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Bailey SM, Kunkel SR, Bedford JS, Cornforth MN. The Central Role of Cytogenetics in Radiation Biology. Radiat Res 2024; 202:227-259. [PMID: 38981612 DOI: 10.1667/rade-24-00038.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/23/2024] [Indexed: 07/11/2024]
Abstract
Radiation cytogenetics has a rich history seldom appreciated by those outside the field. Early radiobiology was dominated by physics and biophysical concepts that borrowed heavily from the study of radiation-induced chromosome aberrations. From such studies, quantitative relationships between biological effect and changes in absorbed dose, dose rate and ionization density were codified into key concepts of radiobiological theory that have persisted for nearly a century. This review aims to provide a historical perspective of some of these concepts, including evidence supporting the contention that chromosome aberrations underlie development of many, if not most, of the biological effects of concern for humans exposed to ionizing radiations including cancer induction, on the one hand, and tumor eradication on the other. The significance of discoveries originating from these studies has widened and extended far beyond their original scope. Chromosome structural rearrangements viewed in mitotic cells were first attributed to the production of breaks by the radiations during interphase, followed by the rejoining or mis-rejoining among ends of other nearby breaks. These relatively modest beginnings eventually led to the discovery and characterization of DNA repair of double-strand breaks by non-homologous end joining, whose importance to various biological processes is now widely appreciated. Two examples, among many, are V(D)J recombination and speciation. Rapid technological advancements in cytogenetics, the burgeoning fields of molecular radiobiology and third-generation sequencing served as a point of confluence between the old and new. As a result, the emergent field of "cytogenomics" now becomes uniquely positioned for the purpose of more fully understanding mechanisms underlying the biological effects of ionizing radiation exposure.
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Affiliation(s)
- Susan M Bailey
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
| | - Stephen R Kunkel
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas
| | - Joel S Bedford
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, Colorado
| | - Michael N Cornforth
- Department of Radiation Oncology, University of Texas Medical Branch, Galveston, Texas
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2
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Karamysheva TV, Lebedev IN, Minaycheva LI, Nazarenko LP, Kashevarova AA, Fedotov DA, Skryabin NA, Lopatkina ME, Cheremnykh AD, Fonova EA, Nikitina TV, Sazhenova EA, Skleimova MM, Kolesnikov NA, Drozdov GV, Yakovleva YS, Seitova GN, Orishchenko KE, Rubtsov NB. A case report of Pallister-Killian syndrome with an unusual mosaic supernumerary marker chromosome 12 with interstitial 12p13.1-p12.1 duplication. Front Genet 2024; 15:1331066. [PMID: 38528911 PMCID: PMC10961358 DOI: 10.3389/fgene.2024.1331066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/22/2024] [Indexed: 03/27/2024] Open
Abstract
Pallister-Killian syndrome (PKS) is a rare inherited disease with multiple congenital anomalies, profound intellectual disability, and the presence in the karyotype of sSMC - i(12)(p10). The frequency of PKS may be underestimated due to problems with cytogenetic diagnosis caused by tissue-specific mosaicism and usually a low percentage of peripheral blood cells containing sSMC. Such tissue-specific mosaicism also complicates a detailed analysis of the sSMC, which, along with the assessment of mosaicism in different tissues, is an important part of cytogenetic diagnosis in PKS. Unfortunately, a full-fledged diagnosis in PKS is either practically impossible or complicated. On the one hand, this is due to problems with the biopsy of various tissues (skin biopsy with fibroblast culture is most often used in practice); on the other - a low percentage of dividing peripheral blood cells containing sSMC, which often significantly complicates the analysis of its composition and organization. In the present study, a detailed analysis of sSMC was carried out in a patient with a characteristic clinical picture of PKS. A relatively high percentage of peripheral blood cells with sSMC (50%) made it possible to perform a detailed molecular cytogenetic analysis of de novo sSMC using chromosomal in situ suppression hybridization (CISS-hybridization), multicolor FISH (mFISH), multicolor chromosome banding (MCB), array CGH (aCGH), and quantitative real-time PCR (qPCR), and short tandem repeat (STR) - analysis. As a result, it was found that the sSMC is not a typical PKS derivative of chromosome 12. In contrast to the classical i(12)(p10) for PKS, the patient's cells contained an acrocentric chromosome consisting of 12p material. Clusters of telomeric repeats were found at the both ends of the sSMC. Furthemore, the results of aCGH and qPCR indicate the presence of interstitial 8.9 Mb duplication at 12p13.1-p12.1 within the sSMC, which leads to different representations of DNA from different segments of 12p within cells containing sSMC. The obtained data raise the question of the instability of the sSMC and, as a consequence, the possible presence of additional rearrangements, which, in traditional cytogenetic analysis of patients with PKS, are usually described as i(12)(p10).
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Affiliation(s)
- T. V. Karamysheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk, Russia
| | - I. N. Lebedev
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
- Department of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - L. I. Minaycheva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - L. P. Nazarenko
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
- Department of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - A. A. Kashevarova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - D. A. Fedotov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N. A. Skryabin
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M. E. Lopatkina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - A. D. Cheremnykh
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E. A. Fonova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
- Department of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - T. V. Nikitina
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - E. A. Sazhenova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - M. M. Skleimova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - N. A. Kolesnikov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - G. V. Drozdov
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - Y. S. Yakovleva
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
- Department of Medical Genetics, Siberian State Medical University, Tomsk, Russia
| | - G. N. Seitova
- Research Institute of Medical Genetics, Tomsk National Research Medical Center of the Russian Academy of Sciences, Tomsk, Russia
| | - K. E. Orishchenko
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk, Russia
| | - N. B. Rubtsov
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences (SB RAS), Novosibirsk, Russia
- Department of Genetic Technologies, Novosibirsk State University, Novosibirsk, Russia
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3
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The Precise Breakpoint Mapping in Paracentric Inversion 10q22.2q23.3 by Comprehensive Cytogenomic Analysis, Multicolor Banding, and Single-Copy Chromosome Sequencing. Biomedicines 2022; 10:biomedicines10123255. [PMID: 36552011 PMCID: PMC9775520 DOI: 10.3390/biomedicines10123255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/29/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
Detection and precise genomic mapping of balanced chromosomal abnormalities in patients with impaired fertility or a clinical phenotype represent a challenge for current cytogenomics owing to difficulties with precise breakpoint localization in the regions enriched for DNA repeats and high genomic variation in such regions. Here, we present a comprehensive cytogenomic approach to breakpoint mapping in a rare paracentric inversion on 10q (in a patient with oligoasthenoteratozoospermia and necrozoospermia) that does not affect other phenotype traits. Multicolor banding, chromosomal microarray analysis, chromosome microdissection with reverse painting, and single-copy sequencing of the rearranged chromosome were performed to determine the length and position of the inverted region as well as to rule out a genetic imbalance at the breakpoints. As a result, a paracentric 19.251 Mbp inversion at 10q22.2q23.3 was described. The most probable location of the breakpoints was predicted using the hg38 assembly. The problems of genetic counseling associated with enrichment for repeats and high DNA variability of usual breakpoint regions were discussed. Possible approaches for cytogenomic assessment of couples with balanced chromosome rearrangements and problems like reproductive failures were considered and suggested as useful part of effective genetic counseling.
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Wang Q, Lee Y, Pujol-Canadell M, Perrier JR, Smilenov L, Harken A, Garty G, Brenner DJ, Ponnaiya B, Turner HC. Cytogenetic Damage of Human Lymphocytes in Humanized Mice Exposed to Neutrons and X Rays 24 h After Exposure. Cytogenet Genome Res 2021; 161:352-361. [PMID: 34488220 PMCID: PMC8455411 DOI: 10.1159/000516529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 04/02/2021] [Indexed: 11/19/2022] Open
Abstract
Detonation of an improvised nuclear device highlights the need to understand the risk of mixed radiation exposure as prompt radiation exposure could produce significant neutron and gamma exposures. Although the neutron component may be a relatively small percentage of the total absorbed dose, the large relative biological effectiveness (RBE) can induce larger biological DNA damage and cell killing. The objective of this study was to use a hematopoietically humanized mouse model to measure chromosomal DNA damage in human lymphocytes 24 h after in vivo exposure to neutrons (0.3 Gy) and X rays (1 Gy). The human dicentric and cytokinesis-block micronucleus assays were performed to measure chromosomal aberrations in human lymphocytes in vivo from the blood and spleen, respectively. The mBAND assay based on fluorescent in situ hybridization labeling was used to detect neutron-induced chromosome 1 inversions in the blood lymphocytes of the neutron-irradiated mice. Cytogenetics endpoints, dicentrics and micronuclei showed that there was no significant difference in yields between the 2 irradiation types at the doses tested, indicating that neutron-induced chromosomal DNA damage in vivo was more biologically effective (RBE ∼3.3) compared to X rays. The mBAND assay, which is considered a specific biomarker of high-LET neutron exposure, confirmed the presence of clustered DNA damage in the neutron-irradiated mice but not in the X-irradiated mice, 24 h after exposure.
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Affiliation(s)
- Qi Wang
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Younghyun Lee
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Monica Pujol-Canadell
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Jay R. Perrier
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Lubomir Smilenov
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Andrew Harken
- Radiological Research Accelerator Facility, Columbia University, Irvington, (NY), USA
| | - Guy Garty
- Radiological Research Accelerator Facility, Columbia University, Irvington, (NY), USA
| | - David J. Brenner
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
| | - Brian Ponnaiya
- Radiological Research Accelerator Facility, Columbia University, Irvington, (NY), USA
| | - Helen C. Turner
- Center for Radiological Research, Columbia University Irving Medical Center, New York, (NY), USA
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Hu Q, Maurais EG, Ly P. Cellular and genomic approaches for exploring structural chromosomal rearrangements. Chromosome Res 2020; 28:19-30. [PMID: 31933061 PMCID: PMC7131874 DOI: 10.1007/s10577-020-09626-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 12/20/2019] [Accepted: 01/01/2020] [Indexed: 12/13/2022]
Abstract
Human chromosomes are arranged in a linear and conserved sequence order that undergoes further spatial folding within the three-dimensional space of the nucleus. Although structural variations in this organization are an important source of natural genetic diversity, cytogenetic aberrations can also underlie a number of human diseases and disorders. Approaches for studying chromosome structure began half a century ago with karyotyping of Giemsa-banded chromosomes and has now evolved to encompass high-resolution fluorescence microscopy, reporter-based assays, and next-generation DNA sequencing technologies. Here, we provide a general overview of experimental methods at different resolution and sensitivity scales and discuss how they can be complemented to provide synergistic insight into the study of human chromosome structural rearrangements. These approaches range from kilobase-level resolution DNA fluorescence in situ hybridization (FISH)-based imaging approaches of individual cells to genome-wide sequencing strategies that can capture nucleotide-level information from diverse sample types. Technological advances coupled to the combinatorial use of multiple methods have resulted in the discovery of new rearrangement classes along with mechanistic insights into the processes that drive structural alterations in the human genome.
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Affiliation(s)
- Qing Hu
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth G Maurais
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Peter Ly
- Department of Pathology, Department of Cell Biology, Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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6
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Rubtsova NV, Karamysheva TV, Rubtsov NB. Clusters of Repetitive DNA Sequences in Chromosomes of Voles of the Subgenus Microtus (Microtus, Arvicolidae). RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419090126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Liehr T. From Human Cytogenetics to Human Chromosomics. Int J Mol Sci 2019; 20:E826. [PMID: 30769866 PMCID: PMC6413437 DOI: 10.3390/ijms20040826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 01/30/2019] [Accepted: 02/12/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND The concept of "chromosomics" was introduced by Prof. Uwe Claussen in 2005. Herein, the growing insights into human chromosome structure finally lead to a "chromosomic view" of the three-dimensional constitution and plasticity of genes in interphase nuclei are discussed. This review is dedicated to the memory of Prof. Uwe Claussen (30 April 1945⁻20 July 2008). RECENT FINDINGS Chromosomics is the study of chromosomes, their three-dimensional positioning in the interphase nucleus, the consequences from plasticity of chromosomal subregions and gene interactions, the influence of chromatin-modification-mediated events on cells, and even individuals, evolution, and disease. Progress achieved in recent years is summarized, including the detection of chromosome-chromosome-interactions which, if damaged, lead to malfunction and disease. However, chromosomics in the Human Genetics field is not progressing presently, as research interest has shifted from single cell to high throughput, genomic approaches. CONCLUSION Chromosomics and its impact were predicted correctly in 2005 by Prof. Claussen. Although some progress was achieved, present reconsiderations of the role of the chromosome and the single cell in Human Genetic research are urgently necessary.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Am Klinikum 1, D-07747 Jena, Germany.
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8
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Hill MA. Track to the future: historical perspective on the importance of radiation track structure and DNA as a radiobiological target. Int J Radiat Biol 2018; 94:759-768. [PMID: 29219655 PMCID: PMC6113897 DOI: 10.1080/09553002.2017.1387304] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 09/22/2017] [Accepted: 09/27/2017] [Indexed: 12/04/2022]
Abstract
PURPOSE Understanding the mechanisms behind induced biological response following exposure to ionizing radiation is not only important in assessing the risk associated with human exposure, but potentially can help identify ways of improving the efficacy of radiotherapy. Over the decades, there has been much discussion on what is the key biological target for radiation action and its associated size. It was already known in the 1930s that microscopic features of radiation significantly influenced biological outcomes. This resulted in the development of classic target theory, leading to field of microdosimetry and subsequently nanodosimetry, studying the inhomogeneity and stochastics of interactions, along with the identification of DNA as a key target. CONCLUSIONS Ultimately, the biological response has been found to be dependent on the radiation track structure (spatial and temporal distribution of ionization and excitation events). Clustering of energy deposition on the nanometer scale has been shown to play a critical role in determining biological response, producing not just simple isolated DNA lesions but also complex clustered lesions that are more difficult to repair. The frequency and complexity of these clustered damage sites are typically found to increase with increasing LET. However in order to fully understand the consequences, it is important to look at the relative distribution of these lesions over larger dimensions along the radiation track, up to the micrometer scale. Correlation of energy deposition events and resulting sites of DNA damage can ultimately result in complex gene mutations and complex chromosome rearrangements following repair, with the frequency and spectrum of the resulting rearrangements critically dependent on the spatial and temporal distribution of these sites and therefore the radiation track. Due to limitations in the techniques used to identify these rearrangements it is likely that the full complexity of the genetic rearrangements that occur has yet to be revealed. This paper discusses these issues from a historical perspective, with many of these historical studies still having relevance today. These can not only cast light on current studies but guide future studies, especially with the increasing range of biological techniques available. So, let us build on past knowledge to effectively explore the future.
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Affiliation(s)
- Mark A. Hill
- CRUK/MRC Oxford Institute for Radiation Oncology, University of Oxford, Gray Laboratories, ORCRB Roosevelt Drive, Oxford, UK
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Babu R, Van Dyke DL, Dev VG, Koduru P, Rao N, Mitter NS, Liu M, Fuentes E, Fuentes S, Papa S. Interphase Chromosome Profiling: A Method for Conventional Banded Chromosome Analysis Using Interphase Nuclei. Arch Pathol Lab Med 2017; 142:213-228. [PMID: 28981371 DOI: 10.5858/arpa.2016-0621-oa] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - Chromosome analysis on bone marrow or peripheral blood samples fails in a small proportion of attempts. A method that is more reliable, with similar or better resolution, would be a welcome addition to the armamentarium of the cytogenetics laboratory. OBJECTIVE - To develop a method similar to banded metaphase chromosome analysis that relies only on interphase nuclei. DESIGN - To label multiple targets in an equidistant fashion along the entire length of each chromosome, including landmark subtelomere and centromere regions. Each label so generated by using cloned bacterial artificial chromosome probes is molecularly distinct with unique spectral characteristics, so the number and position of the labels can be tracked to identify chromosome abnormalities. RESULTS - Interphase chromosome profiling (ICP) demonstrated results similar to conventional chromosome analysis and fluorescence in situ hybridization in 55 previously studied cases and obtained useful ICP chromosome analysis results on another 29 cases in which conventional methods failed. CONCLUSIONS - ICP is a new and powerful method to karyotype peripheral blood and bone marrow aspirate preparations without reliance on metaphase chromosome preparations. It will be of particular value for cases with a failed conventional analysis or when a fast turnaround time is required.
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Iannuzzi A, Pereira J, Iannuzzi C, Fu B, Ferguson-Smith M. Pooling strategy and chromosome painting characterize a living zebroid for the first time. PLoS One 2017; 12:e0180158. [PMID: 28700625 PMCID: PMC5507506 DOI: 10.1371/journal.pone.0180158] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/10/2017] [Indexed: 11/19/2022] Open
Abstract
We have investigated the complex karyotype of a living zebra-donkey hybrid for the first time using chromosome-specific painting probes produced from flow-sorted chromosomes from a zebra (Equus burchelli) and horse (Equus caballus). As the chromosomes proved difficult to distinguish from one another, a successful new strategy was devised to resolve the difficulty and characterize each chromosome. This was based on selecting five panels of whole chromosome painting probes that could differentiate zebra and donkey chromosomes by labelling the probes with either FITC or Cy3 fluorochromes. Each panel was hybridized sequentially to the same G-Q-banded metaphases and the results combined so that every zebra and donkey chromosome in each suitable metaphase could be identified. A diploid number of 2n = 53, XY was found, containing haploid sets of 22 chromosomes from the zebra and 31 chromosomes from the donkey, without evidence of chromosome rearrangement. This new strategy, developed for the first time, may have several applications in the resolution of other complex hybrid karyotypes and chromosomal aberrations.
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Affiliation(s)
- Alessandra Iannuzzi
- Laboratory of Animal Cytogenetics and Genomics, National Research Council of Italy, Institute of Animal Production Systems in Mediterranean Environments (ISPAAM), Naples, Italy
- * E-mail:
| | - Jorge Pereira
- Cytocell Ltd., Cambridge Technopark, Cambridge, United Kingdom
| | - Clara Iannuzzi
- Department of Biochemistry, Biophysics and General Pathology, Università degli Studi della Campania “Luigi Vanvitelli”, Naples, Italy
| | - Beiyuan Fu
- Cytogenetic Facility, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Malcolm Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, University of Cambridge Department of Veterinary Medicine, Cambridge, United Kingdom
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Du Y, Chen B. Detection approaches for multidrug resistance genes of leukemia. DRUG DESIGN DEVELOPMENT AND THERAPY 2017; 11:1255-1261. [PMID: 28458519 PMCID: PMC5402920 DOI: 10.2147/dddt.s134529] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Leukemia is a clonal malignant hematopoietic stem cell disease. It is the sixth most lethal cancer and accounts for 4% of all cancers. The main form of treatment for leukemia is chemotherapy. While some cancer types with a higher incidence than leukemia, such as lung and gastric cancer, have shown a sharp decline in mortality rates in recent years, leukemia has not followed this trend. Drug resistance is often regarded as the main clinical obstacle to effective chemotherapy in patients diagnosed with leukemia. Many resistance mechanisms have now been identified, and multidrug resistance (MDR) is considered the most important and prevalent mechanism involved in the failure of chemotherapy in leukemia. In order to reverse MDR and improve leukemia prognosis, effective detection methods are needed to identify drug resistance genes at initial diagnosis. This article provides a comprehensive overview of published approaches for the detection of MDR in leukemia. Identification of relevant MDR genes and methods for early detection of these genes will be needed in order to treat leukemia more effectively.
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Affiliation(s)
- Ying Du
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
| | - Baoan Chen
- Department of Hematology and Oncology (Key Department of Jiangsu Medicine), School of Medicine, Zhongda Hospital, Southeast University, Nanjing, Jiangsu Province, People's Republic of China
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12
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Liehr T, Othman MAK, Rittscher K. Multicolor Karyotyping and Fluorescence In Situ Hybridization-Banding (MCB/mBAND). Methods Mol Biol 2017; 1541:181-187. [PMID: 27910024 DOI: 10.1007/978-1-4939-6703-2_16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Multicolor fluorescence in situ hybridization (mFISH) approaches are routine applications in tumor as well as clinical cytogenetics nowadays. The first approach when thinking about mFISH is multicolor karyotyping using human whole chromosome paints as probes; this can be achieved by narrow-band filter-based multiplex-FISH (M-FISH) or interferometer/spectroscopy-based spectral karyotyping (SKY). Besides, various FISH-based banding approaches were reported in the literature, including multicolor banding (MCB/mBAND) the latter being evaluated by narrow-band filters, and using specific software. Here, we describe the combined application of multicolor karyotyping and MCB/mBAND for the characterization of simple and complex acquired chromosomal changes in cancer cytogenetics.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany.
| | - Moneeb A K Othman
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
| | - Katharina Rittscher
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, D-07743, Jena, Germany
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13
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Abstract
The Philadelphia chromosome was the first chromosomal abnormality discovered in cancer using the cytogenetics technique in 1960, and was consistently associated with chronic myeloid leukemia. Over the past five decades, innovative technical advances in the field of cancer cytogenetics have greatly enhanced the detection ability of chromosomal alterations, and have facilitated the research and diagnostic potential of chromosomal studies in neoplasms. These developments notwithstanding, chromosome analysis of a single cell is still the easiest way to delineate and understand the relationship between clonal evolution and disease progression of cancer cells. The use of advanced fluorescence in situ hybridization (FISH) techniques allows for the further identification of chromosomal alterations that are unresolved by the karyotyping method. It overcame many of the drawbacks of assessing the genetic alterations in cancer cells by karyotyping. Subsequently, the development of DNA microarray technologies provides a high-resolution view of the whole genome, which may add massive amounts of new information and opens the field of cancer cytogenomics. Strikingly, cancer cytogenetics does not only provide key information to improve the care of patients with malignancies, but also acts as a guide to identify the genes responsible for the development of these neoplastic states and has led to the emergence of molecularly targeted therapies in the field of personalized medicine.
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Affiliation(s)
- Thomas S K Wan
- Haematology Division, Department of Anatomical & Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong.
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14
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Fluorescence imaging of chromosomal DNA using click chemistry. Sci Rep 2016; 6:33217. [PMID: 27620982 PMCID: PMC5020420 DOI: 10.1038/srep33217] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 08/23/2016] [Indexed: 11/08/2022] Open
Abstract
Chromosome visualization is essential for chromosome analysis and genetic diagnostics. Here, we developed a click chemistry approach for multicolor imaging of chromosomal DNA instead of the traditional dye method. We first demonstrated that the commercially available reagents allow for the multicolor staining of chromosomes. We then prepared two pro-fluorophore moieties that served as light-up reporters to stain chromosomal DNA based on click reaction and visualized the clear chromosomes in multicolor. We applied this strategy in fluorescence in situ hybridization (FISH) and identified, with high sensitivity and specificity, telomere DNA at the end of the chromosome. We further extended this approach to observe several basic stages of cell division. We found that the click reaction enables direct visualization of the chromosome behavior in cell division. These results suggest that the technique can be broadly used for imaging chromosomes and may serve as a new approach for chromosome analysis and genetic diagnostics.
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Rebner K, Ostertag E, Kessler RW. Hyperspectral backscatter imaging: a label-free approach to cytogenetics. Anal Bioanal Chem 2016; 408:5701-5709. [DOI: 10.1007/s00216-016-9670-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Revised: 05/02/2016] [Accepted: 05/25/2016] [Indexed: 02/01/2023]
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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] [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.
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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.
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Berardinelli F, De Vitis M, Nieri D, Cherubini R, De Nadal V, Gerardi S, Tanzarella C, Sgura A, Antoccia A. mBAND and mFISH analysis of chromosomal aberrations and breakpoint distribution in chromosome 1 of AG01522 human fibroblasts that were exposed to radiation of different qualities. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 793:55-63. [DOI: 10.1016/j.mrgentox.2015.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 05/27/2015] [Indexed: 11/26/2022]
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Schmälter AK, Righolt CH, Kuzyk A, Mai S. Changes in Nuclear Orientation Patterns of Chromosome 11 during Mouse Plasmacytoma Development. Transl Oncol 2015; 8:417-423. [PMID: 26500032 PMCID: PMC4631097 DOI: 10.1016/j.tranon.2015.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 11/19/2022] Open
Abstract
Studying changes in nuclear architecture is a unique approach toward the understanding of nuclear remodeling during tumor development. One aspect of nuclear architecture is the orientation of chromosomes in the three-dimensional nuclear space. We studied mouse chromosome 11 in lymphocytes of [T38HxBALB/c]N mice with a reciprocal translocation between chromosome X and 11 (T38HT(X;11)) exhibiting a long chromosome T(11;X) and a short chromosome T(X;11) and in fast-onset plasmacytomas (PCTs) induced in the same strain. We determined the three-dimensional orientation of chromosome 11 using a mouse chromosome 11 specific multicolor banding probe. We also examined the nuclear position of the small translocation chromosome T(X;11) which contains cytoband 11E2 and parts of E1. Chromosomes can point either with their centromeric or with their telomeric end toward the nuclear center or periphery, or their position is found in parallel to the nuclear border. In T38HT(X;11) nuclei, the most frequently observed orientation pattern was with both chromosomes 11 in parallel to the nuclear border ("PP"). PCT cells showed nuclei with two or more copies of chromosome 11. In PCTs, the most frequent orientation pattern was with one chromosome in parallel and the other pointing with its centromeric end toward the nuclear periphery ("CP"). There is a significant difference between the orientation patterns observed in T38HT(X;11) and in PCT nuclei (P < .0001).
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Affiliation(s)
- Ann-Kristin Schmälter
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Christiaan H Righolt
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada; Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Alexandra Kuzyk
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada
| | - Sabine Mai
- Manitoba Institute of Cell Biology, University of Manitoba, CancerCare Manitoba, Winnipeg, MB, Canada.
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19
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Hill MA. Fishing for radiation quality: chromosome aberrations and the role of radiation track structure. RADIATION PROTECTION DOSIMETRY 2015; 166:295-301. [PMID: 25883310 DOI: 10.1093/rpd/ncv151] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The yield of chromosome aberrations is not only dependent on dose but also on radiation quality, with high linear energy transfer (LET) typically having a greater biological effectiveness per unit dose than those of low-LET radiation. Differences in radiation track structure and cell morphology can also lead to quantitative differences in the spectra of the resulting chromosomal rearrangements, especially at low doses associated with typical human exposures. The development of combinatorial fluorescent labelling techniques (such as mFISH and mBAND) has helped to reveal the complexity of rearrangements, showing increasing complexity of observed rearrangements with increasing LET but has a resolution limited to ∼10 MBp. High-LET particles have not only been shown to produce clustered sites of DNA damage but also produce multiple correlated breaks along its path resulting in DNA fragments smaller than the resolution of these techniques. Additionally, studies have shown that the vast majority of radiation-induced HPRT mutations were also not detectable using fluorescent in situ hybridisation (FISH) techniques, with correlation of breaks along the track being reflected in the complexity of mutations, with intra- and inter-chromosomal insertions, and inversions occurring at the sites of some of the deletions. Therefore, the analysis of visible chromosomal rearrangements observed using current FISH techniques is likely to represent just the tip of the iceberg, considerably underestimating the extent and complexity of radiation induced rearrangements.
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Affiliation(s)
- M A Hill
- CRUK/MRC Oxford Institute for Radiation Oncology, Gray Laboratories, University of Oxford, ORCRB Roosevelt Drive, Oxford OX3 7DQ, UK
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20
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Righolt CH, Schmälter AK, Kuzyk A, Young IT, van Vliet LJ, Mai S. Measuring murine chromosome orientation in interphase nuclei. Cytometry A 2015; 87:733-40. [PMID: 25891972 DOI: 10.1002/cyto.a.22674] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 03/25/2015] [Accepted: 03/31/2015] [Indexed: 11/08/2022]
Abstract
The nuclear architecture of a cell may change as a result of various diseases, including cancer. A variety of nuclear features are, therefore, of interest to cell biologists. Recently, several studies have investigated the orientation of chromosomes in the interphase nucleus either visually or semi-automatically. In this article an automated method to measure this orientation is presented. The theoretical difference between performing these measurements in two and three dimensions is discussed and experimentally verified. The results computed from measurements of murine nuclei correspond with results from visual inspection. We found significant differences in the orientation of chromosome 11 between nuclei from a PreB cell line of BALB/c origin and primary B nuclei from congenic [T38HxBALB/c]N wild-type mice. Since our new automatic method concurs with both the visual and semi-automatic methods, we conclude that the automatic method can replace these methods in assessing chromosome orientation.
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Affiliation(s)
- Christiaan H Righolt
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Ann-Kristin Schmälter
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada.,Institute for Human Genetics, Ludwig Maximilian University, Munich, Germany
| | - Alexandra Kuzyk
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ian T Young
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Lucas J van Vliet
- Department of Imaging Physics, Delft University of Technology, Delft, The Netherlands
| | - Sabine Mai
- Manitoba Institute of Cell Biology, CancerCare Manitoba, University of Manitoba, Winnipeg, Manitoba, Canada
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21
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Ferguson-Smith MA. History and evolution of cytogenetics. Mol Cytogenet 2015; 8:19. [PMID: 25810762 PMCID: PMC4373004 DOI: 10.1186/s13039-015-0125-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/04/2015] [Indexed: 11/21/2022] Open
Abstract
The events that have led to the development of cytogenetics as a specialty within the life sciences are described, with special attention to the early history of human cytogenetics. Improvements in the resolution of chromosome analysis has followed closely the introduction of innovative technology. The review provides a brief account of the structure of somatic and meiotic chromosomes, stressing the high conservation of structure in plants and animals, with emphasis on aspects that require further research. The future of molecular cytogenetics is likely to depend on a better knowledge of chromosome structure and function.
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Affiliation(s)
- Malcolm A Ferguson-Smith
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES UK
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22
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Bogomolov AG, Karamysheva TV, Rubtsov NB. Fluorescence in situ hybridization with DNA probes derived from individual chromosomes and chromosome regions. Mol Biol 2014. [DOI: 10.1134/s002689331406003x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Prediction of individual response to anticancer therapy: historical and future perspectives. Cell Mol Life Sci 2014; 72:729-57. [PMID: 25387856 PMCID: PMC4309902 DOI: 10.1007/s00018-014-1772-3] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 10/23/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023]
Abstract
Since the introduction of chemotherapy for cancer treatment in the early 20th century considerable efforts have been made to maximize drug efficiency and at the same time minimize side effects. As there is a great interpatient variability in response to chemotherapy, the development of predictive biomarkers is an ambitious aim for the rapidly growing research area of personalized molecular medicine. The individual prediction of response will improve treatment and thus increase survival and life quality of patients. In the past, cell cultures were used as in vitro models to predict in vivo response to chemotherapy. Several in vitro chemosensitivity assays served as tools to measure miscellaneous endpoints such as DNA damage, apoptosis and cytotoxicity or growth inhibition. Twenty years ago, the development of high-throughput technologies, e.g. cDNA microarrays enabled a more detailed analysis of drug responses. Thousands of genes were screened and expression levels were correlated to drug responses. In addition, mutation analysis became more and more important for the prediction of therapeutic success. Today, as research enters the area of -omics technologies, identification of signaling pathways is a tool to understand molecular mechanism underlying drug resistance. Combining new tissue models, e.g. 3D organoid cultures with modern technologies for biomarker discovery will offer new opportunities to identify new drug targets and in parallel predict individual responses to anticancer therapy. In this review, we present different currently used chemosensitivity assays including 2D and 3D cell culture models and several -omics approaches for the discovery of predictive biomarkers. Furthermore, we discuss the potential of these assays and biomarkers to predict the clinical outcome of individual patients and future perspectives.
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24
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Wan TSK. Cancer cytogenetics: methodology revisited. Ann Lab Med 2014; 34:413-25. [PMID: 25368816 PMCID: PMC4215412 DOI: 10.3343/alm.2014.34.6.413] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 07/31/2014] [Accepted: 10/06/2014] [Indexed: 01/14/2023] Open
Abstract
The Philadelphia chromosome was the first genetic abnormality discovered in cancer (in 1960), and it was found to be consistently associated with CML. The description of the Philadelphia chromosome ushered in a new era in the field of cancer cytogenetics. Accumulating genetic data have been shown to be intimately associated with the diagnosis and prognosis of neoplasms; thus, karyotyping is now considered a mandatory investigation for all newly diagnosed leukemias. The development of FISH in the 1980s overcame many of the drawbacks of assessing the genetic alterations in cancer cells by karyotyping. Karyotyping of cancer cells remains the gold standard since it provides a global analysis of the abnormalities in the entire genome of a single cell. However, subsequent methodological advances in molecular cytogenetics based on the principle of FISH that were initiated in the early 1990s have greatly enhanced the efficiency and accuracy of karyotype analysis by marrying conventional cytogenetics with molecular technologies. In this review, the development, current utilization, and technical pitfalls of both the conventional and molecular cytogenetics approaches used for cancer diagnosis over the past five decades will be discussed.
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Affiliation(s)
- Thomas S. K. Wan
- Haematology Division, Department of Pathology, The University of Hong Kong, Hong Kong
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25
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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.
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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
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26
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Mutually exclusive FGFR2, HER2, and KRAS gene amplifications in gastric cancer revealed by multicolour FISH. Cancer Lett 2014; 353:167-75. [PMID: 25086186 DOI: 10.1016/j.canlet.2014.07.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/11/2014] [Accepted: 07/11/2014] [Indexed: 12/15/2022]
Abstract
Gastric cancer (GC) is a major cause of global cancer mortality. Previous genomic studies have reported that several RTK-RAS pathway components are amplified in GC, with individual tumours often amplifying one component and not others ("mutual exclusivity"). Here, we sought to validate these findings for three RTK/RAS components (FGFR2, HER2, KRAS) using fluorescence in situ hybridisation (FISH) on a series of gastric tumours, cell lines and patient-derived xenografts. Applying dual-colour FISH on 137 gastric tumours (89 FFPE surgical resections and 48 diagnostic biopsies), we observed FGFR2 amplification in 7.3% and HER2 amplification in 2.2% of GCs. GCs exhibiting FGFR2 amplification were associated with high tumour grade (p = 0.034). In FISH positive tumours, striking differences in copy number levels between cancer cells in the same tumour were observed, suggesting intra-tumour heterogeneity. Using a multicolour FISH assay allowing simultaneous detection of FGFR2, HER2, and KRAS amplifications, we confirmed that these components exhibited a mutually exclusive pattern of gene amplification across patients. The FISH data were also strongly correlated with Q-PCR levels and at the protein level by immunohistochemistry. Our data confirm that RTK/RAS components are mutually exclusively amplified in GC, and demonstrate the feasibility of identifying multiple aneuploidies using a single FISH assay. Application of this assay to GC samples, particularly diagnostic biopsies, may facilitate enrollment of GC patients into clinical trials evaluating RTK/RAS directed therapies. However, the presence of intra-tumour heterogeneity may require multiple biopsy samples to be obtained per patient before a definitive diagnosis can be attained.
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27
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Schmälter AK, Kuzyk A, Righolt CH, Neusser M, Steinlein OK, Müller S, Mai S. Distinct nuclear orientation patterns for mouse chromosome 11 in normal B lymphocytes. BMC Cell Biol 2014; 15:22. [PMID: 24923307 PMCID: PMC4078936 DOI: 10.1186/1471-2121-15-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 05/30/2014] [Indexed: 11/15/2022] Open
Abstract
Background Characterizing the nuclear orientation of chromosomes in the three-dimensional (3D) nucleus by multicolor banding (mBANDing) is a new approach towards understanding nuclear organization of chromosome territories. An mBANDing paint is composed of multiple overlapping subchromosomal probes that represent different regions of a single chromosome. In this study, we used it for the analysis of chromosome orientation in 3D interphase nuclei. We determined whether the nuclear orientation of the two chromosome 11 homologs was random or preferential, and if it was conserved between diploid mouse Pre B lymphocytes of BALB/c origin and primary B lymphocytes of congenic [T38HxBALB/c]N wild-type mice. The chromosome orientation was assessed visually and through a semi-automated quantitative analysis of the radial and angular orientation patterns observed in both B cell types. Results Our data indicate that there are different preferential patterns of chromosome 11 orientation, which are not significantly different between both mouse cell types (p > 0.05). In the most common case for both cell types, both copies of chromosome 11 were oriented in parallel with the nuclear border. The second most common pattern in both types of B lymphocytes was with one homolog of chromosome 11 positioned with its telomeric end towards the nuclear center and with its centromeric end towards the periphery, while the other chromosome 11 was found parallel with the nuclear border. In addition to these two most common orientations present in approximately 50% of nuclei from each cell type, other orientations were observed at lower frequencies. Conclusions We conclude that there are probabilistic, non-random orientation patterns for mouse chromosome 11 in the mouse B lymphocytes we investigated (p < 0.0001).
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Affiliation(s)
| | | | | | | | | | - Stefan Müller
- Manitoba Institute of Cell Biology, University of Manitoba, Cancer Care Manitoba, 675 McDermot Avenue, Winnipeg, Manitoba, Canada.
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Bint SM, Davies AF, Ogilvie CM. Multicolor banding remains an important adjunct to array CGH and conventional karyotyping. Mol Cytogenet 2013; 6:55. [PMID: 24314262 PMCID: PMC3906906 DOI: 10.1186/1755-8166-6-55] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 10/21/2013] [Indexed: 11/10/2022] Open
Abstract
Background Array comparative genomic hybridization (CGH) for high resolution detection of chromosome imbalance, and karyotype analysis using G-banded chromosomes for detection of chromosome rearrangements, provide a powerful diagnostic armoury for clinical cytogenetics. However, abnormalities detected by karyotype analysis cannot always be characterised by scrutinising the G-banded pattern alone, and imbalance detected by array CGH cannot always be visualised in the context of metaphase chromosomes. In some cases further techniques are needed for detailed characterisation of chromosomal abnormalities. We investigated seven cases involving structural chromosome rearrangements detected by karyotype analysis, and one case where imbalance was primarily detected by array CGH. Multicolor banding (MCB) was used in all cases and proved invaluable in understanding the detailed structure of the abnormalities. Findings Karyotype analysis detected structural chromosome rearrangements in 7 cases and MCB was used to help refine the karyotype for each case. Array CGH detected imbalance in an eighth case, where previously, G-banded chromosome analysis had reported a normal karyotype. Karyotype analysis of a second tissue type revealed this abnormality in mosaic form; however, MCB was needed in order to characterise this rearrangement. MCB provided information for the delineation of small deletions, duplications, insertions and inversions and helped to assign breakpoints which were difficult to identify from G-banded preparations due to ambiguous banding patterns. Conclusion Despite the recent advance of array CGH in molecular cytogenetics we conclude that fluorescence in situ hybridization, including MCB, is still required for the elucidation of structural chromosome rearrangements, and remains an essential adjunct in modern diagnostic laboratories.
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Affiliation(s)
- Susan M Bint
- Cytogenetics department, GSTS-Pathology, Guy's and St, Thomas' Hospital NHS Foundation Trust, London SE1 9RT, UK.
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29
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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] [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.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena D-07743, Germany.
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30
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Das K, Tan P. Molecular cytogenetics: recent developments and applications in cancer. Clin Genet 2013; 84:315-25. [DOI: 10.1111/cge.12229] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/02/2013] [Accepted: 07/02/2013] [Indexed: 12/13/2022]
Affiliation(s)
- K Das
- Cancer and Stem Cell Biology; Duke-NUS Graduate Medical School; Singapore Singapore
| | - P Tan
- Cancer and Stem Cell Biology; Duke-NUS Graduate Medical School; Singapore Singapore
- Cancer Science Institute of Singapore, Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
- Genome Institute of Singapore; Singapore Singapore
- Cellular and Molecular Research; National Cancer Centre of Singapore; Singapore Singapore
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Chen C, Bartenhagen C, Gombert M, Okpanyi V, Binder V, Röttgers S, Bradtke J, Teigler-Schlegel A, Harbott J, Ginzel S, Thiele R, Fischer U, Dugas M, Hu J, Borkhardt A. Next-generation-sequencing-based risk stratification and identification of new genes involved in structural and sequence variations in near haploid lymphoblastic leukemia. Genes Chromosomes Cancer 2013; 52:564-79. [DOI: 10.1002/gcc.22054] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/29/2013] [Indexed: 01/10/2023] Open
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32
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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] [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.
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Affiliation(s)
- Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, Jena, D-07743, Germany.
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Abstract
SUMMARY Cytogenetic analysis is now considered a mandatory investigation in the diagnostic work-up of hematologic malignancies. Recurring structural aberrations serve as powerful markers not only for diagnosis and prognosis of these conditions, but also guide the selection of targeted drugs for personalized oncology. The FISH approach is established as an indispensable tool to complement conventional cytogenetics, in addition to basic and clinical research applications. FISH is used to identify specific chromosomal aberrations through the detection of target DNA sequences by fluorescently labeled DNA probes. Multicolor FISH analysis allows the accurate identification of recurring translocations in neoplastic cells by means of genomic probes that flank the breakpoints. This review summarizes the panel of FISH probes for selection and the current utilization of these FISH techniques in unraveling chromosomal aberrations. The niche of FISH analysis is also highlighted. Variant signal patterns of the clinically useful FISH probes for hematologic oncology illustrated here provide useful interpretative reference for molecular pathology laboratories. In addition, the recent application of FISH tests in contributing information on drug targets at the genomic level to support personalized oncology will also be discussed.
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Affiliation(s)
- Thomas SK Wan
- Division of Haematology, Department of Pathology, Queen Mary Hospital, The University of Hong Kong, 102, Pokfulam Road, Hong Kong, China
| | - Edmond SK Ma
- Department of Pathology, Hong Kong Sanatorium & Hospital, Hong Kong, China
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Hu B, Grabham P, Nie J, Balajee AS, Zhou H, Hei TK, Geard CR. Intrachromosomal Changes and Genomic Instability in Site-Specific Microbeam-Irradiated and Bystander Human-Hamster Hybrid Cells. Radiat Res 2012; 177:25-34. [DOI: 10.1667/rr2757.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Hada M, Wu H, Cucinotta FA. mBAND analysis for high- and low-LET radiation-induced chromosome aberrations: a review. Mutat Res 2011; 711:187-192. [PMID: 21232544 DOI: 10.1016/j.mrfmmm.2010.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2010] [Revised: 12/17/2010] [Accepted: 12/17/2010] [Indexed: 05/30/2023]
Abstract
During long-term space travel or cancer therapy, humans are exposed to high linear energy transfer (LET) energetic heavy ions. High-LET radiation is much more effective than low-LET radiation in causing various biological effects, including cell inactivation, genetic mutations, cataracts and cancer induction. Most of these biological endpoints are closely related to chromosomal damage, and cytogenetic damage can be utilized as a biomarker for radiation insults. Epidemiological data, mainly from survivors of the atomic bomb detonations in Japan, have enabled risk estimation from low-LET radiation exposures. The identification of a cytogenetic signature that distinguishes high- from low-LET exposure remains a long-term goal in radiobiology. Recently developed fluorescence in situ hybridization (FISH)-painting methodologies have revealed unique endpoints related to radiation quality. Heavy-ions induce a high fraction of complex-type exchanges, and possibly unique chromosome rearrangements. This review will concentrate on recent data obtained with multicolor banding in situ hybridization (mBAND) methods in mammalian cells exposed to low- and high-LET radiations. Chromosome analysis with mBAND technique allows detection of both inter- and intrachromosomal exchanges, and also distribution of the breakpoints of aberrations.
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Affiliation(s)
- Megumi Hada
- NASA Johnson Space Center, Houston, TX 77058, USA; Universities Space Research Association, Houston, TX 77058, USA.
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Hada M, Zhang Y, Feiveson A, Cucinotta FA, Wu H. Association of inter- and intrachromosomal exchanges with the distribution of low- and high-LET radiation-induced breaks in chromosomes. Radiat Res 2011; 176:25-37. [PMID: 21466383 DOI: 10.1667/rr2433.1] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
To study the effects of low- and high-linear energy transfer (LET) radiation on break locations within a chromosome, we exposed human epithelial cells in vitro to (137)Cs γ rays at both low and high dose rates, secondary neutrons at a low dose rate, and 600 MeV/u iron ions at a high dose rate. Breakpoints were identified using multicolor banding in situ hybridization (mBAND), which paints chromosome 3 in 23 different colored bands. For all four radiation scenarios, breakpoint distributions were found to be different from the predicted distribution based on band width. Detailed analysis of chromosome fragment ends involved in inter- or intrachromosomal exchanges revealed that the distributions of fragment ends participating in interchromosomal exchanges were similar between the two low-LET radiation dose rates and between the two high-LET radiation types, but the distributions were less similar between low- and high-LET radiations. For fragment ends participating in intrachromosomal exchanges, the distributions for all four radiation scenarios were similar, with clusters of breaks found in three regions. Analysis of the locations of the two fragment ends in chromosome 3 that joined to form an intrachromosomal exchange demonstrated that two breaks with a greater genomic separation can be more likely to rejoin than two closer breaks, indicating that chromatin folding can play an important role in the rejoining of chromosome breaks. Comparison of the breakpoint distributions to the distributions of genes indicated that the gene-rich regions do not necessarily contain more breaks. In general, breakpoint distributions depend on whether a chromosome fragment joins with another fragment in the same chromosome or with a fragment from a different chromosome.
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Affiliation(s)
- Megumi Hada
- NASA Johnson Space Center, Houston, Texas 77058, USA
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Mackinnon RN, Chudoba I. The use of M-FISH and M-BAND to define chromosome abnormalities. Methods Mol Biol 2011; 730:203-18. [PMID: 21431644 DOI: 10.1007/978-1-61779-074-4_15] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Multicolour fluorescence in situ hybridisation (M-FISH) and multicolour banding (M-BAND) are advanced chromosome painting techniques combining multiple chromosome- or region-specific paints in one step. M-FISH identifies all chromosomes or chromosome arms at once, whereas M-BAND identifies the different regions of a single chromosome. The use of either or both can improve the accuracy of karyotyping and help identify cryptic chromosome rearrangements. These probes are prepared by pooling multiple chromosome- or chromosome region-specific DNA libraries, each labelled with a unique combination of fluorochromes. Commercial probes are available, avoiding the need for probe preparation. In the protocol described here, a commercial probe is used. Well-spread metaphases are prepared according to standard techniques, followed by alkaline denaturation and application of the denatured probe. After an incubation period, the slides are washed. A fluorescence microscope with filter sets specific to the fluorescent labels is used for analysis, together with specialised image analysis software. The software interprets the combination of fluorochromes to identify each chromosome and produce a false colour image specific for each chromosome or region. The single colour galleries - which show the hybridisation patterns of the individual fluorochromes - are useful to help interpret and confirm the false colour images produced by the software, including ambiguous signals.
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Affiliation(s)
- Ruth N Mackinnon
- Victorian Cancer Cytogenetics Service, St. Vincent's Hospital Melbourne, Fitzroy, VIC, Australia.
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Abstract
Molecular cytogenetics and especially fluorescence in situ hybridization (FISH) banding approaches are nowadays standard for the exact characterization of simple, complex, and cryptic chromosomal aberrations within the human genome. FISH-banding techniques are any kind of FISH techniques, which provide the possibility to characterize simultaneously several chromosomal subregions smaller than a chromosome arm. FISH banding methods fitting that definition may have quite different characteristics, but share the ability to produce a DNA-specific chromosomal banding. While the standard techniques such as G-bands by Trypsin using Giemsa banding lead to a protein-related black and white banding pattern, FISH-banding techniques are DNA-specific, more colorful, and thus, more informative. At present, the most frequently applied FISH banding technique is the multicolor banding (MCB/m-band) approach. MCB/m-band is based on region-specific microdissection libraries, producing changing fluorescence intensity ratios along the chromosomes. Here we describe the FISH-banding technique MCB/m-band and illustrate how to apply it for characterization of chromosomal breakpoints with a minimal number of FISH experiments.
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Nagasawa H, Brogan JR, Peng Y, Little JB, Bedford JS. Some unsolved problems and unresolved issues in radiation cytogenetics: A review and new data on roles of homologous recombination and non-homologous end joining. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2010; 701:12-22. [DOI: 10.1016/j.mrgentox.2010.03.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2010] [Accepted: 03/09/2010] [Indexed: 12/14/2022]
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Park IY, Shin JC, Kwon JY, Koo BK, Kim M, Lim J, Kim Y, Han K. Prenatal diagnosis of Pallister-Killian syndrome associated with pulmonary stenosis and right ventricular dilatation. Korean J Lab Med 2009; 29:366-70. [PMID: 19726901 DOI: 10.3343/kjlm.2009.29.4.366] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Pallister-Killian syndrome (PKS) is a rare disorder characterized cytogenetically by tetrasomy 12p for isochromosome of the short arm of chromosome 12. PKS is diagnosed by prenatal genetic analysis through chorionic villous sampling, genetic amniocentesis, and cordocentesis, or by chromosomal analysis of skin fibroblasts, but is not usually detected by chromosomal analysis of peripheral blood cells. Herein, we report a case of a gravida at 23 weeks gestation with pulmonary stenosis and right ventricular dilation of the heart which were detected by sonography. Fluorescence in situ hybridization and a multicolor banding technique were performed to verify the diagnosis as 47,XX, +mar.ish i(12)(p10)(TEL++)[16]/46,XX[4], and an autopsy confirmed the cardiac anomalies detected on antenatal sonography.
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Affiliation(s)
- In Yang Park
- Department of Obstetrics and Gynecology, The Catholic University of Korea, Seoul, Korea
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Lee NC, Chang SP, Chang CS, Chen CH, Lee DJ, Lin CC, Hwu WL, Chen M. Cryptic subtelomeric deletion plus inverted duplication at chromosome 18q in a fetus: molecular delineation by multicolor banding. Prenat Diagn 2009; 29:1058-60. [DOI: 10.1002/pd.2332] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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Benkhaled L, Barrios L, Mestres M, Caballin MR, Ribas M, Barquinero JF. Analysis of γ-rays induced chromosome aberrations: A fingerprint evaluation with a combination of pan-centromeric and pan-telomeric probes. Int J Radiat Biol 2009; 82:869-75. [PMID: 17178627 DOI: 10.1080/09553000600979092] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE To evaluate the types of induced chromosome aberrations after the exposure of peripheral blood to gamma-rays by the simultaneous detection of all centromeres and telomeres; and to analyse the suitability of different radiation fingerprints for the assessment of radiation quality in cases of recent exposures. MATERIAL AND METHODS Peripheral blood samples were irradiated at 2, 4 and 6 Gy of gamma-rays. Cytogenetic analysis was carried out by fluorescence in situ hybridization (FISH) technique with pan-centromeric and peptide nucleic acid (PNA)-telomeric DNA probes. Cells were analysed using a Cytovision FISH workstation, chromosome aberrations and the length of the acentric fragments were recorded. RESULTS The total number of the incomplete chromosome elements was 276. The ratio between incomplete elements and multicentrics was 0.38. The number of acentrics was 1096, 71% were complete acentrics, 15% incomplete acentrics, and 14% interstitial fragments. The relative length of complete, incomplete and interstitial acentrics fragments were 2.70 +/- 0.04, 1.91 +/- 0.07, and 1.42 +/- 0.04 respectively. The mean value of the F-ratio was 11.5 higher than the one, 5.5, previously obtained for alpha-particles. For the G-ratio there was no difference between gamma-rays and alpha-particles, 2.8 and 2.8 respectively. The mean value of the H-ratio for gamma-rays, 0.25, was lower than for alpha-particles 0.40. CONCLUSION The results support that the percentage of incomplete chromosome aberrations depends on radiation type; low-linear energy transfer (LET) radiation would produces less incomplete aberrations than high-LET radiation. The F- and H-ratios seem to be good indicators of radiation quality, although a real estimation of the H-ratio is only possible using pan-telomeric probes.
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Affiliation(s)
- L Benkhaled
- Unitat d'Antropologia, Dpt. Biologia Animal, Biologia Vegetal i Ecologia, Facultat de Ciències, Universitat Autònoma de Barcelona, Bellaterra, Spain
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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.
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Affiliation(s)
- Joëlle Tchinda
- Institut für Humangenetik, Universitätsklinikum Münster, Vesaliusweg 12-14, 48129 Münster, Germany.
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Aktas D, Weise A, Utine E, Alehan D, Mrasek K, von Eggeling F, Thieme H, Tuncbilek E, Liehr T. Clinically abnormal case with paternally derived partial trisomy 8p23.3 to 8p12 including maternal isodisomy of 8p23.3: a case report. Mol Cytogenet 2009; 2:14. [PMID: 19566937 PMCID: PMC2715415 DOI: 10.1186/1755-8166-2-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Accepted: 06/30/2009] [Indexed: 01/30/2023] Open
Abstract
Background Because of low copy repeats (LCRs) and common inversion polymorphisms, the human chromosome 8p is prone to a number of recurrent rearrangements. Each of these rearrangements is associated with several phenotypic features. We report on a patient with various clinical malformations and developmental delay in connection with an inverted duplication event, involving chromosome 8p. Methods Chromosome analysis, multicolor banding analysis (MCB), extensive fluorescence in situ hybridization (FISH) analysis and microsatellite analysis were performed. Results The karyotype was characterized in detail by multicolor banding (MCB), subtelomeric and centromere-near probes as 46,XY,dup(8)(pter->p23.3::p12->p23.3::p23.3->qter). Additionally, microsatellite analysis revealed the paternal origin of the duplication and gave hints for a mitotic recombination involving about 6 MB in 8p23.3. Conclusion A comprehensive analysis of the derivative chromosome 8 suggested a previously unreported mechanism of formation, which included an early mitotic aberration leading to maternal isodisomy, followed by an inverted duplication of the 8p12p23.3 region.
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Affiliation(s)
- Dilek Aktas
- Hacettepe University Faculty of Medicine, Department of Genetics, 06100 Sihhiye, Ankara, Turkey.
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Shen Y, Wu BL. Designing a simple multiplex ligation-dependent probe amplification (MLPA) assay for rapid detection of copy number variants in the genome. J Genet Genomics 2009; 36:257-65. [DOI: 10.1016/s1673-8527(08)60113-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Revised: 10/14/2008] [Accepted: 10/18/2008] [Indexed: 11/26/2022]
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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.
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Abstract
Cytogenetic characterization of murine chromosomes using banding techniques like R- or G-banding is technically demanding due to the similar size and the acrocentric structure of all chromosomes. The molecular cytogenetic technique of spectral karyotyping (SKY) overcomes that difficulty by karyotyping metaphase chromosomes after different and simultaneous fluorescence labeling of the whole genome. SKY allows the detection and identification of numerical as well as structural chromosome aberrations with a resolution of approximately 2 Mb. The technique is applicable to all fast-proliferating cells, e.g., cells of the hematopoietic system like stem cells or T- and B-lymphocytes. It is also applicable to murine embryonic fibroblast or cells isolated from tissues with increased proliferation-especially tumor tissues. Furthermore, SKY is recommended for the cytogenetic characterization of newly established cell lines.
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Kosyakova N, Weise A, Mrasek K, Claussen U, Liehr T, Nelle H. The hierarchically organized splitting of chromosomal bands for all human chromosomes. Mol Cytogenet 2009; 2:4. [PMID: 19171032 PMCID: PMC2636822 DOI: 10.1186/1755-8166-2-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 01/26/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromosome banding is widely used in cytogenetics. However, the biological nature of hierarchically organized splitting of chromosomal bands of human chromosomes is an enigma and has not been, as yet, studied. RESULTS Here we present for the first time the hierarchically organized splitting of chromosomal bands in their sub-bands for all human chromosomes. To do this, array-proved multicolor banding (aMCB) probe-sets for all human chromosomes were applied to normal metaphase spreads of three different G-band levels. We confirmed for all chromosomes to be a general principle that only Giemsa-dark bands split into dark and light sub-bands, as we demonstrated previously by chromosome stretching. Thus, the biological band splitting is in > 50% of the sub-bands different than implemented by the ISCN nomenclature suggesting also a splitting of G-light bands. Locus-specific probes exemplary confirmed the results of MCB. CONCLUSION Overall, the present study enables a better understanding of chromosome architecture. The observed difference of biological and ISCN band-splitting may be an explanation why mapping data from human genome project do not always fit the cytogenetic mapping.
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Affiliation(s)
- Nadezda Kosyakova
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
| | - Anja Weise
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
| | - Kristin Mrasek
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
| | - Uwe Claussen
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
| | - Thomas Liehr
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
| | - Heike Nelle
- Universitätsklinikum Jena, Institut für Humangenetik und Anthropologie, Jena, Germany
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Abstract
Pharmacogenomics encompasses several major areas including the identification and analysis of variations of DNA and RNA that affect the efficacy and toxicity of drug therapy. It represents an integration of analytical approaches including DNA and RNA detection and quantitation which may be applied to either candidate genes or a global genome analysis.
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Stumm M, Tönnies H. Fluorescence in situ hybridization techniques in medical diagnostics. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2008; 2:1381-1390. [PMID: 23496784 DOI: 10.1517/17530050802558899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BACKGROUND Fluorescence in situ hybridization (FISH) has become a well-established method in medical diagnostics. FISH methods complement conventional cytogenetic banding techniques and offer extra clinical applications. FISH is based on the binding of complementary, single-stranded fluorescence-labeled nucleic acid sequences to the fixed and denatured target DNA of metaphases, interphase nuclei or isolated DNA sequences (BACs, oligonucleotides). OBJECTIVE The intent of this article is to review the development of molecular cytogenetic techniques available at present and to summarize the most efficient and appropriate use of these techniques in medical diagnostics. The technical aspects and most important applications of FISH assays are described. CONCLUSION FISH is bridging the gap between conventional cytogenetic banding analysis and molecular genetic DNA studies. The use of FISH techniques enhances the correct interpretation of numerical and structural chromosome aberrations.
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Affiliation(s)
- Markus Stumm
- Centre for Prenatal Diagnosis, Kudamm 199, Berlin 10719, Germany
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