101
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Møller HD, Lin L, Xiang X, Petersen TS, Huang J, Yang L, Kjeldsen E, Jensen UB, Zhang X, Liu X, Xu X, Wang J, Yang H, Church GM, Bolund L, Regenberg B, Luo Y. CRISPR-C: circularization of genes and chromosome by CRISPR in human cells. Nucleic Acids Res 2018; 46:e131. [PMID: 30551175 PMCID: PMC6294522 DOI: 10.1093/nar/gky767] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/28/2018] [Accepted: 08/20/2018] [Indexed: 12/18/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) and ring chromosomes are genetic alterations found in humans with genetic disorders. However, there is a lack of genetic engineering tools to recapitulate and study the biogenesis of eccDNAs. Here, we created a dual-fluorescence biosensor cassette, which upon the delivery of pairs of CRISPR/Cas9 guide RNAs, CRISPR-C, allows us to study the biogenesis of a specific fluorophore expressing eccDNA in human cells. We show that CRISPR-C can generate functional eccDNA, using the novel eccDNA biosensor system. We further reveal that CRISPR-C also can generate eccDNAs from intergenic and genic loci in human embryonic kidney 293T cells and human mammary fibroblasts. EccDNAs mainly forms by end-joining mediated DNA-repair and we show that CRISPR-C is able to generate endogenous eccDNAs in sizes from a few hundred base pairs and ranging up to 207 kb. Even a 47.4 megabase-sized ring chromosome 18 can be created by CRISPR-C. Our study creates a new territory for CRISPR gene editing and highlights CRISPR-C as a useful tool for studying the cellular impact, persistence and function of eccDNAs.
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MESH Headings
- Base Sequence
- Biosensing Techniques
- CRISPR-Associated Protein 9/genetics
- CRISPR-Associated Protein 9/metabolism
- CRISPR-Cas Systems
- Cell Line
- Chromosomes, Human, Pair 18/chemistry
- Chromosomes, Human, Pair 18/metabolism
- Clustered Regularly Interspaced Short Palindromic Repeats
- DNA End-Joining Repair
- DNA, Circular/genetics
- DNA, Circular/metabolism
- Fibroblasts
- Fluorescent Dyes/chemistry
- Fluorescent Dyes/metabolism
- Gene Editing/methods
- Genes, Reporter
- Genetic Loci
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Genome, Human
- Green Fluorescent Proteins/genetics
- Green Fluorescent Proteins/metabolism
- HEK293 Cells
- Humans
- Luminescent Proteins/genetics
- Luminescent Proteins/metabolism
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
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Affiliation(s)
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Denmark
| | - Xi Xiang
- Department of Biomedicine, Aarhus University, Denmark
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Qingdao, Qingdao 266555, China
| | | | - Jinrong Huang
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Luhan Yang
- eGenesis, Inc., Cambridge, MA 02139, USA
| | - Eigil Kjeldsen
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Uffe Birk Jensen
- Department of Biomedicine, Aarhus University, Denmark
- Department of Clinical Medicine, Aarhus University, Denmark
| | - Xiuqing Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xin Liu
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xun Xu
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Jian Wang
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - Huanming Yang
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- James D. Watson Institute of Genome Science, 310008 Hangzhou, China
| | - George M Church
- eGenesis, Inc., Cambridge, MA 02139, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Lars Bolund
- Department of Biomedicine, Aarhus University, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
| | - Birgitte Regenberg
- Department of Biology, Faculty of Science, University of Copenhagen, Denmark
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Denmark
- BGI-Qingdao, Qingdao 266555, China
- BGI-Shenzhen, Shenzhen 518083, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
- Lars Bolund Institute of Regenerative Medicine, BGI-Qingdao, Qingdao 266555, China
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102
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Mizuno S, Hanamura I, Ota A, Karnan S, Kanasugi J, Nakamura A, Takasugi S, Uchino K, Horio T, Goto M, Murakami S, Gotou M, Yamamoto H, Watarai M, Shikami M, Hosokawa Y, Miwa H, Taniwaki M, Ueda R, Nitta M, Takami A. Establishment and characterization of a novel vincristine-resistant diffuse large B-cell lymphoma cell line containing the 8q24 homogeneously staining region. FEBS Open Bio 2018; 8:1977-1991. [PMID: 30524948 PMCID: PMC6275272 DOI: 10.1002/2211-5463.12538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 11/27/2022] Open
Abstract
Chromosome band 8q24 is the most frequently amplified locus in various types of cancers. MYC has been identified as the primary oncogene at the 8q24 locus, whereas a long noncoding gene, PVT1, which lies adjacent to MYC, has recently emerged as another potential oncogenic regulator at this position. In this study, we established and characterized a novel cell line, AMU‐ML2, from a patient with diffuse large B‐cell lymphoma (DLBCL), displaying homogeneously staining regions at the 8q24 locus. Fluorescence in situ hybridization clearly detected an elevation in MYC copy numbers corresponding to the homogenously staining region. In addition, a comparative genomic hybridization analysis using high‐resolution arrays revealed that the 8q24 amplicon size was 1.4 Mb, containing the entire MYC and PVT1 regions. We also demonstrated a loss of heterozygosity for TP53 at 17p13 in conjunction with a TP53 frameshift mutation. Notably, AMU‐ML2 cells exhibited resistance to vincristine, and cell proliferation was markedly inhibited by MYC‐shRNA‐mediated knockdown. Furthermore, genes involved in cyclin D, mTOR, and Ras signaling were downregulated following MYC knockdown, suggesting that MYC expression was closely associated with tumor cell growth. In conclusion, AMU‐ML2 cells are uniquely characterized by homogenously staining regions at the 8q24 locus, thus providing useful insights into the pathogenesis of DLBCL with 8q24 abnormalities.
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Affiliation(s)
- Shohei Mizuno
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ichiro Hanamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akinobu Ota
- Department of Biochemistry Aichi Medical University Japan
| | | | - Jo Kanasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Ayano Nakamura
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Souichi Takasugi
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Kaori Uchino
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Tomohiro Horio
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mineaki Goto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Satsuki Murakami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Mayuko Gotou
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Hidesuke Yamamoto
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masaya Watarai
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Masato Shikami
- Department of Hematology Daiyukai General Hospital Aichi Japan
| | | | | | - Masafumi Taniwaki
- Department of Hematology and Oncology Graduate School of Medical Science Kyoto Prefectural University of Medicine Japan
| | - Ryuzo Ueda
- Department of Tumor Immunology Aichi Medical University School of Medicine Japan
| | - Masakazu Nitta
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
| | - Akiyoshi Takami
- Division of Hematology Department of Internal Medicine Aichi Medical University Japan
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103
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Cai M, Zhang H, Hou L, Gao W, Song Y, Cui X, Li C, Guan R, Ma J, Wang X, Han Y, Lv Y, Chen F, Wang P, Meng X, Fu S. Inhibiting homologous recombination decreases extrachromosomal amplification but has no effect on intrachromosomal amplification in methotrexate-resistant colon cancer cells. Int J Cancer 2018; 144:1037-1048. [PMID: 30070702 PMCID: PMC6586039 DOI: 10.1002/ijc.31781] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 02/23/2018] [Accepted: 07/24/2018] [Indexed: 01/08/2023]
Abstract
Gene amplification, which involves the two major topographical structures double minutes (DMs) and homegeneously stained region (HSR), is a common mechanism of treatment resistance in cancer and is initiated by DNA double‐strand breaks. NHEJ, one of DSB repair pathways, is involved in gene amplification as we demonstrated previously. However, the involvement of homologous recombination, another DSB repair pathway, in gene amplification remains to be explored. To better understand the association between HR and gene amplification, we detected HR activity in DM‐ and HSR‐containing MTX‐resistant HT‐29 colon cancer cells. In DM‐containing MTX‐resistant cells, we found increased homologous recombination activity compared with that in MTX‐sensitive cells. Therefore, we suppressed HR activity by silencing BRCA1, the key player in the HR pathway. The attenuation of HR activity decreased the numbers of DMs and DM‐form amplified gene copies and increased the exclusion of micronuclei and nuclear buds that contained DM‐form amplification; these changes were accompanied by cell cycle acceleration and increased MTX sensitivity. In contrast, BRCA1 silencing did not influence the number of amplified genes and MTX sensitivity in HSR‐containing MTX‐resistant cells. In conclusion, our results suggest that the HR pathway plays different roles in extrachromosomal and intrachromosomal gene amplification and may be a new target to improve chemotherapeutic outcome by decreasing extrachromosomal amplification in cancer. What's new? Double‐strand DNA breaks (DSBs) initiate gene amplification, a phenomenon associated with therapeutic resistance in cancer that involves two topographical structures, double minutes (DMs) and homogeneously staining regions (HSRs). Whether DSB repair pathways, particularly homologous recombination (HR), also influence gene amplification is unknown. Here, in methotrexate‐resistant colon cancer cells, HR inhibition effectively reduced gene amplification, specifically the DM‐form, by blocking DM formation and promoting DM exclusion via micronuclei. HR inhibition had no influence on the HSR‐form of gene amplification. Loss of gene amplification by HR inhibition, through partial reversal of methotrexate resistance, may contribute to improved chemotherapeutic outcome.
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Affiliation(s)
- Mengdi Cai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Huishu Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Liqing Hou
- Department of Genetics, Inner Mongolia Maternal and Child Care Hospital, Hohhot, Inner Mongolia Autonomous Region, China
| | - Wei Gao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Ying Song
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xiaobo Cui
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Chunxiang Li
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jinfa Ma
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xu Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Yue Han
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Yafan Lv
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Feng Chen
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Ping Wang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xiangning Meng
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
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104
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Sequencing of Supernumerary Chromosomes of Red Fox and Raccoon Dog Confirms a Non-Random Gene Acquisition by B Chromosomes. Genes (Basel) 2018; 9:genes9080405. [PMID: 30103445 PMCID: PMC6116037 DOI: 10.3390/genes9080405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 07/29/2018] [Accepted: 08/07/2018] [Indexed: 12/23/2022] Open
Abstract
B chromosomes (Bs) represent a variable addition to the main karyotype in some lineages of animals and plants. Bs accumulate through non-Mendelian inheritance and become widespread in populations. Despite the presence of multiple genes, most Bs lack specific phenotypic effects, although their influence on host genome epigenetic status and gene expression are recorded. Previously, using sequencing of isolated Bs of ruminants and rodents, we demonstrated that Bs originate as segmental duplications of specific genomic regions, and subsequently experience pseudogenization and repeat accumulation. Here, we used a similar approach to characterize Bs of the red fox (Vulpes vulpes L.) and the Chinese raccoon dog (Nyctereutes procyonoides procyonoides Gray). We confirm the previous findings of the KIT gene on Bs of both species, but demostrate an independent origin of Bs in these species, with two reused regions. Comparison of gene ensembles in Bs of canids, ruminants, and rodents once again indicates enrichment with cell-cycle genes, development-related genes, and genes functioning in the neuron synapse. The presence of B-chromosomal copies of genes involved in cell-cycle regulation and tissue differentiation may indicate importance of these genes for B chromosome establishment.
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105
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Ausiannikava D, Mitchell L, Marriott H, Smith V, Hawkins M, Makarova KS, Koonin EV, Nieduszynski CA, Allers T. Evolution of Genome Architecture in Archaea: Spontaneous Generation of a New Chromosome in Haloferax volcanii. Mol Biol Evol 2018; 35:1855-1868. [PMID: 29668953 PMCID: PMC6063281 DOI: 10.1093/molbev/msy075] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The common ancestry of archaea and eukaryotes is evident in their genome architecture. All eukaryotic and several archaeal genomes consist of multiple chromosomes, each replicated from multiple origins. Three scenarios have been proposed for the evolution of this genome architecture: 1) mutational diversification of a multi-copy chromosome; 2) capture of a new chromosome by horizontal transfer; 3) acquisition of new origins and splitting into two replication-competent chromosomes. We report an example of the third scenario: the multi-origin chromosome of the archaeon Haloferax volcanii has split into two elements via homologous recombination. The newly generated elements are bona fide chromosomes, because each bears "chromosomal" replication origins, rRNA loci, and essential genes. The new chromosomes were stable during routine growth but additional genetic manipulation, which involves selective bottlenecks, provoked further rearrangements. To the best of our knowledge, rearrangement of a naturally evolved prokaryotic genome to generate two new chromosomes has not been described previously.
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Affiliation(s)
- Darya Ausiannikava
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Laura Mitchell
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Hannah Marriott
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Victoria Smith
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Michelle Hawkins
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD
| | | | - Thorsten Allers
- School of Life Sciences, University of Nottingham, Queen’s Medical Centre, Nottingham, United Kingdom
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106
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Dennin RH. Overlooked: Extrachromosomal DNA and Their Possible Impact on Whole Genome Sequencing. Malays J Med Sci 2018; 25:20-26. [PMID: 30918452 PMCID: PMC6422590 DOI: 10.21315/mjms2018.25.2.3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/05/2018] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal (ec) DNA in eukaryotic cells has been known for decades. The structures described range from linear double stranded (ds) DNA to circular dsDNA, distinct from mitochondrial (mt) DNA. The sizes of circular forms are described from some hundred base pairs (bp) up to more than 150 kbp. The number of molecules per cell ranges from several hundred to a thousand. Semi-quantitative determinations of circular dsDNA show proportions as high as several percentages of the total DNA per cell. These ecDNA fractions harbor sequences that are known to be present in chromosomal DNA (chrDNA) too. Sequencing projects on, for example the human genome, have to take into account the ecDNA sequences which are simultaneously ascertained; corrections cannot be performed retrospectively. Concerning the results of sequencings derived from extracted whole DNA: if the ecDNA fractions contained therein are not taken into account, erroneous conclusions at the chromosomal level may result.
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Affiliation(s)
- Reinhard H Dennin
- Department of Infectious Diseases and Microbiology, University of Luebeck, UKSH, Campus Luebeck, D-23538 Luebeck, Germany
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107
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Discordant inheritance of chromosomal and extrachromosomal DNA elements contributes to dynamic disease evolution in glioblastoma. Nat Genet 2018; 50:708-717. [PMID: 29686388 PMCID: PMC5934307 DOI: 10.1038/s41588-018-0105-0] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 02/28/2018] [Indexed: 01/09/2023]
Abstract
To understand how genomic heterogeneity of glioblastoma contributes to the poor response to therapy characteristic of this disease, we performed DNA and RNA sequencing on GBM tumor samples and the neurospheres and orthotopic xenograft models derived from them. We used the resulting data set to show that somatic driver alterations including single nucleotide variants, focal DNA alterations, and oncogene amplification on extrachromosomal DNA (ecDNA) elements were in majority propagated from tumor to model systems. In several instances, ecDNAs and chromosomal alterations demonstrated divergent inheritance patterns and clonal selection dynamics during cell culture and xenografting. We infer that ecDNA inherited unevenly between offspring cells, a characteristic that affects the oncogenic potential of cells with more or fewer ecDNAs. Longitudinal patient tumor profiling found that oncogenic ecDNAs are frequently retained throughout the course of disease. Our analysis shows that extrachromosomal elements allow rapid increase of genomic heterogeneity during glioblastoma evolution, independent of chromosomal DNA alterations.
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108
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Paulsen T, Kumar P, Koseoglu MM, Dutta A. Discoveries of Extrachromosomal Circles of DNA in Normal and Tumor Cells. Trends Genet 2018; 34:270-278. [PMID: 29329720 PMCID: PMC5881399 DOI: 10.1016/j.tig.2017.12.010] [Citation(s) in RCA: 132] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/24/2017] [Accepted: 12/13/2017] [Indexed: 10/18/2022]
Abstract
While the vast majority of cellular DNA in eukaryotes is contained in long linear strands in chromosomes, we have long recognized some exceptions like mitochondrial DNA, plasmids in yeasts, and double minutes (DMs) in cancer cells where the DNA is present in extrachromosomal circles. In addition, specialized extrachromosomal circles of DNA (eccDNA) have been noted to arise from repetitive genomic sequences like telomeric DNA or rDNA. Recently eccDNA arising from unique (nonrepetitive) DNA have been discovered in normal and malignant cells, raising interesting questions about their biogenesis, function and clinical utility. Here, we review recent results and future directions of inquiry on these new forms of eccDNA.
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MESH Headings
- Animals
- Chromosomes, Human/chemistry
- Chromosomes, Human/metabolism
- DNA, Chloroplast/chemistry
- DNA, Chloroplast/genetics
- DNA, Chloroplast/metabolism
- DNA, Circular/chemistry
- DNA, Circular/genetics
- DNA, Circular/metabolism
- DNA, Kinetoplast/chemistry
- DNA, Kinetoplast/genetics
- DNA, Kinetoplast/metabolism
- DNA, Mitochondrial/chemistry
- DNA, Mitochondrial/genetics
- DNA, Mitochondrial/metabolism
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- DNA, Neoplasm/metabolism
- Eukaryotic Cells/chemistry
- Eukaryotic Cells/metabolism
- Humans
- Kinetoplastida/genetics
- Kinetoplastida/metabolism
- Neoplasms/genetics
- Neoplasms/metabolism
- Neoplasms/pathology
- Neoplastic Cells, Circulating/chemistry
- Neoplastic Cells, Circulating/metabolism
- Plants/genetics
- Plants/metabolism
- Plasmids/chemistry
- Plasmids/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Telomere/chemistry
- Telomere/metabolism
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Affiliation(s)
- Teressa Paulsen
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Pankaj Kumar
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - M Murat Koseoglu
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA
| | - Anindya Dutta
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, USA.
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109
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Koo DH, Molin WT, Saski CA, Jiang J, Putta K, Jugulam M, Friebe B, Gill BS. Extrachromosomal circular DNA-based amplification and transmission of herbicide resistance in crop weed Amaranthus palmeri. Proc Natl Acad Sci U S A 2018; 115:3332-3337. [PMID: 29531028 PMCID: PMC5879691 DOI: 10.1073/pnas.1719354115] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri, a crop weed, can develop herbicide resistance to glyphosate [N-(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene, the molecular target of glyphosate. However, biological questions regarding the source of the amplified EPSPS, the nature of the amplified DNA structures, and mechanisms responsible for maintaining this gene amplification in cells and their inheritance remain unknown. Here, we report that amplified EPSPS copies in glyphosate-resistant (GR) A. palmeri are present in the form of eccDNAs with various conformations. The eccDNAs are transmitted during cell division in mitosis and meiosis to the soma and germ cells and the progeny by an as yet unknown mechanism of tethering to mitotic and meiotic chromosomes. We propose that eccDNAs are one of the components of McClintock's postulated innate systems [McClintock B (1978) Stadler Genetics Symposium] that can rapidly produce soma variation, amplify EPSPS genes in the sporophyte that are transmitted to germ cells, and modulate rapid glyphosate resistance through genome plasticity and adaptive evolution.
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Affiliation(s)
- Dal-Hoe Koo
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - William T Molin
- Crop Production Systems Research Unit, US Department of Agriculture-Agricultural Research Services, Stoneville, MS 38776
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824
- Department of Horticulture, Michigan State University, East Lansing, MI 48824
| | - Karthik Putta
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Mithila Jugulam
- Department of Agronomy, Kansas State University, Manhattan, KS 66506
| | - Bernd Friebe
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506
| | - Bikram S Gill
- Wheat Genetics Resource Center and Department of Plant Pathology, Kansas State University, Manhattan, KS 66506;
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110
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Abstract
The human genome is generally organized into stable chromosomes, and only tumor cells are known to accumulate kilobase (kb)-sized extrachromosomal circular DNA elements (eccDNAs). However, it must be expected that kb eccDNAs exist in normal cells as a result of mutations. Here, we purify and sequence eccDNAs from muscle and blood samples from 16 healthy men, detecting ~100,000 unique eccDNA types from 16 million nuclei. Half of these structures carry genes or gene fragments and the majority are smaller than 25 kb. Transcription from eccDNAs suggests that eccDNAs reside in nuclei and recurrence of certain eccDNAs in several individuals implies DNA circularization hotspots. Gene-rich chromosomes contribute to more eccDNAs per megabase and the most transcribed protein-coding gene in muscle, TTN (titin), provides the most eccDNAs per gene. Thus, somatic genomes are rich in chromosome-derived eccDNAs that may influence phenotypes through altered gene copy numbers and transcription of full-length or truncated genes. Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences.
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111
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Hagenbuchner J, Lungkofler L, Kiechl-Kohlendorfer U, Viola G, Ferlin MG, Ausserlechner MJ, Obexer P. The tubulin inhibitor MG-2477 induces autophagy-regulated cell death, ROS accumulation and activation of FOXO3 in neuroblastoma. Oncotarget 2018; 8:32009-32026. [PMID: 28415610 PMCID: PMC5458265 DOI: 10.18632/oncotarget.16434] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 03/08/2017] [Indexed: 12/29/2022] Open
Abstract
Neuroblastoma is the most frequent extra-cranial solid tumor in children with still high mortality in stage M. Here we studied the tubulin-inhibitor MG-2477 as a possible therapeutic agent for neuroblastoma therapy and uncovered that MG-2477 induces death in neuroblastoma cells independent of PKB-activation status and stage. MG-2477 triggers within 30 minutes extensive autophagosome-formation that finally leads to cell death associated with mitotic catastrophe. Autophagy is critical for MG-2477-induced death and is regulated by the BH3-only protein PMAIP1/NOXA which sequesters the anti-apoptotic BCL2-protein BCLXL and thereby displaces and activates the autophagy-regulator BECN1/beclin1. Knockdown of NOXA or overexpression of its pro-survival binding partners MCL1 and BCLXL counteracts MG-2477-induced cell death. MG-2477 also rapidly induces the repression of the anti-apoptotic protein Survivin, which promotes autophagy and cell death. We further observed the accumulation of reactive oxygen species (ROS) that triggers autophagy induction suggesting a change of the PI3 kinase-III/BECN1 complex and activates the transcription factor FOXO3, which contributes to final cell death induction. The combined data suggest that MG-2477 induces a sequential process of ROS-accumulation, autophagy and FOXO3-activation that leads to cell death in neuroblastoma cells.
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Affiliation(s)
- Judith Hagenbuchner
- Department of Pediatrics II, Medical University Innsbruck, Innsbruck, Austria
| | | | | | - Giampietro Viola
- Department of Woman's and Child's Health, Oncohematology Laboratory University of Padova, Padova, Italy
| | - Maria Grazia Ferlin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padova, Italy
| | | | - Petra Obexer
- Department of Pediatrics II, Medical University Innsbruck, Innsbruck, Austria.,Tyrolean Cancer Research Institute, Innsbruck, Austria
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112
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MYC-containing amplicons in acute myeloid leukemia: genomic structures, evolution, and transcriptional consequences. Leukemia 2018; 32:2152-2166. [PMID: 29467491 PMCID: PMC6170393 DOI: 10.1038/s41375-018-0033-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/27/2017] [Accepted: 11/13/2017] [Indexed: 01/05/2023]
Abstract
Double minutes (dmin), homogeneously staining regions, and ring chromosomes are vehicles of gene amplification in cancer. The underlying mechanism leading to their formation as well as their structure and function in acute myeloid leukemia (AML) remain mysterious. We combined a range of high-resolution genomic methods to investigate the architecture and expression pattern of amplicons involving chromosome band 8q24 in 23 cases of AML (AML-amp). This revealed that different MYC-dmin architectures can coexist within the same leukemic cell population, indicating a step-wise evolution rather than a single event origin, such as through chromothripsis. This was supported also by the analysis of the chromothripsis criteria, that poorly matched the model in our samples. Furthermore, we found that dmin could evolve toward ring chromosomes stabilized by neocentromeres. Surprisingly, amplified genes (mainly PVT1) frequently participated in fusion transcripts lacking a corresponding DNA template. We also detected a significant overexpression of the circular RNA of PVT1 (circPVT1) in AML-amp cases versus AML with a normal karyotype. Our results show that 8q24 amplicons in AML are surprisingly plastic DNA structures with an unexpected association to novel fusion transcripts and circular RNAs.
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113
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The Hidden Genomic and Transcriptomic Plasticity of Giant Marker Chromosomes in Cancer. Genetics 2017; 208:951-961. [PMID: 29279323 DOI: 10.1534/genetics.117.300552] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 12/11/2017] [Indexed: 01/16/2023] Open
Abstract
Genome amplification in the form of rings or giant rod-shaped marker chromosomes (RGMs) is a common genetic alteration in soft tissue tumors. The mitotic stability of these structures is often rescued by perfectly functioning analphoid neocentromeres, which therefore significantly contribute to cancer progression. Here, we disentangled the genomic architecture of many neocentromeres stabilizing marker chromosomes in well-differentiated liposarcoma and lung sarcomatoid carcinoma samples. In cells carrying heavily rearranged RGMs, these structures were assembled as patchworks of multiple short amplified sequences, disclosing an extremely high level of complexity and definitely ruling out the existence of regions prone to neocentromere seeding. Moreover, by studying two well-differentiated liposarcoma samples derived from the onset and the recurrence of the same tumor, we documented an expansion of the neocentromeric domain that occurred during tumor progression, which reflects a strong selective pressure acting toward the improvement of the neocentromeric functionality in cancer. In lung sarcomatoid carcinoma cells we documented, extensive "centromere sliding" phenomena giving rise to multiple, closely mapping neocentromeric epialleles on separate coexisting markers occur, likely due to the instability of neocentromeres arising in cancer cells. Finally, by investigating the transcriptional activity of neocentromeres, we came across a burst of chimeric transcripts, both by extremely complex genomic rearrangements, and cis/trans-splicing events. Post-transcriptional editing events have been reported to expand and variegate the genetic repertoire of higher eukaryotes, so they might have a determining role in cancer. The increased incidence of fusion transcripts, might act as a driving force for the genomic amplification process, together with the increased transcription of oncogenes.
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114
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Chakraborty A, Ay F. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics 2017; 34:338-345. [PMID: 29048467 DOI: 10.1093/bioinformatics/btx664] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/21/2017] [Accepted: 10/17/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities [e.g. copy number variations (CNVs) and translocations] altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g. Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. RESULTS In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), (ii) to call inter-chromosomal translocations and their boundaries (HiCtrans) from Hi-C experiments and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities (AveSim) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing data among chromosomes with CNV events for a breast cancer cell line (r = 0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes and homogeneously staining regions. Considering the inherent limitations of existing techniques for karyotyping (i.e. missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100-300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. AVAILABILITY AND IMPLEMENTATION CNV calling: https://github.com/ay-lab/HiCnv, Translocation calling: https://github.com/ay-lab/HiCtrans and Hi-C simulation: https://github.com/ay-lab/AveSim. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
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115
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Chen W, Robertson AJ, Ganesamoorthy D, Coin LJM. sCNAphase: using haplotype resolved read depth to genotype somatic copy number alterations from low cellularity aneuploid tumors. Nucleic Acids Res 2017; 45:e34. [PMID: 27903916 PMCID: PMC5389684 DOI: 10.1093/nar/gkw1086] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/26/2016] [Indexed: 02/03/2023] Open
Abstract
Accurate identification of copy number alterations is an essential step in understanding the events driving tumor progression. While a variety of algorithms have been developed to use high-throughput sequencing data to profile copy number changes, no tool is able to reliably characterize ploidy and genotype absolute copy number from tumor samples that contain less than 40% tumor cells. To increase our power to resolve the copy number profile from low-cellularity tumor samples, we developed a novel approach that pre-phases heterozygote germline single nucleotide polymorphisms (SNPs) in order to replace the commonly used ‘B-allele frequency’ with a more powerful ‘parental-haplotype frequency’. We apply our tool—sCNAphase—to characterize the copy number and loss-of-heterozygosity profiles of four publicly available breast cancer cell-lines. Comparisons to previous spectral karyotyping and microarray studies revealed that sCNAphase reliably identified overall ploidy as well as the individual copy number mutations from each cell-line. Analysis of artificial cell-line mixtures demonstrated the capacity of this method to determine the level of tumor cellularity, consistently identify sCNAs and characterize ploidy in samples with as little as 10% tumor cells. This novel methodology has the potential to bring sCNA profiling to low-cellularity tumors, a form of cancer unable to be accurately studied by current methods.
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Affiliation(s)
- Wenhan Chen
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Alan J Robertson
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Lachlan J M Coin
- Institute for Molecular Bioscience, The University of Queensland, St Lucia, Queensland, 4072, Australia
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116
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Valgôde FGS, da Silva MA, Vieira DP, Ribela MTCP, Bartolini P, Okazaki K. Cytotoxic and genotoxic effects of 131 I and 60 Co in follicular thyroid cancer cell (WRO) with and without recombinant human thyroid-stimulating hormone treatment. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:451-461. [PMID: 28561379 DOI: 10.1002/em.22099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/22/2017] [Accepted: 04/24/2017] [Indexed: 06/07/2023]
Abstract
Normally, differentiated thyroid cancer (DTC) tends to be biologically indolent, highly curable and has an excellent prognosis. However, the treatment may fail when the cancer has lost radioiodine avidity. The present study was carried out in order to evaluate the cytotoxic and genotoxic effects of 131 I and 60 Co and radioiodine uptake in WRO cells, derived from DTC, harboring the BRAFV600E mutation. WRO cells showed a relatively slow cell cycle of 96.3 h with an unstable karyotype containing various double minutes. The genotoxicity assay (micronucleus test) showed a relative high radioresistance to 131 I (0.07-3.70 MBq/mL), independent of treatment with recombinant human thyroid-stimulating hormone (rhTSH). For the cytotoxicity assay, WRO cells were also relatively resistant to 60 Co (range: 0.2-8.3 Gy), but with a gradual decrease of viability as a function of time for higher doses (20 and 40 Gy, starting from the fifth to sixth day). For internal irradiation with 131 I, WRO cells showed a decline in viability at radioactive concentration higher than 1.85 MBq/mL; this was even more effective at 3.70 MBq/mL, but only when preceded by rhTSH, in coincidence with the highest level of 131 I uptake. These data show promising results, since the loss of the ability of thyroid cells to concentrate radioiodine is considered to be one of the main factors responsible for the failure of 131 I therapy in patients with DTC. The use of tumor-derived cell lines as a model for in vivo tumor requires, however, further investigations and deep evaluation of the corresponding in vivo effects. Environ. Mol. Mutagen. 58:451-461, 2017. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Flávia Gomes Silva Valgôde
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
| | - Márcia Augusta da Silva
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
| | - Daniel Perez Vieira
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
| | - Maria Teresa Carvalho Pinto Ribela
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
| | - Paolo Bartolini
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
| | - Kayo Okazaki
- Centro de Biotecnologia, Instituto de Pesquisas Energéticas e Nucleares, IPEN-CNEN/SP, Av. Prof. Lineu Prestes, 2242, CEP 05508-900, Caixa Postal 11049, Cidade Universitária, São Paulo, Brazil
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Daniele G, Simonetti G, Fusilli C, Iacobucci I, Lonoce A, Palazzo A, Lomiento M, Mammoli F, Marsano RM, Marasco E, Mantovani V, Quentmeier H, Drexler HG, Ding J, Palumbo O, Carella M, Nadarajah N, Perricone M, Ottaviani E, Baldazzi C, Testoni N, Papayannidis C, Ferrari S, Mazza T, Martinelli G, Storlazzi CT. Epigenetically induced ectopic expression of UNCX impairs the proliferation and differentiation of myeloid cells. Haematologica 2017; 102:1204-1214. [PMID: 28411256 PMCID: PMC5566027 DOI: 10.3324/haematol.2016.163022] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 04/12/2017] [Indexed: 11/09/2022] Open
Abstract
We here describe a leukemogenic role of the homeobox gene UNCX,
activated by epigenetic modifications in acute myeloid leukemia (AML). We found
the ectopic activation of UNCX in a leukemia patient harboring
a t(7;10)(p22;p14) translocation, in 22 of 61 of additional cases [a
total of 23 positive patients out of 62 (37.1%)], and in 6 of 75
(8%) of AML cell lines. UNCX is embedded within a
low-methylation region (canyon) and encodes for a transcription factor involved
in somitogenesis and neurogenesis, with specific expression in the eye, brain,
and kidney. UNCX expression turned out to be associated, and
significantly correlated, with DNA methylation increase at its canyon borders
based on data in our patients and in archived data of patients from The Cancer
Genome Atlas. UNCX-positive and -negative patients displayed
significant differences in their gene expression profiles. An enrichment of
genes involved in cell proliferation and differentiation, such as
MAP2K1 and CCNA1, was revealed. Similar
results were obtained in UNCX-transduced CD34+
cells, associated with low proliferation and differentiation arrest.
Accordingly, we showed that UNCX expression characterizes
leukemia cells at their early stage of differentiation, mainly M2 and M3
subtypes carrying wild-type NPM1. We also observed that
UNCX expression significantly associates with an increased
frequency of acute promyelocytic leukemia with PML-RARA and AML
with t(8;21)(q22;q22.1); RUNX1-RUNX1T1 classes, according to
the World Health Organization disease classification. In summary, our findings
suggest a novel leukemogenic role of UNCX, associated with
epigenetic modifications and with impaired cell proliferation and
differentiation in AML.
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Affiliation(s)
- Giulia Daniele
- Department of Biology, University of Bari "A. Moro", Italy
| | - Giorgia Simonetti
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Caterina Fusilli
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Ilaria Iacobucci
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Angelo Lonoce
- Department of Biology, University of Bari "A. Moro", Italy
| | | | - Mariana Lomiento
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Fabiana Mammoli
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Vilma Mantovani
- Center for Applied Biomedical Research (CRBA), S. Orsola-Malpighi Hospital, Bologna, Italy.,Unit of Medical Genetics, Department of Medical and Surgical Sciences, S. Orsola-Malpighi Hospital University of Bologna, Italy
| | - Hilmar Quentmeier
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Hans G Drexler
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Jie Ding
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Human and Animal Cell Lines, Braunschweig, Germany
| | - Orazio Palumbo
- Medical Genetics Unit, IRCCS "Casa Sollievo della Sofferenza (CSS)" Hospital, San Giovanni Rotondo, Italy
| | - Massimo Carella
- Medical Genetics Unit, IRCCS "Casa Sollievo della Sofferenza (CSS)" Hospital, San Giovanni Rotondo, Italy
| | | | - Margherita Perricone
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Emanuela Ottaviani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Carmen Baldazzi
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Nicoletta Testoni
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Cristina Papayannidis
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
| | - Sergio Ferrari
- Department of Life Science, University of Modena and Reggio Emilia, Modena, Italy
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics Unit, San Giovanni Rotondo, Italy
| | - Giovanni Martinelli
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Italy
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118
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Turner KM, Deshpande V, Beyter D, Koga T, Rusert J, Lee C, Li B, Arden K, Ren B, Nathanson DA, Kornblum HI, Taylor MD, Kaushal S, Cavenee WK, Wechsler-Reya R, Furnari FB, Vandenberg SR, Rao PN, Wahl GM, Bafna V, Mischel PS. Extrachromosomal oncogene amplification drives tumour evolution and genetic heterogeneity. Nature 2017; 543:122-125. [PMID: 28178237 PMCID: PMC5334176 DOI: 10.1038/nature21356] [Citation(s) in RCA: 416] [Impact Index Per Article: 59.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 12/23/2016] [Indexed: 02/06/2023]
Abstract
Human cells have twenty-three pairs of chromosomes. In cancer, however, genes can be amplified in chromosomes or in circular extrachromosomal DNA (ecDNA), although the frequency and functional importance of ecDNA are not understood. We performed whole-genome sequencing, structural modelling and cytogenetic analyses of 17 different cancer types, including analysis of the structure and function of chromosomes during metaphase of 2,572 dividing cells, and developed a software package called ECdetect to conduct unbiased, integrated ecDNA detection and analysis. Here we show that ecDNA was found in nearly half of human cancers; its frequency varied by tumour type, but it was almost never found in normal cells. Driver oncogenes were amplified most commonly in ecDNA, thereby increasing transcript level. Mathematical modelling predicted that ecDNA amplification would increase oncogene copy number and intratumoural heterogeneity more effectively than chromosomal amplification. We validated these predictions by quantitative analyses of cancer samples. The results presented here suggest that ecDNA contributes to accelerated evolution in cancer.
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Affiliation(s)
- Kristen M. Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Viraj Deshpande
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Doruk Beyter
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Tomoyuki Koga
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Jessica Rusert
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Catherine Lee
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Karen Arden
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - David A. Nathanson
- Department of Medical and Molecular Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Harley I. Kornblum
- Department of Medical and Molecular Pharmacology, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
- Neuropsychiatric Institute–Semel Institute for Neuroscience and Human Behavior and Department of Psychiatry and Biobehavioral Sciences, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Michael D. Taylor
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Sharmeela Kaushal
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Webster K. Cavenee
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Robert Wechsler-Reya
- Tumor Initiation and Maintenance Program, NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Frank B. Furnari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Scott R. Vandenberg
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - P. Nagesh Rao
- Department of Pathology and Laboratory Medicine, David Geffen UCLA School of Medicine, Los Angeles, CA, USA
| | - Geoffrey M. Wahl
- Gene Expression Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Paul S. Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
- Department of Pathology, University of California at San Diego, La Jolla, CA, USA
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120
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Chen JR, Chien HP, Chen KS, Hwang CC, Chen HY, Yeh KY, Hsieh TY, Chang LC, Hsu YC, Lu RJ, Hua CC. Amplification of HER2 and TOP2A and deletion of TOP2A genes in a series of Taiwanese breast cancer. Medicine (Baltimore) 2017; 96:e5582. [PMID: 28079792 PMCID: PMC5266154 DOI: 10.1097/md.0000000000005582] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The prognostic relevance of topoisomerase II alpha (TOP2A) copy number change remains not well established. This study is aimed to investigate the frequency and pattern of TOP2A aberrations; to correlate TOP2A alterations with human epidermal growth factor receptor 2 (HER2) status and clinicopathological parameters, and further to explore prognostic value of TOP2A and HER2 status in breast cancer in Taiwan. METHODS We analyzed tissue samples from 311 invasive carcinomas in tissue microarrays for TOP2A and HER2 status by fluorescent in situ hybridization. RESULTS TOP2A copy number change is an infrequent genetic event (9.8% amplification and 2.7% deletion) and is present in both HER2-amplified and nonamplified tumors. TOP2A amplification is statistically associated with age >50 at diagnosis (P = 0.016) and HER2 amplification (P < 0.001). HER2 amplification, but not TOP2A amplification, is a predictor of unfavorable prognosis (P = 0.002). Univariate and multivariate analysis showed that higher histologic grading, positive nodal involvement, and HER2 positivity were associated with poorer overall survival. Cytogenetically, double minutes-type amplification is the predominant pattern for both genes (HER2: 64% and TOP2A: 93.1%). Homogeneous staining region-type signals of both genes are resistant to RNase digestion, supporting that these were not nuclear accumulation of mRNA transcripts. CONCLUSION Our results demonstrate the prognostic value of tumor grading, nodal involvement, and HER2 status in Taiwanese breast cancer. TOP2A aberrations are an infrequent event independent of HER2 status, and TOP2A amplification carries no prognostic value. The predictive value of TOP2A aberrations in patients of breast cancer taking athracycline-containing treatment in Taiwan remains to be determined in prospectively well-designed clinical trials.
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Affiliation(s)
- Jim-Ray Chen
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Hui-Ping Chien
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Kuo-Su Chen
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
- Department of Nephrology, Division of Medicine Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Cheng-Cheng Hwang
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Huang-Yang Chen
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
- Department of General Surgery, Division of Surgery, Keelung Chang Gung Memorial Hospital, Taiwan
| | - Kun-Yan Yeh
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
- Department of Oncology and Hematology, Division of Medicine, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
| | - Tsan-Yu Hsieh
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Liang-Che Chang
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Yuan-Chun Hsu
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Ren-Jie Lu
- Department of Pathology, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
| | - Chung-Ching Hua
- College of Medicine, Chang Gung University, Kwei-Shan, Taoyuan, Taiwan
- Department of Internal Medicine, Keelung Chang Gung Memorial Hospital, Keelung, Taiwan
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121
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Ndrg1b and fam49ab modulate the PTEN pathway to control T-cell lymphopoiesis in the zebrafish. Blood 2016; 128:3052-3060. [PMID: 27827822 DOI: 10.1182/blood-2016-09-742502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 11/04/2016] [Indexed: 02/07/2023] Open
Abstract
During hematopoiesis, the balance between proliferation, differentiation, and apoptosis is tightly regulated in order to maintain homeostasis. Failure in these processes can ultimately lead to uncontrolled proliferation and leukemia. Phosphatase and tensin homolog (PTEN) is one of the molecular pathways involved in this balance. By opposing PI3-kinases, PTEN inhibits proliferation and promotes differentiation and is thus considered a tumor suppressor. Indeed, PTEN is frequently mutated in many cancers, including leukemias. Loss of PTEN often leads to lymphoid cancers. However, little is known about the molecular events that regulate PTEN signaling during lymphopoiesis. In this study, we used zebrafish to address this. We report that N-myc downstream-regulated gene 1b (ndrg1b) rescues lymphoid differentiation after PTEN inhibition. We also show that a previously uncharacterized gene, fam49ab, inhibits T-cell differentiation, a phenotype that can be rescued by ndrg1b We propose that ndrg1b and fam49ab are 2 new modulators of PTEN signaling that control lymphoid differentiation in the zebrafish thymus.
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122
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Koka R, Mainor CB, Banerjee A, Baer MR, Zou YS. Concomitant amplification of the MLL gene on a ring chromosome and a homogeneously staining region (hsr) in acute myeloid leukemia: mechanistic implications. Leuk Lymphoma 2016; 58:1250-1253. [PMID: 27733077 DOI: 10.1080/10428194.2016.1233539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Rima Koka
- a Department of Pathology , University of Maryland School of Medicine , Baltimore , MD , USA.,b University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD , USA
| | - Candace B Mainor
- b University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD , USA.,c Department of Medicine , University of Maryland School of Medicine , Baltimore , MD , USA
| | - Arnob Banerjee
- b University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD , USA.,c Department of Medicine , University of Maryland School of Medicine , Baltimore , MD , USA
| | - Maria R Baer
- b University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD , USA.,c Department of Medicine , University of Maryland School of Medicine , Baltimore , MD , USA
| | - Ying S Zou
- a Department of Pathology , University of Maryland School of Medicine , Baltimore , MD , USA.,b University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center , Baltimore , MD , USA
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123
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Møller HD, Bojsen RK, Tachibana C, Parsons L, Botstein D, Regenberg B. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells. J Vis Exp 2016:e54239 |. [PMID: 27077531 DOI: 10.3791/54239] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.
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Affiliation(s)
| | - Rasmus K Bojsen
- National Veterinary Institute, Technical University of Denmark
| | | | - Lance Parsons
- Lewis-Sigler Institute for Integrative Genomics, Princeton University
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124
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Abstract
Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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125
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Formation of Nup98-containing nuclear bodies in HeLa sublines is linked to genomic rearrangements affecting chromosome 11. Chromosoma 2015; 125:789-805. [PMID: 26685999 DOI: 10.1007/s00412-015-0567-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 12/06/2015] [Accepted: 12/10/2015] [Indexed: 01/23/2023]
Abstract
Nup98 is an important component of the nuclear pore complex (NPC) and also a rare but recurrent target for chromosomal translocation in leukaemogenesis. Nup98 contains multiple cohesive Gly-Leu-Phe-Gly (GLFG) repeats that are critical notably for the formation of intranuclear GLFG bodies. Previous studies have reported the existence of GLFG bodies in cells overexpressing exogenous Nup98 or in a HeLa subline (HeLa-C) expressing an unusual elevated amount of endogenous Nup98. Here, we have analysed the presence of Nup98-containing bodies in several human cell lines. We found that HEp-2, another HeLa subline, contains GLFG bodies that are distinct from those identified in HeLa-C. Rapid amplification of cDNA ends (RACE) revealed that HEp-2 cells express additional truncated forms of Nup98 fused to a non-coding region of chromosome 11q22.1. Cytogenetic analyses using FISH and array-CGH further revealed chromosomal rearrangements that were distinct from those observed in leukaemic cells. Indeed, HEp-2 cells feature a massive amplification of juxtaposed NUP98 and 11q22.1 loci on a chromosome marker derived from chromosome 3. Unexpectedly, minor co-amplifications of NUP98 and 11q22.1 loci were also observed in other HeLa sublines, but on rearranged chromosomes 11. Altogether, this study reveals that distinct genomic rearrangements affecting NUP98 are associated with the formation of GLFG bodies in specific HeLa sublines.
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126
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Leibowitz ML, Zhang CZ, Pellman D. Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. Annu Rev Genet 2015; 49:183-211. [DOI: 10.1146/annurev-genet-120213-092228] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mitchell L. Leibowitz
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
| | - Cheng-Zhong Zhang
- Department of Pediatric Oncology,
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215;
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
| | - David Pellman
- Department of Pediatric Oncology,
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115;
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
- Howard Hughes Medical Institute, Boston, Massachusetts 02115
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127
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Bagci O, Kurtgöz S. Amplification of Cellular Oncogenes in Solid Tumors. NORTH AMERICAN JOURNAL OF MEDICAL SCIENCES 2015; 7:341-6. [PMID: 26417556 PMCID: PMC4561439 DOI: 10.4103/1947-2714.163641] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The term gene amplification refers to an increase in copy number of a gene. Upregulation of gene expression through amplification is a general mechanism to increase gene dosage. Oncogene amplifications have been shown in solid human cancers and they are often associated with progression of cancer. Defining oncogene amplification is useful since it is used as a prognostic marker in clinical oncology nowadays, especially v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (HER2) targeted agents are used in breast cancer patients with high level of HER2 overexpression as a therapeutic approach. However, patients without HER2 overexpression do not appear to benefit from these agents. We concluded that determination of oncogene amplification in solid tumors is an important factor in treatment of human cancers with many unknowns. We have referred to PubMed and some databases to prepare this article.
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Affiliation(s)
- Ozkan Bagci
- Department of Medical Genetics, Suleyman Demirel University, School of Medicine, Isparta, Turkey
| | - Serkan Kurtgöz
- Department of Medical Genetics, Suleyman Demirel University, School of Medicine, Isparta, Turkey
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128
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Matsui A, Ihara T, Suda H, Mikami H, Semba K. Gene amplification: mechanisms and involvement in cancer. Biomol Concepts 2015; 4:567-82. [PMID: 25436757 DOI: 10.1515/bmc-2013-0026] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/02/2013] [Indexed: 11/15/2022] Open
Abstract
Gene amplification was recognized as a physiological process during the development of Drosophila melanogaster. Intriguingly, mammalian cells use this mechanism to overexpress particular genes for survival under stress, such as during exposure to cytotoxic drugs. One well-known example is the amplification of the dihydrofolate reductase gene observed in methotrexate-resistant cells. Four models have been proposed for the generation of amplifications: extrareplication and recombination, the breakage-fusion-bridge cycle, double rolling-circle replication, and replication fork stalling and template switching. Gene amplification is a typical genetic alteration in cancer, and historically many oncogenes have been identified in the amplified regions. In this regard, novel cancer-associated genes may remain to be identified in the amplified regions. Recent comprehensive approaches have further revealed that co-amplified genes also contribute to tumorigenesis in concert with known oncogenes in the same amplicons. Considering that cancer develops through the alteration of multiple genes, gene amplification is an effective acceleration machinery to promote tumorigenesis. Identification of cancer-associated genes could provide novel and effective therapeutic targets.
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129
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Abstract
Examples of extrachromosomal circular DNAs (eccDNAs) are found in many organisms, but their impact on genetic variation at the genome scale has not been investigated. We mapped 1,756 eccDNAs in the Saccharomyces cerevisiae genome using Circle-Seq, a highly sensitive eccDNA purification method. Yeast eccDNAs ranged from an arbitrary lower limit of 1 kb up to 38 kb and covered 23% of the genome, representing thousands of genes. EccDNA arose both from genomic regions with repetitive sequences ≥ 15 bases long and from regions with short or no repetitive sequences. Some eccDNAs were identified in several yeast populations. These eccDNAs contained ribosomal genes, transposon remnants, and tandemly repeated genes (HXT6/7, ENA1/2/5, and CUP1-1/-2) that were generally enriched on eccDNAs. EccDNAs seemed to be replicated and 80% contained consensus sequences for autonomous replication origins that could explain their maintenance. Our data suggest that eccDNAs are common in S. cerevisiae, where they might contribute substantially to genetic variation and evolution.
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130
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Zhang CZ, Spektor A, Cornils H, Francis JM, Jackson EK, Liu S, Meyerson M, Pellman D. Chromothripsis from DNA damage in micronuclei. Nature 2015; 522:179-84. [PMID: 26017310 PMCID: PMC4742237 DOI: 10.1038/nature14493] [Citation(s) in RCA: 762] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 04/20/2015] [Indexed: 01/01/2023]
Abstract
Genome sequencing has uncovered a new mutational phenomenon in cancer and congenital disorders called chromothripsis. Chromothripsis is characterized by extensive genomic rearrangements and an oscillating pattern of DNA copy number levels, all curiously restricted to one or a few chromosomes. The mechanism for chromothripsis is unknown, but we previously proposed that it could occur through the physical isolation of chromosomes in aberrant nuclear structures called micronuclei. Here, using a combination of live cell imaging and single-cell genome sequencing, we demonstrate that micronucleus formation can indeed generate a spectrum of genomic rearrangements, some of which recapitulate all known features of chromothripsis. These events are restricted to the mis-segregated chromosome and occur within one cell division. We demonstrate that the mechanism for chromothripsis can involve the fragmentation and subsequent reassembly of a single chromatid from a micronucleus. Collectively, these experiments establish a new mutational process of which chromothripsis is one extreme outcome.
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Affiliation(s)
- Cheng-Zhong Zhang
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [4] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alexander Spektor
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Hauke Cornils
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joshua M Francis
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Emily K Jackson
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
| | - Shiwei Liu
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Matthew Meyerson
- 1] Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA [4] Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - David Pellman
- 1] Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA [3] Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA [4] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA
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131
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Hayes M, Li J. An integrative framework for the identification of double minute chromosomes using next generation sequencing data. BMC Genet 2015; 16 Suppl 2:S1. [PMID: 25953282 PMCID: PMC4423570 DOI: 10.1186/1471-2156-16-s2-s1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Double minute chromosomes are circular fragments of DNA whose presence is associated with the onset of certain cancers. Double minutes are lethal, as they are highly amplified and typically contain oncogenes. Locating double minutes can supplement the process of cancer diagnosis, and it can help to identify therapeutic targets. However, there is currently a dearth of computational methods available to identify double minutes. We propose a computational framework for the idenfication of double minute chromosomes using next-generation sequencing data. Our framework integrates predictions from algorithms that detect DNA copy number variants, and it also integrates predictions from algorithms that locate genomic structural variants. This information is used by a graph-based algorithm to predict the presence of double minute chromosomes. RESULTS Using a previously published copy number variant algorithm and two structural variation prediction algorithms, we implemented our framework and tested it on a dataset consisting of simulated double minute chromosomes. Our approach uncovered double minutes with high accuracy, demonstrating its plausibility. CONCLUSIONS Although we only tested the framework with three programs (RDXplorer, BreakDancer, Delly), it can be extended to incorporate results from programs that 1) detect amplified copy number and from programs that 2) detect genomic structural variants like deletions, translocations, inversions, and tandem repeats. The software that implements the framework can be accessed here: https://github.com/mhayes20/DMFinder
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132
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MYC amplification in multiple marker chromosomes and EZH2 microdeletion in a man with acute myeloid leukemia. Cancer Genet 2015; 208:96-100. [PMID: 25800664 DOI: 10.1016/j.cancergen.2015.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 01/28/2015] [Accepted: 01/30/2015] [Indexed: 12/21/2022]
Abstract
The role of MYC and EZH2 in acute myeloid leukemia (AML) pathogenesis is poorly understood. Herein we present a case of AML with MYC amplification in marker chromosomes and a microdeletion of chromosome 7 below cytogenetic resolution. The karyotype of the patient's bone marrow aspirate showed three to five marker chromosomes in all dividing cells without other structural or numerical chromosomal abnormalities. Analysis by fluorescence in situ hybridization (FISH) with a probe specific for the human MYC gene revealed amplification of the oncogene localized to the marker chromosomes. Using whole genome single nucleotide polymorphism (SNP) microarray analysis, an approximately 4.4 Mb amplicon containing the MYC gene was identified with an estimated amplification of about 30 copies per leukemic cell and, thus, an average of about 8 copies per marker chromosome. A 6.4 Mb hemizygous microdeletion of chromosome 7 within band q36.1 was also found by SNP microarray analysis in a cellular-equivalent dosage of 50%. The microdeletion spans multiple genes, including EZH2, a gene with well-known cancer association. No mutation was found in the remaining EZH2 allele by next generation gene sequencing. The combination of MYC amplification and EZH2 deletion, which has not been described previously in AML, may suggest a synergistic role of the two oncogenes in the pathogenesis of the patient's acute leukemia.
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133
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Makunin AI, Dementyeva PV, Graphodatsky AS, Volobouev VT, Kukekova AV, Trifonov VA. Genes on B chromosomes of vertebrates. Mol Cytogenet 2014; 7:99. [PMID: 25538793 PMCID: PMC4274688 DOI: 10.1186/s13039-014-0099-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 12/05/2014] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND There is a growing body of evidence that B chromosomes, once regarded as totally heterochromatic and genetically inert, harbor multiple segmental duplications containing clusters of ribosomal RNA genes, processed pseudogenes and protein-coding genes. Application of novel molecular approaches further supports complex composition and possible phenotypic effects of B chromosomes. RESULTS Here we review recent findings of gene-carrying genomic segments on B chromosomes from different vertebrate groups. We demonstrate that the genetic content of B chromosomes is highly heterogeneous and some B chromosomes contain multiple large duplications derived from various chromosomes of the standard karyotype. Although B chromosomes seem to be mostly homologous to each other within a species, their genetic content differs between species. There are indications that some genomic regions are more likely to be located on B chromosomes. CONCLUSIONS The discovery of multiple autosomal genes on B chromosomes opens a new discussion about their possible effects ranging from sex determination to fitness and adaptation, their complex interactions with host genome and role in evolution.
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Affiliation(s)
- Alexey I Makunin
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia
| | - Polina V Dementyeva
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
| | - Alexander S Graphodatsky
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
| | - Vitaly T Volobouev
- />Museum National d’Histoire Naturelle, Origine, Structure et Evolution de la Biodiversite, Paris, France
| | - Anna V Kukekova
- />Department of Animal Sciences, The University of Illinois at Urbana-Champaign, Champaign, USA
| | - Vladimir A Trifonov
- />Institute of Molecular and Cellular Biology SВ RAS, Novosibirsk, 630090 Russia
- />Novosibirsk State University, Novosibirsk, Russia
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134
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Extrachromosomal driver mutations in glioblastoma and low-grade glioma. Nat Commun 2014; 5:5690. [PMID: 25471132 PMCID: PMC4338529 DOI: 10.1038/ncomms6690] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 10/29/2014] [Indexed: 01/04/2023] Open
Abstract
Alteration of the number of copies of Double Minutes (DMs) with oncogenic EGFR mutations in response to tyrosine kinase inhibitors (TKIs) is a novel adaptive mechanism of glioblastoma. Here we provide evidence that such mutations in DMs, called here Amplification-Linked Extrachromosomal Mutations (ALEMs), originate extrachromosomally and could therefore be completely eliminated from the cancer cells. By exome sequencing of 7 glioblastoma patients we reveal ALEMs in EGFR, PDGFRA and other genes. These mutations together with DMs are lost by cancer cells in culture. We confirm the extrachromosomal origin of such mutations by showing that wild type and mutated DMs may coexist in the same tumor. Analysis of 4198 tumors suggests the presence of ALEMs across different tumor types with the highest prevalence in glioblastomas and low grade gliomas. The extrachromosomal nature of ALEMs explains the observed drastic changes in the amounts of mutated oncogenes (like EGFR or PDGFRA) in glioblastoma in response to environmental changes.
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135
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Vogt N, Gibaud A, Lemoine F, de la Grange P, Debatisse M, Malfoy B. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res 2014; 42:13194-205. [PMID: 25378339 PMCID: PMC4245956 DOI: 10.1093/nar/gku1101] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/18/2023] Open
Abstract
The mechanisms of gene amplification in tumour cells are poorly understood and the relationship between extrachromosomal DNA molecules, named double minutes (dmins), and intrachromosomal homogeneously staining regions (hsr) is not documented at nucleotide resolution. Using fluorescent in situ hybridization and whole genome sequencing, we studied a xenografted human oligodendroglioma where the co-amplification of the EGFR and MYC loci was present in the form of dmins at early passages and of an hsr at later passages. The amplified regions underwent multiple rearrangements and deletions during the formation of the dmins and their transformation into hsr. In both forms of amplification, non-homologous end-joining and microhomology-mediated end-joining rather than replication repair mechanisms prevailed in fusions. Small fragments, some of a few tens of base pairs, were associated in contigs. They came from clusters of breakpoints localized hundreds of kilobases apart in the amplified regions. The characteristics of some pairs of junctions suggest that at least some fragments were not fused randomly but could result from the concomitant repair of neighbouring breakpoints during the interaction of remote DNA sequences. This characterization at nucleotide resolution of the transition between extra- and intrachromosome amplifications highlights a hitherto uncharacterized organization of the amplified regions suggesting the involvement of new mechanisms in their formation.
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Affiliation(s)
- Nicolas Vogt
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | - Anne Gibaud
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | | | | | - Michelle Debatisse
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
| | - Bernard Malfoy
- Institut Curie, Centre de Recherche, F-75248 Paris, France CNRS, UMR3244, F-75248 Paris, France UPMC, F-75248 Paris, France
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136
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Macchia G, Nord KH, Zoli M, Purgato S, D'Addabbo P, Whelan CW, Carbone L, Perini G, Mertens F, Rocchi M, Storlazzi CT. Ring chromosomes, breakpoint clusters, and neocentromeres in sarcomas. Genes Chromosomes Cancer 2014; 54:156-67. [PMID: 25421174 DOI: 10.1002/gcc.22228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 11/03/2014] [Indexed: 01/04/2023] Open
Abstract
Gene amplification is relatively common in tumors. In certain subtypes of sarcoma, it often occurs in the form of ring and/or giant rod-shaped marker (RGM) chromosomes whose mitotic stability is frequently rescued by ectopic novel centromeres (neocentromeres). Little is known about the origin and structure of these RGM chromosomes, including how they arise, their internal organization, and which sequences underlie the neocentromeres. To address these questions, 42 sarcomas with RGM chromosomes were investigated to detect regions prone to double strand breaks and possible functional or structural constraints driving the amplification process. We found nine breakpoint cluster regions potentially involved in the genesis of RGM chromosomes, which turned out to be significantly enriched in poly-pyrimidine traits. Some of the clusters were located close to genes already known to be relevant for sarcomas, thus indicating a potential functional constraint, while others mapped to transcriptionally inactive chromatin domains enriched in heterochromatic sites. Of note, five neocentromeres were identified after analyzing 13 of the cases by fluorescent in situ hybridization. ChIP-on-chip analysis with antibodies against the centromeric protein CENP-A showed that they were a patchwork of small genomic segments derived from different chromosomes, likely joint to form a contiguous sequence during the amplification process.
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Affiliation(s)
- Gemma Macchia
- Department of Biology, University of Bari, Bari, Italy; Department of Clinical Genetics, University and Regional Laboratories, Lund University, Lund, Sweden
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137
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Poddighe PJ, Wessels H, Merle P, Westers M, Bhola S, Loonen A, Zweegman S, Ossenkoppele GJ, Wondergem MJ. Genomic amplification of MYC as double minutes in a patient with APL-like leukemia. Mol Cytogenet 2014; 7:67. [PMID: 25392715 PMCID: PMC4228273 DOI: 10.1186/s13039-014-0067-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 09/27/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML) characterized by a PML-RARA fusion due to a translocation t(15;17). Its sensitivity to treatment with all-trans retinoic acid (ATRA), which causes differentiation of the abnormal promyelocytes, combined with anthracycline based chemotherapy makes it the best curable subtype of acute myeloid leukemia. A rapid and accurate diagnosis is needed in the first place to prevent (more) bleeding problems. Here we present a patient with a leukemia with an APL-like morphology but no detectable PML-RARA fusion, as demonstrated by RT-PCR and cytogenetic analysis. RESULTS Unexpectedly, karyotyping revealed numerous double minutes (dmins). Fluorescence in situ hybridization (FISH) with DNA probes specific for the MYC-region showed the presence of multiple MYC amplicons. SNP-array analysis uncovered amplification of the 8q24.13-q24.21 region, including the MYC-gene, flanked by deletions in 8q24.13 and 8q24.21-q24.22, and a homozygous deletion in 9p21.3, flanked by heterozygous deletions in the same chromosome region. CONCLUSIONS The diagnosis was revised to AML, not otherwise specified (AML, NOS) and therefore therapy with ATRA was discontinued.
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Affiliation(s)
- Pino J Poddighe
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, PK 0X011, Amsterdam, 1081 HV The Netherlands
| | - Hans Wessels
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, PK 0X011, Amsterdam, 1081 HV The Netherlands
| | - Pauline Merle
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Marisa Westers
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Shama Bhola
- Department of Clinical Genetics, VU University Medical Center, De Boelelaan 1117, PK 0X011, Amsterdam, 1081 HV The Netherlands
| | - Anne Loonen
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Sonja Zweegman
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Gert J Ossenkoppele
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Marielle J Wondergem
- Department of Haematology, VU University Medical Center, Amsterdam, The Netherlands
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138
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L'Abbate A, Macchia G, D'Addabbo P, Lonoce A, Tolomeo D, Trombetta D, Kok K, Bartenhagen C, Whelan CW, Palumbo O, Severgnini M, Cifola I, Dugas M, Carella M, De Bellis G, Rocchi M, Carbone L, Storlazzi CT. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res 2014; 42:9131-45. [PMID: 25034695 PMCID: PMC4132716 DOI: 10.1093/nar/gku590] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The mechanism for generating double minutes chromosomes (dmin) and homogeneously staining regions (hsr) in cancer is still poorly understood. Through an integrated approach combining next-generation sequencing, single nucleotide polymorphism array, fluorescent in situ hybridization and polymerase chain reaction-based techniques, we inferred the fine structure of MYC-containing dmin/hsr amplicons harboring sequences from several different chromosomes in seven tumor cell lines, and characterized an unprecedented number of hsr insertion sites. Local chromosome shattering involving a single-step catastrophic event (chromothripsis) was recently proposed to explain clustered chromosomal rearrangements and genomic amplifications in cancer. Our bioinformatics analyses based on the listed criteria to define chromothripsis led us to exclude it as the driving force underlying amplicon genesis in our samples. Instead, the finding of coexisting heterogeneous amplicons, differing in their complexity and chromosome content, in cell lines derived from the same tumor indicated the occurrence of a multi-step evolutionary process in the genesis of dmin/hsr. Our integrated approach allowed us to gather a complete view of the complex chromosome rearrangements occurring within MYC amplicons, suggesting that more than one model may be invoked to explain the origin of dmin/hsr in cancer. Finally, we identified PVT1 as a target of fusion events, confirming its role as breakpoint hotspot in MYC amplification.
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Affiliation(s)
| | - Gemma Macchia
- Department of Biology, University of Bari, Bari, Italy
| | | | - Angelo Lonoce
- Department of Biology, University of Bari, Bari, Italy
| | - Doron Tolomeo
- Department of Biology, University of Bari, Bari, Italy
| | - Domenico Trombetta
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Klaas Kok
- Department of Genetics, University of Groningen, Groningen, The Netherlands
| | | | | | - Orazio Palumbo
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Marco Severgnini
- Institute for Biomedical Technologies, National Research Council, Milan, Italy
| | - Ingrid Cifola
- Institute for Biomedical Technologies, National Research Council, Milan, Italy
| | - Martin Dugas
- Institute of Medical Informatics, University of Münster, Münster, Germany
| | - Massimo Carella
- Medical Genetics Unit, IRCCS Casa Sollievo della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Gianluca De Bellis
- Institute for Biomedical Technologies, National Research Council, Milan, Italy
| | | | - Lucia Carbone
- National Primate Research Center, Beaverton, Oregon, USA
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139
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Chen JR, Hsieh TY, Chen HY, Yeh KY, Chen KS, ChangChien YC, Pintye M, Chang LC, Hwang CC, Chien HP, Hsu YC. Absence of estrogen receptor alpha (ESR1) gene amplification in a series of breast cancers in Taiwan. Virchows Arch 2014; 464:689-99. [PMID: 24756215 DOI: 10.1007/s00428-014-1576-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 03/18/2014] [Accepted: 03/21/2014] [Indexed: 11/28/2022]
Abstract
Immunohistochemical expression of ERα, encoded by the ESR1 (estrogen receptor 1) gene located at 6q25.1, is the most important determinant of responsiveness to endocrine therapy in breast cancer. The prevalence and significance of ESR1 amplification in breast cancer remain controversial. We set out to assess ESR1 status and its relevance in breast cancer in Taiwan. We tested tissue samples from 311 invasive carcinomas in a tissue microarray for ESR1 status by fluorescent in situ hybridization (FISH) and chromogenic in situ hybridization (CISH). In order to examine its association with ERα and ESR1 status, HER2 status was determined by FISH. Of the carcinomas, 58.8 % (183/311) was ERα positive. None of the carcinomas showed amplification of ESR1 by either method, whereas 24.1 % (75/311) of the carcinomas harbored HER2 amplification. Of the carcinomas, 9.6 % (26/301) showed ESR1 gain (1.3 ≤ ratio ESR1/chromosome 6 < 2) by FISH and 10 % (24/299) by CISH. FISH and CISH results showed a good correlation (κ-coefficient = 0.786). ESR1 gain by FISH and CISH was significantly associated with high-grade (P = 0.0294 and 0.0417, respectively) but not with ERα expression, HER2 status, or overall survival. ERα positivity was significantly associated with better overall survival (P = 0.039). HER2 amplification was significantly related with poor overall survival (P = 0.002). Our data confirm that in breast cancer, HER2 amplification is a frequent genetic aberration and a negative prognostic factor, and show that ESR1 amplification is not a key genetic abnormality in the tumorigenesis of breast cancer in Taiwan.
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Affiliation(s)
- Jim-Ray Chen
- Department of Pathology, Keelung Chang Gung Memorial Hospital, 222 Maijin Road, Keelung, 204, Taiwan,
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140
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Beltran H. The N-myc Oncogene: Maximizing its Targets, Regulation, and Therapeutic Potential. Mol Cancer Res 2014; 12:815-22. [PMID: 24589438 DOI: 10.1158/1541-7786.mcr-13-0536] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
N-myc (MYCN), a member of the Myc family of basic-helix-loop-helix-zipper (bHLHZ) transcription factors, is a central regulator of many vital cellular processes. As such, N-myc is well recognized for its classic oncogenic activity and association with human neuroblastoma. Amplification and overexpression of N-myc has been described in other tumor types, particularly those of neural origin and neuroendocrine tumors. This review outlines N-myc's contribution to normal development and oncogenic progression. In addition, it highlights relevant transcriptional targets and mechanisms of regulation. Finally, the clinical implications of N-Myc as a biomarker and potential as a target using novel therapeutic approaches are discussed.
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Affiliation(s)
- Himisha Beltran
- Author's Affiliation: Weill Cornell Medical College, New York, New York
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141
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Zheng S, Verhaak RGW. Intragenic breakpoint: a marker of genome instability in glioblastoma. Cell Cycle 2013; 12:3705-6. [PMID: 24145229 PMCID: PMC3905055 DOI: 10.4161/cc.26874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Siyuan Zheng
- Department of Bioinformatics and Computational Biology; The University of Texas MD Anderson Cancer Center; Houston TX USA
| | - Roel G W Verhaak
- Department of Bioinformatics and Computational Biology; The University of Texas MD Anderson Cancer Center; Houston TX USA; Department of Genomic Medicine; The University of Texas MD Anderson Cancer Center; Houston TX USA
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142
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Zhang CZ, Leibowitz ML, Pellman D. Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements. Genes Dev 2013; 27:2513-30. [PMID: 24298051 PMCID: PMC3861665 DOI: 10.1101/gad.229559.113] [Citation(s) in RCA: 177] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recent genome sequencing studies have identified several classes of complex genomic rearrangements that appear to be derived from a single catastrophic event. These discoveries identify ways that genomes can be altered in single large jumps rather than by many incremental steps. Here we compare and contrast these phenomena and examine the evidence that they arise "all at once." We consider the impact of massive chromosomal change for the development of diseases such as cancer and for evolution more generally. Finally, we summarize current models for underlying mechanisms and discuss strategies for testing these models.
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Affiliation(s)
- Cheng-Zhong Zhang
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
| | - Mitchell L. Leibowitz
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - David Pellman
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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143
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Lipska BS, Koczkowska M, Wierzba J, Ploszynska A, Iliszko M, Izycka-Swieszewska E, Adamkiewicz-Drozynska E, Limon J. On the significance of germline cytogenetic rearrangements at MYCN locus in neuroblastoma. Mol Cytogenet 2013; 6:43. [PMID: 24131700 PMCID: PMC3819649 DOI: 10.1186/1755-8166-6-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 09/20/2013] [Indexed: 01/11/2023] Open
Abstract
Background MYCN oncogene amplification is the most important prognostic factor in neuroblastoma. 25% neuroblastoma tumors have somatic amplifications at this locus but little is known about its constitutional aberrations and their potential role in carcinogenesis. Here, we have performed an array-CGH and qPCR characterization of two patients with constitutional partial 2p trisomy including MYCN genomic region. Results One of the patients had congenital neuroblastoma and showed presence of minute areas of gains and losses within the common fragile site FRA2C at 2p24 encompassing MYCN. The link between 2p24 germline rearrangements and neuroblastoma development was reassessed by reviewing similar cases in the literature. Conclusions It appears that constitutional rearrangements involving chromosome 2p24 may play role in NB development.
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Affiliation(s)
- Beata S Lipska
- Department of Biology and Genetics, Medical University of Gdansk, Debinki 1str, 80211 Gdansk, Poland.
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144
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Nord KH, Macchia G, Tayebwa J, Nilsson J, Vult von Steyern F, Brosjö O, Mandahl N, Mertens F. Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas. Hum Mol Genet 2013; 23:878-88. [PMID: 24070870 DOI: 10.1093/hmg/ddt479] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Gene amplification is a common phenomenon in malignant neoplasms of all types. One mechanism behind increased gene copy number is the formation of ring chromosomes. Such structures are mitotically unstable and during tumor progression they accumulate material from many different parts of the genome. Hence, their content varies considerably between and within tumors. Partly due to this extensive variation, the genetic content of many ring-containing tumors remains poorly characterized. Ring chromosomes are particularly prevalent in specific subtypes of sarcoma. Here, we have combined fluorescence in situ hybridization (FISH), global genomic copy number and gene expression data on ring-containing soft tissue sarcomas and show that they harbor two fundamentally different types of ring chromosome: MDM2-positive and MDM2-negative rings. While the former are often found in an otherwise normal chromosome complement, the latter seem to arise in the context of general chromosomal instability. In line with this, sarcomas with MDM2-negative rings commonly show complete loss of either CDKN2A or RB1 -both known to be important for genome integrity. Sarcomas with MDM2-positive rings instead show co-amplification of a variety of potential driver oncogenes. More than 100 different genes were found to be involved, many of which are known to induce cell growth, promote proliferation or inhibit apoptosis. Several of the amplified and overexpressed genes constitute potential drug targets.
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Affiliation(s)
- Karolin H Nord
- Department of Clinical Genetics, University and Regional Laboratories, Skåne University Hospital, Lund University, 221 84 Lund, Sweden
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145
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Peng M, Bakker JL, Dicioccio RA, Gille JJP, Zhao H, Odunsi K, Sucheston L, Jaafar L, Mivechi NF, Waisfisz Q, Ko L. Inactivating Mutations in GT198 in Familial and Early-Onset Breast and Ovarian Cancers. Genes Cancer 2013; 4:15-25. [PMID: 23946868 DOI: 10.1177/1947601913486344] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 03/16/2013] [Indexed: 01/03/2023] Open
Abstract
The human GT198 gene (gene symbol PSMC3IP) is located at chromosome 17q21, 470 kb proximal to BRCA1, a locus previously linked to breast and ovarian cancer predisposition. Its protein product (also known as TBPIP and Hop2) has been shown to regulate steroid hormone receptor-mediated gene activation and to stimulate homologous recombination in DNA repair. Here, we screened germline mutations in GT198 in familial and early-onset breast and ovarian cancer patients. We have identified 8 germline variants in a total of 212 index patients including reoccurring nonsense mutation c.310C>T (p.Q104X) and 5' UTR mutation c.-37A>T, each found in 2 unrelated families. Most identified index patients from cancer families had early onsets with a median age of 35 years. c.310C>T was absent in a total of 564 control individuals analyzed. GT198 gene amplification with an imbalanced mutant copy gain was identified in the blood DNA of one of the patients carrying c.310C>T. When tested, this truncating mutation abolished DNA damage-induced Rad51 foci formation. In addition, we have identified 15 somatic mutations in 2 tumors from 1 patient carrying germline mutation c.-37A>T. The presence of a somatic mutation on the wild-type allele showed that GT198 was biallelically mutated in the tumor. The somatic mutations identified near a splicing junction site caused defective alternative splicing and truncated the open reading frame. Therefore, distinct mutations may cause a similar consequence by truncating the full-length protein and inducing a loss of the wild type. Our study provides the first evidence of the presence of inactivating mutations in GT198 in familial and early-onset breast and ovarian cancer patients. Mutations in GT198, a gene regulating DNA repair, potentially contribute to an increased risk in familial breast and ovarian cancers.
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Affiliation(s)
- Min Peng
- Cancer Center, Institute of Molecular Medicine and Genetics, Medical College of Georgia, Georgia Regents University, Augusta, GA, USA
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146
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Sanborn JZ, Salama SR, Grifford M, Brennan CW, Mikkelsen T, Jhanwar S, Katzman S, Chin L, Haussler D. Double minute chromosomes in glioblastoma multiforme are revealed by precise reconstruction of oncogenic amplicons. Cancer Res 2013; 73:6036-45. [PMID: 23940299 DOI: 10.1158/0008-5472.can-13-0186] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA sequencing offers a powerful tool in oncology based on the precise definition of structural rearrangements and copy number in tumor genomes. Here, we describe the development of methods to compute copy number and detect structural variants to locally reconstruct highly rearranged regions of the tumor genome with high precision from standard, short-read, paired-end sequencing datasets. We find that circular assemblies are the most parsimonious explanation for a set of highly amplified tumor regions in a subset of glioblastoma multiforme samples sequenced by The Cancer Genome Atlas (TCGA) consortium, revealing evidence for double minute chromosomes in these tumors. Further, we find that some samples harbor multiple circular amplicons and, in some cases, further rearrangements occurred after the initial amplicon-generating event. Fluorescence in situ hybridization analysis offered an initial confirmation of the presence of double minute chromosomes. Gene content in these assemblies helps identify likely driver oncogenes for these amplicons. RNA-seq data available for one double minute chromosome offered additional support for our local tumor genome assemblies, and identified the birth of a novel exon made possible through rearranged sequences present in the double minute chromosomes. Our method was also useful for analysis of a larger set of glioblastoma multiforme tumors for which exome sequencing data are available, finding evidence for oncogenic double minute chromosomes in more than 20% of clinical specimens examined, a frequency consistent with previous estimates.
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Affiliation(s)
- J Zachary Sanborn
- Authors' Affiliations: Five3 Genomics, LLC; Center for Biomolecular Science and Engineering, University of California; Howard Hughes Medical Institute, Santa Cruz, California; Human Oncology & Pathogenesis Program and Department of Neurosurgery; Cytogenetics Laboratory, Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York; Departments of Neurology & Neurosurgery, Henry Ford Hospital, Detroit, Michigan; and Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
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147
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Yang L, Luquette LJ, Gehlenborg N, Xi R, Haseley PS, Hsieh CH, Zhang C, Ren X, Protopopov A, Chin L, Kucherlapati R, Lee C, Park PJ. Diverse mechanisms of somatic structural variations in human cancer genomes. Cell 2013; 153:919-29. [PMID: 23663786 DOI: 10.1016/j.cell.2013.04.010] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Revised: 02/28/2013] [Accepted: 03/29/2013] [Indexed: 01/09/2023]
Abstract
Identification of somatic rearrangements in cancer genomes has accelerated through analysis of high-throughput sequencing data. However, characterization of complex structural alterations and their underlying mechanisms remains inadequate. Here, applying an algorithm to predict structural variations from short reads, we report a comprehensive catalog of somatic structural variations and the mechanisms generating them, using high-coverage whole-genome sequencing data from 140 patients across ten tumor types. We characterize the relative contributions of different types of rearrangements and their mutational mechanisms, find that ~20% of the somatic deletions are complex deletions formed by replication errors, and describe the differences between the mutational mechanisms in somatic and germline alterations. Importantly, we provide detailed reconstructions of the events responsible for loss of CDKN2A/B and gain of EGFR in glioblastoma, revealing that these alterations can result from multiple mechanisms even in a single genome and that both DNA double-strand breaks and replication errors drive somatic rearrangements.
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Affiliation(s)
- Lixing Yang
- Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
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148
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Gibaud A, Vogt N, Brison O, Debatisse M, Malfoy B. Characterization at nucleotide resolution of the homogeneously staining region sites of insertion in two cancer cell lines. Nucleic Acids Res 2013; 41:8210-9. [PMID: 23821669 PMCID: PMC3783161 DOI: 10.1093/nar/gkt566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The mechanisms of formation of intrachromosomal amplifications in tumours are still poorly understood. By using quantitative polymerase chain reaction, DNA sequencing, chromosome walking, in situ hybridization on metaphase chromosomes and whole-genome analysis, we studied two cancer cell lines containing an MYC oncogene amplification with acquired copies ectopically inserted in rearranged chromosomes 17. These intrachromosomal amplifications result from the integration of extrachromosomal DNA molecules. Replication stress could explain the formation of the double-strand breaks involved in their insertion and in the rearrangements of the targeted chromosomes. The sequences of the junctions indicate that homologous recombination was not involved in their formation and support a non-homologous end-joining process. The replication stress-inducible common fragile sites present in the amplicons may have driven the intrachromosomal amplifications. Mechanisms associating break-fusion-bridge cycles and/or chromosome fragmentation may have led to the formation of the uncovered complex structures. To our knowledge, this is the first characterization of an intrachromosomal amplification site at nucleotide resolution.
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Affiliation(s)
- Anne Gibaud
- Institut Curie, Centre de Recherche, CNRS, UMR3244 and UPMC, 26 Rue d'Ulm, F-75248 Paris, France
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149
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Zheng S, Fu J, Vegesna R, Mao Y, Heathcock LE, Torres-Garcia W, Ezhilarasan R, Wang S, McKenna A, Chin L, Brennan CW, Yung WKA, Weinstein JN, Aldape KD, Sulman EP, Chen K, Koul D, Verhaak RGW. A survey of intragenic breakpoints in glioblastoma identifies a distinct subset associated with poor survival. Genes Dev 2013; 27:1462-72. [PMID: 23796897 DOI: 10.1101/gad.213686.113] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
With the advent of high-throughput sequencing technologies, much progress has been made in the identification of somatic structural rearrangements in cancer genomes. However, characterization of the complex alterations and their associated mechanisms remains inadequate. Here, we report a comprehensive analysis of whole-genome sequencing and DNA copy number data sets from The Cancer Genome Atlas to relate chromosomal alterations to imbalances in DNA dosage and describe the landscape of intragenic breakpoints in glioblastoma multiforme (GBM). Gene length, guanine-cytosine (GC) content, and local presence of a copy number alteration were closely associated with breakpoint susceptibility. A dense pattern of repeated focal amplifications involving the murine double minute 2 (MDM2)/cyclin-dependent kinase 4 (CDK4) oncogenes and associated with poor survival was identified in 5% of GBMs. Gene fusions and rearrangements were detected concomitant within the breakpoint-enriched region. At the gene level, we noted recurrent breakpoints in genes such as apoptosis regulator FAF1. Structural alterations of the FAF1 gene disrupted expression and led to protein depletion. Restoration of the FAF1 protein in glioma cell lines significantly increased the FAS-mediated apoptosis response. Our study uncovered a previously underappreciated genomic mechanism of gene deregulation that can confer growth advantages on tumor cells and may generate cancer-specific vulnerabilities in subsets of GBM.
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Affiliation(s)
- Siyuan Zheng
- Department of Bioinformatics and Computational Biology
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150
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Coleman AE, McNeil N, Kovalchuck AL, Wangsa D, Ried T, Wang H. Cellular exposure to muscle relaxants and propofol could lead to genomic instability in vitro. J Biomed Res 2013; 26:117-24. [PMID: 23554740 PMCID: PMC3597328 DOI: 10.1016/s1674-8301(12)60021-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2011] [Revised: 01/05/2012] [Accepted: 01/28/2012] [Indexed: 11/25/2022] Open
Abstract
Anesthesia is widely used in several medical settings and accepted as safe. However, there is some evidence that anesthetic agents can induce genomic changes leading to neural degeneration or apoptosis. Although chromosomal changes have not been observed in vivo, this is most likely due to DNA repair mechanisms, apoptosis, or cellular senescence. Potential chromosomal alterations after exposure to common anesthetic agents may be relevant in patients with genomic instability syndromes or with aggressive treatment of malignancies. In this study, the P388 murine B cells were cultured in vitro, and spectral karyotyping (SKY) was utilized to uncover genome-wide changes. Clinically relevant doses of cisatracurium and propofol increased structural and numerical chromosomal instability. These results may be relevant in patients with underlying chromosomal instability syndromes or concurrently being exposed to chemotherapeutic agents. Future studies may include utilization of stimulated peripheral blood lymphocytes to further confirm the significance of these results.
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Affiliation(s)
- Allen Edward Coleman
- Department of Anesthesiology, Wayne State University, Detroit Medical Center, Detroit, Michigan 48201, USA
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