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Abubakar SD. Characterization of Chromosomal Abnormalities in Cancer by Spectral Karyotyping. MEDICAL LABORATORY JOURNAL 2019. [DOI: 10.29252/mlj.13.6.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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Bloomfield M, Duesberg P. Inherent variability of cancer-specific aneuploidy generates metastases. Mol Cytogenet 2016; 9:90. [PMID: 28018487 PMCID: PMC5160004 DOI: 10.1186/s13039-016-0297-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 11/14/2016] [Indexed: 12/14/2022] Open
Abstract
Background The genetic basis of metastasis is still unclear because metastases carry individual karyotypes and phenotypes, rather than consistent mutations, and are rare compared to conventional mutation. There is however correlative evidence that metastasis depends on cancer-specific aneuploidy, and that metastases are karyotypically related to parental cancers. Accordingly we propose that metastasis is a speciation event. This theory holds that cancer-specific aneuploidy varies the clonal karyotypes of cancers automatically by unbalancing thousands of genes, and that rare variants form new autonomous subspecies with metastatic or other non-parental phenotypes like drug-resistance – similar to conventional subspeciation. Results To test this theory, we analyzed the karyotypic and morphological relationships between seven cancers and corresponding metastases. We found (1) that the cellular phenotypes of metastases were closely related to those of parental cancers, (2) that metastases shared 29 to 96% of their clonal karyotypic elements or aneusomies with the clonal karyotypes of parental cancers and (3) that, unexpectedly, the karyotypic complexity of metastases was very similar to that of the parental cancer. This suggests that metastases derive cancer-specific autonomy by conserving the overall complexity of the parental karyotype. We deduced from these results that cancers cause metastases by karyotypic variations and selection for rare metastatic subspecies. Further we asked whether metastases with multiple metastasis-specific aneusomies are assembled in one or multiple, sequential steps. Since (1) no stable karyotypic intermediates of metastases were observed in cancers here and previously by others, and (2) the karyotypic complexities of cancers are conserved in metastases, we concluded that metastases are generated from cancers in one step – like subspecies in conventional speciation. Conclusions We conclude that the risk of cancers to metastasize is proportional to the degree of cancer-specific aneuploidy, because aneuploidy catalyzes the generation of subspecies, including metastases, at aneuploidy-dependent rates. Since speciation by random chromosomal rearrangements and selection is unpredictable, the theory that metastases are karyotypic subspecies of cancers also explains Foulds’ rules, which hold that the origins of metastases are “abrupt” and that their phenotypes are “unpredictable.”
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Affiliation(s)
- Mathew Bloomfield
- Department of Molecular and Cell Biology; Donner Laboratory, University of California at Berkeley, Berkeley, CA 94720 USA ; Present address: Department of Natural Sciences and Mathematics, Dominican University of California, San Rafael, CA USA
| | - Peter Duesberg
- Department of Molecular and Cell Biology; Donner Laboratory, University of California at Berkeley, Berkeley, CA 94720 USA
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Barnabas N, Sanchez J, Chitale D, Adeyinka A. Array-CGH Shows Amplification of 8q Including MYC as the Sole Aberration in a Leiomyosarcoma of the Female Lower Genital Tract. Cytogenet Genome Res 2014; 142:245-8. [DOI: 10.1159/000362523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/14/2014] [Indexed: 11/19/2022] Open
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Abstract
Metastasis is responsible for most cancer mortality. The process of metastasis is complex, requiring the coordinated expression and fine regulation of many genes in multiple pathways in both the tumor and host tissues. Identification and characterization of the genetic programs that regulate metastasis is critical to understanding the metastatic process and discovering molecular targets for the prevention and treatment of metastasis. Genomic approaches and functional genomic analyses can systemically discover metastasis genes. In this review, we summarize the genetic tools and methods that have been used to identify and characterize the genes that play critical roles in metastasis.
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Affiliation(s)
- Jinchun Yan
- University of Washington Medical Center, 1959 N. E. Pacific Street, Seattle, WA 98195, USA.
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Bayani J, Paliouras M, Planque C, Shan SJC, Graham C, Squire JA, Diamandis EP. Impact of cytogenetic and genomic aberrations of the kallikrein locus in ovarian cancer. Mol Oncol 2008; 2:250-60. [PMID: 19383346 DOI: 10.1016/j.molonc.2008.07.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2008] [Accepted: 07/14/2008] [Indexed: 11/19/2022] Open
Abstract
The tissue kallikrein (KLK) genes are a new source for biomarkers in ovarian cancer. However, there has been no systematic analysis of copy number and structural rearrangements related to their protein expression. Chromosomal rearrangements and copy number changes of the KLK region were studied by FISH with protein levels measured by ELISA. Ovarian cancer and cell lines revealed the KLK region was subject to copy number imbalances or involved in unbalanced translocations and were associated with increased protein expression of KLKs 5, 6, 7, 8, 9, 10 and 11. In this initial study, we introduce the potential for long-range chromosomal effects and copy number as a mechanism for the previously reported aberrant expression of many KLK genes in ovarian cancers.
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Affiliation(s)
- Jane Bayani
- Department of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, University Health Network, Toronto, Ontario, M5G 2M9, Canada
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Howarth KD, Blood KA, Ng BL, Beavis JC, Chua Y, Cooke SL, Raby S, Ichimura K, Collins VP, Carter NP, Edwards PAW. Array painting reveals a high frequency of balanced translocations in breast cancer cell lines that break in cancer-relevant genes. Oncogene 2008; 27:3345-59. [PMID: 18084325 PMCID: PMC2423006 DOI: 10.1038/sj.onc.1210993] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2007] [Revised: 11/13/2007] [Accepted: 11/15/2007] [Indexed: 12/21/2022]
Abstract
Chromosome translocations in the common epithelial cancers are abundant, yet little is known about them. They have been thought to be almost all unbalanced and therefore dismissed as mostly mediating tumour suppressor loss. We present a comprehensive analysis by array painting of the chromosome translocations of breast cancer cell lines HCC1806, HCC1187 and ZR-75-30. In array painting, chromosomes are isolated by flow cytometry, amplified and hybridized to DNA microarrays. A total of 200 breakpoints were identified and all were mapped to 1 Mb resolution on bacterial artificial chromosome (BAC) arrays, then 40 selected breakpoints, including all balanced breakpoints, were further mapped on tiling-path BAC arrays or to around 2 kb resolution using oligonucleotide arrays. Many more of the translocations were balanced at 1 Mb resolution than expected, either reciprocal (eight in total) or balanced for at least one participating chromosome (19 paired breakpoints). Second, many of the breakpoints were at genes that are plausible targets of oncogenic translocation, including balanced breaks at CTCF, EP300/p300 and FOXP4. Two gene fusions were demonstrated, TAX1BP1-AHCY and RIF1-PKD1L1. Our results support the idea that chromosome rearrangements may play an important role in common epithelial cancers such as breast cancer.
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Affiliation(s)
- KD Howarth
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - KA Blood
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - BL Ng
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - JC Beavis
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - Y Chua
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - SL Cooke
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - S Raby
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
| | - K Ichimura
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - VP Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Box 231 Addenbrookes Hospital, Hills Road, Cambridge, U.K
| | - NP Carter
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K
| | - PAW Edwards
- Hutchison-MRC Research Centre, Department of Pathology, University of Cambridge, Hills Road, Cambridge CB2 0XZ, U.K
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Urquidi V, Goodison S. Genomic signatures of breast cancer metastasis. Cytogenet Genome Res 2007; 118:116-29. [PMID: 18000362 DOI: 10.1159/000108292] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2006] [Accepted: 09/28/2006] [Indexed: 01/04/2023] Open
Abstract
Despite significant advances in the treatment of primary cancer, the ability to predict the metastatic behavior of a patient's cancer, as well as to detect and eradicate such recurrences, remain major clinical challenges in oncology. While many potential molecular biomarkers have been identified and tested previously, none have greatly improved the accuracy of specimen evaluation over routine histopathological criteria and they predict individual outcomes poorly. However, the recent introduction of high-throughput microarray technology has opened new avenues in genomic investigation of cancer, and through application in tissue-based studies and appropriate animal models, has facilitated the identification of gene expression signatures that are associated with the lethal progression of breast cancer. The use of these approaches has the potential to greatly impact our knowledge of tumor biology, to provide efficient biomarkers, and enable development towards customized prognostication and therapies for the individual.
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Affiliation(s)
- V Urquidi
- Department of Medicine, University of Florida, Jacksonville, FL, USA
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Gelsi-Boyer V, Orsetti B, Cervera N, Finetti P, Sircoulomb F, Rougé C, Lasorsa L, Letessier A, Ginestier C, Monville F, Esteyriès S, Adélaïde J, Esterni B, Henry C, Ethier SP, Bibeau F, Mozziconacci MJ, Charafe-Jauffret E, Jacquemier J, Bertucci F, Birnbaum D, Theillet C, Chaffanet M. Comprehensive Profiling of 8p11-12 Amplification in Breast Cancer. Mol Cancer Res 2005; 3:655-67. [PMID: 16380503 DOI: 10.1158/1541-7786.mcr-05-0128] [Citation(s) in RCA: 169] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In human carcinomas, especially breast cancer, chromosome arm 8p is frequently involved in complex chromosomal rearrangements that combine amplification at 8p11-12, break in the 8p12-21 region, and loss of 8p21-ter. Several studies have identified putative oncogenes in the 8p11-12 amplicon. However, discrepancies and the lack of knowledge on the structure of this amplification lead us to think that the actual identity of the oncogenes is not definitively established. We present here a comprehensive study combining genomic, expression, and chromosome break analyses of the 8p11-12 region in breast cell lines and primary breast tumors. We show the existence of four amplicons at 8p11-12 using array comparative genomic hybridization. Gene expression analysis of 123 samples using DNA microarrays identified 14 genes significantly overexpressed in relation to amplification. Using fluorescence in situ hybridization analysis on tissue microarrays, we show the existence of a cluster of breakpoints spanning a region just telomeric to and associated with the amplification. Finally, we show that 8p11-12 amplification has a pejorative effect on survival in breast cancer.
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Affiliation(s)
- Véronique Gelsi-Boyer
- Marseilles Cancer Institute, Department of Molecular Oncology, UMR599 Institut National de la Sante et de la Recherche Medicale, France
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Letessier A, Mozziconacci MJ, Murati A, Juriens J, Adélaïde J, Birnbaum D, Chaffanet M. Multicolour-banding fluorescence in situ hybridisation (mbanding-FISH) to identify recurrent chromosomal alterations in breast tumour cell lines. Br J Cancer 2005; 92:382-8. [PMID: 15655561 PMCID: PMC2361837 DOI: 10.1038/sj.bjc.6602228] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Recurrent chromosome breakpoints in tumour cells may point to cancer genes, but not many have been molecularly characterised. We have used multicolour-banding fluorescence in situ hybridisation (mbanding-FISH) on breast tumour cell lines to identify regions of chromosome break created by inversions, duplications, insertions and translocations on chromosomes 1, 5, 8, 12 and 17. We delineate a total of 136 regions of break, some of them occurring with high frequency. We further describe two examples of dual-colour FISH characterisation of breakpoints, which target the 1p36 and 5p11–12 regions. Both breaks involve genes whose function is unknown to date. The mbanding-FISH strategy constitutes an efficient first step in the search for potential cancer genes.
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Affiliation(s)
- A Letessier
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - M-J Mozziconacci
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Department of Biopathology, Paoli-Calmettes Institute, Marseille, France
| | - A Murati
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Department of Biopathology, Paoli-Calmettes Institute, Marseille, France
| | - J Juriens
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - J Adélaïde
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - D Birnbaum
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
| | - M Chaffanet
- Laboratory of Molecular Cytogenetics, Department of Molecular Oncology, Paoli-Calmettes Institute-UMR599 INSERM, Marseille Cancer Research Institute, Marseille, France
- Institut Paoli-Calmettes, 232, Bd Sainte Marguerite BP156, 13273 Marseille Cedex 9, France. E-mail:
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Davidson JM, Gorringe KL, Chin SF, Orsetti B, Besret C, Courtay-Cahen C, Roberts I, Theillet C, Caldas C, Edwards PA. Molecular cytogenetic analysis of breast cancer cell lines. Br J Cancer 2000; 83:1309-17. [PMID: 11044355 PMCID: PMC2408781 DOI: 10.1054/bjoc.2000.1458] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The extensive chromosome rearrangements of breast carcinomas must contribute to tumour development, but have been largely intractable to classical cytogenetic banding. We report here the analysis by 24-colour karyotyping and comparative genomic hybridization (CGH) of 19 breast carcinoma cell lines and one normal breast epithelial cell line, which provide model examples of karyotype patterns and translocations present in breast carcinomas. The CGH was compared with CGH of 106 primary breast cancers. The lines varied from perfectly diploid to highly aneuploid. Translocations were very varied and over 98% were unbalanced. The most frequent in the carcinomas were 8;11 in five lines; and 8;17, 1;4 and 1;10 in four lines. The most frequently involved chromosome was 8. Several lines showed complex multiply-translocated chromosomes. The very aneuploid karyotypes appeared to fall into two groups that evolved by different routes: one that steadily lost chromosomes and at one point doubled their entire karyotype; and another that steadily gained chromosomes, together with abnormalities. All karyotypes fell within the range seen in fresh material and CGH confirmed that the lines were broadly representative of fresh tumours. The karyotypes provide a resource for the cataloguing and analysis of translocations in these tumours, accessible at http://www.path.cam.ac.uk/ approximately pawefish.
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Affiliation(s)
- J M Davidson
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP
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