCID: PMC3141436 DOI: 10.1186/1471-2148-11-186] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Accepted: 06/30/2011] [Indexed: 11/13/2022] Open
Abstract
Background The Erythrinidae fish family is characterized by a large variation with respect to diploid chromosome numbers and sex-determining systems among its species, including two multiple X1X2Y sex systems in Hoplias malabaricus and Erythrinus erythrinus. At first, the occurrence of a same sex chromosome system within a family suggests that the sex chromosomes are correlated and originated from ancestral XY chromosomes that were either homomorphic or at an early stage of differentiation. To identify the origin and evolution of these X1X2Y sex chromosomes, we performed reciprocal cross-species FISH experiments with two sex-chromosome-specific probes designed from microdissected X1 and Y chromosomes of H. malabaricus and E. erythrinus, respectively. Results Our results yield valuable information regarding the origin and evolution of these sex chromosome systems. Our data indicate that these sex chromosomes evolved independently in these two closed related Erythrinidae species. Different autosomes were first converted into a poorly differentiated XY sex pair in each species, and additional chromosomal rearrangements produced both X1X2Y sex systems that are currently present. Conclusions Our data provide new insights into the origin and evolution of sex chromosomes, which increases our knowledge about fish sex chromosome evolution.
Collapse
Affiliation(s)
- Marcelo B Cioffi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
| | | | | | | | | | | | | |
Collapse
|
50
|
Liehr T, Ewers E, Hamid AB, Kosyakova N, Voigt M, Weise A, Manvelyan M. Small supernumerary marker chromosomes and uniparental disomy have a story to tell. J Histochem Cytochem 2011; 59:842-8. [PMID: 21673185 DOI: 10.1369/0022155411412780] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Small supernumerary maker chromosomes (sSMC) and uniparental disomy (UPD) are rare, and a combination of both is rarely encountered. Accordingly, only 46 sSMC cases UPD have been reported. Despite of its rareness, UPD has to be considered, especially in prenatal cases with sSMC. Here, the authors reviewed all sSMC cases with UPD (sSMC(U+)) and compared them to sSMC without UPD (sSMC(U-)), which resulted in the following correlations: 1) every sSMC, irrespective of its chromosomal origin, may be principally connected with UPD; 2) mixed hetero- and iso-UPD (hUPD/iUPD) can be observed most often in sSMC(U+) cases followed by complete iUPD, complete hUPD, and segmental iUPD; 3) UPD of chromosomes 6, 7, 14, 15, 16, and 20 is most often reported in sSMC(U+); 4) maternal UPD was approximately nine times more frequent than paternal UPD; 5) if mosaic with a normal cell line, acrocentric-derived sSMC had a three times higher chance of occurrence than the corresponding nonmosaic sSMC cases; 6) UPD in connection with a parentally inherited sSMC is, if existent at all, a rare event; and 7) the gender type and shape of sSMC had no effect on UPD formation. Overall, sSMC(U+) cases may have a story to tell about chromosome number control mechanisms in early embryogenesis.
Collapse
Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Jena, Germany.
| | | | | | | | | | | | | |
Collapse
|