1
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Youk J, Kwon HW, Lim J, Kim E, Kim T, Kim R, Park S, Yi K, Nam CH, Jeon S, An Y, Choi J, Na H, Lee ES, Cho Y, Min DW, Kim H, Kang YR, Choi SH, Bae MJ, Lee CG, Kim JG, Kim YS, Yu T, Lee WC, Shin JY, Lee DS, Kim TY, Ku T, Kim SY, Lee JH, Koo BK, Lee H, Yi OV, Han EC, Chang JH, Kim KS, Son TG, Ju YS. Quantitative and qualitative mutational impact of ionizing radiation on normal cells. CELL GENOMICS 2024; 4:100499. [PMID: 38359788 PMCID: PMC10879144 DOI: 10.1016/j.xgen.2024.100499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 02/17/2024]
Abstract
The comprehensive genomic impact of ionizing radiation (IR), a carcinogen, on healthy somatic cells remains unclear. Using large-scale whole-genome sequencing (WGS) of clones expanded from irradiated murine and human single cells, we revealed that IR induces a characteristic spectrum of short insertions or deletions (indels) and structural variations (SVs), including balanced inversions, translocations, composite SVs (deletion-insertion, deletion-inversion, and deletion-translocation composites), and complex genomic rearrangements (CGRs), including chromoplexy, chromothripsis, and SV by breakage-fusion-bridge cycles. Our findings suggest that 1 Gy IR exposure causes an average of 2.33 mutational events per Gb genome, comprising 2.15 indels, 0.17 SVs, and 0.01 CGRs, despite a high level of inter-cellular stochasticity. The mutational burden was dependent on total irradiation dose, regardless of dose rate or cell type. The findings were further validated in IR-induced secondary cancers and single cells without clonalization. Overall, our study highlights a comprehensive and clear picture of IR effects on normal mammalian genomes.
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Affiliation(s)
- Jeonghwan Youk
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Hyun Woo Kwon
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Korea University College of Medicine, Seoul, Republic of Korea
| | - Joonoh Lim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Eunji Kim
- Department of Radiation Oncology, Seoul Metropolitan Government-Seoul National University Boramae Medical Center, 20, Boramae-ro 5 Gil, Dongjak-gu, Seoul 07061, Republic of Korea; Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Taewoo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Ryul Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Seongyeol Park
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Kijong Yi
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA
| | - Chang Hyun Nam
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sara Jeon
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Yohan An
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Jinwook Choi
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Hyelin Na
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Eon-Seok Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Youngwon Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Dong-Wook Min
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - HyoJin Kim
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Yeong-Rok Kang
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Si Ho Choi
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Min Ji Bae
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Chang Geun Lee
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Joon-Goon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Young Seo Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Tosol Yu
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Dongnam Institute of Radiological and Medical Science, Busan 46033, Republic of Korea
| | | | | | - Dong Soo Lee
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Department of Nuclear Medicine, Seoul National University College of Medicine, Seoul 03080, Republic of Korea
| | - Tae-You Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul 08826, Republic of Korea; Cancer Research Institute, Seoul National University, Seoul, Republic of Korea; Department of Internal Medicine, Seoul National University Hospital, Seoul 03080, Republic of Korea
| | - Taeyun Ku
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; KI for Health Science and Technology, KAIST, Daejeon 34141, Republic of Korea
| | - Su Yeon Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Joo-Hyeon Lee
- Wellcome - MRC Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, University of Cambridge, CB2 0AW Cambridge, UK; Department of Physiology, Development and Neuroscience, University of Cambridge, CB2 3EL Cambridge, UK
| | - Bon-Kyoung Koo
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Hyunsook Lee
- Department of Biological Sciences & IMBG, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - On Vox Yi
- Department of Breast Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Eon Chul Han
- Department of Surgery, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea
| | - Ji Hyun Chang
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Kyung Su Kim
- Department of Radiation Oncology, Seoul National University College of Medicine, Seoul 03080, Republic of Korea; Department of Radiation Oncology, Seoul National University Hospital, Seoul, Republic of Korea.
| | - Tae Gen Son
- Research Center, Dongnam Institute of Radiological and Medical Science, Busan, Republic of Korea.
| | - Young Seok Ju
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea; Genome Insight, Inc., San Diego, CA 92121, USA.
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2
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Dehkordi SR, Wong ITL, Ni J, Luebeck J, Zhu K, Prasad G, Krockenberger L, Xu G, Chowdhury B, Rajkumar U, Caplin A, Muliaditan D, Coruh C, Jin Q, Turner K, Teo SX, Pang AWC, Alexandrov LB, Chua CEL, Furnari FB, Paulson TG, Law JA, Chang HY, Yue F, DasGupta R, Zhao J, Mischel PS, Bafna V. Breakage fusion bridge cycles drive high oncogene copy number, but not intratumoral genetic heterogeneity or rapid cancer genome change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.12.571349. [PMID: 38168210 PMCID: PMC10760206 DOI: 10.1101/2023.12.12.571349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Oncogene amplification is a major driver of cancer pathogenesis. Breakage fusion bridge (BFB) cycles, like extrachromosomal DNA (ecDNA), can lead to high copy numbers of oncogenes, but their impact on intratumoral heterogeneity, treatment response, and patient survival are not well understood due to difficulty in detecting them by DNA sequencing. We describe a novel algorithm that detects and reconstructs BFB amplifications using optical genome maps (OGMs), called OM2BFB. OM2BFB showed high precision (>93%) and recall (92%) in detecting BFB amplifications in cancer cell lines, PDX models and primary tumors. OM-based comparisons demonstrated that short-read BFB detection using our AmpliconSuite (AS) toolkit also achieved high precision, albeit with reduced sensitivity. We detected 371 BFB events using whole genome sequences from 2,557 primary tumors and cancer lines. BFB amplifications were preferentially found in cervical, head and neck, lung, and esophageal cancers, but rarely in brain cancers. BFB amplified genes show lower variance of gene expression, with fewer options for regulatory rewiring relative to ecDNA amplified genes. BFB positive (BFB (+)) tumors showed reduced heterogeneity of amplicon structures, and delayed onset of resistance, relative to ecDNA(+) tumors. EcDNA and BFB amplifications represent contrasting mechanisms to increase the copy numbers of oncogene with markedly different characteristics that suggest different routes for intervention.
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Affiliation(s)
- Siavash Raeisi Dehkordi
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Ivy Tsz-Lo Wong
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Jing Ni
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Bioinformatics and Systems Biology Graduate Program, University of California San Diego, San Diego, CA, USA
| | - Kaiyuan Zhu
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Gino Prasad
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Lena Krockenberger
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Guanghui Xu
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Biswanath Chowdhury
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Ann Caplin
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
| | - Daniel Muliaditan
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- ClearNote Health, San Diego, CA 92121 USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
| | | | - Shu Xian Teo
- Singapore Nuclear Research and Safety Initiative, National University of Singapore
| | | | - Ludmil B Alexandrov
- Moores Cancer Center, UC San Diego Health, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | | | - Frank B Furnari
- Department of Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Thomas G Paulson
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL, USA
| | - Ramanuj DasGupta
- Laboratory of Precision Oncology and Cancer Evolution, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Jean Zhao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115 USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, San Diego, CA, USA
- Halıcıoğlu Data Science Institute, University of California at San Diego, La Jolla, CA, USA
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3
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Malchers F, Nogova L, van Attekum MH, Maas L, Brägelmann J, Bartenhagen C, Girard L, Bosco G, Dahmen I, Michels S, Weeden CE, Scheel AH, Meder L, Golfmann K, Schuldt P, Siemanowski J, Rehker J, Merkelbach-Bruse S, Menon R, Gautschi O, Heuckmann JM, Brambilla E, Asselin-Labat ML, Persigehl T, Minna JD, Walczak H, Ullrich RT, Fischer M, Reinhardt HC, Wolf J, Büttner R, Peifer M, George J, Thomas RK. Somatic rearrangements causing oncogenic ectodomain deletions of FGFR1 in squamous cell lung cancer. J Clin Invest 2023; 133:e170217. [PMID: 37606995 PMCID: PMC10617767 DOI: 10.1172/jci170217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023] Open
Abstract
The discovery of frequent 8p11-p12 amplifications in squamous cell lung cancer (SQLC) has fueled hopes that FGFR1, located inside this amplicon, might be a therapeutic target. In a clinical trial, only 11% of patients with 8p11 amplification (detected by FISH) responded to FGFR kinase inhibitor treatment. To understand the mechanism of FGFR1 dependency, we performed deep genomic characterization of 52 SQLCs with 8p11-p12 amplification, including 10 tumors obtained from patients who had been treated with FGFR inhibitors. We discovered somatically altered variants of FGFR1 with deletion of exons 1-8 that resulted from intragenic tail-to-tail rearrangements. These ectodomain-deficient FGFR1 variants (ΔEC-FGFR1) were expressed in the affected tumors and were tumorigenic in both in vitro and in vivo models of lung cancer. Mechanistically, breakage-fusion-bridges were the source of 8p11-p12 amplification, resulting from frequent head-to-head and tail-to-tail rearrangements. Generally, tail-to-tail rearrangements within or in close proximity upstream of FGFR1 were associated with FGFR1 dependency. Thus, the genomic events shaping the architecture of the 8p11-p12 amplicon provide a mechanistic explanation for the emergence of FGFR1-driven SQLC. Specifically, we believe that FGFR1 ectodomain-deficient and FGFR1-centered amplifications caused by tail-to-tail rearrangements are a novel somatic genomic event that might be predictive of therapeutically relevant FGFR1 dependency.
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Affiliation(s)
- Florian Malchers
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lucia Nogova
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Martijn H.A. van Attekum
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Lukas Maas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Johannes Brägelmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Mildred Scheel School of Oncology, Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
| | - Luc Girard
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Graziella Bosco
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Ilona Dahmen
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
| | - Sebastian Michels
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Clare E. Weeden
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Andreas H. Scheel
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Lydia Meder
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Kristina Golfmann
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Philipp Schuldt
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Janna Siemanowski
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Jan Rehker
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Sabine Merkelbach-Bruse
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | | | - Oliver Gautschi
- University of Berne and Cantonal Hospital of Lucerne, Cantonal Hospital of Lucerne, Lucerne, Switzerland
| | | | | | - Marie-Liesse Asselin-Labat
- Personalized Oncology Division, Walter and Eliza Hall Institute of Medical Research, Department of Medical Biology, The University of Melbourne, Parkville, Australia
| | - Thorsten Persigehl
- Institute for Diagnostic and Interventional Radiology, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
| | - John D. Minna
- University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Henning Walczak
- Institute of Biochemistry I, Medical Faculty, University of Cologne, Cologne, Germany
- CECAD Cluster of Excellence, University of Cologne, Cologne, Germany
- Centre for Cell Death, Cancer, and Inflammation (CCCI), UCL Cancer Institute, University College London, London, United Kingdom
| | - Roland T. Ullrich
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children’s Hospital of Cologne, University Hospital Cologne, Medical Faculty, Cologne, Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Hans Christian Reinhardt
- Department of Hematology and Stem Cell Transplantation, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Jürgen Wolf
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department I of Internal Medicine, Center for Integrated Oncology Aachen Bonn, Cologne Duesseldorf, Cologne, Germany
| | - Reinhard Büttner
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Martin Peifer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Center for Molecular Medicine Cologne (CMMC), Cologne, Germany
| | - Julie George
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- Department of Head and Neck Surgery, Medical Faculty, University Hospital Cologne, Cologne, Germany
| | - Roman K. Thomas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Department of Translational Genomics, Cologne, Germany Germany
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
- German Cancer Consortium (DKTK), partner site Heidelberg and German Cancer Research Center (DKFZ), Heidelberg, Germany
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4
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Rodriguez-Fos E, Planas-Fèlix M, Burkert M, Puiggròs M, Toedling J, Thiessen N, Blanc E, Szymansky A, Hertwig F, Ishaque N, Beule D, Torrents D, Eggert A, Koche RP, Schwarz RF, Haase K, Schulte JH, Henssen AG. Mutational topography reflects clinical neuroblastoma heterogeneity. CELL GENOMICS 2023; 3:100402. [PMID: 37868040 PMCID: PMC10589636 DOI: 10.1016/j.xgen.2023.100402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/13/2023] [Accepted: 08/11/2023] [Indexed: 10/24/2023]
Abstract
Neuroblastoma is a pediatric solid tumor characterized by strong clinical heterogeneity. Although clinical risk-defining genomic alterations exist in neuroblastomas, the mutational processes involved in their generation remain largely unclear. By examining the topography and mutational signatures derived from all variant classes, we identified co-occurring mutational footprints, which we termed mutational scenarios. We demonstrate that clinical neuroblastoma heterogeneity is associated with differences in the mutational processes driving these scenarios, linking risk-defining pathognomonic variants to distinct molecular processes. Whereas high-risk MYCN-amplified neuroblastomas were characterized by signs of replication slippage and stress, homologous recombination-associated signatures defined high-risk non-MYCN-amplified patients. Non-high-risk neuroblastomas were marked by footprints of chromosome mis-segregation and TOP1 mutational activity. Furthermore, analysis of subclonal mutations uncovered differential activity of these processes through neuroblastoma evolution. Thus, clinical heterogeneity of neuroblastoma patients can be linked to differences in the mutational processes that are active in their tumors.
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Affiliation(s)
- Elias Rodriguez-Fos
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Mercè Planas-Fèlix
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Burkert
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Joern Toedling
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Nina Thiessen
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Eric Blanc
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center – Center for Genomic Regulation – Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Angelika Eggert
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Richard P. Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Roland F. Schwarz
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany
| | - Kerstin Haase
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Johannes H. Schulte
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anton G. Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Berlin Institute of Health at Charité – Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
- German Cancer Consortium (DKTK), Partner Site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
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5
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Li C, Chen L, Pan G, Zhang W, Li SC. Deciphering complex breakage-fusion-bridge genome rearrangements with Ambigram. Nat Commun 2023; 14:5528. [PMID: 37684230 PMCID: PMC10491683 DOI: 10.1038/s41467-023-41259-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Breakage-fusion-bridge (BFB) is a complex rearrangement that leads to tumor malignancy. Existing models for detecting BFBs rely on the ideal BFB hypothesis, ruling out the possibility of BFBs entangled with other structural variations, that is, complex BFBs. We propose an algorithm Ambigram to identify complex BFB and reconstruct the rearranged structure of the local genome during the cancer subclone evolution process. Ambigram handles data from short, linked, long, and single-cell sequences, and optical mapping technologies. Ambigram successfully deciphers the gold- or silver-standard complex BFBs against the state-of-the-art in multiple cancers. Ambigram dissects the intratumor heterogeneity of complex BFB events with single-cell reads from melanoma and gastric cancer. Furthermore, applying Ambigram to liver and cervical cancer data suggests that the BFB mechanism may mediate oncovirus integrations. BFB also exists in noncancer genomics. Investigating the complete human genome reference with Ambigram suggests that the BFB mechanism may be involved in two genome reorganizations of Homo Sapiens during evolution. Moreover, Ambigram discovers the signals of recurrent foldback inversions and complex BFBs in whole genome data from the 1000 genome project, and congenital heart diseases, respectively.
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Affiliation(s)
- Chaohui Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Lingxi Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Guangze Pan
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Wenqian Zhang
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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6
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Yüksel A, Altungöz O. Gene amplifications and extrachromosomal circular DNAs: function and biogenesis. Mol Biol Rep 2023; 50:7693-7703. [PMID: 37433908 DOI: 10.1007/s11033-023-08649-1] [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] [Received: 08/17/2022] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
Gene amplification is an increase in the copy number of restricted chromosomal segments that contain gene(s) and frequently results in the over-expression of the corresponding gene(s). Amplification may be found in the form of extrachromosomal circular DNAs (eccDNAs) or as linear repetitive amplicon regions that are integrated into chromosomes, which may form cytogenetically observable homogeneously staining regions or may be scattered throughout the genome. eccDNAs are structurally circular and in terms of their function and content, they can be classified into various subtypes. They play pivotal roles in many physiological and pathological phenomena such as tumor pathogenesis, aging, maintenance of telomere length and ribosomal DNAs (rDNAs), and gain of resistance against chemotherapeutic agents. Amplification of oncogenes is consistently seen in various types of cancers and can be associated with prognostic factors. eccDNAs are known to be originated from chromosomes as a consequence of various cellular events such as repair processes of damaged DNA or DNA replication errors. In this review, we highlighted the role of gene amplification in cancer, the functional aspects of eccDNAs subtypes, the proposed biogenesis mechanisms, and their role in gene or segmental-DNA amplification.
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Affiliation(s)
- Ali Yüksel
- Department of Medical Biology and Genetics, Institute of Health Sciences, Dokuz Eylul University, 35330, Izmir, Turkey.
| | - Oğuz Altungöz
- Department of Medical Biology and Genetics, Institute of Health Sciences, Dokuz Eylul University, 35330, Izmir, Turkey.
- Department of Medical Biology, Dokuz Eylül Medical School, 35330, Izmir, Turkey.
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7
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Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications. Front Oncol 2023; 13:1194405. [PMID: 37448518 PMCID: PMC10338009 DOI: 10.3389/fonc.2023.1194405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characteristics, functions, mechanisms of formation, and detection methods of ecDNA, with a focus on the potential clinical implications of ecDNA in cancer. Specifically, we consider the role of ecDNA in acquired drug resistance, as a diagnostic and prognostic biomarker, and as a therapeutic target in the context of cancer. As the pathological and clinical significance of ecDNA continues to be explored, it is anticipated that ecDNA will have broad applications in the diagnosis, prognosis, and treatment of patients with cancer.
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Affiliation(s)
- Yucheng Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi He
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyu Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li He
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Yongchang Zheng
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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8
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [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] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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9
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Montalvo-Javé EE, Nuño-Lámbarri N, López-Sánchez GN, Ayala-Moreno EA, Gutierrez-Reyes G, Beane J, Pawlik TM. Pancreatic Cancer: Genetic Conditions and Epigenetic Alterations. J Gastrointest Surg 2023; 27:1001-1010. [PMID: 36749558 DOI: 10.1007/s11605-022-05553-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 11/19/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND Pancreatic cancer is a lethal proliferative disease driven by multiple genetic and epigenetic alterations. Microarrays and omics-based sequencing techniques are potent tools that have facilitated a broader understanding of the complex biological processes that drive pancreatic ductal adenocarcinoma (PDAC). In turn, these tools have resulted in the identification of novel disease markers, prognostic factors, and therapeutic targets. Herein, we provide a review of the genetic and epigenetic drivers of PDAC relative to recent discoveries that impact patient management. METHODS A review of PubMed, Medline, Clinical Key, and Index Medicus was conducted to identify literature from January 1995 to July 2022 that is related to PDAC genetics and epigenetics. Articles in Spanish and English were considered during selection. RESULTS Molecular, genetic, and epigenetic diagnostic tools, novel biomarkers, and promising therapeutic targets have emerged in the treatment of pancreatic cancer. The implementation of microarray technology and application of large omics-based data repositories have facilitated recent discoveries in PDAC. Multiple molecular analyses based on RNA interference have been instrumental in the identification of novel therapeutic targets for patients with PDAC. Moreover, microarrays and next-generation omics-based discoveries have been instrumental in the characterization of subtypes of pancreatic cancer, thereby improving prognostication and refining patient selection for available targeted therapies. CONCLUSION Advances in molecular biology, genetics, and epigenetics have ushered in a new era of discovery in the pathobiology of PDAC. Current efforts are underway to translate these findings into clinical tools and therapies to improve outcomes in patients with PDAC.
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Affiliation(s)
- Eduardo E Montalvo-Javé
- Hepatopancreatobiliary Clinic, Department of Surgery, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico. .,Department of Surgery, Faculty of Medicine, Universidad Nacional Autónoma de México, Mexico City, Mexico.
| | | | | | - Edwin A Ayala-Moreno
- Department of Surgery, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Gabriela Gutierrez-Reyes
- Liver, Pancreas and Motility Laboratory, Unit of Experimental Medicine, Hospital General de México "Dr. Eduardo Liceaga", Mexico City, Mexico
| | - Joal Beane
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Timothy M Pawlik
- Department of Surgery, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
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10
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Funnell T, O'Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, Shah SP, Aparicio S. Single-cell genomic variation induced by mutational processes in cancer. Nature 2022; 612:106-115. [PMID: 36289342 PMCID: PMC9712114 DOI: 10.1038/s41586-022-05249-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
Abstract
How cell-to-cell copy number alterations that underpin genomic instability1 in human cancers drive genomic and phenotypic variation, and consequently the evolution of cancer2, remains understudied. Here, by applying scaled single-cell whole-genome sequencing3 to wild-type, TP53-deficient and TP53-deficient;BRCA1-deficient or TP53-deficient;BRCA2-deficient mammary epithelial cells (13,818 genomes), and to primary triple-negative breast cancer (TNBC) and high-grade serous ovarian cancer (HGSC) cells (22,057 genomes), we identify three distinct 'foreground' mutational patterns that are defined by cell-to-cell structural variation. Cell- and clone-specific high-level amplifications, parallel haplotype-specific copy number alterations and copy number segment length variation (serrate structural variations) had measurable phenotypic and evolutionary consequences. In TNBC and HGSC, clone-specific high-level amplifications in known oncogenes were highly prevalent in tumours bearing fold-back inversions, relative to tumours with homologous recombination deficiency, and were associated with increased clone-to-clone phenotypic variation. Parallel haplotype-specific alterations were also commonly observed, leading to phylogenetic evolutionary diversity and clone-specific mono-allelic expression. Serrate variants were increased in tumours with fold-back inversions and were highly correlated with increased genomic diversity of cellular populations. Together, our findings show that cell-to-cell structural variation contributes to the origins of phenotypic and evolutionary diversity in TNBC and HGSC, and provide insight into the genomic and mutational states of individual cancer cells.
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Affiliation(s)
- Tyler Funnell
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ciara H O'Flanagan
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Steven McKinney
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Farhia Kabeer
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hakwoo Lee
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Salehi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ignacio Vázquez-García
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Emily Leventhal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tehmina Masud
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Damian Yap
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Allen W Zhang
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jamie L P Lim
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Beixi Wang
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jazmine Brimhall
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Justina Biele
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jerome Ting
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Vinci Au
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Michael Van Vliet
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Yi Fei Liu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sean Beatty
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Daniel Lai
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jenifer Pham
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Diljot Grewal
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Douglas Abrams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eliyahu Havasov
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Samantha Leung
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Richard A Moore
- Michael Smith Genome Sciences Centre, Vancouver, British Columbia, Canada
| | - Nicole Rusk
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Florian Uhlitz
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adam C Weiner
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elena Zaikova
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - J Maxwell Douglas
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Dmitriy Zamarin
- GYN Medical Oncology, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sarah H Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Spencer D Martin
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yangguang Li
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Hong Xu
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Teresa Ruiz de Algara
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - So Ra Lee
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Viviana Cerda Llanos
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
| | - David G Huntsman
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jessica N McAlpine
- Department of Gynecology and Obstetrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Samuel Aparicio
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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12
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Chromosomal Instability in Chronic Myeloid Leukemia: Mechanistic Insights and Effects. Cancers (Basel) 2022; 14:cancers14102533. [PMID: 35626137 PMCID: PMC9140097 DOI: 10.3390/cancers14102533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 12/15/2022] Open
Abstract
The most recent two decades have seen tremendous progress in the understanding and treatment of chronic myeloid leukemia, a disease defined by the characteristic Philadelphia chromosome and the ensuing BCR::ABL fusion protein. However, the biology of the disease extends beyond the Philadelphia chromosome into a nebulous arena of chromosomal and genetic instability, which makes it a genetically heterogeneous disease. The BCR::ABL oncoprotein creates a fertile backdrop for oxidative damage to the DNA, along with impairment of genetic surveillance and the favoring of imprecise error-prone DNA repair pathways. These factors lead to growing chromosomal instability, manifested as additional chromosomal abnormalities along with other genetic aberrations. This worsens with disease progression to accelerated and blast phase, and modulates responses to tyrosine kinase inhibitors. Treatment options that target the genetic aberrations that mitigate chromosome instability might be a potential area for research in patients with advanced phase CML.
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13
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Rosswog C, Bartenhagen C, Welte A, Kahlert Y, Hemstedt N, Lorenz W, Cartolano M, Ackermann S, Perner S, Vogel W, Altmüller J, Nürnberg P, Hertwig F, Göhring G, Lilienweiss E, Stütz AM, Korbel JO, Thomas RK, Peifer M, Fischer M. Chromothripsis followed by circular recombination drives oncogene amplification in human cancer. Nat Genet 2021; 53:1673-1685. [PMID: 34782764 DOI: 10.1038/s41588-021-00951-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/10/2021] [Indexed: 12/24/2022]
Abstract
The mechanisms behind the evolution of complex genomic amplifications in cancer have remained largely unclear. Using whole-genome sequencing data of the pediatric tumor neuroblastoma, we here identified a type of amplification, termed 'seismic amplification', that is characterized by multiple rearrangements and discontinuous copy number levels. Overall, seismic amplifications occurred in 9.9% (274 of 2,756) of cases across 38 cancer types, and were associated with massively increased copy numbers and elevated oncogene expression. Reconstruction of the development of seismic amplification showed a stepwise evolution, starting with a chromothripsis event, followed by formation of circular extrachromosomal DNA that subsequently underwent repetitive rounds of circular recombination. The resulting amplicons persisted as extrachromosomal DNA circles or had reintegrated into the genome in overt tumors. Together, our data indicate that the sequential occurrence of chromothripsis and circular recombination drives oncogene amplification and overexpression in a substantial fraction of human malignancies.
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Affiliation(s)
- Carolina Rosswog
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Else Kröner Forschungskolleg Clonal Evolution in Cancer, University Hospital Cologne, Cologne, Germany
| | - Christoph Bartenhagen
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Anne Welte
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Yvonne Kahlert
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Nadine Hemstedt
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Witali Lorenz
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Maria Cartolano
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sandra Ackermann
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Sven Perner
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Pathology Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Wenzel Vogel
- Institute of Pathology, University of Luebeck and University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.,Pathology Research Center Borstel, Leibniz Lung Center, Borstel, Germany
| | - Janine Altmüller
- Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Core Facility Genomics, Berlin, Germany.,Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Peter Nürnberg
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.,Cologne Center for Genomics (CCG), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School (MHH), Hannover, Germany
| | - Esther Lilienweiss
- Department of Internal Medicine, University of Cologne, Cologne, Germany
| | - Adrian M Stütz
- European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany
| | - Jan O Korbel
- European Molecular Biology Laboratory Genome Biology Unit, Heidelberg, Germany
| | - Roman K Thomas
- Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.,Department of Pathology, University of Cologne, Cologne, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Martin Peifer
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Department of Translational Genomics, Medical Faculty, University of Cologne, Cologne, Germany.
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
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14
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Zhao XK, Xing P, Song X, Zhao M, Zhao L, Dang Y, Lei LL, Xu RH, Han WL, Wang PP, Yang MM, Hu JF, Zhong K, Zhou FY, Han XN, Meng CL, Ji JJ, Chen X, Wang LD. Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma. Nat Commun 2021; 12:6489. [PMID: 34764264 PMCID: PMC8586158 DOI: 10.1038/s41467-021-26745-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 10/21/2021] [Indexed: 01/24/2023] Open
Abstract
The role of focal amplifications and extrachromosomal DNA (ecDNA) is unknown in gastric cardia adenocarcinoma (GCA). Here, we identify frequent focal amplifications and ecDNAs in Chinese GCA patient samples, and find focal amplifications in the GCA cohort are associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits. We observe diverse correlations between the presence of oncogene focal amplifications and prognosis, where ERBB2 focal amplifications positively correlate with prognosis and EGFR focal amplifications negatively correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients show survival probability of ERBB2 positive patients is lower than that of ERBB2 negative patients when their surviving time is under 2 years, however, the tendency is opposite when their surviving time is longer than 2 years. Our observations indicate that the ERBB2 focal amplifications may represent a good prognostic marker in GCA patients.
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Affiliation(s)
- Xue-Ke Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Yonglong Dang
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Ling-Ling Lei
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Rui-Hua Xu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Wen-Li Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Pan-Pan Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Miao-Miao Yang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Jing-Feng Hu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Kan Zhong
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Fu-You Zhou
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Xue-Na Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Chao-Long Meng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Jia-Jia Ji
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden.
| | - Li-Dong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China.
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15
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Human chromosome 3p21.3 carries TERT transcriptional regulators in pancreatic cancer. Sci Rep 2021; 11:15355. [PMID: 34321527 PMCID: PMC8319171 DOI: 10.1038/s41598-021-94711-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 07/15/2021] [Indexed: 11/23/2022] Open
Abstract
Frequent loss of heterozygosity (LOH) on the short arm of human chromosome 3 (3p) region has been found in pancreatic cancer (PC), which suggests the likely presence of tumor suppressor genes in this region. However, the functional significance of LOH in this region in the development of PC has not been clearly defined. The human telomerase reverse transcriptase gene (hTERT) contributes to unlimited proliferative and tumorigenicity of malignant tumors. We previously demonstrated that hTERT expression was suppressed by the introduction of human chromosome 3 in several cancer cell lines. To examine the functional role of putative TERT suppressor genes on chromosome 3 in PC, we introduced an intact human chromosome 3 into the human PK9 and murine LTPA PC cell lines using microcell-mediated chromosome transfer. PK9 microcell hybrids with an introduced human chromosome 3 showed significant morphological changes and rapid growth arrest. Intriguingly, microcell hybrid clones of LTPA cells with an introduced human chromosome 3 (LTPA#3) showed suppression of mTert transcription, cell proliferation, and invasion compared with LTPA#4 cells containing human chromosome 4 and parental LTPA cells. Additionally, the promoter activity of mTert was downregulated in LTPA#3. Furthermore, we confirmed that TERT regulatory gene(s) are present in the 3p21.3 region by transfer of truncated chromosomes at arbitrary regions. These results provide important information on the functional significance of the LOH at 3p for development and progression of PC.
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16
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Hadi K, Yao X, Behr JM, Deshpande A, Xanthopoulakis C, Tian H, Kudman S, Rosiene J, Darmofal M, DeRose J, Mortensen R, Adney EM, Shaiber A, Gajic Z, Sigouros M, Eng K, Wala JA, Wrzeszczyński KO, Arora K, Shah M, Emde AK, Felice V, Frank MO, Darnell RB, Ghandi M, Huang F, Dewhurst S, Maciejowski J, de Lange T, Setton J, Riaz N, Reis-Filho JS, Powell S, Knowles DA, Reznik E, Mishra B, Beroukhim R, Zody MC, Robine N, Oman KM, Sanchez CA, Kuhner MK, Smith LP, Galipeau PC, Paulson TG, Reid BJ, Li X, Wilkes D, Sboner A, Mosquera JM, Elemento O, Imielinski M. Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs. Cell 2021; 183:197-210.e32. [PMID: 33007263 DOI: 10.1016/j.cell.2020.08.006] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 04/08/2020] [Accepted: 08/03/2020] [Indexed: 12/12/2022]
Abstract
Cancer genomes often harbor hundreds of somatic DNA rearrangement junctions, many of which cannot be easily classified into simple (e.g., deletion) or complex (e.g., chromothripsis) structural variant classes. Applying a novel genome graph computational paradigm to analyze the topology of junction copy number (JCN) across 2,778 tumor whole-genome sequences, we uncovered three novel complex rearrangement phenomena: pyrgo, rigma, and tyfonas. Pyrgo are "towers" of low-JCN duplications associated with early-replicating regions, superenhancers, and breast or ovarian cancers. Rigma comprise "chasms" of low-JCN deletions enriched in late-replicating fragile sites and gastrointestinal carcinomas. Tyfonas are "typhoons" of high-JCN junctions and fold-back inversions associated with expressed protein-coding fusions, breakend hypermutation, and acral, but not cutaneous, melanomas. Clustering of tumors according to genome graph-derived features identified subgroups associated with DNA repair defects and poor prognosis.
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Affiliation(s)
- Kevin Hadi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Xiaotong Yao
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Julie M Behr
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Aditya Deshpande
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | - Huasong Tian
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Sarah Kudman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joel Rosiene
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Madison Darmofal
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Tri-institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | | | | | - Emily M Adney
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA
| | - Alon Shaiber
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Zoran Gajic
- New York Genome Center, New York, NY 10013, USA
| | - Michael Sigouros
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Kenneth Eng
- Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jeremiah A Wala
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | - Minita Shah
- New York Genome Center, New York, NY 10013, USA
| | | | | | - Mayu O Frank
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Robert B Darnell
- New York Genome Center, New York, NY 10013, USA; Laboratory of Molecular Neuro-Oncology and Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA
| | - Mahmoud Ghandi
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Franklin Huang
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; School of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sally Dewhurst
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - John Maciejowski
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Titia de Lange
- Laboratory of Cell Biology and Genetics, The Rockefeller University, New York, NY 10065, USA
| | - Jeremy Setton
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Immunogenomics and Precision Oncology Platform, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Jorge S Reis-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - David A Knowles
- New York Genome Center, New York, NY 10013, USA; Department of Computer Science, Columbia University, New York, NY 10027, USA
| | - Ed Reznik
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bud Mishra
- Departments of Computer Science, Mathematics and Cell Biology, Courant Institute and NYU School of Medicine, New York University, New York, NY 10012, USA
| | - Rameen Beroukhim
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Departments of Medical Oncology and Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | | | - Kenji M Oman
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Carissa A Sanchez
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Mary K Kuhner
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lucian P Smith
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Patricia C Galipeau
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Thomas G Paulson
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Brian J Reid
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Xiaohong Li
- Divisions of Human Biology and Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - David Wilkes
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Andrea Sboner
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Juan Miguel Mosquera
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Olivier Elemento
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Marcin Imielinski
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10021, USA; New York Genome Center, New York, NY 10013, USA; Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA; Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA.
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17
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Stok C, Kok Y, van den Tempel N, van Vugt MATM. Shaping the BRCAness mutational landscape by alternative double-strand break repair, replication stress and mitotic aberrancies. Nucleic Acids Res 2021; 49:4239-4257. [PMID: 33744950 PMCID: PMC8096281 DOI: 10.1093/nar/gkab151] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/18/2021] [Accepted: 03/05/2021] [Indexed: 12/16/2022] Open
Abstract
Tumours with mutations in the BRCA1/BRCA2 genes have impaired double-stranded DNA break repair, compromised replication fork protection and increased sensitivity to replication blocking agents, a phenotype collectively known as 'BRCAness'. Tumours with a BRCAness phenotype become dependent on alternative repair pathways that are error-prone and introduce specific patterns of somatic mutations across the genome. The increasing availability of next-generation sequencing data of tumour samples has enabled identification of distinct mutational signatures associated with BRCAness. These signatures reveal that alternative repair pathways, including Polymerase θ-mediated alternative end-joining and RAD52-mediated single strand annealing are active in BRCA1/2-deficient tumours, pointing towards potential therapeutic targets in these tumours. Additionally, insight into the mutations and consequences of unrepaired DNA lesions may also aid in the identification of BRCA-like tumours lacking BRCA1/BRCA2 gene inactivation. This is clinically relevant, as these tumours respond favourably to treatment with DNA-damaging agents, including PARP inhibitors or cisplatin, which have been successfully used to treat patients with BRCA1/2-defective tumours. In this review, we aim to provide insight in the origins of the mutational landscape associated with BRCAness by exploring the molecular biology of alternative DNA repair pathways, which may represent actionable therapeutic targets in in these cells.
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Affiliation(s)
- Colin Stok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Yannick P Kok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Nathalie van den Tempel
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
| | - Marcel A T M van Vugt
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ, Groningen, The Netherlands
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18
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Wang M, Chen X, Yu F, Ding H, Zhang Y, Wang K. Extrachromosomal Circular DNAs: Origin, formation and emerging function in Cancer. Int J Biol Sci 2021; 17:1010-1025. [PMID: 33867825 PMCID: PMC8040306 DOI: 10.7150/ijbs.54614] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 02/05/2021] [Indexed: 02/06/2023] Open
Abstract
The majority of cellular DNAs in eukaryotes are organized into linear chromosomes. In addition to chromosome DNAs, genes also reside on extrachromosomal elements. The extrachromosomal DNAs are commonly found to be circular, and they are referred to as extrachromosomal circular DNAs (eccDNAs). Recent technological advances have enriched our knowledge of eccDNA biology. There is currently increasing concern about the connection between eccDNA and cancer. Gene amplification on eccDNAs is prevalent in cancer. Moreover, eccDNAs commonly harbor oncogenes or drug resistance genes, hence providing a growth or survival advantage to cancer cells. eccDNAs play an important role in tumor heterogeneity and evolution, facilitating tumor adaptation to challenging circumstances. In addition, eccDNAs have recently been identified as cell-free DNAs in circulating system. The altered level of eccDNAs is observed in cancer patients relative to healthy controls. Particularly, eccDNAs are associated with cancer progression and poor outcomes. Thus, eccDNAs could be useful as novel biomarkers for the diagnosis and prognosis of cancer. In this review, we summarize current knowledge regarding the formation, characteristics and biological importance of eccDNAs, with a focus on the molecular mechanisms associated with their roles in cancer progression. We also discuss their potential applications in the detection and treatment of cancer. A better understanding of the functional role of eccDNAs in cancer would facilitate the comprehensive analysis of molecular mechanisms involved in cancer pathogenesis.
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Affiliation(s)
- Man Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Xinzhe Chen
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Fei Yu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Han Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Yuan Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, China
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19
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Obesity, oxidative DNA damage and vitamin D as predictors of genomic instability in children and adolescents. Int J Obes (Lond) 2021; 45:2095-2107. [PMID: 34158611 PMCID: PMC8380542 DOI: 10.1038/s41366-021-00879-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/18/2021] [Accepted: 05/27/2021] [Indexed: 02/05/2023]
Abstract
BACKGROUND/OBJECTIVES Epidemiological evidence indicates obesity in childhood and adolescence to be an independent risk factor for cancer and premature mortality in adulthood. Pathological implications from excess adiposity may begin early in life. Obesity is concurrent with a state of chronic inflammation, a well-known aetiological factor for DNA damage. In addition, obesity has been associated with micro-nutritional deficiencies. Vitamin D has attracted attention for its anti-inflammatory properties and role in genomic integrity and stability. The aim of this study was to determine a novel approach for predicting genomic instability via the combined assessment of adiposity, DNA damage, systemic inflammation, and vitamin D status. SUBJECTS/METHODS We carried out a cross-sectional study with 132 participants, aged 10-18, recruited from schools and paediatric obesity clinics in London. Anthropometric assessments included BMI Z-score, waist and hip circumference, and body fat percentage via bioelectrical impedance. Inflammation and vitamin D levels in saliva were assessed by enzyme-linked immunosorbent assay. Oxidative DNA damage was determined via quantification of 8-hydroxy-2'-deoxyguanosine in urine. Exfoliated cells from the oral cavity were scored for genomic instability via the buccal cytome assay. RESULTS As expected, comparisons between participants with obesity and normal range BMI showed significant differences in anthropometric measures (p < 0.001). Significant differences were also observed in some measures of genomic instability (p < 0.001). When examining relationships between variables for all participants, markers of adiposity positively correlated with acquired oxidative DNA damage (p < 0.01) and genomic instability (p < 0.001), and negatively correlated with vitamin D (p < 0.01). Multiple regression analyses identified obesity (p < 0.001), vitamin D (p < 0.001), and oxidative DNA damage (p < 0.05) as the three significant predictors of genomic instability. CONCLUSIONS Obesity, oxidative DNA damage, and vitamin D deficiency are significant predictors of genomic instability. Non-invasive biomonitoring and predictive modelling of genomic instability in young patients with obesity may contribute to the prioritisation and severity of clinical intervention measures.
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20
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Toledo F. Mechanisms Generating Cancer Genome Complexity: Back to the Future. Cancers (Basel) 2020; 12:E3783. [PMID: 33334014 PMCID: PMC7765419 DOI: 10.3390/cancers12123783] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/11/2020] [Indexed: 11/16/2022] Open
Abstract
Understanding the mechanisms underlying cancer genome evolution has been a major goal for decades. A recent study combining live cell imaging and single-cell genome sequencing suggested that interwoven chromosome breakage-fusion-bridge cycles, micronucleation events and chromothripsis episodes drive cancer genome evolution. Here, I discuss the "interphase breakage model," suggested from prior fluorescent in situ hybridization data that led to a similar conclusion. In this model, the rapid genome evolution observed at early stages of gene amplification was proposed to result from the interweaving of an amplification mechanism (breakage-fusion-bridge cycles) and of a deletion mechanism (micronucleation and stitching of DNA fragments retained in the nucleus).
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Affiliation(s)
- Franck Toledo
- Genetics of Tumor Suppression, Institut Curie, PSL Research University, Sorbonne University, CNRS UMR3244 Dynamics of Genetic Information, 26 rue d'Ulm, CEDEX 05, 75248 Paris, France
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21
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Aganezov S, Raphael BJ. Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples. Genome Res 2020; 30:1274-1290. [PMID: 32887685 PMCID: PMC7545144 DOI: 10.1101/gr.256701.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 08/07/2020] [Indexed: 12/25/2022]
Abstract
Many cancer genomes are extensively rearranged with aberrant chromosomal karyotypes. Deriving these karyotypes from high-throughput DNA sequencing of bulk tumor samples is complicated because most tumors are a heterogeneous mixture of normal cells and subpopulations of cancer cells, or clones, that harbor distinct somatic mutations. We introduce a new algorithm, Reconstructing Cancer Karyotypes (RCK), to reconstruct haplotype-specific karyotypes of one or more rearranged cancer genomes from DNA sequencing data from a bulk tumor sample. RCK leverages evolutionary constraints on the somatic mutational process in cancer to reduce ambiguity in the deconvolution of admixed sequencing data into multiple haplotype-specific cancer karyotypes. RCK models mixtures containing an arbitrary number of derived genomes and allows the incorporation of information both from short-read and long-read DNA sequencing technologies. We compare RCK to existing approaches on 17 primary and metastatic prostate cancer samples. We find that RCK infers cancer karyotypes that better explain the DNA sequencing data and conform to a reasonable evolutionary model. RCK's reconstructions of clone- and haplotype-specific karyotypes will aid further studies of the role of intra-tumor heterogeneity in cancer development and response to treatment. RCK is freely available as open source software.
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Affiliation(s)
- Sergey Aganezov
- Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, New Jersey 08540, USA
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22
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Luebeck J, Coruh C, Dehkordi SR, Lange JT, Turner KM, Deshpande V, Pai DA, Zhang C, Rajkumar U, Law JA, Mischel PS, Bafna V. AmpliconReconstructor integrates NGS and optical mapping to resolve the complex structures of focal amplifications. Nat Commun 2020; 11:4374. [PMID: 32873787 PMCID: PMC7463033 DOI: 10.1038/s41467-020-18099-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 07/31/2020] [Indexed: 12/15/2022] Open
Abstract
Oncogene amplification, a major driver of cancer pathogenicity, is often mediated through focal amplification of genomic segments. Recent results implicate extrachromosomal DNA (ecDNA) as the primary driver of focal copy number amplification (fCNA) - enabling gene amplification, rapid tumor evolution, and the rewiring of regulatory circuitry. Resolving an fCNA's structure is a first step in deciphering the mechanisms of its genesis and the fCNA's subsequent biological consequences. We introduce a computational method, AmpliconReconstructor (AR), for integrating optical mapping (OM) of long DNA fragments (>150 kb) with next-generation sequencing (NGS) to resolve fCNAs at single-nucleotide resolution. AR uses an NGS-derived breakpoint graph alongside OM scaffolds to produce high-fidelity reconstructions. After validating its performance through multiple simulation strategies, AR reconstructed fCNAs in seven cancer cell lines to reveal the complex architecture of ecDNA, a breakage-fusion-bridge and other complex rearrangements. By reconstructing the rearrangement signatures associated with an fCNA's generative mechanism, AR enables a more thorough understanding of the origins of fCNAs.
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Affiliation(s)
- Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, 92093, USA
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Joshua T Lange
- Biomedical Sciences Graduate Program, University of California at San Diego, La Jolla, CA, 92093, USA
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Viraj Deshpande
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Dave A Pai
- Bionano Genomics, Inc., San Diego, CA, 92121, USA
| | - Chao Zhang
- Bioinformatics and Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, 92093, USA
- Department of Pathology, University of California at San Diego, La Jolla, CA, 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, 92093, USA.
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23
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Greenman CD, Penso-Dolfin L, Wu T. The complexity of genome rearrangement combinatorics under the infinite sites model. J Theor Biol 2020; 501:110335. [DOI: 10.1016/j.jtbi.2020.110335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 04/16/2020] [Accepted: 05/14/2020] [Indexed: 11/30/2022]
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24
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Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet 2020; 52:891-897. [PMID: 32807987 PMCID: PMC7484012 DOI: 10.1038/s41588-020-0678-2] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 12/27/2022]
Abstract
Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.
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Affiliation(s)
- Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Boundless Bio, La Jolla, CA, USA
| | - Kristen Turner
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
- Boundless Bio, La Jolla, CA, USA
| | - Sihan Wu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Viraj Deshpande
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Illumina, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Johannes H Schulte
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Anton G Henssen
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California, San Diego, San Diego, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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25
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Abstract
MOTIVATION Copy number aberrations (CNAs), which delete or amplify large contiguous segments of the genome, are a common type of somatic mutation in cancer. Copy number profiles, representing the number of copies of each region of a genome, are readily obtained from whole-genome sequencing or microarrays. However, modeling copy number evolution is a substantial challenge, because different CNAs may overlap with one another on the genome. A recent popular model for copy number evolution is the copy number distance (CND), defined as the length of a shortest sequence of deletions and amplifications of contiguous segments that transforms one profile into the other. In the CND, all events contribute equally; however, it is well known that rates of CNAs vary by length, genomic position and type (amplification versus deletion). RESULTS We introduce a weighted CND that allows events to have varying weights, or probabilities, based on their length, position and type. We derive an efficient algorithm to compute the weighted CND as well as the associated transformation. This algorithm is based on the observation that the constraint matrix of the underlying optimization problem is totally unimodular. We show that the weighted CND improves phylogenetic reconstruction on simulated data where CNAs occur with varying probabilities, aids in the derivation of phylogenies from ultra-low-coverage single-cell DNA sequencing data and helps estimate CNA rates in a large pan-cancer dataset. AVAILABILITY AND IMPLEMENTATION Code is available at https://github.com/raphael-group/WCND. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ron Zeira
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ 08544, USA
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26
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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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27
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Alagpulinsa DA, Szalat RE, Poznansky MC, Shmookler Reis RJ. Genomic Instability in Multiple Myeloma. Trends Cancer 2020; 6:858-873. [PMID: 32487486 DOI: 10.1016/j.trecan.2020.05.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/18/2022]
Abstract
Genomic instability (GIN), an increased tendency to acquire genomic alterations, is a cancer hallmark. However, its frequency, underlying causes, and disease relevance vary across different cancers. Multiple myeloma (MM), a plasma cell malignancy, evolves through premalignant phases characterized by genomic abnormalities. Next-generation sequencing (NGS) methods are deconstructing the genomic landscape of MM across the continuum of its development, inextricably linking malignant transformation and disease progression with increasing acquisition of genomic alterations, and illuminating the mechanisms that generate these alterations. Although GIN drives disease evolution, it also creates vulnerabilities such as dependencies on 'superfluous' repair mechanisms and the induction of tumor-specific antigens that can be targeted. We review the mechanisms of GIN in MM, the associated vulnerabilities, and therapeutic targeting strategies.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Raphael E Szalat
- Department of Medical Oncology, Dana Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Medical Oncology, Boston University School of Medicine, Boston, MA 02118, USA
| | - Mark C Poznansky
- Vaccine and Immunotherapy Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare Service, Little Rock, AR 72205, USA; Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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28
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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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29
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Wu S, Ou T, Xing N, Lu J, Wan S, Wang C, Zhang X, Yang F, Huang Y, Cai Z. Whole-genome sequencing identifies ADGRG6 enhancer mutations and FRS2 duplications as angiogenesis-related drivers in bladder cancer. Nat Commun 2019; 10:720. [PMID: 30755618 PMCID: PMC6372626 DOI: 10.1038/s41467-019-08576-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 01/18/2019] [Indexed: 12/31/2022] Open
Abstract
Bladder cancer is one of the most common and highly vascularized cancers. To better understand its genomic structure and underlying etiology, we conduct whole-genome and targeted sequencing in urothelial bladder carcinomas (UBCs, the most common type of bladder cancer). Recurrent mutations in noncoding regions affecting gene regulatory elements and structural variations (SVs) leading to gene disruptions are prevalent. Notably, we find recurrent ADGRG6 enhancer mutations and FRS2 duplications which are associated with higher protein expression in the tumor and poor prognosis. Functional assays demonstrate that depletion of ADGRG6 or FRS2 expression in UBC cells compromise their abilities to recruit endothelial cells and induce tube formation. Moreover, pathway assessment reveals recurrent alterations in multiple angiogenesis-related genes. These results illustrate a multidimensional genomic landscape that highlights noncoding mutations and SVs in UBC tumorigenesis, and suggest ADGRG6 and FRS2 as novel pathological angiogenesis regulators that would facilitate vascular-targeted therapies for UBC. Bladder cancer is one of the most common and highly vascularized cancers. Here the authors perform a whole-genome analysis in urothelial bladder carcinomas and identify recurrent genetic alterations in a set of angiogenesis genes, facilitating the understanding of molecular mechanisms underlying pathological angiogenesis in this type of cancer.
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Affiliation(s)
- Song Wu
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China. .,Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China. .,Department of Urology, Minimally Invasive Surgery Center, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510000, China.
| | - Tong Ou
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China.,Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Nianzeng Xing
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100000, China.,Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100000, China
| | - Jiang Lu
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
| | - Shengqing Wan
- Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Changxi Wang
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
| | - Xi Zhang
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
| | - Feiya Yang
- Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100000, China.,Department of Urology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100000, China
| | - Yi Huang
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China.,Shenzhen Following Precision Medical Research Institute, Luohu Hospital Group, Shenzhen, 518000, China
| | - Zhiming Cai
- Urology Institute of Shenzhen University, The Third Affiliated Hospital of Shenzhen University, Shenzhen University, Shenzhen, 518000, China
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30
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Liu J, Nannas NJ, Fu FF, Shi J, Aspinwall B, Parrott WA, Dawe RK. Genome-Scale Sequence Disruption Following Biolistic Transformation in Rice and Maize. THE PLANT CELL 2019; 31:368-383. [PMID: 30651345 PMCID: PMC6447018 DOI: 10.1105/tpc.18.00613] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 12/13/2018] [Accepted: 01/09/2019] [Indexed: 05/20/2023]
Abstract
Biolistic transformation delivers nucleic acids into plant cells by bombarding the cells with microprojectiles, which are micron-scale, typically gold particles. Despite the wide use of this technique, little is known about its effect on the cell's genome. We biolistically transformed linear 48-kb phage lambda and two different circular plasmids into rice (Oryza sativa) and maize (Zea mays) and analyzed the results by whole genome sequencing and optical mapping. Although some transgenic events showed simple insertions, others showed extreme genome damage in the form of chromosome truncations, large deletions, partial trisomy, and evidence of chromothripsis and breakage-fusion bridge cycling. Several transgenic events contained megabase-scale arrays of introduced DNA mixed with genomic fragments assembled by nonhomologous or microhomology-mediated joining. Damaged regions of the genome, assayed by the presence of small fragments displaced elsewhere, were often repaired without a trace, presumably by homology-dependent repair (HDR). The results suggest a model whereby successful biolistic transformation relies on a combination of end joining to insert foreign DNA and HDR to repair collateral damage caused by the microprojectiles. The differing levels of genome damage observed among transgenic events may reflect the stage of the cell cycle and the availability of templates for HDR.
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Affiliation(s)
- Jianing Liu
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Natalie J Nannas
- Department of Biology, Hamilton College, Clinton, New York 13323
| | - Fang-Fang Fu
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Jinghua Shi
- Bionano Genomics, San Diego, California 92121
| | - Brooke Aspinwall
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Wayne A Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, Georgia 30602
| | - R Kelly Dawe
- Department of Genetics, University of Georgia, Athens, Georgia 30602
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
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31
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Deshpande V, Luebeck J, Nguyen NPD, Bakhtiari M, Turner KM, Schwab R, Carter H, Mischel PS, Bafna V. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat Commun 2019; 10:392. [PMID: 30674876 PMCID: PMC6344493 DOI: 10.1038/s41467-018-08200-y] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 12/13/2018] [Indexed: 01/17/2023] Open
Abstract
Focal oncogene amplification and rearrangements drive tumor growth and evolution in multiple cancer types. We present AmpliconArchitect (AA), a tool to reconstruct the fine structure of focally amplified regions using whole genome sequencing (WGS) and validate it extensively on multiple simulated and real datasets, across a wide range of coverage and copy numbers. Analysis of AA-reconstructed amplicons in a pan-cancer dataset reveals many novel properties of copy number amplifications in cancer. These findings support a model in which focal amplifications arise due to the formation and replication of extrachromosomal DNA. Applying AA to 68 viral-mediated cancer samples, we identify a large fraction of amplicons with specific structural signatures suggestive of hybrid, human-viral extrachromosomal DNA. AA reconstruction, integrated with metaphase fluorescence in situ hybridization (FISH) and PacBio sequencing on the cell-line UPCI:SCC090 confirm the extrachromosomal origin and fine structure of a Forkhead box E1 (FOXE1)-containing hybrid amplicon.
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Affiliation(s)
- Viraj Deshpande
- Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Jens Luebeck
- Bioinformatics and Systems Biology Program, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Nam-Phuong D Nguyen
- Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Mehrdad Bakhtiari
- Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Richard Schwab
- Department of Medicine, Division of Hematology-Oncology, School of Medicine, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Moores Cancer Center, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Pathology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
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32
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Macintyre G, Goranova TE, De Silva D, Ennis D, Piskorz AM, Eldridge M, Sie D, Lewsley LA, Hanif A, Wilson C, Dowson S, Glasspool RM, Lockley M, Brockbank E, Montes A, Walther A, Sundar S, Edmondson R, Hall GD, Clamp A, Gourley C, Hall M, Fotopoulou C, Gabra H, Paul J, Supernat A, Millan D, Hoyle A, Bryson G, Nourse C, Mincarelli L, Sanchez LN, Ylstra B, Jimenez-Linan M, Moore L, Hofmann O, Markowetz F, McNeish IA, Brenton JD. Copy number signatures and mutational processes in ovarian carcinoma. Nat Genet 2018; 50:1262-1270. [PMID: 30104763 PMCID: PMC6130818 DOI: 10.1038/s41588-018-0179-8] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 06/19/2018] [Indexed: 01/22/2023]
Abstract
The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.
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Affiliation(s)
| | | | | | - Darren Ennis
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Daoud Sie
- VU University Medical Center, Amsterdam, the Netherlands
| | - Liz-Anne Lewsley
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Aishah Hanif
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cheryl Wilson
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Suzanne Dowson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, London, UK
- University College London Hospital, London, UK
| | | | | | | | | | - Richard Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK
- Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, St Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Christina Fotopoulou
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK
| | - Hani Gabra
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK
- Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Anna Supernat
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - David Millan
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Aoisha Hoyle
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Gareth Bryson
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Craig Nourse
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Laura Mincarelli
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Bauke Ylstra
- VU University Medical Center, Amsterdam, the Netherlands
| | | | | | - Oliver Hofmann
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Iain A McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
- Beatson West of Scotland Cancer Centre, Glasgow, UK.
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK.
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Cambridge, UK.
- Addenbrooke's Hospital, Cambridge, UK.
- Department of Oncology, University of Cambridge, Cambridge, UK.
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33
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Abstract
The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.
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34
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Macintyre G, Goranova TE, De Silva D, Ennis D, Piskorz AM, Eldridge M, Sie D, Lewsley LA, Hanif A, Wilson C, Dowson S, Glasspool RM, Lockley M, Brockbank E, Montes A, Walther A, Sundar S, Edmondson R, Hall GD, Clamp A, Gourley C, Hall M, Fotopoulou C, Gabra H, Paul J, Supernat A, Millan D, Hoyle A, Bryson G, Nourse C, Mincarelli L, Sanchez LN, Ylstra B, Jimenez-Linan M, Moore L, Hofmann O, Markowetz F, McNeish IA, Brenton JD. Copy number signatures and mutational processes in ovarian carcinoma. Nat Genet 2018. [PMID: 30104763 DOI: 10.1038/s41588-018-0179-8]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.
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Affiliation(s)
| | | | | | - Darren Ennis
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | | | - Daoud Sie
- VU University Medical Center, Amsterdam, the Netherlands
| | - Liz-Anne Lewsley
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Aishah Hanif
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Cheryl Wilson
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Suzanne Dowson
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Michelle Lockley
- Barts Cancer Institute, Queen Mary University of London, London, UK.,University College London Hospital, London, UK
| | | | | | | | | | - Richard Edmondson
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, St Mary's Hospital, Manchester, UK.,Department of Obstetrics and Gynaecology, Manchester Academic Health Science Centre, St Mary's Hospital, Central Manchester NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK
| | | | | | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, MRC IGMM, University of Edinburgh, Edinburgh, UK
| | | | - Christina Fotopoulou
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK
| | - Hani Gabra
- Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK.,Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - James Paul
- Cancer Research UK Clinical Trials Unit, Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Anna Supernat
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - David Millan
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Aoisha Hoyle
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Gareth Bryson
- Department of Pathology, Queen Elizabeth University Hospital, Glasgow, UK
| | - Craig Nourse
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Laura Mincarelli
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK
| | | | - Bauke Ylstra
- VU University Medical Center, Amsterdam, the Netherlands
| | | | | | - Oliver Hofmann
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.,Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Iain A McNeish
- Institute of Cancer Sciences, University of Glasgow, Glasgow, UK. .,Beatson West of Scotland Cancer Centre, Glasgow, UK. .,Division of Cancer and Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College, London, UK.
| | - James D Brenton
- Cancer Research UK Cambridge Institute, Cambridge, UK. .,Addenbrooke's Hospital, Cambridge, UK. .,Department of Oncology, University of Cambridge, Cambridge, UK.
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35
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Zeira R, Shamir R. Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions. Bioinformatics 2018; 37:1489-1496. [PMID: 29726899 DOI: 10.1093/bioinformatics/bty381] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 01/30/2023] Open
Abstract
Motivation Problems of genome rearrangement are central in both evolution and cancer research. Most genome rearrangement models assume that the genome contains a single copy of each gene and the only changes in the genome are structural, i.e., reordering of segments. In contrast, tumor genomes also undergo numerical changes such as deletions and duplications, and thus the number of copies of genes varies. Dealing with unequal gene content is a very challenging task, addressed by few algorithms to date. More realistic models are needed to help trace genome evolution during tumorigenesis. Results Here we present a model for the evolution of genomes with multiple gene copies using the operation types double-cut-and-joins, duplications and deletions. The events supported by the model are reversals, translocations, tandem duplications, segmental deletions, and chromosomal amplifications and deletions, covering most types of structural and numerical changes observed in tumor samples. Our goal is to find a series of operations of minimum length that transform one karyotype into the other. We show that the problem is NP-hard and give an integer linear programming formulation that solves the problem exactly under some mild assumptions. We test our method on simulated genomes and on ovarian cancer genomes. Our study advances the state of the art in two ways: It allows a broader set of operations than extant models, thus being more realistic, and it is the first study attempting to reconstruct the full sequence of structural and numerical events during cancer evolution. Availability Code and data are available in https://github.com/Shamir-Lab/Sorting-Cancer-Karyotypes. Contact ronzeira@post.tau.ac.il, rshamir@tau.ac.il. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Ron Shamir
- Blavatnik School of Computer Science, Tel Aviv university, Tel Aviv, 6997801, Israel
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36
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Abstract
Cancer genome sequences contain footprints of somatic mutational processes, whose analysis in large tumor sequencing datasets has revealed novel mutational signatures, correlative features of variant topography, and complex events. Many of these analytic results have yet to reconciled with decades of mechanistic genome integrity research performed in controlled model systems. However, a new generation of genome-integrity experiments combining computational modeling, data analytics, and high-throughput sequencing are emerging to link mechanisms to patterns. Conversely, analytic studies evaluating quantitative footprints of specific genome integrity hypotheses will be critical in fitting naturally occurring mutational patterns to the predictions of a particular mechanistic model. Such quantitative and mechanistic studies will form the foundation of an emerging systems biology of genome integrity.
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Affiliation(s)
- John Maciejowski
- Rockefeller University, New York, USA.,New York Genome Center, New York, USA
| | - Marcin Imielinski
- New York Genome Center, New York, USA.,Weill Cornell Medicine, New York, USA
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37
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Li Y, Zhou S, Schwartz DC, Ma J. Allele-Specific Quantification of Structural Variations in Cancer Genomes. Cell Syst 2016; 3:21-34. [PMID: 27453446 PMCID: PMC4965314 DOI: 10.1016/j.cels.2016.05.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/13/2016] [Accepted: 05/24/2016] [Indexed: 12/21/2022]
Abstract
Aneuploidy and structural variations (SVs) generate cancer genomes containing a mixture of rearranged genomic segments with extensive somatic copy number alterations. However, existing methods can identify either SVs or allele-specific copy number alterations, but not both simultaneously, which provides a limited view of cancer genome structure. Here we introduce Weaver, an algorithm for the quantification and analysis of allele-specific copy numbers of SVs. Weaver uses a Markov Random Field to estimate joint probabilities of allele-specific copy number of SVs and their inter-connectivity based on paired-end whole-genome sequencing data. Weaver also predicts the timing of SVs relative to chromosome amplifications. We demonstrate the accuracy of Weaver using simulations and findings from whole-genome Optical Mapping. We apply Weaver to generate allele-specific copy numbers of SVs for MCF-7 and HeLa cell lines, and identify recurrent SV patterns in 44 TCGA ovarian cancer whole-genome sequencing datasets. Our approach provides a more complete assessment of the complex genomic architectures inherent to many cancer genomes.
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Affiliation(s)
- Yang Li
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Shiguo Zhou
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David C Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jian Ma
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA 15213, USA.
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38
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Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G. A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. Nat Commun 2016; 7:12222. [PMID: 27406316 PMCID: PMC4947184 DOI: 10.1038/ncomms12222] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/12/2016] [Indexed: 02/06/2023] Open
Abstract
HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism.
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Affiliation(s)
- Anthony Ferrari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Anne Vincent-Salomon
- Institut Curie, PSL Research University, Département de Pathologie, INSERM U934, 26 rue d'Ulm, 75248 Paris, France
| | - Xavier Pivot
- Centre Hospitalier Universitaire de Minjoz, UMR INSERM 1098, Boulevard A. Fleming, Besançon 25000, France
| | - Anne-Sophie Sertier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Emilie Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Sandrine Boyault
- Plateforme de génomique des cancers, Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Eskeatnaf Mulugeta
- Institut Curie, UMR 3215 CNRS, Génétique et biologie du développement, Epigénèse et développement des mammifères, U934 Inserm, 26 rue d'Ulm, 75248 Paris, France
| | - Isabelle Treilleux
- Centre Léon Bérard, Département de Pathologie, 28 rue Laënnec, 69008 Lyon, France
| | - Gaëtan MacGrogan
- Département de Biopathologie, Unité Inserm U916, Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux, France
| | - Laurent Arnould
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Vincent Le Texier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Hélène Blanché
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jean-François Deleuze
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jocelyne Jacquemier
- Institut Paoli-Calmettes, Département de Pathologie, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Marie-Christine Mathieu
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Frédérique Penault-Llorca
- Centre Jean Perrin, Département de Biopathologie, EA 4677 ERTICa, Université d'Auvergne, 58 rue Montalembert, 63000 Clermont-Ferrand, France
| | - Frédéric Bibeau
- Institut Régional du Cancer de Montpellier (ICM), Département de Pathologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Odette Mariani
- Institut Curie, PSL Research University, Service de Pathologie, Centre de Ressources Biologiques, BRIF BB-0033-00048, 26 rue d'Ulm, 75248 Paris, France
| | - Cécile Mannina
- Département de Pathologie, Institut Bergonié, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Jean-Yves Pierga
- Institut Curie, PSL Research University, Département d'Oncologie Médicale, Université Paris Descartes, 26 rue d'Ulm, 75248 Paris, France
| | - Olivier Trédan
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Thomas Bachelot
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Hervé Bonnefoi
- Department of Medical Oncology, Institut Bergonié Unicancer, University of Bordeaux, INSERM U916, CIC1401, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Gilles Romieu
- Institut Régional du Cancer de Montpellier (ICM), Oncologie Sénologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Pierre Fumoleau
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Suzette Delaloge
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Maria Rios
- Centre Alexis Vautrin, Département d'Oncologie Médicale, 6 Avenue de Bourgogne, 54511 Vandoeuvre Les Nancy, France
| | - Jean-Marc Ferrero
- Centre Antoine Lacassagne, Département d'Oncologie Médicale, 33 Avenue de Valombrose, 06189 Nice, France
| | - Carole Tarpin
- Institut Paoli-Calmettes, Département d'Oncologie Médicale, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Catherine Bouteille
- Clinique Mutualiste de Bellevue, Chirurgie Gynécologique et Mammaire, 3 rue le Verrier, 42100 Saint-Etienne, France
| | - Fabien Calvo
- Institut Gustave Roussy, Cancer Core Europe, 39 rue Camille Desmoulins, Villejuif 94805, France
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | | | - Iris Pauporté
- Institut National du Cancer, Département de Recherche Clinique, 52 Avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Pierre Saintigny
- INSERM U1052-CNRS 5286, Cancer Research Center of Lyon, F-69008 Lyon, France
- Université de Lyon, F-69622 Lyon, France
- Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Daniel Birnbaum
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Aix-Marseille Université, 232 boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, 38330 Montbonnot-Saint Martin, France
| | - Gilles Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
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39
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Zhang CZ, Pellman D. From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:117-37. [PMID: 26968629 DOI: 10.1101/sqb.2015.80.027623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analysis of mutations in thousands of cancer genomes has revealed many characteristic patterns of mutagenesis. The search for the molecular mechanisms underlying these mutational patterns has not only generated novel biological insight but also led to the development of new experimental strategies to study cell-to-cell variation and genome evolution. In this essay, we discuss recent progress in the study of mutational mechanisms with a particular emphasis on the analysis of mutagenesis at the single-cell level.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 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, 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 Howard Hughes Medical Institute, Boston, Massachusetts 02115
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40
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Greenman CD, Cooke SL, Marshall J, Stratton MR, Campbell PJ. Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process. J Math Biol 2016; 72:47-86. [PMID: 25833184 PMCID: PMC4702116 DOI: 10.1007/s00285-015-0875-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 03/04/2015] [Indexed: 12/11/2022]
Abstract
Breakage-fusion-bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. Here we study the evolution space of breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are [Formula: see text] qualitatively distinct evolutions involving [Formula: see text] breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the process to show these evolutions are not equally likely, and also describe how amplicons become localized. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples.
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Affiliation(s)
- C D Greenman
- School of Computing Sciences, University of East Anglia, Norwich, UK.
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK.
| | - S L Cooke
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - J Marshall
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - M R Stratton
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
| | - P J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
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41
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Abstract
The Breakage Fusion Bridge (BFB) process is a key marker for genomic instability, producing highly rearranged genomes in relatively small numbers of cell cycles. While the process itself was observed during the late 1930s, little is known about the extent of BFB in tumor genome evolution. Moreover, BFB can dramatically increase copy numbers of chromosomal segments, which in turn hardens the tasks of both reference-assisted and ab initio genome assembly. Based on available data such as Next Generation Sequencing (NGS) and Array Comparative Genomic Hybridization (aCGH) data, we show here how BFB evidence may be identified, and how to enumerate all possible evolutions of the process with respect to observed data. Specifically, we describe practical algorithms that, given a chromosomal arm segmentation and noisy segment copy number estimates, produce all segment count vectors supported by the data that can be produced by BFB, and all corresponding BFB architectures. This extends the scope of analyses described in our previous work, which produced a single count vector and architecture per instance. We apply these analyses to a comprehensive human cancer dataset, demonstrate the effectiveness and efficiency of the computation, and suggest methods for further assertions of candidate BFB samples. Source code of our tool can be found online.
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Affiliation(s)
- Shay Zakov
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, California
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42
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Chen HS, Hutter CM, Mechanic LE, Amos CI, Bafna V, Hauser ER, Hernandez RD, Li C, Liberles DA, McAllister K, Moore JH, Paltoo DN, Papanicolaou GJ, Peng B, Ritchie MD, Rosenfeld G, Witte JS, Gillanders EM, Feuer EJ. Genetic simulation tools for post-genome wide association studies of complex diseases. Genet Epidemiol 2014; 39:11-19. [PMID: 25371374 DOI: 10.1002/gepi.21870] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 09/02/2014] [Accepted: 09/26/2014] [Indexed: 01/12/2023]
Abstract
Genetic simulation programs are used to model data under specified assumptions to facilitate the understanding and study of complex genetic systems. Standardized data sets generated using genetic simulation are essential for the development and application of novel analytical tools in genetic epidemiology studies. With continuing advances in high-throughput genomic technologies and generation and analysis of larger, more complex data sets, there is a need for updating current approaches in genetic simulation modeling. To provide a forum to address current and emerging challenges in this area, the National Cancer Institute (NCI) sponsored a workshop, entitled "Genetic Simulation Tools for Post-Genome Wide Association Studies of Complex Diseases" at the National Institutes of Health (NIH) in Bethesda, Maryland on March 11-12, 2014. The goals of the workshop were to (1) identify opportunities, challenges, and resource needs for the development and application of genetic simulation models; (2) improve the integration of tools for modeling and analysis of simulated data; and (3) foster collaborations to facilitate development and applications of genetic simulation. During the course of the meeting, the group identified challenges and opportunities for the science of simulation, software and methods development, and collaboration. This paper summarizes key discussions at the meeting, and highlights important challenges and opportunities to advance the field of genetic simulation.
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Affiliation(s)
- Huann-Sheng Chen
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892
| | - Leah E Mechanic
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Christopher I Amos
- Division of Community, Family Medicine, Dartmouth College, Lebanon, NH 03755
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093
| | | | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143
| | - Chun Li
- Department of Biostatistics, Vanderbilt University, Nashville, TN 37235
| | - David A Liberles
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Kimberly McAllister
- Susceptibility and Population Health Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Jason H Moore
- Department of Genetics, Dartmouth College, Lebanon, NH 03755
| | - Dina N Paltoo
- Office of Director, National Institutes of Health, Bethesda, MD 20892
| | - George J Papanicolaou
- Division of Cardiovascular Sciences, Prevention and Population Sciences Program, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Bo Peng
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Marylyn D Ritchie
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802
| | - Gabriel Rosenfeld
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892
| | - John S Witte
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA 94107
| | - Elizabeth M Gillanders
- Epidemiology and Genomics Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Eric J Feuer
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Bethesda, MD 20892
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Cornélio DA, Tavares JCM, Pimentel TVCDA, Cavalcanti GB, Batistuzzo de Medeiros SR. Cytokinesis-block micronucleus assay adapted for analyzing genomic instability of human mesenchymal stem cells. Stem Cells Dev 2014; 23:823-38. [PMID: 24328548 DOI: 10.1089/scd.2013.0383] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Human mesenchymal stem cells (hMSCs) are multipotent cells used in cell therapy research. One of the problems involving hMSCs is the possibility of genetic instability during in vitro expansion required to obtain a suitable number of cells for clinical applications. The cytokinesis-block micronucleus (CBMN) assay measures genetic instability by analyzing the presence of micronucleus (MN), nucleoplasmic bridges (NPBs), and nuclear buds (NBUDs) in binucleated cells. The present study describes modifications in the CBMN assay methodology to analyze genetic instability in hMSCs isolated from the umbilical vein and in vitro expanded. The best protocol to achieve binucleated hMSCs with preserved cytoplasm was as follows: cytochalasin B concentration (4.0 μg/mL), use of hypotonic treatment (3 min), and the fixative solution (9 methanol:1 acetic acid). These adaptations were reproduced in three hMSC primary cell cultures and also in XP4PA and A549 cell lines. The frequency of hMSCs treated with mitomycin-C presenting MN was lower than that with other nuclear alterations, indicating that the hMSCs contain mechanisms to avoid a high level of chromosomal breaks. However, a high frequency of cells with NPBs was detected and spontaneous anaphase bridges under normal hMSC in vitro culture were observed. Considering that anaphase bridges are characteristic alterations in tumor cells, the CBMN assay is indicated as an important tool associated with other genetic analyses in order to ensure the safe clinical use of hMSCs in cell therapy.
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Affiliation(s)
- Déborah Afonso Cornélio
- 1 Departamento de Biologia Celular e Genética, Centro de Biociências, Universidade Federal do Rio Grande do Norte , Natal, Brazil
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Oesper L, Mahmoody A, Raphael BJ. THetA: inferring intra-tumor heterogeneity from high-throughput DNA sequencing data. Genome Biol 2013; 14:R80. [PMID: 23895164 PMCID: PMC4054893 DOI: 10.1186/gb-2013-14-7-r80] [Citation(s) in RCA: 146] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 07/29/2013] [Indexed: 12/11/2022] Open
Abstract
Tumor samples are typically heterogeneous, containing admixture by normal, non-cancerous cells and one or more subpopulations of cancerous cells. Whole-genome sequencing of a tumor sample yields reads from this mixture, but does not directly reveal the cell of origin for each read. We introduce THetA (Tumor Heterogeneity Analysis), an algorithm that infers the most likely collection of genomes and their proportions in a sample, for the case where copy number aberrations distinguish subpopulations. THetA successfully estimates normal admixture and recovers clonal and subclonal copy number aberrations in real and simulated sequencing data. THetA is available at http://compbio.cs.brown.edu/software/.
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Kim S, Medvedev P, Paton TA, Bafna V. Reprever: resolving low-copy duplicated sequences using template driven assembly. Nucleic Acids Res 2013; 41:e128. [PMID: 23658221 PMCID: PMC3695505 DOI: 10.1093/nar/gkt339] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Genomic sequence duplication is an important mechanism for genome evolution, often resulting in large sequence variations with implications for disease progression. Although paired-end sequencing technologies are commonly used for structural variation discovery, the discovery of novel duplicated sequences remains an unmet challenge. We analyze duplicons starting from identified high-copy number variants. Given paired-end mapped reads, and a candidate high-copy region, our tool, Reprever, identifies (a) the insertion breakpoints where the extra duplicons inserted into the donor genome and (b) the actual sequence of the duplicon. Reprever resolves ambiguous mapping signatures from existing homologs, repetitive elements and sequencing errors to identify breakpoint. At each breakpoint, Reprever reconstructs the inserted sequence using profile hidden Markov model (PHMM)-based guided assembly. In a test on 1000 artificial genomes with simulated duplication, Reprever could identify novel duplicates up to 97% of genomes within 3 bp positional and 1% sequence errors. Validation on 680 fosmid sequences identified and reconstructed eight duplicated sequences with high accuracy. We applied Reprever to reanalyzing a re-sequenced data set from the African individual NA18507 to identify >800 novel duplicates, including insertions in genes and insertions with additional variation. polymerase chain reaction followed by capillary sequencing validated both the insertion locations of the strongest predictions and their predicted sequence.
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Affiliation(s)
- Sangwoo Kim
- Department of Computer Science and Engineering, 9500 Gilman Dr University of California at San Diego, La Jolla, CA 92122, USA.
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