1
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Murata MM, Igari F, Urbanowicz R, Mouakkad L, Kim S, Chen Z, DiVizio D, Posadas EM, Giuliano AE, Tanaka H. A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.25.564058. [PMID: 37961589 PMCID: PMC10634834 DOI: 10.1101/2023.10.25.564058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Plasma cell-free DNA (cfDNA) is a promising source of gene mutations for cancer detection by liquid biopsy. However, no current tests interrogate chromosomal structural variants (SVs) genome-wide. Here, we report a simple molecular and sequencing workflow called Genome-wide Analysis of Palindrome Formation (GAPF-seq) to probe DNA palindromes, a type of SV that often demarcates gene amplification. With low-throughput next-generation sequencing and automated machine learning, tumor DNA showed skewed chromosomal distributions of high-coverage 1-kb bins (HCBs), which differentiated 39 breast tumors from matched normal DNA with an average Area Under the Curve (AUC) of 0.9819. A proof-of-concept liquid biopsy study using cfDNA from prostate cancer patients and healthy individuals yielded an average AUC of 0.965. HCBs on the X chromosome emerged as a determinant feature and were associated with androgen receptor gene amplification. As a novel agnostic liquid biopsy approach, GAPF-seq could fill the technological gap offering unique cancer-specific SV profiles.
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2
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Tanaka H, Murata M, Igari F, Urbanowicz R, Mouakkad L, Kim S, Chen Z, Di Vizio D, Posadas E, Giuliano A. A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA. RESEARCH SQUARE 2024:rs.3.rs-3492157. [PMID: 38260372 PMCID: PMC10802711 DOI: 10.21203/rs.3.rs-3492157/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Interrogating plasma cell-free DNA (cfDNA) to detect cancer offers promise; however, no current tests scan structural variants (SVs) throughout the genome. Here, we report a simple molecular workflow to enrich a tumorigenic SV (DNA palindromes/fold-back inversions) that often demarcates genomic amplification and its feasibility for cancer detection by combining low-throughput next-generation sequencing with automated machine learning (Genome-wide Analysis of Palindrome Formation, GAPF-seq). Tumor DNA signal manifested as skewed chromosomal distributions of high-coverage 1-kb bins (HCBs), differentiating 39 matched breast tumor DNA from normal DNA with an average AUC of 0.9819. In a proof-of-concept liquid biopsy study, cfDNA from 0.5 mL plasma from prostate cancer patients was sufficient for binary classification against matched buffy coat DNA with an average AUC of 0.965. HCBs on the X chromosome emerged as a determinant feature and were associated with AR amplification. GAPF-seq could generate unique cancer-specific SV profiles in an agnostic liquid biopsy setting.
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3
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Zhang X, Kschischo M. Profiling Numerical and Structural Chromosomal Instability in Different Cancer Types. Methods Mol Biol 2024; 2825:345-360. [PMID: 38913320 DOI: 10.1007/978-1-0716-3946-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Many cancers display whole chromosome instability (W-CIN) and structural chromosomal instability (S-CIN), referring to increased rates of acquiring numerically and structurally abnormal chromosome changes. This protocol provides detailed steps to analyze the W-CIN and S-CIN across cancer types, intending to leverage large-scale bulk sequencing and SNP array data complemented with the computational models to gain a better understanding of W-CIN and S-CIN.
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Affiliation(s)
- Xiaoxiao Zhang
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Maik Kschischo
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany.
- Institute for Computer Science, University of Koblenz, Koblenz, Germany.
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4
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Murata MM, Giuliano AE, Tanaka H. Genome-Wide Analysis of Palindrome Formation with Next-Generation Sequencing (GAPF-Seq) and a Bioinformatics Pipeline for Assessing De Novo Palindromes in Cancer Genomes. Methods Mol Biol 2023; 2660:13-22. [PMID: 37191787 DOI: 10.1007/978-1-0716-3163-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
DNA palindromes are a type of chromosomal aberration that appears frequently during tumorigenesis. They are characterized by sequences of nucleotides that are identical to their reverse complements and often arise due to illegitimate repair of DNA double-strand breaks, fusion of telomeres, or stalled replication forks, all of which are common adverse early events in cancer. Here, we describe the protocol for enriching palindromes from genomic DNA sources with low-input DNA amounts and detail a bioinformatics tool for assessing the enrichment and location of de novo palindrome formation from low-coverage whole-genome sequencing data.
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Affiliation(s)
- Michael M Murata
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
- Department of Surgery, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
- Departments of Surgery and Biomedical Sciences, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA, USA.
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5
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Svetec Miklenić M, Svetec IK. Palindromes in DNA-A Risk for Genome Stability and Implications in Cancer. Int J Mol Sci 2021; 22:2840. [PMID: 33799581 PMCID: PMC7999016 DOI: 10.3390/ijms22062840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
A palindrome in DNA consists of two closely spaced or adjacent inverted repeats. Certain palindromes have important biological functions as parts of various cis-acting elements and protein binding sites. However, many palindromes are known as fragile sites in the genome, sites prone to chromosome breakage which can lead to various genetic rearrangements or even cell death. The ability of certain palindromes to initiate genetic recombination lies in their ability to form secondary structures in DNA which can cause replication stalling and double-strand breaks. Given their recombinogenic nature, it is not surprising that palindromes in the human genome are involved in genetic rearrangements in cancer cells as well as other known recurrent translocations and deletions associated with certain syndromes in humans. Here, we bring an overview of current understanding and knowledge on molecular mechanisms of palindrome recombinogenicity and discuss possible implications of DNA palindromes in carcinogenesis. Furthermore, we overview the data on known palindromic sequences in the human genome and efforts to estimate their number and distribution, as well as underlying mechanisms of genetic rearrangements specific palindromic sequences cause.
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Affiliation(s)
| | - Ivan Krešimir Svetec
- Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia;
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6
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Eisfeldt J, Pettersson M, Petri A, Nilsson D, Feuk L, Lindstrand A. Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier. Hum Genet 2020; 140:775-790. [PMID: 33315133 PMCID: PMC8052244 DOI: 10.1007/s00439-020-02242-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Chromoanagenesis is a genomic event responsible for the formation of complex structural chromosomal rearrangements (CCRs). Germline chromoanagenesis is rare and the majority of reported cases are associated with an affected phenotype. Here, we report a healthy female carrying two de novo CCRs involving chromosomes 4, 19, 21 and X and chromosomes 7 and 11, respectively, with a total of 137 breakpoint junctions (BPJs). We characterized the CCRs using a hybrid-sequencing approach, combining short-read sequencing, nanopore sequencing, and optical mapping. The results were validated using multiple cytogenetic methods, including fluorescence in situ hybridization, spectral karyotyping, and Sanger sequencing. We identified 137 BPJs, which to our knowledge is the highest number of reported breakpoint junctions in germline chromoanagenesis. We also performed a statistical assessment of the positioning of the breakpoints, revealing a significant enrichment of BPJ-affecting genes (96 intragenic BPJs, 26 genes, p < 0.0001), indicating that the CCRs formed during active transcription of these genes. In addition, we find that the DNA fragments are unevenly and non-randomly distributed across the derivative chromosomes indicating a multistep process of scattering and re-joining of DNA fragments. In summary, we report a new maximum number of BPJs (137) in germline chromoanagenesis. We also show that a hybrid sequencing approach is necessary for the correct characterization of complex CCRs. Through in-depth statistical assessment, it was found that the CCRs most likely was formed through an event resembling chromoplexy—a catastrophic event caused by erroneous transcription factor binding.
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Affiliation(s)
- Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Maria Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Petri
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden.,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet Science Park, Solna, Sweden
| | - Lars Feuk
- Science for Life Laboratory Uppsala, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Karolinska University Hospital Solna, 171 76, Stockholm, Sweden. .,Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden.
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7
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Tanaka H, Watanabe T. Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers. Trends Cancer 2020; 6:462-477. [PMID: 32383436 PMCID: PMC7285850 DOI: 10.1016/j.trecan.2020.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Focal copy-number increases (genomic amplification) pinpoint oncogenic driver genes and therapeutic targets in cancer genomes. With the advent of genomic technologies, recurrent genomic amplification has been mapped throughout the genome. Recurrent amplification could be solely due to positive selection for the tumor-promoting effects of amplified gene products. Alternatively, recurrence could result from the susceptibility of the loci to amplification. Distinguishing between these possibilities requires a full understanding of the amplification mechanisms. Two mechanisms, the formation of double minute (DM) chromosomes and breakage-fusion-bridge (BFB) cycles, have been repeatedly linked to genomic amplification, and the impact of both mechanisms has been confirmed in cancer genomics data. We review the details of these mechanisms and discuss the mechanisms underlying recurrence.
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Affiliation(s)
- Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA.
| | - Takaaki Watanabe
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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8
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Asoshina M, Myo G, Tada N, Tajino K, Shimizu N. Targeted amplification of a sequence of interest in artificial chromosome in mammalian cells. Nucleic Acids Res 2019; 47:5998-6006. [PMID: 31062017 PMCID: PMC6582328 DOI: 10.1093/nar/gkz343] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/08/2019] [Accepted: 05/01/2019] [Indexed: 12/14/2022] Open
Abstract
A plasmid with a replication initiation region (IR) and a matrix attachment region (MAR) initiates gene amplification in mammalian cells at a random chromosomal location. A mouse artificial chromosome (MAC) vector can stably carry a large genomic region. In this study we combined these two technologies with the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease (Cas)9 strategy to achieve targeted amplification of a sequence of interest. We previously showed that the IR/MAR plasmid was amplified up to the extrachromosomal tandem repeat; here we demonstrate that cleavage of these tandem plasmids and MAC by Cas9 facilitates homologous recombination between them. The plasmid array on the MAC could be further extended to form a ladder structure with high gene expression by a breakage–fusion–bridge cycle involving breakage at mouse major satellites. Amplification of genes on the MAC has the advantage that the MAC can be transferred between cells. We visualized the MAC in live cells by amplifying the lactose operator array on the MAC in cells expressing lactose repressor-green fluorescent protein fusion protein. This targeted amplification strategy is in theory be applicable to any sequence at any chromosomal site, and provides a novel tool for animal cell technology.
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Affiliation(s)
- Manami Asoshina
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Genki Myo
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
| | - Natsuko Tada
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Koji Tajino
- Chromocenter Inc., Yonago, Tottori 683-0823, Japan
| | - Noriaki Shimizu
- Graduate School of Biosphere Science, Hiroshima University, Higashi-hiroshima, Hiroshima 739-8521, Japan
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9
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Mechanisms of Genomic Instability in Breast Cancer. Trends Mol Med 2019; 25:595-611. [DOI: 10.1016/j.molmed.2019.04.004] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/22/2022]
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10
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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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11
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Independent Mechanisms Lead to Genomic Instability in Hodgkin Lymphoma: Microsatellite or Chromosomal Instability †. Cancers (Basel) 2018; 10:cancers10070233. [PMID: 30011886 PMCID: PMC6071189 DOI: 10.3390/cancers10070233] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Revised: 06/29/2018] [Accepted: 07/03/2018] [Indexed: 12/19/2022] Open
Abstract
Background: Microsatellite and chromosomal instability have been investigated in Hodgkin lymphoma (HL). Materials and Methods: We studied seven HL cell lines (five Nodular Sclerosis (NS) and two Mixed Cellularity (MC)) and patient peripheral blood lymphocytes (100 NS-HL and 23 MC-HL). Microsatellite instability (MSI) was assessed by PCR. Chromosomal instability and telomere dysfunction were investigated by FISH. DNA repair mechanisms were studied by transcriptomic and molecular approaches. Results: In the cell lines, we observed high MSI in L428 (4/5), KMH2, and HDLM2 (3/5), low MSI in L540, L591, and SUP-HD1, and none in L1236. NS-HL cell lines showed telomere shortening, associated with alterations of nuclear shape. Small cells were characterized by telomere loss and deletion, leading to chromosomal fusion, large nucleoplasmic bridges, and breakage/fusion/bridge (B/F/B) cycles, leading to chromosomal instability. The MC-HL cell lines showed substantial heterogeneity of telomere length. Intrachromosmal double strand breaks induced dicentric chromosome formation, high levels of micronucleus formation, and small nucleoplasmic bridges. B/F/B cycles induced complex chromosomal rearrangements. We observed a similar pattern in circulating lymphocytes of NS-HL and MC-HL patients. Transcriptome analysis confirmed the differences in the DNA repair pathways between the NS and MC cell lines. In addition, the NS-HL cell lines were radiosensitive and the MC-cell lines resistant to apoptosis after radiation exposure. Conclusions: In mononuclear NS-HL cells, loss of telomere integrity may present the first step in the ongoing process of chromosomal instability. Here, we identified, MSI as an additional mechanism for genomic instability in HL.
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12
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Watanabe T, Tanaka H, Horiuchi T. Complex repeat structure promotes hyper-amplification and amplicon evolution through rolling-circle replication. Nucleic Acids Res 2018; 46:5097-5108. [PMID: 29718479 PMCID: PMC6007334 DOI: 10.1093/nar/gky275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 04/04/2018] [Indexed: 11/30/2022] Open
Abstract
Inverted repeats (IRs) are abundant in genomes and frequently serve as substrates for chromosomal aberrations, including gene amplification. In the early stage of amplification, repeated cycles of chromosome breakage and rearrangement, called breakage-fusion-bridge (BFB), generate a large inverted structure, which evolves into highly-amplified, complex end products. However, it remains to be determined how IRs mediate chromosome rearrangements and promote subsequent hyper-amplification and amplicon evolutions. To dissect the complex processes, we constructed repetitive structures in a yeast chromosome and selected amplified cells using genetic markers with limited expression. The genomic architecture was associated with replication stress and produced extra-/intra-chromosomal amplification. Genetic analysis revealed structure-specific endonucleases, Mus81 and Rad27, and post-replication DNA repair protein, Rad18, suppress the amplification processes. Following BFB cycles, the intra-chromosomal products undergo intensive rearrangements, such as frequent inversions and deletions, indicative of rolling-circle replication. This study presents an integrated view linking BFB cycles to hyper-amplification driven by rolling-circle replication.
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Affiliation(s)
- Takaaki Watanabe
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA.,Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA.,Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Takashi Horiuchi
- Department of Molecular Life Science, Division of Basic Molecular Science and Molecular Medicine, School of Medicine, Tokai University, Isehara, Kanagawa, Japan.,National Institute for Basic Biology, Okazaki, Aichi, Japan
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13
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Marotta M, Onodera T, Johnson J, Budd GT, Watanabe T, Cui X, Giuliano AE, Niida A, Tanaka H. Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors. Sci Rep 2017; 7:41921. [PMID: 28211519 PMCID: PMC5314454 DOI: 10.1038/srep41921] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022] Open
Abstract
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors. We applied two genomic approaches to investigate amplification mechanisms: sequencing of DNA libraries enriched with tumor-derived palindromic DNA (Genome-wide Analysis of Palindrome Formation) and whole genome sequencing (WGS). We observed significant enrichment of palindromic DNA within amplified ERBB2 genomic segments. Palindromic DNA was particularly enriched at amplification peaks and at boundaries between amplified and normal copy-number regions. Thus, palindromic gene amplification shaped the amplified ERBB2 locus. The enrichment of palindromic DNA throughout the amplified segments leads us to propose that the ERBB2 locus is amplified through the mechanism that repeatedly generates palindromic DNA, such as Breakage-Fusion-Bridge cycles. The genomic architecture surrounding ERBB2 in the normal genome, such as segmental duplications, could promote the locus-specific mechanism.
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Affiliation(s)
- Michael Marotta
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA
| | - Taku Onodera
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jeffrey Johnson
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - G Thomas Budd
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Takaaki Watanabe
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA.,Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Atsushi Niida
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hisashi Tanaka
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA.,Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
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14
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Krøigård AB, Larsen MJ, Lænkholm AV, Knoop AS, Jensen JD, Bak M, Mollenhauer J, Kruse TA, Thomassen M. Clonal expansion and linear genome evolution through breast cancer progression from pre-invasive stages to asynchronous metastasis. Oncotarget 2016; 6:5634-49. [PMID: 25730902 PMCID: PMC4467391 DOI: 10.18632/oncotarget.3111] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 01/08/2015] [Indexed: 11/29/2022] Open
Abstract
Evolution of the breast cancer genome from pre-invasive stages to asynchronous metastasis is complex and mostly unexplored, but highly demanded as it may provide novel markers for and mechanistic insights in cancer progression. The increasing use of personalized therapy of breast cancer necessitates knowledge of the degree of genomic concordance between different steps of malignant progression as primary tumors often are used as surrogates of systemic disease. Based on exome sequencing we performed copy number profiling and point mutation detection on successive steps of breast cancer progression from one breast cancer patient, including two different regions of Ductal Carcinoma In Situ (DCIS), primary tumor and an asynchronous metastasis. We identify a remarkable landscape of somatic mutations, retained throughout breast cancer progression and with new mutational events emerging at each step. Our data, contrary to the proposed model of early dissemination of metastatic cells and parallel progression of primary tumors and metastases, provide evidence of linear progression of breast cancer with relatively late dissemination from the primary tumor. The genomic discordance between the different stages of tumor evolution in this patient emphasizes the importance of molecular profiling of metastatic tissue directing molecularly targeted therapy at recurrence.
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Affiliation(s)
- Anne Bruun Krøigård
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | - Martin Jakob Larsen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark
| | | | - Ann S Knoop
- Department of Oncology, Rigshospitalet, 2100 Copenhagen, Denmark
| | - Jeanette D Jensen
- Department of Oncology, Odense University Hospital, 5000 Odense C, Denmark
| | - Martin Bak
- Department of Pathology, Odense University Hospital, 5000 Odense C, Denmark
| | - Jan Mollenhauer
- Lundbeckfonden Center of Excellence NanoCAN, 5000 Odense C, Denmark.,Molecular Oncology Group, Institute of Molecular Medicine, University of Southern Denmark, 5000 Odense C, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark.,Lundbeckfonden Center of Excellence NanoCAN, 5000 Odense C, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark.,Human Genetics, Institute of Clinical Research, University of Southern Denmark, 5000 Odense C, Denmark.,Lundbeckfonden Center of Excellence NanoCAN, 5000 Odense C, Denmark
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15
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Deng SK, Yin Y, Petes TD, Symington LS. Mre11-Sae2 and RPA Collaborate to Prevent Palindromic Gene Amplification. Mol Cell 2016; 60:500-8. [PMID: 26545079 DOI: 10.1016/j.molcel.2015.09.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 08/20/2015] [Accepted: 09/28/2015] [Indexed: 12/17/2022]
Abstract
Foldback priming at DNA double-stranded breaks is one mechanism proposed to initiate palindromic gene amplification, a common feature of cancer cells. Here, we show that small (5-9 bp) inverted repeats drive the formation of large palindromic duplications, the major class of chromosomal rearrangements recovered from yeast cells lacking Sae2 or the Mre11 nuclease. RPA dysfunction increased the frequency of palindromic duplications in Sae2 or Mre11 nuclease-deficient cells by ∼ 1,000-fold, consistent with intra-strand annealing to create a hairpin-capped chromosome that is subsequently replicated to form a dicentric isochromosome. The palindromic duplications were frequently associated with duplication of a second chromosome region bounded by a repeated sequence and a telomere, suggesting the dicentric chromosome breaks and repairs by recombination between dispersed repeats to acquire a telomere. We propose secondary structures within single-stranded DNA are potent instigators of genome instability, and RPA and Mre11-Sae2 play important roles in preventing their formation and propagation, respectively.
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Affiliation(s)
- Sarah K Deng
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Yi Yin
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Thomas D Petes
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Medical Center, New York, NY 10032, USA.
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16
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Lopez V, Barinova N, Onishi M, Pobiega S, Pringle JR, Dubrana K, Marcand S. Cytokinesis breaks dicentric chromosomes preferentially at pericentromeric regions and telomere fusions. Genes Dev 2015; 29:322-36. [PMID: 25644606 PMCID: PMC4318148 DOI: 10.1101/gad.254664.114] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. Lopez et al. find that dicentrics without internal telomere sequences preferentially break at pericentromeric regions. In all cases, cleavage does not occur in anaphase but instead requires cytokinesis. Dicentrics cause the spindle pole bodies and centromeres to relocate to the bud neck during cytokinesis, explaining how cytokinesis can sever dicentrics near centromeres. Dicentric chromosomes are unstable products of erroneous DNA repair events that can lead to further genome rearrangements and extended gene copy number variations. During mitosis, they form anaphase bridges, resulting in chromosome breakage by an unknown mechanism. In budding yeast, dicentrics generated by telomere fusion break at the fusion, a process that restores the parental karyotype and protects cells from rare accidental telomere fusion. Here, we observed that dicentrics lacking telomere fusion preferentially break within a 25- to 30-kb-long region next to the centromeres. In all cases, dicentric breakage requires anaphase exit, ruling out stretching by the elongated mitotic spindle as the cause of breakage. Instead, breakage requires cytokinesis. In the presence of dicentrics, the cytokinetic septa pinch the nucleus, suggesting that dicentrics are severed after actomyosin ring contraction. At this time, centromeres and spindle pole bodies relocate to the bud neck, explaining how cytokinesis can sever dicentrics near centromeres.
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Affiliation(s)
- Virginia Lopez
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Natalja Barinova
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - Masayuki Onishi
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Sabrina Pobiega
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France
| | - John R Pringle
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karine Dubrana
- UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France; Laboratoire Instabilité Génétique et Organisation Nucléaire, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France
| | - Stéphane Marcand
- Laboratoire Télomères et Réparation du Chromosome, Service Instabilité Génétique Réparation et Recombinaison, Institut de Radiobiologie Moléculaire et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, 92265 Fontenay-aux-Roses, France; UMR967, Institut National de la Santé et de la Recherche Médicale, 92265 Fontenay-aux-Roses, France;
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17
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Kondratova A, Watanabe T, Marotta M, Cannon M, Segall AM, Serre D, Tanaka H. Replication fork integrity and intra-S phase checkpoint suppress gene amplification. Nucleic Acids Res 2015; 43:2678-90. [PMID: 25672394 PMCID: PMC4357702 DOI: 10.1093/nar/gkv084] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Gene amplification is a phenotype-causing form of chromosome instability and is initiated by DNA double-strand breaks (DSBs). Cells with mutant p53 lose G1/S checkpoint and are permissive to gene amplification. In this study we show that mammalian cells become proficient for spontaneous gene amplification when the function of the DSB repair protein complex MRN (Mre11/Rad50/Nbs1) is impaired. Cells with impaired MRN complex experienced severe replication stress and gained substrates for gene amplification during replication, as evidenced by the increase of replication-associated single-stranded breaks that were converted to DSBs most likely through replication fork reversal. Impaired MRN complex directly compromised ATM/ATR-mediated checkpoints and allowed cells to progress through cell cycle in the presence of DSBs. Such compromised intra-S phase checkpoints promoted gene amplification independently from mutant p53. Finally, cells adapted to endogenous replication stress by globally suppressing genes for DNA replication and cell cycle progression. Our results indicate that the MRN complex suppresses gene amplification by stabilizing replication forks and by securing DNA damage response to replication-associated DSBs.
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Affiliation(s)
- Anna Kondratova
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Takaaki Watanabe
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Michael Marotta
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Matthew Cannon
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Anca M Segall
- Department of Biology, San Diego State University, San Diego, CA 92182, USA
| | - David Serre
- Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA
| | - Hisashi Tanaka
- Department of Molecular Genetics, Cleveland Clinic Lerner Research Institute, Cleveland, OH, USA Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
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18
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How a replication origin and matrix attachment region accelerate gene amplification under replication stress in mammalian cells. PLoS One 2014; 9:e103439. [PMID: 25061979 PMCID: PMC4111587 DOI: 10.1371/journal.pone.0103439] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 07/02/2014] [Indexed: 11/19/2022] Open
Abstract
The gene amplification plays a critical role in the malignant transformation of mammalian cells. The most widespread method for amplifying a target gene in cell culture is the use of methotrexate (Mtx) treatment to amplify dihydrofolate reductase (Dhfr). Whereas, we found that a plasmid bearing both a mammalian origin of replication (initiation region; IR) and a matrix attachment region (MAR) was spontaneously amplified in mammalian cells. In this study, we attempted to uncover the underlying mechanism by which the IR/MAR sequence might accelerate Mtx induced Dhfr amplification. The plasmid containing the IR/MAR was extrachromosomally amplified, and then integrated at multiple chromosomal locations within individual cells, increasing the likelihood that the plasmid might be inserted into a chromosomal environment that permits high expression and further amplification. Efficient amplification of this plasmid alleviated the genotoxicity of Mtx. Clone-based cytogenetic and sequence analysis revealed that the plasmid was amplified in a chromosomal context by breakage-fusion-bridge cycles operating either at the plasmid repeat or at the flanking fragile site activated by Mtx. This mechanism explains how a circular molecule bearing IR/MAR sequences of chromosomal origin might be amplified under replication stress, and also provides insight into gene amplification in human cancer.
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