1
|
Scott C, Downes DJ, Brown JM, Beagrie R, Olijnik AA, Gosden M, Schwessinger R, Fisher CA, Rose A, Ferguson DJP, Johnson E, Hill QA, Okoli S, Renella R, Ryan K, Brand M, Hughes J, Roy NBA, Higgs DR, Babbs C, Buckle VJ. Recapitulation of erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities. Haematologica 2021; 106:2960-2970. [PMID: 33121234 PMCID: PMC8561284 DOI: 10.3324/haematol.2020.260158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 09/17/2020] [Indexed: 11/19/2022] Open
Abstract
The investigation of inherited disorders of erythropoiesis has elucidated many of the principles underlying the production of normal red blood cells and how this is perturbed in human disease. Congenital Dyserythropoietic Anaemia type 1 (CDA-I) is a rare form of anaemia caused by mutations in two genes of unknown function: CDAN1 and CDIN1 (previously called C15orf41), whilst in some cases, the underlying genetic abnormality is completely unknown. Consequently, the pathways affected in CDA-I remain to be discovered. To enable detailed analysis of this rare disorder we have validated a culture system which recapitulates all of the cardinal haematological features of CDA-I, including the formation of the pathognomonic 'spongy' heterochromatin seen by electron microscopy. Using a variety of cell and molecular biological approaches we discovered that erythroid cells in this condition show a delay during terminal erythroid differentiation, associated with increased proliferation and widespread changes in chromatin accessibility. We also show that the proteins encoded by CDAN1 and CDIN1 are enriched in nucleoli which are structurally and functionally abnormal in CDA-I. Together these findings provide important pointers to the pathways affected in CDA-I which for the first time can now be pursued in the tractable culture system utilised here.
Collapse
Affiliation(s)
- Caroline Scott
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford.
| | - Damien J Downes
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Jill M Brown
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Robert Beagrie
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | | | - Matthew Gosden
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Ron Schwessinger
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | | | - Anna Rose
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - David J P Ferguson
- Ultrastructural Morphology Group, NDCLS, John Radcliffe Hospital, Oxford
| | - Errin Johnson
- Sir William Dunn School of Pathology, Oxford University, Oxford
| | | | - Steven Okoli
- Imperial College, The Commonwealth Building, The Hammersmith Hospital, Du Cane Rd, London
| | - Raffaele Renella
- Pediatric Hematology-Oncology Research Laboratory, CHUV-UNIL Lausanne Switzerland
| | - Kate Ryan
- Department of Haematology, Manchester Royal Infirmary, Oxford Rd, Manchester
| | - Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa
| | - Jim Hughes
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Noemi B A Roy
- Department of Haematology, Oxford University Hospitals NHS Trust, Churchill Hospital, Old Rd, Headington, and NIHR Biomedical Research Centre, Oxford
| | - Douglas R Higgs
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Christian Babbs
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford
| | - Veronica J Buckle
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford.
| |
Collapse
|
2
|
|
3
|
Rahman MM, Uddin KF, Al Jezawi NK, Karuvantevida N, Akter H, Dity NJ, Rahaman MA, Begum M, Rahaman MA, Baqui MA, Salwa Z, Islam S, Woodbury-Smith M, Basiruzzaman M, Uddin M. Gonadal mosaicism of large terminal de novo duplication and deletion in siblings with variable intellectual disability phenotypes. Mol Genet Genomic Med 2019; 7:e00954. [PMID: 31475484 PMCID: PMC6785528 DOI: 10.1002/mgg3.954] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/15/2022] Open
Abstract
Background Intellectual disability (ID) is a complex condition that can impact multiple domains of development. The genetic contribution to ID’s etiology is significant, with more than 100 implicated genes and loci currently identified. The majority of such variants are rare and de novo genetic mutations. Methods We have applied whole‐genome microarray to identify large, rare, clinically relevant copy number variants (CNVs). We have applied well‐established algorithms for variants call. Quantitative polymerase chain reaction (qPCR) was applied to validate the variants using three technical replicates for each family member. To assess whether the copy number variation was due to balanced translocation or mosaicism, we further conducted droplet digital PCR (ddPCR) on the whole family. We have, as well, applied “critical‐exon” mapping, human developmental brain transcriptome, and a database of known associated neurodevelopmental disorder variants to identify candidate genes. Results Here we present two siblings who are both impacted by a large terminal duplication and a deletion. Whole‐genome microarray revealed an 18.82 megabase (MB) duplication at terminal locus (7q34‐q36.3) of chromosome 7 and a 3.90 MB deletion impacting the terminal locus (15q26.3) of chromosome 15. qPCR and ddPCR experiments confirmed the de novo origin of the variants and the co‐occurrence of these two de novo events among the siblings, but their absence in both parents, implicates an unbalanced translocation that could have mal‐segregated among the siblings or a possible germline mosaicism. These terminal events impact IGF1R, CNTNAP2, and DPP6, shown to be strongly associated with neurodevelopmental disorders. Detailed clinical examination of the siblings revealed the presence of both shared and distinct phenotypic features. Conclusions This study identified two large rare terminal de novo events impacting two siblings. Further phenotypic investigation highlights that even in the presence of identical large high penetrant variants, spectrum of clinical features can be different between the siblings.
Collapse
Affiliation(s)
| | - Km Furkan Uddin
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Nesreen K Al Jezawi
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,Department of Biotechnology, Bharathidasan University, Tiruchirappalli, India
| | | | | | | | | | | | - Md Abdul Baqui
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | | | | | - Marc Woodbury-Smith
- Institute of Neuroscience, Newcastle University, Newcastle upon Tyne, UK.,The Centre for Applied Genomics, Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohammed Basiruzzaman
- NeuroGen Technologies Ltd., Dhaka, Bangladesh.,Department of Neurology, Dhaka Medical College Hospital, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates.,The Centre for Applied Genomics, Department of Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| |
Collapse
|
4
|
Brown JM, Roberts NA, Graham B, Waithe D, Lagerholm C, Telenius JM, De Ornellas S, Oudelaar AM, Scott C, Szczerbal I, Babbs C, Kassouf MT, Hughes JR, Higgs DR, Buckle VJ. A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions. Nat Commun 2018; 9:3849. [PMID: 30242161 PMCID: PMC6155075 DOI: 10.1038/s41467-018-06248-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 08/24/2018] [Indexed: 11/08/2022] Open
Abstract
Self-interacting chromatin domains encompass genes and their cis-regulatory elements; however, the three-dimensional form a domain takes, whether this relies on enhancer-promoter interactions, and the processes necessary to mediate the formation and maintenance of such domains, remain unclear. To examine these questions, here we use a combination of high-resolution chromosome conformation capture, a non-denaturing form of fluorescence in situ hybridisation and super-resolution imaging to study a 70 kb domain encompassing the mouse α-globin regulatory locus. We show that this region forms an erythroid-specific, decompacted, self-interacting domain, delimited by frequently apposed CTCF/cohesin binding sites early in terminal erythroid differentiation, and does not require transcriptional elongation for maintenance of the domain structure. Formation of this domain does not rely on interactions between the α-globin genes and their major enhancers, suggesting a transcription-independent mechanism for establishment of the domain. However, absence of the major enhancers does alter internal domain interactions. Formation of a loop domain therefore appears to be a mechanistic process that occurs irrespective of the specific interactions within.
Collapse
Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Nigel A Roberts
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Bryony Graham
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Dominic Waithe
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, Oxford, OX3 9DS, UK
| | - Jelena M Telenius
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Sara De Ornellas
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - A Marieke Oudelaar
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Caroline Scott
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Izabela Szczerbal
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wolynska 33, 60-637 Poznan, Poland
| | - Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Mira T Kassouf
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK.
| |
Collapse
|
5
|
Chakraborty K, Veetil AT, Jaffrey SR, Krishnan Y. Nucleic Acid-Based Nanodevices in Biological Imaging. Annu Rev Biochem 2017; 85:349-73. [PMID: 27294440 DOI: 10.1146/annurev-biochem-060815-014244] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The nanoscale engineering of nucleic acids has led to exciting molecular technologies for high-end biological imaging. The predictable base pairing, high programmability, and superior new chemical and biological methods used to access nucleic acids with diverse lengths and in high purity, coupled with computational tools for their design, have allowed the creation of a stunning diversity of nucleic acid-based nanodevices. Given their biological origin, such synthetic devices have a tremendous capacity to interface with the biological world, and this capacity lies at the heart of several nucleic acid-based technologies that are finding applications in biological systems. We discuss these diverse applications and emphasize the advantage, in terms of physicochemical properties, that the nucleic acid scaffold brings to these contexts. As our ability to engineer this versatile scaffold increases, its applications in structural, cellular, and organismal biology are clearly poised to massively expand.
Collapse
Affiliation(s)
- Kasturi Chakraborty
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Aneesh T Veetil
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , ,
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Medical College of Cornell University, New York, New York 10065;
| | - Yamuna Krishnan
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637; , , .,Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior, University of Chicago, Chicago, Illinois 60637
| |
Collapse
|
6
|
Pauciullo A, Perucatti A, Cosenza G, Iannuzzi A, Incarnato D, Genualdo V, Di Berardino D, Iannuzzi L. Sequential cross-species chromosome painting among river buffalo, cattle, sheep and goat: a useful tool for chromosome abnormalities diagnosis within the family Bovidae. PLoS One 2014; 9:e110297. [PMID: 25330006 PMCID: PMC4201488 DOI: 10.1371/journal.pone.0110297] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 09/18/2014] [Indexed: 11/18/2022] Open
Abstract
The main goal of this study was to develop a comparative multi-colour Zoo-FISH on domestic ruminants metaphases using a combination of whole chromosome and sub-chromosomal painting probes obtained from the river buffalo species (Bubalus bubalis, 2n = 50,XY). A total of 13 DNA probes were obtained through chromosome microdissection and DOP-PCR amplification, labelled with two fluorochromes and sequentially hybridized on river buffalo, cattle (Bos taurus, 2n = 60,XY), sheep (Ovis aries, 2n = 54,XY) and goat (Capra hircus, 2n = 60,XY) metaphases. The same set of paintings were then hybridized on bovine secondary oocytes to test their potential use for aneuploidy detection during in vitro maturation. FISH showed excellent specificity on metaphases and interphase nuclei of all the investigated species. Eight pairs of chromosomes were simultaneously identified in buffalo, whereas the same set of probes covered 13 out 30 chromosome pairs in the bovine and goat karyotypes and 40% of the sheep karyotype (11 out of 27 chromosome pairs). This result allowed development of the first comparative M-FISH karyotype within the domestic ruminants. The molecular resolution of complex karyotypes by FISH is particularly useful for the small chromosomes, whose similarity in the banding patterns makes their identification very difficult. The M-FISH karyotype also represents a practical tool for structural and numerical chromosome abnormalities diagnosis. In this regard, the successful hybridization on bovine secondary oocytes confirmed the potential use of this set of probes for the simultaneous identification on the same germ cell of 12 chromosome aneuploidies. This is a fundamental result for monitoring the reproductive health of the domestic animals in relation to management errors and/or environmental hazards.
Collapse
Affiliation(s)
- Alfredo Pauciullo
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| | - Angela Perucatti
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| | - Gianfranco Cosenza
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Alessandra Iannuzzi
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| | - Domenico Incarnato
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| | - Viviana Genualdo
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| | - Dino Di Berardino
- Department of Agriculture, University of Naples Federico II, Portici, Italy
| | - Leopoldo Iannuzzi
- Institute for Animal Production System in Mediterranean Environment, National Research Council, Naples, Italy
| |
Collapse
|
7
|
Perche O, Menuet A, Marcos M, Liu L, Pâris A, Utami KH, Kervran D, Cacheux V, Laudier B, Briault S. Combined deletion of two Condensin II system genes (NCAPG2 and MCPH1) in a case of severe microcephaly and mental deficiency. Eur J Med Genet 2013; 56:635-41. [PMID: 24013099 DOI: 10.1016/j.ejmg.2013.07.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 07/29/2013] [Indexed: 01/13/2023]
Abstract
7qter deletion syndrome includes prenatal and/or postnatal growth retardation, microcephaly, psychomotor delay or mental retardation and a characteristic dysmorphism. If clinical features are well described, the molecular mechanisms underlying the 7qter deletion syndrome remain unknown. Those deletions usually arise de novo. Here, we describe a young boy with an abnormal phenotype consistent with a 7qter deletion syndrome. High resolution genomic analysis (Affymetrix Human Genome Wide SNP 6.0) revealed a 7q36.3 deletion encompassing NCAPG2, ESYT2, WDR60 and VIPR2, inherited from his asymptomatic father and paternal grandfather. In addition, the patient also harbored a MCPH1 deletion inherited from his healthy mother. Combined NCAPG2 and MCPH1 deletions were correlated with low mRNA levels and protein expression in the patient. MCPH1 and NCAPG2 proteins interaction is known to control chromosome structure and we thus propose that double heterozygosity for null mutations of those two genes of the Condensin II system contribute to mental deficiency with severe microcephaly phenotype.
Collapse
Affiliation(s)
- Olivier Perche
- UMR7355, CNRS, Orleans, France; Experimental and Molecular Immunology and Neurogenetics, University of Orleans, 3b rue de la Férollerie, 45071 Orleans Cedex 2, France; Genetic Department, Regional Hospital, 14 Avenue de l'Hôpital, 45100 Orleans, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Schödel J, Bardella C, Sciesielski LK, Brown JM, Pugh CW, Buckle V, Tomlinson IP, Ratcliffe PJ, Mole DR. Common genetic variants at the 11q13.3 renal cancer susceptibility locus influence binding of HIF to an enhancer of cyclin D1 expression. Nat Genet 2012; 44:420-5, S1-2. [PMID: 22406644 PMCID: PMC3378637 DOI: 10.1038/ng.2204] [Citation(s) in RCA: 123] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2011] [Accepted: 01/30/2012] [Indexed: 12/18/2022]
Abstract
Although genome-wide association studies (GWAS) have identified the existence of numerous population-based cancer susceptibility loci, mechanistic insights remain limited, particularly for intergenic polymorphisms. Here, we show that polymorphism at a remote intergenic region on chromosome 11q13.3, recently identified as a susceptibility locus for renal cell carcinoma, modulates the binding and function of hypoxia-inducible factor (HIF) at a previously unrecognized transcriptional enhancer of CCND1 (encoding cyclin D1) that is specific for renal cancers characterized by inactivation of the von Hippel-Lindau tumor suppressor (pVHL). The protective haplotype impairs binding of HIF-2, resulting in an allelic imbalance in cyclin D1 expression, thus affecting a link between hypoxia pathways and cell cycle control.
Collapse
Affiliation(s)
- Johannes Schödel
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Chiara Bardella
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Lina K Sciesielski
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Jill M Brown
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX4 9DS, United Kingdom
| | - Chris W Pugh
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Veronica Buckle
- Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX4 9DS, United Kingdom
| | - Ian P Tomlinson
- Molecular and Population Genetics Laboratory, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
- Oxford NIHR Comprehensive Biomedical Research Centre, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - Peter J Ratcliffe
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - David R Mole
- Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, United Kingdom
| |
Collapse
|
9
|
Submicroscopic subtelomeric aberrations in Chinese patients with unexplained developmental delay/mental retardation. BMC MEDICAL GENETICS 2010; 11:72. [PMID: 20459802 PMCID: PMC2892449 DOI: 10.1186/1471-2350-11-72] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 05/11/2010] [Indexed: 01/16/2023]
Abstract
BACKGROUND Subtelomeric imbalance is widely accepted as related to developmental delay/mental retardation (DD/MR). Fine mapping of aberrations in gene-enriched subtelomeric regions provides essential clues for localizing critical regions, and provides a strategy for identifying new candidate genes. To date, no large-scale study has been conducted on subtelomeric aberrations in DD/MR patients in mainland China. METHODS This study included 451 Chinese children with moderate to severe clinically unexplained DD/MR. The subtelomere-MLPA (multiplex ligation dependent probe amplification) and Affymetrix human SNP array 6.0 were used to determine the subtelomeric copy number variations. The exact size and the breakpoint of each identified aberration were well defined. RESULTS The submicroscopic subtelomeric aberrations were identified in 23 patients, with a detection rate of 5.1%. 16 patients had simple deletions, 2 had simple duplications and 5 with both deletions and duplications. The deletions involved 14 different subtelomeric regions (1p, 2p, 4p, 6p, 7p, 7q, 8p, 9p, 10p, 11q, 14q, 15q, 16p and 22q), and duplications involved 7 subtelomeric regions (3q, 4p, 6q, 7p, 8p, 12p and 22q). Of all the subtelomeric aberrations found in Chinese subjects, the most common was 4p16.3 deletion. The sizes of the deletions varied from 0.6 Mb to 12 Mb, with 5-143 genes inside. Duplicated regions were 0.26 Mb to 11 Mb, with 6-202 genes inside. In this study, four deleted subtelomeric regions and one duplicated region were smaller than any other previously reported, specifically the deletions in 11q25, 8p23.3, 7q36.3, 14q32.33, and the duplication in 22q13. Candidate genes inside each region were proposed. CONCLUSIONS Submicroscopic subtelomeric aberrations were detected in 5.1% of Chinese children with clinically unexplained DD/MR. Four deleted subtelomeric regions and one duplicated region found in this study were smaller than any previously reported, which will be helpful for further defining the candidate dosage sensitive gene associated with DD/MR.
Collapse
|
10
|
Tchinda J, Volpert S, McNeil N, Neumann T, Kennerknecht I, Ried T, Büchner T, Serve H, Berdel WE, Horst J, Hilgenfeld E. Multicolor Karyotyping in Acute Myeloid Leukemia. Leuk Lymphoma 2009; 44:1843-53. [PMID: 14738135 DOI: 10.1080/10428190310001603605] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cytogenetic data have significantly contributed to our understanding of the heterogeneity of acute myeloid leukemia (AML). In AML, numerous recurrent chromosomal aberrations have been identified, and several of them, e.g. t(8;21)(q22;q22), t(15;17)(q22;q11-12), inv(16)(p13q22), are specific for distinct subgroups. Furthermore, chromosomal aberrations have proved to be of paramount prognostic importance for remission induction and survival. Chromosome analysis using classical cytogenetic banding techniques often fails to completely resolve complex karyotypes and cryptic translocations not identifiable by these techniques have been detected using molecular cytogenetic methods. While fluorescence in situ hybridization (FISH) has become an indispensable tool for screening and follow-up of known aberrations, the techniques of spectral karyotyping (SKY) and multiplex-fluorescence in situ hybridization (M-FISH) allow for the simultaneous visualization of all chromosomes of a metaphase in a single hybridization step, and thereby enable screening for the aberrations present without their prior knowledge. Therefore, with the introduction of these techniques in 1996 the comprehensive analysis of complex karyotypes and the identification of new, hitherto cryptic translocations and, ultimately, the identification of new disease subgroups seemed possible. Since, more than 600 cases of AML and MDS have been analyzed. Herein, we attempt to summarize the data published and discuss what has been achieved towards realization of these goals.
Collapse
Affiliation(s)
- Joëlle Tchinda
- Institut für Humangenetik, Universitätsklinikum Münster, Vesaliusweg 12-14, 48129 Münster, Germany.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
11
|
|
12
|
Specialized fluorescence in situ hybridization (FISH) techniques for leukaemia research. Methods Mol Biol 2009. [PMID: 19277577 DOI: 10.1007/978-1-59745-418-6_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorescence in situ hybridization (FISH) provides one of the few ways of analysing the genotype of individual cells, an important consideration for mixed cell populations such as those found in leukaemia. A more sophisticated variation combines fluorescence immunophenotyping and FISH for specific leukaemia-associated chromosome rearrangements. Combined immunophenotyping and FISH is a powerful tool to identify the cell lineage in which the leukaemia-specific chromosome rearrangement occurs and has been used to identify putative pre-leukaemic cells in normal cord blood. Another valuable FISH-based research technique is multi-fluor FISH (M-FISH). This multicolour approach is effectively a molecular karyotype of individual cells and has a range of applications, from chromosome breakage studies and characterising mouse models of leukaemia, to providing a perfect complementary approach to the emerging genomic microarray technologies.
Collapse
|
13
|
FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 2008; 45:385-6, 388, 390 passim. [PMID: 18855767 DOI: 10.2144/000112811] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The introduction of FISH (fluorescence in situ hybridization) marked the beginning of a new era for the study of chromosome structure and function. As a combined molecular and cytological approach, the major advantage of this visually appealing technique resides in its unique ability to provide an intermediate degree of resolution between DNA analysis and chromosomal investigations while retaining information at the single-cell level. Used to support large-scale mapping and sequencing efforts related to the human genome project, FISH accuracy and versatility were subsequently capitalized on in biological and medical research, providing a wealth of diverse applications and FISH-based diagnostic assays. The diversification of the original FISH protocol into the impressive number of procedures available these days has been promoted throughout the years by a number of interconnected factors: the improvement in sensitivity, specificity and resolution, together with the advances in the fields of fluorescence microscopy and digital imaging, and the growing availability of genomic and bioinformatic resources. By assembling in a glossary format many of the "acronymed" FISH applications published so far, this review intends to celebrate the ability of FISH to re-invent itself and thus remain at the forefront of biomedical research.
Collapse
|
14
|
Geigl JB, Uhrig S, Speicher MR. Multiplex-fluorescence in situ hybridization for chromosome karyotyping. Nat Protoc 2007; 1:1172-84. [PMID: 17406400 DOI: 10.1038/nprot.2006.160] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Multiplex-fluorescence in situ hybridization (M-FISH) was initially developed to stain human chromosomes--the 22 autosomes and X and Y sex chromosomes--with uniquely distinctive colors to facilitate karyotyping. The characteristic spectral signatures of all different combinations of fluorochromes are determined by multichannel image-analysis methods. Advantages of M-FISH include rapid analysis of metaphase spreads, even in complex cases with multiple chromosomal rearrangements, and identification of marker chromosomes. The M-FISH technology has been extended to other species, such as the mouse. Furthermore, in addition to painting probes, the method has been used with a variety of region-specific probes. M-FISH has even recently been used for 3D studies to analyze the distribution of human chromosomes in intact and preserved interphase nuclei. Hence, M-FISH has evolved into an essential tool for both clinical diagnostics and basic research. In this protocol, we describe how to use M-FISH to karyotype chromosomes, a procedure that takes approximately 14 d if new M-FISH probes have to be generated and 3 d if the M-FISH probes are ready to use.
Collapse
Affiliation(s)
- Jochen B Geigl
- Institute of Medical Biology and Human Genetics, Medical University of Graz, Harrachgasse 21/8, A-8010 Graz, Austria
| | | | | |
Collapse
|
15
|
Paulsson K, Johansson B. Trisomy 8 as the sole chromosomal aberration in acute myeloid leukemia and myelodysplastic syndromes. ACTA ACUST UNITED AC 2007; 55:37-48. [PMID: 16697122 DOI: 10.1016/j.patbio.2006.04.007] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Accepted: 04/05/2006] [Indexed: 10/24/2022]
Abstract
Trisomy 8 as the sole abnormality is the most common karyotypic finding in acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), occurring in approximately 5% and 10% of the cytogenetically abnormal cases, respectively. However, despite the high frequency of +8, much remains to be elucidated as regards its epidemiology, etiology, clinical impact, association with other chromosomal abnormalities, cell of origin, and functional and pathogenetic consequences. Here, we summarize and review these various aspects of trisomy 8, focusing on AMLs and MDS harboring this abnormality as a single change.
Collapse
Affiliation(s)
- K Paulsson
- Department of Clinical Genetics, University Hospital, SE-221 85 Lund, Sweden.
| | | |
Collapse
|
16
|
Kearney L. Multiplex-FISH (M-FISH): technique, developments and applications. Cytogenet Genome Res 2006; 114:189-98. [PMID: 16954655 DOI: 10.1159/000094202] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2006] [Accepted: 04/06/2006] [Indexed: 01/08/2023] Open
Abstract
Multiplex FISH (M-FISH) represents one of the most significant developments in molecular cytogenetics of the past decade. Originally designed to generate 24 colour karyotyping, the technique has spawned many variations and an equally diverse range of applications. In tumour and leukaemia cytogenetics, the two groups that have been targeted represent both ends of the cytogenetic spectrum: those with an apparently normal karyotype (suspected of harbouring small rearrangements not detectable by conventional cytogenetics) and those with a complex aberrant karyotype (which are difficult to karyotype accurately due to the sheer number of aberrations). In research, mouse M-FISH provides a powerful tool to characterize mouse models of a disease. In addition, the ability to accurately karyotype single metaphases without selection makes M-FISH the perfect tool in chromosome breakage studies and for characterizing clonal evolution of tumours. Finally, M-FISH has emerged as the perfect partner for the developing genomic microarray (array CGH) technologies, providing a powerful approach to gene discovery.
Collapse
Affiliation(s)
- L Kearney
- Section of Haemato-Oncology, Institute of Cancer Research, London, UK.
| |
Collapse
|
17
|
Brown JM, Leach J, Reittie JE, Atzberger A, Lee-Prudhoe J, Wood WG, Higgs DR, Iborra FJ, Buckle VJ. Coregulated human globin genes are frequently in spatial proximity when active. ACTA ACUST UNITED AC 2006; 172:177-87. [PMID: 16418531 PMCID: PMC2063548 DOI: 10.1083/jcb.200507073] [Citation(s) in RCA: 177] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The organization of genes within the nucleus may influence transcription. We have analyzed the nuclear positioning of the coordinately regulated α- and β-globin genes and show that the gene-dense chromatin surrounding the human α-globin genes is frequently decondensed, independent of transcription. Against this background, we show the frequent juxtaposition of active α- and β-globin genes and of homologous α-globin loci that occurs at nuclear speckles and correlates with transcription. However, we did not see increased colocalization of signals, which would be expected with direct physical interaction. The same degree of proximity does not occur between human β-globin genes or between murine globin genes, which are more constrained to their chromosome territories. Our findings suggest that the distribution of globin genes within erythroblast nuclei is the result of a self-organizing process, involving transcriptional status, diffusional ability of chromatin, and physical interactions with nuclear proteins, rather than a directed form of higher-order control.
Collapse
Affiliation(s)
- Jill M Brown
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford OX3 9DS, England, UK
| | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Davidsson J, Paulsson K, Johansson B. Multicolor fluorescence in situ hybridization characterization of cytogenetically polyclonal hematologic malignancies. ACTA ACUST UNITED AC 2006; 163:180-3. [PMID: 16337865 DOI: 10.1016/j.cancergencyto.2005.05.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2005] [Revised: 05/30/2005] [Accepted: 05/31/2005] [Indexed: 11/28/2022]
Abstract
Several different investigations and methodologies have provided data supporting a monoclonal origin of neoplasia. For example, the vast majority of neoplastic disorders are cytogenetically monoclonal. Occasionally, however, clones with unrelated karyotypic anomalies are found, as, for example, in approximately 2% of acute myeloid leukemias (AML), myelodysplastic syndromes (MDS), and chronic myeloproliferative disorders (CMD). Whether such a cytogenetic polyclonality represents a polyclonal origin or whether different clones share a submicroscopic primary change, indicating a monoclonal origin, remains to be elucidated. Our objective was to ascertain if cryptic aberrations can be found in cytogenetically polyclonal hematologic malignancies using multicolor fluorescence in situ hybridization (M-FISH). Fourteen AML, MDS, and CMD cases were investigated. In none of these was a cryptic aberration found, common to all subclones, although the karyotypes were revised in two AMLs and one MDS. Thus, all malignancies were still classified as polyclonal after the M-FISH analyses. Based on the present results, we conclude that M-FISH, in general, does not reveal primary cryptic aberrations supporting a monoclonal origin of cytogenetically polyclonal hematologic malignancies.
Collapse
Affiliation(s)
- Josef Davidsson
- Department of Clinical Genetics, Lund University Hospital, SE - 221 85 Lund, Sweden.
| | | | | |
Collapse
|
19
|
Speicher MR, Carter NP. The new cytogenetics: blurring the boundaries with molecular biology. Nat Rev Genet 2005; 6:782-92. [PMID: 16145555 DOI: 10.1038/nrg1692] [Citation(s) in RCA: 250] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Exciting advances in fluorescence in situ hybridization and array-based techniques are changing the nature of cytogenetics, in both basic research and molecular diagnostics. Cytogenetic analysis now extends beyond the simple description of the chromosomal status of a genome and allows the study of fundamental biological questions, such as the nature of inherited syndromes, the genomic changes that are involved in tumorigenesis and the three-dimensional organization of the human genome. The high resolution that is achieved by these techniques, particularly by microarray technologies such as array comparative genomic hybridization, is blurring the traditional distinction between cytogenetics and molecular biology.
Collapse
|
20
|
Beyer V, Mühlematter D, Parlier V, Cabrol C, Bougeon-Mamin S, Solenthaler M, Tobler A, Pugin P, Gregor M, Hitz F, Hess U, Chapuis B, Laurencet F, Schanz U, Schmidt PM, van Melle G, Jotterand M. Polysomy 8 defines a clinico-cytogenetic entity representing a subset of myeloid hematologic malignancies associated with a poor prognosis: report on a cohort of 12 patients and review of 105 published cases. ACTA ACUST UNITED AC 2005; 160:97-119. [PMID: 15993266 DOI: 10.1016/j.cancergencyto.2004.12.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Revised: 11/16/2004] [Accepted: 12/10/2004] [Indexed: 01/14/2023]
Abstract
Tetrasomy, pentasomy, and hexasomy 8 (polysomy 8) are relatively rare compared to trisomy 8. Here we report on a series of 12 patients with acute myeloid leukemia (AML), myelodysplastic syndrome (MDS), or myeloproliferative disorder (MPD) associated with polysomy 8 as detected by conventional cytogenetics and fluorescence in situ hybridization (FISH). In an attempt to better characterize the clinical and hematological profile of this cytogenetic entity, our data were combined with those of 105 published patients. Tetrasomy 8 was the most common presentation of polysomy 8. In 60.7% of patients, polysomy 8 occurred as part of complex changes (16.2% with 11q23 rearrangements). No cryptic MLL rearrangements were found in cases in which polysomy 8 was the only karyotypic change. Our study demonstrates the existence of a polysomy 8 syndrome, which represents a subtype of AML, MDS, and MPD characterized by a high incidence of secondary diseases, myelomonocytic or monocytic involvement in AML and poor overall survival (6 months). Age significantly reduced median survival, but associated cytogenetic abnormalities did not modify it. Cytogenetic results further demonstrate an in vitro preferential growth of the cells with a high level of aneuploidy suggesting a selective advantage for polysomy 8 cells.
Collapse
Affiliation(s)
- Valérie Beyer
- Service de Génétique Médicale, Centre Hospitalier Universitaire Vaudois, Lausanne CH-1011, Switzerland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Abstract
In this chapter, we focus on the genetic basis of mental retardation (MR), specifically the use of subtelomeric probes to provide new diagnoses in idiopathic MR. We discuss both the background to the clinical demand for diagnoses and the technological advances that culminated in the development of subtelomeric testing strategies. We explain the theory behind these strategies and briefly outline the protocols involved, giving the advantages, limitations, and pitfalls of the analyses. Finally, we give an overview of the MR subtelomeric studies to date and how subtelomeric testing has become a widely used tool in clinical diagnostic laboratories, particularly in the diagnosis of unexplained MR, but also in other fields of clinical medicine. The conclusion addresses the overall impact that subtelomeric testing has had on the diagnosis of MR, the implications for patients and their families, and future research avenues for exploring the genetic causes of MR and improving our overall understanding of neurocognitive development.
Collapse
Affiliation(s)
- Samantha J L Knight
- The Wellcome Trust Centre for Human Genetics, Churchill Hospital, Headington, Oxford, Oxfordshire OX3 7BN, United Kingdom
| | | |
Collapse
|
22
|
Rooms L, Reyniers E, Kooy RF. Subtelomeric rearrangements in the mentally retarded: A comparison of detection methods. Hum Mutat 2005; 25:513-24. [PMID: 15880643 DOI: 10.1002/humu.20185] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
In recent years, subtelomeric rearrangements, e.g., chromosome deletions or duplications too small to be detected by conventional cytogenetic analysis, have emerged as a significant cause of both idiopathic and familial mental retardation. As mental retardation is a common disorder, many patients need to be tested on a routine basis. In this review, we will discuss the different methods that have been applied in laboratories worldwide, including multiprobe fluorescence in situ hybridization (FISH), multiallelic marker analysis, multiplex amplifiable probe hybridization (MAPH), multiplex ligation-dependent probe amplification (MLPA), quantitative real-time PCR, comparative genomic hybridization (CGH), and multicolor FISH, including spectral karyotyping (SKY), subtelomeric combined binary ratio labeling FISH (S-COBRA FISH), multiplex FISH telomere integrity assay (M-TEL), telomeric multiplex FISH (TM-FISH), and primed in situ labeling (PRINS).
Collapse
Affiliation(s)
- Liesbeth Rooms
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | |
Collapse
|
23
|
Speicher MR. Monitoring chromosome rearrangements. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2005; 570:19-41. [PMID: 18727497 DOI: 10.1007/1-4020-3764-3_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
|
24
|
Klaus M, Haferlach T, Schnittger S, Kern W, Hiddemann W, Schoch C. Cytogenetic profile in de novo acute myeloid leukemia with FAB subtypes M0, M1, and M2: a study based on 652 cases analyzed with morphology, cytogenetics, and fluorescence in situ hybridization. ACTA ACUST UNITED AC 2004; 155:47-56. [PMID: 15527902 DOI: 10.1016/j.cancergencyto.2004.03.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2004] [Accepted: 03/15/2004] [Indexed: 11/28/2022]
Abstract
In about 55% of acute myeloid leukemia (AML) cases, chromosome aberrations are detectable by cytogenetics. Close correlations between cytomorphology and cytogenetics have been reported. To determine a pattern of cytogenetic abnormalities within the French-American-British (FAB) subtypes AML M0, M1, and M2, we analyzed 48 AML M0, 179 AML M1, and 425 AML M2 and compared cytogenetic data to a cohort of 1,062 AML M3/3v, M4, M4eo, M5a/5b, M6, and M7. Cytogenetic abnormalities were significantly more frequent in AML M0 (71%) compared to M1 (49%), M2 (53%), and the total cohort (56%; P < 0.02). While +8 was the most common numeric abnormality in all FAB subtypes, +13, +14, and +11 were associated with AML M0-M2. The only recurring balanced translocation that was associated with one of these FAB subtypes was t(8;21) in M2 (12.5%) and, rarely, M1 (1.7%) (M0, 0% and M3-7, 0.09%; P=0.001). To evaluate the frequency of cytogenetically undetectable abnormalities, we performed fluorescence in situ hybridization (FISH) analyses in 273 AML M0-M2 with normal karyotype using probes for ETO, ABL, MLL, TEL, RB, P53, AML1, and BCR. In two cases we identified numerical aberrations of RB only in interphases nuclei. In seven additional cases, TEL and MLL abnormalities were found. In conclusion, t(8;21), +11, +13, and +14 are strongly associated with AML M0, M1, and M2. The FISH screening analyses identified abnormalities in an additional 3% in normal karyotypes.
Collapse
Affiliation(s)
- Mirjam Klaus
- Department of Internal Medicine III, Laboratory for Leukemia Diagnostics, Ludwig-Maximilians-University, Marchioninistrasse 15, 81377 Munich, Germany.
| | | | | | | | | | | |
Collapse
|
25
|
Boehm D, Herold S, Kuechler A, Liehr T, Laccone F. Rapid detection of subtelomeric deletion/duplication by novel real-time quantitative PCR using SYBR-green dye. Hum Mutat 2004; 23:368-78. [PMID: 15024731 DOI: 10.1002/humu.20011] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, miscarriages, and hematological malignancies. Automated detection of subtle deletions and duplications involving telomeres is essential for high-throughput screening procedures, but impractical when conventional cytogenetic methods are used. Novel real-time PCR quantitative genotyping of subtelomeric amplicons using SYBR-green dye allows high-resolution screening of single copy number gains and losses by their relative quantification against a diploid genome. To assess the applicability of the technique in the screening and diagnosis of subtelomeric imbalances, we describe here a blinded study in which DNA from 20 negative controls and 20 patients with known unbalanced cytogenetic abnormalities involving at least one or more telomeres were analyzed using a novel human subtelomere-specific primer set, producing altogether 86 amplicons, in the SYBR-green I-based real-time quantitative PCR screening approach. Screening of the DNA samples from 20 unrelated controls for copy number polymorphism do not detect any polymorphism in the set of amplicons, but single-copy-number gains and losses were accurately detected by quantitative PCR in all patients, except the copy number alterations of the subtelomeric p-arms of the acrocentric chromosomes in two cases. Furthermore, a detailed mapping of the deletion/translocation breakpoint was demonstrated in two cases by novel real-time PCR "primer-jumping." Because of the simplicity and flexibility of the SYBR-green I-based real-time detection, the primer-set can easily be extended, either to perform further detailed molecular characterization of breakpoints or to include amplicons for the detection and/or analysis of syndromes that are associated with genomic copy number alterations, e.g., deletion/duplication-syndromes and malignant cancers.
Collapse
Affiliation(s)
- Detlef Boehm
- Institute of Human Genetics, University of Goettingen, Goettingen, Germany.
| | | | | | | | | |
Collapse
|
26
|
Engels H, Ehrbrecht A, Zahn S, Bosse K, Vrolijk H, White S, Kalscheuer V, Hoovers JMN, Schwanitz G, Propping P, Tanke HJ, Wiegant J, Raap AK. Comprehensive analysis of human subtelomeres with combined binary ratio labelling fluorescence in situ hybridisation. Eur J Hum Genet 2003; 11:643-51. [PMID: 12939649 DOI: 10.1038/sj.ejhg.5201028] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Cryptic subtelomeric chromosome rearrangements play an important role in the aetiology of mental retardation, congenital anomalies, miscarriages and neoplasia. To facilitate a comprehensive molecular-cytogenetic analysis of these extremely gene-rich and mutation-prone chromosome regions, novel multicolour fluorescence in situ hybridisation (FISH) techniques are being developed. As yet, subtelomeric FISH methods have either had limited multiplicities, making it necessary to perform many hybridisations per patient, or a limited scope of analysable chromosome mutation types, thus not detecting some aberration types such as pericentric inversions or very small aberrations. COBRA (COmbined Binary RAtio) labelling is a generic multicolour FISH technique that combines ratio and combinatorial labelling to attain especially high multiplicities with few fluorochromes. The Subtelomere COBRA FISH method ("S-COBRA FISH") described here detects efficiently all 41 BAC and PAC FISH probes necessary for a complete subtelomere screening in only two hybridisations. It was applied to the analysis of 10 cases with known and partially known aberrations and successfully detected balanced and unbalanced translocations, deletions and an unbalanced pericentric inversion in a mosaic situation. The ability of S-COBRA FISH to efficiently detect all types of balanced and unbalanced subtelomeric chromosome aberrations makes it the most comprehensive diagnostic procedure for human subtelomeric chromosome regions described to date.
Collapse
Affiliation(s)
- Hartmut Engels
- Institute of Human Genetics, University of Bonn, Wilhelmstrasse 31, D-53111 Bonn, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
27
|
Lafage-Pochitaloff M. [Essentials of conventional and molecular cytogenetics: application to diagnosis of hematological malignancies]. PATHOLOGIE-BIOLOGIE 2003; 51:307-11. [PMID: 12927887 DOI: 10.1016/s0369-8114(03)00115-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- M Lafage-Pochitaloff
- Département de Biopathologie, Institut Paoli-Calmettes, 232, boulevard Sainte-Marguerite, 13009 Marseille, France.
| |
Collapse
|
28
|
Flint J, Knight S. The use of telomere probes to investigate submicroscopic rearrangements associated with mental retardation. Curr Opin Genet Dev 2003; 13:310-6. [PMID: 12787795 DOI: 10.1016/s0959-437x(03)00049-2] [Citation(s) in RCA: 103] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Idiopathic mental retardation is a common condition the origins of which are poorly understood. Following initial reports that small chromosomal rearrangements affecting telomeres could be an important aetiological contributor, several new methods for screening patients have been developed. Over the past few years, 22 studies have reported results from 2585 patients. The prevalence of abnormalities in the entire group is 5.1%; but the figure is higher (6.8%) in individuals with moderate to severe mental retardation. About half the cases are caused by a de novo deletion, and about half by a balanced translocation segregating in a patient's family. Despite the large sample size available, it is still not clear whether a combination of thorough clinical examination and assiduous cytogenetic investigation might not be as effective at detecting subtelomeric anomalies as molecular assays.
Collapse
Affiliation(s)
- Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | | |
Collapse
|
29
|
Trifonov V, Seidel J, Starke H, Martina P, Beensen V, Ziegler M, Hartmann I, Heller A, Nietzel A, Claussen U, Liehr T. Enlarged chromosome 13 p-arm hiding a cryptic partial trisomy 6p22.2-pter. Prenat Diagn 2003; 23:427-30. [PMID: 12749042 DOI: 10.1002/pd.595] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
30
|
Paulsson K, Fioretos T, Strömbeck B, Mauritzson N, Tanke HJ, Johansson B. Trisomy 8 as the sole chromosomal aberration in myelocytic malignancies: a multicolor and locus-specific fluorescence in situ hybridization study. CANCER GENETICS AND CYTOGENETICS 2003; 140:66-9. [PMID: 12550762 DOI: 10.1016/s0165-4608(02)00628-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Trisomy 8 is the most common chromosomal aberration in myelocytic malignancies, occurring both as a sole change as well as in addition to other abnormalities. In spite of this, next to nothing is known about its pathogenetic importance or its molecular genetic consequences. Possible mechanisms involved in the transformation process include dosage effects of genes mapping to chromosome 8 and presence of specific mutations or cryptic fusion genes on the duplicated chromosome. In the latter case, +8 would be secondary to a cryptic primary rearrangement and not involved in leukemogenesis as such, but rather in tumor evolution. Although hidden genetic changes have been found in some trisomies, for example, mutations in KIT in acute myelocytic leukemia (AML) with +4 and in MET in hereditary papillary kidney carcinoma with trisomy 7, none associated with +8 have so far been discovered. To address this issue, we have investigated a total of 13 cases of AML, myelodysplastic syndromes, and chronic myeloproliferative disorders with trisomy 8 as the sole chromosomal anomaly. All cases were studied by combined binary ratio multicolor fluorescence in situ hybridization (FISH) and with FISH using locus-specific probes for both arms of chromosome 8, the subtelomeric regions of 8p and 8q, and the leukemia-associated genes FGFR1, MOZ, ETO, and MYC. No cryptic changes were detected, thus excluding the possibility of gross genetic rearrangements or aberrations involving these loci on chromosome 8.
Collapse
Affiliation(s)
- Kajsa Paulsson
- Department of Clinical Genetics, University Hospital, SE-221 85, Lund, Sweden.
| | | | | | | | | | | |
Collapse
|
31
|
Ness GO, Lybaek H, Houge G. Usefulness of high-resolution comparative genomic hybridization (CGH) for detecting and characterizing constitutional chromosome abnormalities. AMERICAN JOURNAL OF MEDICAL GENETICS 2002; 113:125-36. [PMID: 12407702 DOI: 10.1002/ajmg.10593] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Comparative genomic hybridization (CGH) is a technique for detection of chromosomal imbalances in a genomic DNA sample. We here report the application of the recently developed method of high-resolution CGH on DNA samples from 66 children having various degrees of delayed psychomotor development with or without clear dysmorphic features and congenital malformations. In 5 of 50 patients with apparently normal karyotypes, a deletion or duplication was revealed by CGH. Only one of these cases had a subtelomeric rearrangement. In one of seven cases with a de novo apparently balanced translocation, deletions were found. In all nine cases where the origin of a marker chromosome or additional chromosomal material was difficult to determine, CGH gave a precise identification. The following findings were from cases having a deletion or duplication as the sole chromosomal imbalance; dup(2)(p16p21), del(4)(q21q21), del(6)(q14q15), del(6)(p12p12), dup(6)(q24qter), and dup(15)(q11q13). One case had dup(9)(p11pter) combined with a very small subtelomeric deletion on 6q. In our hands, CGH is highly useful not only for identifying known chromosomal imbalances, but also for finding elusive deletions or duplications in the large group of children with developmental delay with or without congenital abnormalities. In such cases, the diagnostic yield of CGH appears to be higher than what has been reported from subtelomeric FISH screening.
Collapse
Affiliation(s)
- Gro Oddveig Ness
- Center for Medical Genetics and Molecular Medicine, Haukeland University Hospital, Bergen, Norway
| | | | | |
Collapse
|
32
|
Mozziconacci MJ, Rosenauer A, Restouin A, Fanelli M, Shao W, Fernandez F, Toiron Y, Viscardi J, Gambacorti-Passerini C, Miller WH, Lafage-Pochitaloff M. Molecular cytogenetics of the acute promyelocytic leukemia-derived cell line NB4 and of four all-trans retinoic acid-resistant subclones. Genes Chromosomes Cancer 2002; 35:261-70. [PMID: 12353268 DOI: 10.1002/gcc.10117] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The retinoic acid (RA)-sensitive NB4 cell line was the first established acute promyelocytic leukemia (APL) permanent cell line. It harbors the (15;17) translocation, which fuses the PML and RARA genes. Given the low frequency of APLs, their generally low white blood cell count, and the difficulty to work on APL patient cells, this cell line represents a remarkable tool for biomolecular studies. To investigate possible mechanisms of retinoid resistance, subclones of NB4 resistant to all-trans retinoic acid (ATRA) were established. To characterize better the parental NB4 cell line and four ATRA-resistant subclones (NB4-R4, NB4-A1, NB4-B1, and NB4-007/6), we have performed both conventional and 24-color FISH karyotyping. Thus, we could identify all chromosomal abnormalities including marker chromosomes that were unclassified with R banding. Moreover, we have performed dual-color FISH by use of specific PML and RARA probes, to evaluate the number of copies for each gene and fusion gene. Interestingly, the number of copies of PML, RARA, and fusion genes was different for each cell line. Finally, we assessed the presence of the PML, RARA, PML/RARA, and RARA/PML transcripts by RT-PCR and of the PML/RARA and RARA proteins by Western blotting in all the cell lines. These data could focus further research for a better understanding of the molecular mechanisms underlying response or resistance to differentiating and/or apoptotic reagents.
Collapse
MESH Headings
- Chromosome Banding/methods
- Chromosome Painting/methods
- Clone Cells
- Cytogenetic Analysis/methods
- DNA Probes/genetics
- DNA, Neoplasm/genetics
- Drug Resistance, Neoplasm/genetics
- Humans
- In Situ Hybridization, Fluorescence/methods
- Karyotyping/methods
- Leukemia, Promyelocytic, Acute/genetics
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Neoplasm Proteins/genetics
- Oncogene Proteins, Fusion/genetics
- Protein Isoforms/genetics
- Translocation, Genetic/genetics
- Tretinoin/metabolism
- Tumor Cells, Cultured
Collapse
|
33
|
Barbouti A, Johansson B, Höglund M, Mauritzson N, Strömbeck B, Nilsson PG, Tanke HJ, Hagemeijer A, Mitelman F, Fioretos T. Multicolor COBRA-FISH analysis of chronic myeloid leukemia reveals novel cryptic balanced translocations during disease progression. Genes Chromosomes Cancer 2002; 35:127-37. [PMID: 12203776 DOI: 10.1002/gcc.10099] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
During the initial indolent chronic phase of chronic myeloid leukemia (CML), the t(9;22)(q34;q11), resulting in the Philadelphia chromosome (Ph), is usually the sole cytogenetic anomaly, but as the disease progresses into the accelerated phase (AP), and eventually into aggressive blast crisis (BC), secondary aberrations, mainly unbalanced changes such as +8, i(17q), and +Ph, are frequent. To date, molecular genetic studies of CML BC have mainly focused on alterations of well-known tumor-suppressor genes (e.g., TP53, CDKN2A, and RB1) and oncogenes (e.g., RAS and MYC), whereas limited knowledge is available about the molecular genetic correlates of the unbalanced chromosomal abnormalities. Balanced secondary changes are rare in CML AP/BC, but it is not known whether cryptic chromosomal translocations, generating fusion genes, may be responsible for disease progression in a subgroup of CML. To address this issue, we used multicolor combined binary ratio fluorescence in situ hybridization (FISH), which allows the simultaneous visualization of all 24 chromosomes in different colors, verified by locus-specific FISH in a series of 33 CML cases. Two cryptic balanced translocations, t(7;17)(q32-34;q23) and t(7;17)(p15;q23), were found in two of the five cases showing the t(9;22) as the only cytogenetic change. Using several BAC clones, the breakpoints at 17q23 in both cases were mapped within a 350-kb region. In the case with the 7p15 breakpoint, a BAC clone containing the HOXA gene cluster displayed a split signal, suggesting a possible creation of a fusion gene involving a member of the HOXA family. Furthermore, one case with a partially cryptic t(9;11)(p21-22;q23) and an MLL rearrangement as well as a previously unreported t(3;10)(p22;p12-13) were identified. Altogether, a refined karyotypic description was achieved in 12 (36%) of the 33 investigated cases, illustrating the value of using multicolor FISH for identifying pathogenetically important aberrations in CML AP/BC.
Collapse
|
34
|
Satoh T, Hatanaka M, Yamamoto K, Kuro-o M, Sofuni T. Application of mFISH for the analysis of chemically-induced chromosomal aberrations: a model for the formation of triradial chromosomes. Mutat Res 2002; 504:57-65. [PMID: 12106646 DOI: 10.1016/s0027-5107(02)00079-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Using a human lymphoblastoid cell line WTK-1, we applied multicolor fluorescence in situ hybridization (mFISH) technique to analyze mitomycin C (MMC)-induced chromatid exchanges, focusing especially on the triradial chromosomes. It was found that the triradial chromosomes were formed with a specific rearrangement, "recipient and donor" relationship. The exchange sites of the recipient chromosomes were on single chromatid breaks and distributed randomly throughout the interstitial, pericentromeric, and terminal regions. In counterpart, donor chromosomes exchanged on isochromatid breaks of their telomeric and/or subtelomeric regions with the single chromatid breaks of recipient chromosomes. More than 80% of the scored triradial chromosomes were formed with such rearrangements, and few acentric chromosome fragments derived from the donor chromosomes could be detected in the metaphases observed. We therefore suggest that biological mechanisms of breakages between the recipient and donor chromosomes are different: the former due to direct DNA-damage by MMC, but the latter due to indirect DNA-damage depending on telomeric specific structure/function.
Collapse
Affiliation(s)
- Takatomo Satoh
- Life Science Technology Research Center, Olympus Optical Co. Ltd., 2-3 Kuboyama-cho, Hachioji, Tokyo, Japan.
| | | | | | | | | |
Collapse
|
35
|
Veltman JA, Schoenmakers EFPM, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 2002; 70:1269-76. [PMID: 11951177 PMCID: PMC447601 DOI: 10.1086/340426] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2001] [Accepted: 02/25/2002] [Indexed: 12/08/2022] Open
Abstract
Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome-specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure.
Collapse
Affiliation(s)
- Joris A Veltman
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Abstract
Subtelomeres are extraordinarily dynamic and variable regions near the ends of chromosomes. They are defined by their unusual structure: patchworks of blocks that are duplicated near the ends of multiple chromosomes. Duplications among subtelomeres have spawned small gene families, making inter-individual variation in subtelomeres a potential source of phenotypic diversity. The ectopic recombination that occurs between subtelomeres might also have a role in reconstituting telomeres in the absence of telomerase. However, the propensity for subtelomeres to interchange is a double-edged sword, as extensive subtelomeric homology can mediate deleterious rearrangements of the ends of chromosomes to cause human disease.
Collapse
Affiliation(s)
- Heather C Mefford
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
| | | |
Collapse
|
37
|
Lee C, Lemyre E, Miron PM, Morton CC. Multicolor fluorescence in situ hybridization in clinical cytogenetic diagnostics. Curr Opin Pediatr 2001; 13:550-5. [PMID: 11753105 DOI: 10.1097/00008480-200112000-00010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Multicolor fluorescence in situ hybridization is a technology that has vastly expanded the diagnostic repertoire of the clinical cytogenetics laboratory. The limitations of conventional chromosome banding analysis can often be overcome by the high sensitivity and specificity of multicolor fluorescence in situ hybridization tests. This article reviews the latest multicolor fluorescence in situ hybridization tests (including multiplex fluorescence in situ hybridization, spectral karyotyping, cross-species color banding, and comparative genomic hybridization) that are currently limited to a few select clinical cytogenetic laboratories, but may soon have more dominant roles in clinical cytogenetic practice.
Collapse
Affiliation(s)
- C Lee
- Department of Pathology, Brigham and Women's Hospital, Boston Massachusetts, USA.
| | | | | | | |
Collapse
|
38
|
Fauth C, Speicher MR. Classifying by colors: FISH-based genome analysis. CYTOGENETICS AND CELL GENETICS 2001; 93:1-10. [PMID: 11474168 DOI: 10.1159/000056937] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In recent years a fascinating evolution of different multicolor fluorescence in situ hybridization (FISH) technologies could be witnessed. The various approaches to cohybridize multiple DNA probes in different colors opened new avenues for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. These developments had a remarkable impact on microscopy design and the usage of highly sensitive area imagers. In addition, they led to the introduction of new fluorochromes with appropriate filter combinations, refinements of hybridization protocols, novel probe sets, and innovative software for automated chromosome analysis. This paper attempts to summarize the various multicolor approaches and discusses the application of the individual technologies.
Collapse
Affiliation(s)
- C Fauth
- Institut für Anthropologie und Humangenetik, Ludwig-Maximilians-Universität München, Goethestrasse 31, D-80336 Münich, Germany
| | | |
Collapse
|
39
|
Abstract
Refinements in cytogenetic techniques over the past 30 years have allowed the increasingly sensitive detection of chromosome abnormalities in haematological malignancies. In particular, the advent of fluorescence in situ hybridization techniques has provided significant advances in both diagnosis and research of leukaemias. The application of new multicolour karyotyping techniques has allowed the complete dissection of complex chromosome rearrangements and provides the prospect of identifying new recurrent chromosome rearrangements. Both comparative genomic hybridization and interphase fluorescence in situ hybridization avoid the use of metaphase chromosomes altogether and have allowed the genetic analysis of previously intractable targets. Recent developments in comparative genomic hybridization to DNA microarrays provide the promise of high resolution and automated screening for chromosomal imbalances. Rather than replacing conventional cytogenetics, however, these techniques have extended the range of cytogenetic analyses when applied in a complementary fashion.
Collapse
Affiliation(s)
- L Kearney
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headington, Oxford, OX3 9DS, UK
| |
Collapse
|