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Hayes M, Nguyen A, Islam R, Butler C, Tran E, Mullins D, Hicks C. HolistIC: leveraging Hi-C and whole genome shotgun sequencing for double minute chromosome discovery. Bioinformatics 2022; 38:1208-1215. [PMID: 34888626 PMCID: PMC9991898 DOI: 10.1093/bioinformatics/btab816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 01/05/2023] Open
Abstract
MOTIVATION Double minute (DM) chromosomes are acentric extrachromosomal DNA artifacts that are frequently observed in the cells of numerous cancers. They are highly amplified and contain oncogenes and drug-resistance genes, making their presence a challenge for effective cancer treatment. Algorithmic discovery of DM can potentially improve bench-derived therapies for cancer treatment. A hindrance to this task is that DMs evolve, yielding circular chromatin that shares segments from progenitor DMs. This creates DMs with overlapping amplicon coordinates. Existing DM discovery algorithms use whole genome shotgun sequencing (WGS) in isolation, which can potentially incorrectly classify DMs that share overlapping coordinates. RESULTS In this study, we describe an algorithm called 'HolistIC' that can predict DMs in tumor genomes by integrating WGS and Hi-C sequencing data. The consolidation of these sources of information resolves ambiguity in DM amplicon prediction that exists in DM prediction with WGS data used in isolation. We implemented and tested our algorithm on the tandem Hi-C and WGS datasets of three cancer datasets and a simulated dataset. Results on the cancer datasets demonstrated HolistIC's ability to predict DMs from Hi-C and WGS data in tandem. The results on the simulated data showed the HolistIC can accurately distinguish DMs that have overlapping amplicon coordinates, an advance over methods that predict extrachromosomal amplification using WGS data in isolation. AVAILABILITY AND IMPLEMENTATION Our software, named 'HolistIC', is available at http://www.github.com/mhayes20/HolistIC. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Matthew Hayes
- Department of Physics and Computer Science, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Angela Nguyen
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Rahib Islam
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Caryn Butler
- Department of Public Health Sciences, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Ethan Tran
- Department of Biology, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Derrick Mullins
- Department of Physics and Computer Science, Xavier University of Louisiana, New Orleans, LA 70125, USA
| | - Chindo Hicks
- Department of Genetics, Louisiana State University Health Sciences Center New Orleans, New Orleans, LA 70112, USA
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52
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Wu S, Bafna V, Chang HY, Mischel PS. Extrachromosomal DNA: An Emerging Hallmark in Human Cancer. ANNUAL REVIEW OF PATHOLOGY 2022; 17:367-386. [PMID: 34752712 PMCID: PMC9125980 DOI: 10.1146/annurev-pathmechdis-051821-114223] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Human genes are arranged on 23 pairs of chromosomes, but in cancer, tumor-promoting genes and regulatory elements can free themselves from chromosomes and relocate to circular, extrachromosomal pieces of DNA (ecDNA). ecDNA, because of its nonchromosomal inheritance, drives high-copy-number oncogene amplification and enables tumors to evolve their genomes rapidly. Furthermore, the circular ecDNA architecture fundamentally alters gene regulation and transcription, and the higher-order organization of ecDNA contributes to tumor pathogenesis. Consequently, patients whose cancers harbor ecDNA have significantly shorter survival. Although ecDNA was first observed more than 50 years ago, its critical importance has only recently come to light. In this review, we discuss the current state of understanding of how ecDNAs form and function as well as how they contribute to drug resistance and accelerated cancer evolution.
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Affiliation(s)
- Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA;
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes and Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
| | - Paul S Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA;
- Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, California, USA
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53
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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: 52] [Impact Index Per Article: 17.3] [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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54
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Hung KL, Yost KE, Xie L, Shi Q, Helmsauer K, Luebeck J, Schöpflin R, Lange JT, Chamorro González R, Weiser NE, Chen C, Valieva ME, Wong ITL, Wu S, Dehkordi SR, Duffy CV, Kraft K, Tang J, Belk JA, Rose JC, Corces MR, Granja JM, Li R, Rajkumar U, Friedlein J, Bagchi A, Satpathy AT, Tjian R, Mundlos S, Bafna V, Henssen AG, Mischel PS, Liu Z, Chang HY. ecDNA hubs drive cooperative intermolecular oncogene expression. Nature 2021; 600:731-736. [PMID: 34819668 PMCID: PMC9126690 DOI: 10.1038/s41586-021-04116-8] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 10/08/2021] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA) is prevalent in human cancers and mediates high expression of oncogenes through gene amplification and altered gene regulation1. Gene induction typically involves cis-regulatory elements that contact and activate genes on the same chromosome2,3. Here we show that ecDNA hubs-clusters of around 10-100 ecDNAs within the nucleus-enable intermolecular enhancer-gene interactions to promote oncogene overexpression. ecDNAs that encode multiple distinct oncogenes form hubs in diverse cancer cell types and primary tumours. Each ecDNA is more likely to transcribe the oncogene when spatially clustered with additional ecDNAs. ecDNA hubs are tethered by the bromodomain and extraterminal domain (BET) protein BRD4 in a MYC-amplified colorectal cancer cell line. The BET inhibitor JQ1 disperses ecDNA hubs and preferentially inhibits ecDNA-derived-oncogene transcription. The BRD4-bound PVT1 promoter is ectopically fused to MYC and duplicated in ecDNA, receiving promiscuous enhancer input to drive potent expression of MYC. Furthermore, the PVT1 promoter on an exogenous episome suffices to mediate gene activation in trans by ecDNA hubs in a JQ1-sensitive manner. Systematic silencing of ecDNA enhancers by CRISPR interference reveals intermolecular enhancer-gene activation among multiple oncogene loci that are amplified on distinct ecDNAs. Thus, protein-tethered ecDNA hubs enable intermolecular transcriptional regulation and may serve as units of oncogene function and cooperative evolution and as potential targets for cancer therapy.
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Affiliation(s)
- King L Hung
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Liangqi Xie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Quanming Shi
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Konstantin Helmsauer
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jens Luebeck
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Robert Schöpflin
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Joshua T Lange
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Rocío Chamorro González
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natasha E Weiser
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Celine Chen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Maria E Valieva
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ivy Tsz-Lo Wong
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Sihan Wu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Siavash R Dehkordi
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Connor V Duffy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Katerina Kraft
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jun Tang
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Julia A Belk
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Computer Science, Stanford University, Stanford, CA, USA
| | - John C Rose
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Jordan Friedlein
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Anindya Bagchi
- Tumor Initiation and Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Robert Tjian
- Department of Molecular and Cell Biology, Li Ka Shing Center for Biomedical and Health Sciences, CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA, USA
- Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Stefan Mundlos
- Development and Disease Research Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Anton G Henssen
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC), Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center DKFZ, Heidelberg, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Paul S Mischel
- ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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55
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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: 24] [Impact Index Per Article: 8.0] [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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56
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Sun Z, Ji N, Zhao R, Liang J, Jiang J, Tian H. Extrachromosomal circular DNAs are common and functional in esophageal squamous cell carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1464. [PMID: 34734016 PMCID: PMC8506789 DOI: 10.21037/atm-21-4372] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/09/2021] [Indexed: 01/17/2023]
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is the leading cause of cancer-related mortality. While recent studies have documented the presence of extrachromosomal circular DNAs (eccDNAs) in various tumors, to date, there have been no studies examining the distribution and function of eccDNAs in ESCC. Methods The eccDNAs from three surgically matched ESCC tissue samples were extracted and amplified by rolling circle amplification after removal of linear DNA and mitochondrial circular DNA. High-throughput eccDNA sequencing and bioinformatics analysis was performed to study the distribution pattern and the level of eccDNA expression. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed on the genes associated with the differentially expressed eccDNAs. Five up-regulated and five down-regulated candidate eccDNAs were validated by routine polymerase chain reaction (PCR), TOPO-TA cloning and Sanger sequencing. The nucleotides flanking the eccDNA junctions were analyzed to explore the mechanisms of eccDNA formation. Results A total of 184,557 eccDNAs was identified. The overall length distribution ranged from 33 to 968,842 base pairs (bp), with the peak at approximately 360 bp. These eccDNAs mainly originated from 5'- and 3'-untranslated regions (UTRs), and rarely from exons, introns, LINE, or Alu repeat regions. The chromosome distribution, length distribution, and genomic annotation of the eccDNAs were comparable between ESCC samples and matched normal epithelium. Nevertheless, 16,031 eccDNAs were found to be differentially expressed between ESCC and matched normal epithelium, including 10,126 up-regulated eccDNAs and 5,905 down-regulated eccDNAs. GO analysis and KEGG pathway analysis showed enriched in cancer pathways, mitogen-activated protein kinase (MAPK) pathway, GTPase-related activity, and cytoskeleton function. PCR, TOPO-TA cloning, and Sanger sequencing validated the junctional sites of five up-regulated candidate eccDNAs and four other unexpected eccDNAs. A repeat nucleotide pattern between the position flanking the start site and that flanking the end site was detected. Conclusions This study demonstrated the genome-wide presence of eccDNAs, explored the differential expression of eccDNAs, and revealed the potential mechanisms of eccDNAs in ESCC. This work provides further insights into our understanding of genome plasticity, the role of eccDNAs in ESCC, and may contribute to the development of potential clinical therapies.
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Affiliation(s)
- Zhenguo Sun
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Na Ji
- Medical Division, Shandong Provincial Western Hospital, Shandong Provincial Ear Nose Throat Hospital, Jinan, China
| | - Renchang Zhao
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jinghui Liang
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jin Jiang
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hui Tian
- Department of Thoracic Surgery, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
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57
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Lu W, Yu K, Li X, Ge Q, Liang G, Bai Y. Identification of full-length circular nucleic acids using long-read sequencing technologies. Analyst 2021; 146:6102-6113. [PMID: 34549740 DOI: 10.1039/d1an01147b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Unlike the traditional perception in genomic DNA or linear RNA, circular nucleic acids are a class of functional biomolecules with a circular configuration and are often observed in nature. These circular molecules encompass the full spectrum of size and play an important role in organisms, making circular nucleic acids research worthy. Due to the low abundance of most types of circular nucleic acids and the disadvantages of short-read sequencing platforms, accurate and full-length circular nucleic acid sequencing and identification is difficult. In this review, we have provided insights into full-length circular nucleic acid detection methods using long-read sequencing technologies, with a focus on the experimental and bioinformatics strategies to obtain accurate sequences.
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Affiliation(s)
- Wenxiang Lu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Kequan Yu
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Xiaohan Li
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Qinyu Ge
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Geyu Liang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, Jiangsu, 210096, China
| | - Yunfei Bai
- State Key Lab of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
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58
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Karami Fath M, Akbari Oryani M, Ramezani A, Barjoie Mojarad F, Khalesi B, Delazar S, Anjomrooz M, Taghizadeh A, Taghizadeh S, Payandeh Z, Pourzardosht N. Extra chromosomal DNA in different cancers: Individual genome with important biological functions. Crit Rev Oncol Hematol 2021; 166:103477. [PMID: 34534658 DOI: 10.1016/j.critrevonc.2021.103477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/30/2021] [Accepted: 09/03/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer can be caused by various factors, including the malfunction of tumor suppressor genes and the hyper-activation of proto-oncogenes. Tumor-associated extrachromosomal circular DNA (eccDNA) has been shown to adversely affect human health and accelerate malignant actions. Whole-genome sequencing (WGS) on different cancer types suggested that the amplification of ecDNA has increased the oncogene copy number in various cancers. The unique structure and function of ecDNA, its profound significance in cancer, and its help in the comprehension of current cancer genome maps, renders it as a hotspot to explore the tumor pathogenesis and evolution. Illumination of the basic mechanisms of ecDNA may provide more insights into cancer therapeutics. Despite the recent advances, different features of ecDNA require further elucidation. In the present review, we primarily discussed the characteristics, biogenesis, genesis, and origin of ecDNA and later highlighted its functions in both tumorigenesis and therapeutic resistance of different cancers.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Mahsa Akbari Oryani
- Department of Pathology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Arefeh Ramezani
- Department of Microbiology and Virology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Barjoie Mojarad
- Department of Radiology, Faculty of Paramedical Sciences, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Bahman Khalesi
- Department of Research and Production of Poultry Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research Education and Extension Organization, Karaj, Iran
| | - Sina Delazar
- Department of Radiology, Tehran University of Medical Sciences, Tehran, Iran
| | - Mehran Anjomrooz
- Department of Radiology, Shariati Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Arvin Taghizadeh
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahin Taghizadeh
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Navid Pourzardosht
- Biochemistry Department, Guilan University of Medical Sciences, Rasht, Iran.
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59
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Ling X, Han Y, Meng J, Zhong B, Chen J, Zhang H, Qin J, Pang J, Liu L. Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer. Mol Cancer 2021; 20:113. [PMID: 34479546 PMCID: PMC8414719 DOI: 10.1186/s12943-021-01413-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/22/2021] [Indexed: 12/13/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) refers to a type of circular DNA that originate from but are likely independent of chromosomes. Due to technological advancements, eccDNAs have recently emerged as multifunctional molecules with numerous characteristics. The unique topological structure and genetic characteristics of eccDNAs shed new light on the monitoring, early diagnosis, treatment, and prediction of cancer. EccDNAs are commonly observed in both normal and cancer cells and function via different mechanisms in the stress response to exogenous and endogenous stimuli, aging, and carcinogenesis and in drug resistance during cancer treatment. The structural diversity of eccDNAs contributes to the function and numerical diversity of eccDNAs and thereby endows eccDNAs with powerful roles in evolution and in cancer initiation and progression by driving genetic plasticity and heterogeneity from extrachromosomal sites, which has been an ignored function in evolution in recent decades. EccDNAs show great potential in cancer, and we summarize the features, biogenesis, evaluated functions, functional mechanisms, related methods, and clinical utility of eccDNAs with a focus on their role in evolution and cancer.
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Affiliation(s)
- Xiaoxuan Ling
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Yali Han
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jinxue Meng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Bohuan Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jialong Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - He Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jiheng Qin
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jing Pang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Linhua Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China. .,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.
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60
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Hong J, Zheng S, Jiang D. The contributions of extrachromosomal DNA elements in neoplasm progression. Am J Cancer Res 2021; 11:2417-2429. [PMID: 34249408 PMCID: PMC8263671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/13/2021] [Indexed: 06/13/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is a small, circular structure of DNA found outside chromosomes, in the cytoplasm and outside cells. Since the discovery of ecDNA in 1964, more studies have verified the significant prospect and application potential of its use in oncology. The presence of ecDNA is associated with a series of tumor activities such as the increasing or decreasing of oncogene copies, carcinogenic transmission, and activation of related signaling pathways. This review focuses on discussing the structure of ecDNA and its relevance in carcinogenesis, angiogenesis, drug resistance and metastasis.
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Affiliation(s)
- Jiawei Hong
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, China
- NHFPC Key Laboratory of Combined Multi-organ TransplantationHangzhou 310000, China
| | - Shusen Zheng
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, China
- NHFPC Key Laboratory of Combined Multi-organ TransplantationHangzhou 310000, China
- Key Laboratory of The Diagnosis and Treatment of Organ Transplantation, CAMSChina
- Key Laboratory of Organ TransplantationHangzhou 310003, Zhejiang Province, China
- Collaborative Innovation Center for Diagnosis Treatment of Infectious DiseasesHangzhou 310000, China
| | - Donghai Jiang
- Department of Surgery, Division of Hepatobiliary and Pancreatic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang UniversityHangzhou 310000, China
- NHFPC Key Laboratory of Combined Multi-organ TransplantationHangzhou 310000, China
- Key Laboratory of The Diagnosis and Treatment of Organ Transplantation, CAMSChina
- Key Laboratory of Organ TransplantationHangzhou 310003, Zhejiang Province, China
- Collaborative Innovation Center for Diagnosis Treatment of Infectious DiseasesHangzhou 310000, China
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61
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Wang T, Zhang H, Zhou Y, Shi J. Extrachromosomal circular DNA: a new potential role in cancer progression. J Transl Med 2021; 19:257. [PMID: 34112178 PMCID: PMC8194206 DOI: 10.1186/s12967-021-02927-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is considered a circular DNA molecule that exists widely in nature and is independent of conventional chromosomes. eccDNA can be divided into small polydispersed circular DNA (spcDNA), telomeric circles (t-circles), microDNA, and extrachromosomal DNA (ecDNA) according to its size and sequence. Multiple studies have shown that eccDNA is the product of genomic instability, has rich and important biological functions, and is involved in the occurrence of many diseases, including cancer. In this review, we focus on the discovery history, formation process, characteristics, and physiological functions of eccDNAs; the potential functions of various eccDNAs in human cancer; and the research methods employed to study eccDNA.
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Affiliation(s)
- Tianyi Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China. .,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.
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62
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FLT3 Amplification as Double Minute Chromosomes in a Patient with Chronic Myelomonocytic Leukemia. DISEASE MARKERS 2021; 2021:9932837. [PMID: 34194582 PMCID: PMC8203365 DOI: 10.1155/2021/9932837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 05/03/2021] [Accepted: 05/20/2021] [Indexed: 11/17/2022]
Abstract
Double minute chromosomes (dmins) are a form of gene amplification presenting as small spherical paired chromatin bodies. Dmins are rare in hematologic malignancies and are generally associated with a poor prognosis. Some case reports identified MYC or MLL gene amplification performing as dmin in myeloid neoplasms. FLT3 (FMS-related tyrosine kinase 3) acts as an oncogene in myeloid neoplasms which is associated with several signal transduction pathways. Genomic amplification of FLT3 has not been reported in hematological disease. The current study attempts to demonstrate the existence of double minute chromosomes via FLT3 gene amplification in a patient diagnosed with chronic myelomonocytic leukemia (CMML). Routine G-banded karyotype, array-based comparative genomic hybridization, and fluorescence in situ hybridization analyses were used to characterize the cytogenetic abnormality in the patient's bone marrow. FLT3 amplification as dmins in a patient with CMML was revealed. This case study reports a rare double minute chromosome via FLT3 amplification in CMML by using array-based comparative genomic hybridization and fluorescence in situ hybridization analyses. The study also proposed another possible mechanism of FLT3 genes in leukemogenesis.
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63
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Integrative reconstruction of cancer genome karyotypes using InfoGenomeR. Nat Commun 2021; 12:2467. [PMID: 33927198 PMCID: PMC8085216 DOI: 10.1038/s41467-021-22671-6] [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] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/23/2021] [Indexed: 02/02/2023] Open
Abstract
Annotation of structural variations (SVs) and base-level karyotyping in cancer cells remains challenging. Here, we present Integrative Framework for Genome Reconstruction (InfoGenomeR)-a graph-based framework that can reconstruct individual SVs into karyotypes based on whole-genome sequencing data, by integrating SVs, total copy number alterations, allele-specific copy numbers, and haplotype information. Using whole-genome sequencing data sets of patients with breast cancer, glioblastoma multiforme, and ovarian cancer, we demonstrate the analytical potential of InfoGenomeR. We identify recurrent derivative chromosomes derived from chromosomes 11 and 17 in breast cancer samples, with homogeneously staining regions for CCND1 and ERBB2, and double minutes and breakage-fusion-bridge cycles in glioblastoma multiforme and ovarian cancer samples, respectively. Moreover, we show that InfoGenomeR can discriminate private and shared SVs between primary and metastatic cancer sites that could contribute to tumour evolution. These findings indicate that InfoGenomeR can guide targeted therapies by unravelling cancer-specific SVs on a genome-wide scale.
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64
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Wang Y, Huang R, Zheng G, Shen J. Small ring has big potential: insights into extrachromosomal DNA in cancer. Cancer Cell Int 2021; 21:236. [PMID: 33902601 PMCID: PMC8077740 DOI: 10.1186/s12935-021-01936-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/13/2021] [Indexed: 12/23/2022] Open
Abstract
Recent technical advances have led to the discovery of novel functions of extrachromosomal DNA (ecDNA) in multiple cancer types. Studies have revealed that cancer-associated ecDNA shows a unique circular shape and contains oncogenes that are more frequently amplified than that in linear chromatin DNA. Importantly, the ecDNA-mediated amplification of oncogenes was frequently found in most cancers but rare in normal tissues. Multiple reports have shown that ecDNA has a profound impact on oncogene activation, genomic instability, drug sensitivity, tumor heterogeneity and tumor immunology, therefore may offer the potential for cancer diagnosis and therapeutics. Nevertheless, the underlying mechanisms and future applications of ecDNA remain to be determined. In this review, we summarize the basic concepts, biological functions and molecular mechanisms of ecDNA. We also provide novel insights into the fundamental role of ecDNA in cancer.
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Affiliation(s)
- Yihao Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Rui Huang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Guopei Zheng
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China
| | - Jianfeng Shen
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 200025, China.
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200025, China.
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65
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Qin XY, Gailhouste L. Non-Genomic Control of Dynamic MYCN Gene Expression in Liver Cancer. Front Oncol 2021; 10:618515. [PMID: 33937011 PMCID: PMC8085327 DOI: 10.3389/fonc.2020.618515] [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] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Upregulated MYCN gene expression is restricted to specialized cell populations such as EpCAM+ cancer stem cells in liver cancer, regardless of DNA amplification and mutation. Here, we reviewed the role of MYCN gene expression in liver homeostasis, regeneration, and tumorigenesis, and discussed the potential non-genomic mechanisms involved in controlling MYCN gene expression in liver cancer, with a focus on inflammation-mediated signal transduction and microRNA-associated post-transcriptional regulation. We concluded that dynamic MYCN gene expression is an integrated consequence of multiple signals in the tumor microenvironment, including tumor growth-promoting signals, lipid desaturation-mediated endoplasmic reticulum stress adaptation signals, and tumor suppressive miRNAs, making it a potential predictive biomarker of tumor stemness and plasticity. Therefore, understanding and tracing the dynamic changes and functions of MYCN gene expression will shed light on the origin of liver tumorigenesis at the cellular level and the development of novel therapeutic and diagnostic strategies for liver cancer treatment.
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Affiliation(s)
- Xian-Yang Qin
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Luc Gailhouste
- Liver Cancer Prevention Research Unit, RIKEN Cluster for Pioneering Research, Wako, Japan
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66
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Torgunakov NY, Kizilova EA, Karamysheva TV, Malinovskaya LP, Bikchurina TI, Borodin PM. Homogeneously Staining Regions (HSR) in Chromosome 1 of the House Mouse: Synapsis and Recombination at Meiosis. Cytogenet Genome Res 2021; 161:14-22. [PMID: 33725692 DOI: 10.1159/000513266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/16/2020] [Indexed: 11/19/2022] Open
Abstract
Amplified sequences constitute a large part of mammalian genomes. A chromosome 1 containing 2 large (up to 50 Mb) homogeneously staining regions (HSRs) separated by a small inverted euchromatic region is present in many natural populations of the house mouse (Mus musculus musculus). The HSRs are composed of a long-range repeat cluster, Sp100-rs, with a repeat length of 100 kb. In order to understand the organization and function of HSRs in meiotic chromosomes, we examined synapsis and recombination in male mice hetero- and homozygous for the HSR-carrying chromosome using FISH with an HSR-specific DNA probe and immunolocalization of the key meiotic proteins. In all homozygous and heterozygous pachytene nuclei, we observed fully synapsed linear homomorphic bivalents 1 marked by the HSR FISH probe. The synaptic adjustment in the heterozygotes was bilateral: the HSR-carrying homolog was shortened and the wild-type homolog was elongated. The adjustment was reversible: desynapsis at diplotene was accompanied by elongation of the HSRs. Immunolocalization of H3K9me2/3 indicated that the HSRs in the meiotic chromosome retained the epigenetic modification typical for C-heterochromatin in somatic cells. MLH1 foci, marking mature recombination nodules, were detected in the proximal HSR band in heterozygotes and in both HSR bands of homozygotes. Unequal crossing over within the long-range repeat cluster can cause variation in size of the HSRs, which has been detected in the natural populations of the house mouse.
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Affiliation(s)
- Nikita Y Torgunakov
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Elena A Kizilova
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Tatyana V Karamysheva
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Lyubov P Malinovskaya
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Tatiana I Bikchurina
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation, .,Novosibirsk State University, Novosibirsk, Russian Federation,
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67
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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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Vasudevan A, Schukken KM, Sausville EL, Girish V, Adebambo OA, Sheltzer JM. Aneuploidy as a promoter and suppressor of malignant growth. Nat Rev Cancer 2021; 21:89-103. [PMID: 33432169 DOI: 10.1038/s41568-020-00321-1] [Citation(s) in RCA: 84] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/12/2020] [Indexed: 12/13/2022]
Abstract
Aneuploidy has been recognized as a hallmark of tumorigenesis for more than 100 years, but the connection between chromosomal errors and malignant growth has remained obscure. New evidence emerging from both basic and clinical research has illuminated a complicated relationship: despite its frequency in human tumours, aneuploidy is not a universal driver of cancer development and instead can exert substantial tumour-suppressive effects. The specific consequences of aneuploidy are highly context dependent and are influenced by a cell's genetic and environmental milieu. In this Review, we discuss the diverse facets of cancer biology that are shaped by aneuploidy, including metastasis, drug resistance and immune recognition, and we highlight aneuploidy's distinct roles as both a tumour promoter and an anticancer vulnerability.
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69
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Jasiak A, Krawczyńska N, Iliszko M, Czarnota K, Buczkowski K, Stefanowicz J, Adamkiewicz-Drożyńska E, Cichosz G, Iżycka-Świeszewska E. Expression of BARD1 β Isoform in Selected Pediatric Tumors. Genes (Basel) 2021; 12:genes12020168. [PMID: 33530592 PMCID: PMC7911681 DOI: 10.3390/genes12020168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/20/2022] Open
Abstract
Currently, many new possible biomarkers and mechanisms are being searched and tested to analyse pathobiology of pediatric tumours for the development of new treatments. One such candidate molecular factor is BARD1 (BRCA1 Associated RING Domain 1)—a tumour-suppressing gene involved in cell cycle control and genome stability, engaged in several types of adult-type tumours. The data on BARD1 significance in childhood cancer is limited. This study determines the expression level of BARD1 and its isoform beta (β) in three different histogenetic groups of pediatric cancer—neuroblastic tumours, and for the first time in chosen germ cell tumours (GCT), and rhabdomyosarcoma (RMS), using the qPCR method. We found higher expression of beta isoform in tumour compared to healthy tissue with no such changes concerning BARD1 full-length. Additionally, differences in expression of BARD1 β between histological types of neuroblastic tumours were observed, with higher levels in ganglioneuroblastoma and ganglioneuroma. Furthermore, a higher expression of BARD1 β characterized yolk sac tumours (GCT type) and RMS when comparing with non-neoplastic tissue. These tumours also showed a high expression of the TERT (Telomerase Reverse Transcriptase) gene. In two RMS cases we found deep decrease of BARD1 β in post-chemotherapy samples. This work supports the oncogenicity of the beta isoform in pediatric tumours, as well as demonstrates the differences in its expression depending on the histological type of neoplasm, and the level of maturation in neuroblastic tumours.
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Affiliation(s)
- Anna Jasiak
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Natalia Krawczyńska
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, 407S Goodwin Ave, Urbana, IL 61801, USA;
| | - Mariola Iliszko
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
- Laboratory of Clinical Genetics, University Clinical Centre, 17 Smoluchowskiego St., 80-210 Gdansk, Poland
| | - Katarzyna Czarnota
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
| | - Kamil Buczkowski
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
| | - Joanna Stefanowicz
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Elżbieta Adamkiewicz-Drożyńska
- Department of Pediatrics, Hematology, Oncology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (J.S.); (E.A.-D.)
| | - Grzegorz Cichosz
- Department of Biology and Medical Genetics, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (A.J.); (M.I.); (G.C.)
| | - Ewa Iżycka-Świeszewska
- Department of Pathology and Neuropathology, Medical University of Gdansk, 1 Debinki St., 80-211 Gdansk, Poland; (K.C.); (K.B.)
- Department of Pathomorphology, Copernicus Hospitals, 1-6 Nowe Ogrody St., 80-803 Gdansk, Poland
- Correspondence:
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Wu S, Bafna V, Mischel PS. Extrachromosomal DNA (ecDNA) in cancer pathogenesis. Curr Opin Genet Dev 2021; 66:78-82. [PMID: 33477016 DOI: 10.1016/j.gde.2021.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/19/2022]
Abstract
In cancer, oncogenes and surrounding regulatory regions can untether themselves from chromosomes, forming extrachromosomal DNA particles (ecDNAs). Because of their non-chromosomal inheritance, ecDNA drives high oncogene copy number and intratumoral genetic heterogeneity, endowing tumors with the ability to rapidly change their genomes, accelerating tumor evolution, and contributing to therapeutic resistance. Further, the circular topology of ecDNA leads to enhanced chromatin accessibility, altered gene regulation, and massive oncogene transcription, driving tumor growth and progression, and placing ecDNA at the interface of cancer genomics and epigenetics. Recent studies show that ecDNA is a common event in many of the most aggressive forms of cancer, potentially challenging our current precision oncology approaches. In this review, we discuss what is known about ecDNA and its biological and clinical impact, highlighting new research and suggesting the promise, and some of the challenges ahead for the field.
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Affiliation(s)
- Sihan Wu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA; Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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71
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Liang X, Chen H, Li L, An R, Komiyama M. Ring-Structured DNA and RNA as Key Players In Vivoand In Vitro. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20200235] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Hui Chen
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Lin Li
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Ran An
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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72
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Xing J, Ning Q, Tang D, Mo Z, Lei X, Tang S. Progress on the role of extrachromosomal DNA in tumor pathogenesis and evolution. Clin Genet 2020; 99:503-512. [PMID: 33314031 DOI: 10.1111/cge.13896] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/03/2020] [Accepted: 12/09/2020] [Indexed: 12/23/2022]
Abstract
The amplification of oncogenes on extrachromosomal DNA (ecDNA) provides a new mechanism for cancer cells to adapt to the changes in the tumor microenvironment and accelerate tumor evolution. These extrachromosomal elements contain oncogenes, and their chromatin structures are more open than linear chromosomes and therefore have stronger oncogene transcriptional activity. ecDNA always contains enhancer elements, and genes on ecDNA can be reintegrated into the linear genome to regulate the selective expression of genes. ecDNA lacks centromeres, and the inheritance from the parent cell to the daughter cell is uneven. This non-Mendelian genetic mechanism results in the increase of tumor heterogeneity with daughter cells that can gain a competitive advantage through a large number of copies of oncogenes. ecDNA promotes tumor invasiveness and provides a mechanism for drug resistance associated with poorer survival outcomes. Recent studies have demonstrated that the overall proportion of ecDNA in tumors is approximately 40%. In this review, we summarize the current knowledge of ecDNA in the field of tumorigenesis and development.
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Affiliation(s)
- Jichen Xing
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, and Institute of Pharmacy & Pharmacology, University of South China, Hengyang, China.,Hunan Province Key Laboratory for Antibody-Based Drug and Intelligent Delivery System, Hunan University of Medicine, Huaihua, China
| | - Qian Ning
- Hunan Province Key Laboratory for Antibody-Based Drug and Intelligent Delivery System, Hunan University of Medicine, Huaihua, China
| | - Diya Tang
- Department of Medical Oncology, Xiangya Hospital Central South University, Changsha, China
| | - Zhongcheng Mo
- Institute of Basic Medical Sciences, College of Basic Medicine, Guilin Medical University, Guilin, Guangxi, China
| | - Xiaoyong Lei
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, and Institute of Pharmacy & Pharmacology, University of South China, Hengyang, China
| | - Shengsong Tang
- Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, and Institute of Pharmacy & Pharmacology, University of South China, Hengyang, China.,Hunan Province Key Laboratory for Antibody-Based Drug and Intelligent Delivery System, Hunan University of Medicine, Huaihua, China
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73
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Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nat Commun 2020; 11:5823. [PMID: 33199677 PMCID: PMC7669906 DOI: 10.1038/s41467-020-19452-y] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 09/30/2020] [Indexed: 12/16/2022] Open
Abstract
MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA (ecDNA). The exact amplicon structure has not been described thus far and the functional relevance of its rearrangements is unknown. Here, we analyze the MYCN amplicon structure using short-read and Nanopore sequencing and its chromatin landscape using ChIP-seq, ATAC-seq and Hi-C. This reveals two distinct classes of amplicons which explain the regulatory requirements for MYCN overexpression. The first class always co-amplifies a proximal enhancer driven by the noradrenergic core regulatory circuit (CRC). The second class of MYCN amplicons is characterized by high structural complexity, lacks key local enhancers, and instead contains distal chromosomal fragments harboring CRC-driven enhancers. Thus, ectopic enhancer hijacking can compensate for the loss of local gene regulatory elements and explains a large component of the structural diversity observed in MYCN amplification. MYCN amplification is common in neuroblastomas. Here the authors analyse the MYCN amplicon structure and its epigenetic regulation by integrating short- and longread genomic and epigenomic data and find two classes of MYCN amplicons in neuroblastomas, one driven by local enhancers and the other by hijacking of distal regulatory elements.
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74
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Wei J, Wu C, Meng H, Li M, Niu W, Zhan Y, Jin L, Duan Y, Zeng Z, Xiong W, Li G, Zhou M. The biogenesis and roles of extrachromosomal oncogene involved in carcinogenesis and evolution. Am J Cancer Res 2020; 10:3532-3550. [PMID: 33294253 PMCID: PMC7716155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/14/2020] [Indexed: 06/12/2023] Open
Abstract
More and more extrachromosomal DNA (ecDNA) was found in human tumor cells in recent years, which has a high copy number in tumors and changes the expression of oncogenes, thus different from normal chromosomal DNA. These circular structures were identified to originate from chromosomes, and play critical roles in rapid carcinogenesis, tumor evolution and multidrug resistance. Therefore, this review mostly focuses on the biogenesis and regulation of extrachromosomal oncogene in ecDNA as well as its function and mechanism in tumors, which are of great significance for our comprehensive understanding of the role of ecDNA in tumor carcinogenic mechanism and are expected to provide ecDNA with the potential to be a new molecular target for the diagnosis and treatment of tumors.
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Affiliation(s)
- Jianxia Wei
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Chunchun Wu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Hanbing Meng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Mengna Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
| | - Weihong Niu
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Yuting Zhan
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
- Department of Pathology, The Second Xiangya Hospital, Central South UniversityChangsha 410011, Hunan, China
| | - Long Jin
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Yumei Duan
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
| | - Ming Zhou
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
- Cancer Research Institute and School of Basic Medical Sciences, Central South UniversityChangsha 410078, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South UniversityChangsha 410078, Hunan, China
- Hunan Key Laboratory of Oncotarget Gene, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South UniversityChangsha 410013, Hunan, China
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75
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Jia X, Guan R, Cui X, Zhu J, Liu P, Zhang L, Wang D, Zhang Y, Dong K, Wu J, Ji W, Ji G, Bai J, Yu J, Yu Y, Sun W, Zhang F, Fu S. Molecular structure and evolution mechanism of two populations of double minutes in human colorectal cancer cells. J Cell Mol Med 2020; 24:14205-14216. [PMID: 33124133 PMCID: PMC7754069 DOI: 10.1111/jcmm.16035] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/26/2020] [Accepted: 10/11/2020] [Indexed: 12/13/2022] Open
Abstract
Gene amplification chiefly manifests as homogeneously stained regions (HSRs) or double minutes (DMs) in cytogenetically and extrachromosomal DNA (ecDNA) in molecular genetics. Evidence suggests that gene amplification is becoming a hotspot for cancer research, which may be a new treatment strategy for cancer. DMs usually carry oncogenes or chemoresistant genes that are associated with cancer progression, occurrence and prognosis. Defining the molecular structure of DMs will facilitate understanding of the molecular mechanism of tumorigenesis. In this study, we re‐identified the origin and integral sequence of DMs in human colorectal adenocarcinoma cell line NCI‐H716 by genetic mapping and sequencing strategy, employing high‐resolution array‐based comparative genomic hybridization, high‐throughput sequencing, multiplex‐fluorescence in situ hybridization and chromosome walking techniques. We identified two distinct populations of DMs in NCI‐H716, confirming their heterogeneity in cancer cells, and managed to construct their molecular structure, which were not investigated before. Research evidence of amplicons distribution in two different populations of DMs suggested that a multi‐step evolutionary model could fit the module of DM genesis better in NCI‐H716 cell line. In conclusion, our data implicated that DMs play a very important role in cancer progression and further investigation is necessary to uncover the role of the DMs.
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Affiliation(s)
- Xueyuan Jia
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Rongwei Guan
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Xiaobo Cui
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Jing Zhu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Peng Liu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Ling Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Dong Wang
- Scientific Research Centre, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Zhang
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China
| | - Kexian Dong
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Jie Wu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Wei Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Guohua Ji
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Jing Bai
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Jingcui Yu
- Scientific Research Centre, the Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Yang Yu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Wenjing Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
| | - Feng Zhang
- Obstetrics and Gynecology Hospital, State Key Laboratory of Genetic Engineering at School of Life Sciences, Institute of Reproduction and Development, Fudan University, Shanghai, China.,Key Laboratory of Reproduction Regulation of NPFPC, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai, China
| | - Songbin Fu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, China.,Key Laboratory of Preservation of Human Genetic Resources and Disease Control in China, Ministry of Education, Harbin Medical University, Harbin, China
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76
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Gu X, Yu J, Chai P, Ge S, Fan X. Novel insights into extrachromosomal DNA: redefining the onco-drivers of tumor progression. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2020; 39:215. [PMID: 33046109 PMCID: PMC7552444 DOI: 10.1186/s13046-020-01726-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/05/2020] [Indexed: 02/07/2023]
Abstract
Extrachromosomal DNA (ecDNA), gene-encoding extrachromosomal particles of DNA, is often present in tumor cells. Recent studies have revealed that oncogene amplification via ecDNA is widespread across a diverse range of cancers. ecDNA is involved in increasing tumor heterogeneity, reverting tumor phenotypes, and enhancing gene expression and tumor resistance to chemotherapy, indicating that it plays a significant role in tumorigenesis. In this review, we summarize the characteristics and genesis of ecDNA, connect these characteristics with their concomitant influences on tumorigenesis, enumerate the oncogenes encoded by ecDNA in multiple cancers, elaborate the roles of ecDNA in tumor pathogenesis and progression, and propose the considerable research and therapeutic prospects of ecDNA in cancer.
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Affiliation(s)
- Xiang Gu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Jie Yu
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Peiwei Chai
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P. R. China.,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China
| | - Shengfang Ge
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P. R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
| | - Xianqun Fan
- Department of Ophthalmology, Ninth People's Hospital, Shanghai JiaoTong University School of Medicine, Shanghai, 20025, P. R. China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 20025, People's Republic of China.
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77
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Yan Y, Guo G, Huang J, Gao M, Zhu Q, Zeng S, Gong Z, Xu Z. Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance. J Hematol Oncol 2020; 13:124. [PMID: 32928268 PMCID: PMC7491193 DOI: 10.1186/s13045-020-00960-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/03/2020] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.
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Affiliation(s)
- Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.,Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhicheng Gong
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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78
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Rizeq B, Sif S, Nasrallah GK, Ouhtit A. Novel role of BRCA1 interacting C-terminal helicase 1 (BRIP1) in breast tumour cell invasion. J Cell Mol Med 2020; 24:11477-11488. [PMID: 32888398 PMCID: PMC7576304 DOI: 10.1111/jcmm.15761] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/21/2020] [Accepted: 08/05/2020] [Indexed: 12/14/2022] Open
Abstract
Breast cancer (BC) is the most common malignancy and the leading cause of death in women worldwide. Only 5%‐10% of mutations in BRCA genes are associated with familial breast tumours in Eastern countries, suggesting the contribution of other genes. Using a microarray gene expression profiling study of BC, we have recently identified BRIP1 (fivefold up‐regulation) as a potential gene associated with BC progression in the Omani population. Although BRIP1 regulates DNA repair and cell proliferation, the precise role of BRIP1 in BC cell invasion/metastasis has not been explored yet; this prompted us to test the hypothesis that BRIP1 promotes BC cell proliferation and invasion. Using a combination of cellular and molecular approaches, our results revealed differential overexpression of BRIP1 in different BC cell lines. Functional assays validated further the physiological relevance of BRIP1 in tumour malignancy, and siRNA‐mediated BRIP1 knockdown significantly reduced BC cell motility by targeting key motility‐associated genes. Moreover, down‐regulation of BRIP1 expression significantly attenuated cell proliferation via cell cycle arrest. Our study is the first to show the novel function of BRIP1 in promoting BC cell invasion by regulating expression of various downstream target genes. Furthermore, these findings provide us with a unique opportunity to identify BRIP1‐induced pro‐invasive genes that could serve as biomarkers and/or targets to guide the design of appropriate BC targeted therapies.
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Affiliation(s)
- Balsam Rizeq
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar.,Biomedical Research Center, Qatar University, Doha, Qatar
| | - Saïd Sif
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar
| | - Gheyath K Nasrallah
- Biomedical Research Center, Qatar University, Doha, Qatar.,Biomedical Science Department, College of Health Sciences, Qatar University, Doha, Qatar
| | - Allal Ouhtit
- Department of Biological and Environmental Sciences, College of Arts & Sciences, Qatar University, Doha, Qatar
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79
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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: 42] [Impact Index Per Article: 10.5] [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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80
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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: 214] [Impact Index Per Article: 53.5] [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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81
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Liao Z, Jiang W, Ye L, Li T, Yu X, Liu L. Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression. Biochim Biophys Acta Rev Cancer 2020; 1874:188392. [PMID: 32735964 DOI: 10.1016/j.bbcan.2020.188392] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/26/2020] [Accepted: 07/10/2020] [Indexed: 02/08/2023]
Abstract
Although the eukaryotic genome is mainly comprised of linear chromosomal DNA, genes can also be found outside of chromosomes. The unconventional presence of extrachromosomal genes is usually found to be circular, and these structures are named extrachromosomal circular DNA (eccDNA), which are often observed in cancer cells. Various types of eccDNA including small polydispersed DNA (spcDNA), telomeric cirlces, microDNA, etc. have been discovered. Among these eccDNA, extrachromosomal DNA (ecDNA), which encompasses the full spectrum of large, gene-containing extrachromosomal particles, has regained great research interest due to recent technological advances such as next-generation sequencing and super-resolution microscopy. In this review, we summarize the different types of eccDNA and discuss the role of eccDNA, especially ecDNA in tumor heterogeneity and progression. Additionally, we discuss some possible future investigative directions related to ecDNA biogenesis and its clinical application.
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Affiliation(s)
- Zhenyu Liao
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wang Jiang
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Longyun Ye
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Tianjiao Li
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Liang Liu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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82
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Molin WT, Yaguchi A, Blenner M, Saski CA. The EccDNA Replicon: A Heritable, Extranuclear Vehicle That Enables Gene Amplification and Glyphosate Resistance in Amaranthus palmeri. THE PLANT CELL 2020; 32:2132-2140. [PMID: 32327538 PMCID: PMC7346551 DOI: 10.1105/tpc.20.00099] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/09/2020] [Accepted: 04/21/2020] [Indexed: 05/10/2023]
Abstract
Gene copy number variation is a predominant mechanism used by organisms to respond to selective pressures from the environment. This often results in unbalanced structural variations that perpetuate as adaptations to sustain life. However, the underlying mechanisms that give rise to gene proliferation are poorly understood. Here, we show a unique result of genomic plasticity in Amaranthus palmeri: a massive, ∼400-kb extrachromosomal circular DNA (eccDNA) that harbors the 5-ENOYLPYRUVYLSHIKIMATE-3-PHOSPHATE SYNTHASE (EPSPS) gene and 58 other genes whose encoded functions traverse detoxification, replication, recombination, transposition, tethering, and transport. Gene expression analysis under glyphosate stress showed transcription of 41 of these 59 genes, with high expression of EPSPS, as well as genes coding for aminotransferases, zinc finger proteins, and several uncharacterized proteins. The genomic architecture of the eccDNA replicon is composed of a complex arrangement of repeat sequences and mobile genetic elements interspersed among arrays of clustered palindromes that may be crucial for stability, DNA duplication and tethering, and/or a means of nuclear integration of the adjacent and intervening sequences. Comparative analysis of orthologous genes in grain amaranth (Amaranthus hypochondriacus) and waterhemp (Amaranthus tuberculatus) suggests that higher order chromatin interactions contribute to the genomic origins of the A. palmeri eccDNA replicon structure.
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Affiliation(s)
- William T Molin
- Crop Protection Systems Research Unit, U.S. Department of Agriculture-Agricultural Research Service, Stoneville, Mississippi 38776
| | - Allison Yaguchi
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634
| | - Mark Blenner
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634
| | - Christopher A Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina 29634
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83
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The adaptive potential of circular DNA accumulation in ageing cells. Curr Genet 2020; 66:889-894. [PMID: 32296868 PMCID: PMC7497353 DOI: 10.1007/s00294-020-01069-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/12/2020] [Accepted: 03/14/2020] [Indexed: 12/20/2022]
Abstract
Carefully maintained and precisely inherited chromosomal DNA provides long-term genetic stability, but eukaryotic cells facing environmental challenges can benefit from the accumulation of less stable DNA species. Circular DNA molecules lacking centromeres segregate randomly or asymmetrically during cell division, following non-Mendelian inheritance patterns that result in high copy number instability and massive heterogeneity across populations. Such circular DNA species, variously known as extrachromosomal circular DNA (eccDNA), microDNA, double minutes or extrachromosomal DNA (ecDNA), are becoming recognised as a major source of the genetic variation exploited by cancer cells and pathogenic eukaryotes to acquire drug resistance. In budding yeast, circular DNA molecules derived from the ribosomal DNA (ERCs) have been long known to accumulate with age, but it is now clear that aged yeast also accumulate other high-copy protein-coding circular DNAs acquired through both random and environmentally-stimulated recombination processes. Here, we argue that accumulation of circular DNA provides a reservoir of heterogeneous genetic material that can allow rapid adaptation of aged cells to environmental insults, but avoids the negative fitness impacts on normal growth of unsolicited gene amplification in the young population.
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84
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Bailey C, Shoura MJ, Mischel PS, Swanton C. Extrachromosomal DNA-relieving heredity constraints, accelerating tumour evolution. Ann Oncol 2020; 31:884-893. [PMID: 32275948 DOI: 10.1016/j.annonc.2020.03.303] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/26/2020] [Indexed: 12/31/2022] Open
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) provides a mechanism by which cancer cells can rapidly adapt to changes in the tumour microenvironment. These circular structures contain oncogenes and their regulatory elements, and, lacking centromeres, they are subject to unequal segregation during mitosis. This non-Mendelian mechanism of inheritance results in increased tumour heterogeneity with daughter cells that can contain increasingly amplified oncogene copy number. These structures also contain favourable epigenetic modifications including transcriptionally active chromatin, further fuelling positive selection. ecDNA drives aggressive tumour behaviour, is related to poorer survival outcomes and provides mechanisms of drug resistance. Recent evidence suggests one in four solid tumours contain cells with ecDNA structures. The concept of tumour evolution is one in which cancer cells compete to survive in a diverse tumour microenvironment under the Darwinian principles of variation and fitness heritability. Unconstrained by conventional segregation constraints, ecDNA can accelerate intratumoral heterogeneity and cellular fitness. In this review, we highlight some of the recent discoveries underpinning this process.
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Affiliation(s)
- C Bailey
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK
| | - M J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, USA
| | - P S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, San Diego, USA; San Diego Moores Cancer Center, University of California, La Jolla, USA; Department of Pathology, University of California San Diego, La Jolla, USA
| | - C Swanton
- Cancer Evolution and Genome Instability Laboratory, The Francis Crick Institute, London, UK; Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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85
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Ain Q, Schmeer C, Wengerodt D, Witte OW, Kretz A. Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration. Int J Mol Sci 2020; 21:ijms21072477. [PMID: 32252492 PMCID: PMC7177960 DOI: 10.3390/ijms21072477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.
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Affiliation(s)
- Quratul Ain
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
- Correspondence:
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86
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Onagoruwa OT, Pal G, Ochu C, Ogunwobi OO. Oncogenic Role of PVT1 and Therapeutic Implications. Front Oncol 2020; 10:17. [PMID: 32117705 PMCID: PMC7010636 DOI: 10.3389/fonc.2020.00017] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/07/2020] [Indexed: 12/14/2022] Open
Abstract
PVT1, a long non-coding RNA has been implicated in a variety of human cancers. Recent advancements have led to increasing discovery of the critical roles of PVT1 in cancer initiation and progression. Novel insight is emerging about PVT1's mechanism of action in different cancers. Identifying and understanding the variety of activities of PVT1 involved in cancers is a necessity for the development of PVT1 as a diagnostic biomarker or therapeutic target in cancers where PVT1 is dysregulated. PVT1's varied activities include overexpression, modulation of miRNA expression, protein interactions, targeting of regulatory genes, formation of fusion genes, functioning as a competing endogenous RNA (ceRNA), and interactions with MYC, among many others. Furthermore, bioinformatic analysis of PVT1 interactions in cancers has aided understanding of the numerous pathways involved in PVT1 contribution to carcinogenesis in a cancer type-specific manner. However, these recent findings show that there is much more to be learned to be able to fully exploit PVT1 for cancer prognostication and therapy. In this review, we summarize some of the latest findings on PVT1's oncogenic activities, signaling networks and how targeting these networks can be a strategy for cancer therapy.
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Affiliation(s)
| | - Gargi Pal
- Hunter College (CUNY), New York, NY, United States
| | - Chika Ochu
- Hunter College (CUNY), New York, NY, United States
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87
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Walen KH. Near-Dead Cells to Special Tetraploidy to First Cells to Cancer Diagnostic Morphology: Unlikely Therapy-Gain from For-Profit Industrial Goliath. ACTA ACUST UNITED AC 2020. [DOI: 10.4236/jct.2020.117036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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88
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Circle-Seq: Isolation and Sequencing of Chromosome-Derived Circular DNA Elements in Cells. Methods Mol Biol 2020; 2119:165-181. [PMID: 31989524 DOI: 10.1007/978-1-0716-0323-9_15] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chromosome-derived extrachromosomal circular DNA elements (eccDNAs) are detected in all eukaryotes examined so far. Here I describe the Circle-Seq protocol, applicable for physical enrichment of eccDNAs of a broad size range, combined with sequence confirmation of circular structures.Briefly, by concise alkaline treatment and gentle gravity flow-through an ion-exchange column, eccDNAs are enriched in the eluate fraction. EccDNAs are enzymatically isolated by extensive Plasmid-Safe DNase digestion of linear chromosomes and further enriched by φ29 rolling circle amplification. By means of high throughput sequencing of amplified eccDNA and custom eccDNA mapping software, around ten-thousand unique eccDNA types could be detected at nucleotide resolution in a million human muscle nuclei by this method.
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89
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Koche RP, Rodriguez-Fos E, Helmsauer K, Burkert M, MacArthur IC, Maag J, Chamorro R, Munoz-Perez N, Puiggròs M, Dorado Garcia H, Bei Y, Röefzaad C, Bardinet V, Szymansky A, Winkler A, Thole T, Timme N, Kasack K, Fuchs S, Klironomos F, Thiessen N, Blanc E, Schmelz K, Künkele A, Hundsdörfer P, Rosswog C, Theissen J, Beule D, Deubzer H, Sauer S, Toedling J, Fischer M, Hertwig F, Schwarz RF, Eggert A, Torrents D, Schulte JH, Henssen AG. Extrachromosomal circular DNA drives oncogenic genome remodeling in neuroblastoma. Nat Genet 2019; 52:29-34. [PMID: 31844324 DOI: 10.1038/s41588-019-0547-z] [Citation(s) in RCA: 151] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/12/2019] [Indexed: 01/25/2023]
Abstract
Extrachromosomal circularization of DNA is an important genomic feature in cancer. However, the structure, composition and genome-wide frequency of extrachromosomal circular DNA have not yet been profiled extensively. Here, we combine genomic and transcriptomic approaches to describe the landscape of extrachromosomal circular DNA in neuroblastoma, a tumor arising in childhood from primitive cells of the sympathetic nervous system. Our analysis identifies and characterizes a wide catalog of somatically acquired and undescribed extrachromosomal circular DNAs. Moreover, we find that extrachromosomal circular DNAs are an unanticipated major source of somatic rearrangements, contributing to oncogenic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. Cancer-causing lesions can emerge out of circle-derived rearrangements and are associated with adverse clinical outcome. It is highly probable that circle-derived rearrangements represent an ongoing mutagenic process. Thus, extrachromosomal circular DNAs represent a multihit mutagenic process, with important functional and clinical implications for the origins of genomic remodeling in cancer.
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Affiliation(s)
- Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Elias Rodriguez-Fos
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Konstantin Helmsauer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Burkert
- Department of Biology, Humboldt University, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Ian C MacArthur
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jesper Maag
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rocio Chamorro
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalia Munoz-Perez
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Montserrat Puiggròs
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain
| | - Heathcliff Dorado Garcia
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Yi Bei
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Claudia Röefzaad
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Victor Bardinet
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annabell Szymansky
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annika Winkler
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Theresa Thole
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Natalie Timme
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katharina Kasack
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Fuchs
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Filippos Klironomos
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Eric Blanc
- Berlin Institute of Health, Berlin, Germany
| | - Karin Schmelz
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Künkele
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Patrick Hundsdörfer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carolina Rosswog
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jessica Theissen
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Hedwig Deubzer
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | | | - Joern Toedling
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Fischer
- Department of Experimental Pediatric Oncology, University Children's Hospital of Cologne, Cologne, Germany.,Center for Molecular Medicine Cologne, Medical Faculty, University of Cologne, Cologne, Germany
| | - Falk Hertwig
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland F Schwarz
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Angelika Eggert
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Torrents
- Barcelona Supercomputing Center, Joint Barcelona Supercomputing Center-Centre for Genomic Regulation-Institute for Research in Biomedicine Research Program in Computational Biology, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Johannes H Schulte
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.,Berlin Institute of Health, Berlin, Germany.,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anton G Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany. .,Berlin Institute of Health, Berlin, Germany. .,German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany. .,Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany.
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90
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Hull RM, King M, Pizza G, Krueger F, Vergara X, Houseley J. Transcription-induced formation of extrachromosomal DNA during yeast ageing. PLoS Biol 2019; 17:e3000471. [PMID: 31794573 PMCID: PMC6890164 DOI: 10.1371/journal.pbio.3000471] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/31/2019] [Indexed: 12/22/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) facilitates adaptive evolution by allowing rapid and extensive gene copy number variation and is implicated in the pathology of cancer and ageing. Here, we demonstrate that yeast aged under environmental copper accumulate high levels of eccDNA containing the copper-resistance gene CUP1. Transcription of the tandemly repeated CUP1 gene causes CUP1 eccDNA accumulation, which occurs in the absence of phenotypic selection. We have developed a sensitive and quantitative eccDNA sequencing pipeline that reveals CUP1 eccDNA accumulation on copper exposure to be exquisitely site specific, with no other detectable changes across the eccDNA complement. eccDNA forms de novo from the CUP1 locus through processing of DNA double-strand breaks (DSBs) by Sae2, Mre11 and Mus81, and genome-wide analyses show that other protein coding eccDNA species in aged yeast share a similar biogenesis pathway. Although abundant, we find that CUP1 eccDNA does not replicate efficiently, and high-copy numbers in aged cells arise through frequent formation events combined with asymmetric DNA segregation. The transcriptional stimulation of CUP1 eccDNA formation shows that age-linked genetic change varies with transcription pattern, resulting in gene copy number profiles tailored by environment. Transcription can cause the de novo formation of protein-coding extrachromosomal DNA that accumulates in ageing yeast cells; these extrachromosomal circular DNA molecules form frequently by a DNA double strand break repair mechanism.
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Affiliation(s)
- Ryan M. Hull
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Michelle King
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Grazia Pizza
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Felix Krueger
- Babraham Bioinformatics, Babraham Institute, Cambridge, United Kingdom
| | - Xabier Vergara
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme, Babraham Institute, Cambridge, United Kingdom
- * E-mail:
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91
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Yerlici VT, Lu MW, Hoge CR, Miller RV, Neme R, Khurana JS, Bracht JR, Landweber LF. Programmed genome rearrangements in Oxytricha produce transcriptionally active extrachromosomal circular DNA. Nucleic Acids Res 2019; 47:9741-9760. [PMID: 31504770 PMCID: PMC6765146 DOI: 10.1093/nar/gkz725] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/02/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is both a driver of eukaryotic genome instability and a product of programmed genome rearrangements, but its extent had not been surveyed in Oxytricha, a ciliate with elaborate DNA elimination and translocation during development. Here, we captured rearrangement-specific circular DNA molecules across the genome to gain insight into its processes of programmed genome rearrangement. We recovered thousands of circularly excised Tc1/mariner-type transposable elements and high confidence non-repetitive germline-limited loci. We verified their bona fide circular topology using circular DNA deep-sequencing, 2D gel electrophoresis and inverse polymerase chain reaction. In contrast to the precise circular excision of transposable elements, we report widespread heterogeneity in the circular excision of non-repetitive germline-limited loci. We also demonstrate that circular DNAs are transcribed in Oxytricha, producing rearrangement-specific long non-coding RNAs. The programmed formation of thousands of eccDNA molecules makes Oxytricha a model system for studying nucleic acid topology. It also suggests involvement of eccDNA in programmed genome rearrangement.
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Affiliation(s)
- V Talya Yerlici
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Michael W Lu
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Carla R Hoge
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Richard V Miller
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Rafik Neme
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Jaspreet S Khurana
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - John R Bracht
- Department of Biology, American University, Washington, DC 20016, USA
| | - Laura F Landweber
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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92
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Wu S, Turner KM, Nguyen N, Raviram R, Erb M, Santini J, Luebeck J, Rajkumar U, Diao Y, Li B, Zhang W, Jameson N, Corces MR, Granja JM, Chen X, Coruh C, Abnousi A, Houston J, Ye Z, Hu R, Yu M, Kim H, Law JA, Verhaak RGW, Hu M, Furnari FB, Chang HY, Ren B, Bafna V, Mischel PS. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 2019; 575:699-703. [PMID: 31748743 PMCID: PMC7094777 DOI: 10.1038/s41586-019-1763-5] [Citation(s) in RCA: 281] [Impact Index Per Article: 56.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 09/26/2019] [Indexed: 01/01/2023]
Abstract
Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.
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Affiliation(s)
- Sihan Wu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Kristen M Turner
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Nam Nguyen
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
- Boundless Bio, Inc., La Jolla, CA, USA
| | - Ramya Raviram
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Marcella Erb
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jennifer Santini
- UCSD Light Microscopy Core Facility, Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
| | - Jens Luebeck
- Bioinformatics & Systems Biology Graduate Program, University of California at San Diego, La Jolla, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Yarui Diao
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cell Biology, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
- Department of Orthopaedic Surgery, Regeneration Next Initiative, Duke University School of Medicine, Durham, NC, USA
| | - Bin Li
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Wenjing Zhang
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Nathan Jameson
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Xingqi Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ceyda Coruh
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Armen Abnousi
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jack Houston
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Zhen Ye
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Rong Hu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julie A Law
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Frank B Furnari
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
| | - Bing Ren
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, Center for Epigenomics, University of California at San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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93
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Koduru P, Chen W, Haley B, Ho K, Oliver D, Wilson K. Cytogenomic characterization of double minute heterogeneity in therapy related acute myeloid leukemia. Cancer Genet 2019; 238:69-75. [PMID: 31425928 DOI: 10.1016/j.cancergen.2019.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/24/2019] [Accepted: 08/06/2019] [Indexed: 01/04/2023]
Abstract
Breast cancer patients treated with adjuvant chemotherapy regimens containing alkylating agents and anthracyclines are at an increased risk for secondary myeloid malignancies, either acute myeloid leukemia (AML) or myelodysplastic syndrome (MDS). Complex genomic changes (karyotypes and/or gene amplification) accompany the development of the secondary neoplasms. Here we present a unique case of a breast cancer patient who developed secondary AML within 18 months of treatment with trastuzumab, pertuzumab, docetaxel, carboplatin (TCHP) and radiation. Leukemia cells had catastrophic alterations in chromosomes 8, 11, and 17. Genetic abnormalities in the leukemia cells included amplification of MYC and KMT2A as double minutes, and deletion and mutational inactivation of TP53 Concurrent amplification of different genes at different levels and on different double minutes, we have named "double minute heterogeneity." Clinically, this case highlights the need to identify genes amplified in secondary myeloid malignancies by cytogenomic microarray (CMA) analysis since these may have therapeutic implications.
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Affiliation(s)
- Prasad Koduru
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA.
| | - Weina Chen
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA
| | - Barbara Haley
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA
| | - Kevin Ho
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA
| | - Dwight Oliver
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA
| | - Kathleen Wilson
- Department of Pathology, and Division of Hematology and Oncology, Department of Medicine, UT Southwestern Medical Center, Dallas, USA
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94
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Sakhdari A, Tang Z, Ok CY, Bueso-Ramos CE, Medeiros LJ, Huh YO. Homogeneously staining region (hsr) on chromosome 11 is highly specific for KMT2A amplification in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Cancer Genet 2019; 238:18-22. [PMID: 31425921 DOI: 10.1016/j.cancergen.2019.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 01/01/2023]
Abstract
AML and MDS are most common myeloid neoplasms that affect mainly older patients. Overexpression of certain proto-oncogenes plays an indispensable role in tumorigenesis and overexpression can be a consequence of gene rearrangement, amplification and/or mutation. Rearrangement and amplification of KMT2A located at chromosome band 11q23 is a well-characterized genetic driver in a subset of AML/MDS cases and is associated with a poor prognosis. The presence of homogeneously staining regions (hsr) also has been correlated with amplification of specific proto-oncogenes. In this study, we correlated hsr(11)(q23) with KMT2A in a large cohort of AML/MDS (n = 54) patients. We identified 37 patients with hsr(11)(q23) in the setting of AML (n = 27) and MDS (n = 10). All patients showed a complex karyotype including 12 cases with monosomy 17. KMT2A FISH analysis was available for 35 patients which showed KMT2A amplification in all patients. Among control cases with hsr involving chromosomes other than 11q [non-11q hsr, n = 17], FISH analysis for KMT2A was available in 10 cases and none of these cases showed KMT2A amplification (p = 0.0001, Fisher's exact test, two-tailed). Mutational analysis was performed in 32 patients with hsr(11)(q23). The most common mutated gene was TP53 (n = 29), followed by DNMT3A (n = 4), NF1 (n = 4), and TET2 (n = 3). Thirty (83%) patients died over a median follow-up of 7.6 months (range, 0.4-33.4). In summary, hsr(11)(q23) in AML/MDS cases is associated with a complex karyotype, monosomy 17, KMT2A amplification, and TP53 mutation.
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Affiliation(s)
- Ali Sakhdari
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States.
| | - Zhenya Tang
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States
| | - Chi Young Ok
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States
| | - Carlos E Bueso-Ramos
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States
| | - L Jeffrey Medeiros
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States
| | - Yang O Huh
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas 77030-4009, United States
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95
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Abstract
Recent reports have demonstrated that oncogene amplification on extrachromosomal DNA (ecDNA) is a frequent event in cancer, providing new momentum to explore a phenomenon first discovered several decades ago. The direct consequence of ecDNA gains in these cases is an increase in DNA copy number of the oncogenes residing on the extrachromosomal element. A secondary effect, perhaps even more important, is that the unequal segregation of ecDNA from a parental tumour cell to offspring cells rapidly increases tumour heterogeneity, thus providing the tumour with an additional array of responses to microenvironment-induced and therapy-induced stress factors and perhaps providing an evolutionary advantage. This Perspectives article discusses the current knowledge and potential implications of oncogene amplification on ecDNA in cancer.
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Affiliation(s)
- Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
| | - Vineet Bafna
- Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, San Diego, La Jolla, CA, USA.
- UCSD School of Medicine, La Jolla, CA, USA.
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96
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Dadone-Montaudié B, Burel-Vandenbos F, Soler C, Rosello O, Boyer C, Fabas T, Bianchini L, Pedeutour F. Double minute chromosomes harboring MDM2 amplification in a pediatric atypical lipomatous tumor. Genes Chromosomes Cancer 2019; 58:673-679. [PMID: 30887579 DOI: 10.1002/gcc.22754] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 12/30/2022] Open
Abstract
Adipocytic tumors are rare in children and are mostly benign. Less than 25 cases of pediatric well-differentiated liposarcoma (WDLPS), atypical lipomatous tumors (ALT), and dedifferentiated liposarcoma (DDLPS) have been reported. Among them, only three cases were genetically analyzed. We describe the genetic features of a rapidly growing adipose tumor that occurred in the thigh of a 7-year-old girl. Histologically, it was composed of mature adipocytic cells with a few atypia. Molecular analysis showed high-level amplification of the 12q13-21 region including MDM2 among 64 amplified genes. MDM2 amplification is a diagnostic hallmark of ALT/WDLPS/DDLPS. In adult cases, it is typically located in ring or giant marker chromosomes. In the present case, extra-copies of MDM2 were located on double minute chromosomes (dmin). This raised the hypothesis of dmin being precursors of adult's rings and giant markers and may provide indications for a better understanding of the mechanisms of adipose tumor oncogenesis.
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Affiliation(s)
- Bérengère Dadone-Montaudié
- Laboratory of Solid Tumors Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice, Faculté de Médecine, Nice, France.,Central Laboratory of Pathology, Nice University Hospital, Hôpital Pasteur, Nice, France
| | - Fanny Burel-Vandenbos
- Central Laboratory of Pathology, Nice University Hospital, Hôpital Pasteur, Nice, France
| | - Christine Soler
- Department of Pediatric Onco-hematology, Nice University Hospital, Hôpital Archet 2, Nice, France
| | - Olivier Rosello
- Department of Pediatric Surgery, Hôpital Lenval, Nice, France
| | - Corinne Boyer
- Department of Pediatric Radiology, Hôpital Lenval, Nice, France
| | - Thibault Fabas
- Laboratory of Solid Tumors Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice, Faculté de Médecine, Nice, France
| | - Laurence Bianchini
- Laboratory of Solid Tumors Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice, Faculté de Médecine, Nice, France
| | - Florence Pedeutour
- Laboratory of Solid Tumors Genetics, Institute for Research on Cancer and Aging of Nice (IRCAN), CNRS UMR 7284/INSERM U1081, Université Côte d'Azur (UCA), Centre Hospitalier Universitaire de Nice, Faculté de Médecine, Nice, France
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97
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The roles played by the MYCN, Trk, and ALK genes in neuroblastoma and neural development. Surg Today 2019; 49:721-727. [PMID: 30848386 DOI: 10.1007/s00595-019-01790-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/20/2019] [Indexed: 12/23/2022]
Abstract
Neuroblastoma is one of the most frequent, yet distinctive and challenging childhood tumors. The uniqueness of this tumor depends on its biological markers, which classify neuroblastomas into favorable and unfavorable, with 5-year survival rates ranging from almost 100-30%. In this review, we focus on some biological factors that play major roles in neuroblastoma: MYCN, Trk, and ALK. The MYCN and Trk family genes have been studied for decades and are known to be crucial for the tumorigenesis and progression of neuroblastoma. ALK gene mutations have been recognized recently to be responsible for familial neuroblastomas. Each factor plays an important role in normal neural development, regulating cell proliferation or differentiation by activating several signaling pathways, and interacting with each other. These factors have been studied not only as prognostic factors, but also as targets of neuroblastoma therapy, and some clinical trials are ongoing. We review the basic aspects of MYCN, Trk, and ALK in both neural development and in neuroblastoma.
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98
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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: 131] [Impact Index Per Article: 26.2] [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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99
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Walen KH. Genomic Instability in Cancer II: 4N-Skewed (90°) Reductive Division via Fragile Sites to Fitness Increase for Solid and Hematological Cancer Beginnings. ACTA ACUST UNITED AC 2019. [DOI: 10.4236/jct.2019.107045] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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100
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Xu K, Ding L, Chang TC, Shao Y, Chiang J, Mulder H, Wang S, Shaw TI, Wen J, Hover L, McLeod C, Wang YD, Easton J, Rusch M, Dalton J, Downing JR, Ellison DW, Zhang J, Baker SJ, Wu G. Structure and evolution of double minutes in diagnosis and relapse brain tumors. Acta Neuropathol 2019; 137:123-137. [PMID: 30267146 PMCID: PMC6338707 DOI: 10.1007/s00401-018-1912-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 09/15/2018] [Accepted: 09/16/2018] [Indexed: 11/28/2022]
Abstract
Double minute chromosomes are extrachromosomal circular DNA fragments frequently found in brain tumors. To understand their evolution, we characterized the double minutes in paired diagnosis and relapse tumors from a pediatric high-grade glioma and four adult glioblastoma patients. We determined the full structures of the major double minutes using a novel approach combining multiple types of supporting genomic evidence. Among the double minutes identified in the pediatric patient, only one carrying EGFR was maintained at high abundance in both samples, whereas two others were present in only trace amounts at diagnosis but abundant at relapse, and the rest were found either in the relapse sample only or in the diagnosis sample only. For the EGFR-carrying double minutes, we found a secondary somatic deletion in all copies at relapse, after erlotinib treatment. However, the somatic mutation was present at very low frequency at diagnosis, suggesting potential resistance to the EGFR inhibitor. This mutation caused an in-frame RNA transcript to skip exon 16, a novel transcript isoform absent in EST database, as well as about 700 RNA-seq of normal brains that we reviewed. We observed similar patterns involving longitudinal copy number shift of double minutes in another four pairs (diagnosis/relapse) of adult glioblastoma. Overall, in three of five paired tumor samples, we found that although the same oncogenes were amplified at diagnosis and relapse, they were amplified on different double minutes. Our results suggest that double minutes readily evolve, increasing tumor heterogeneity rapidly. Understanding patterns of double minute evolution can shed light on future therapeutic solutions to brain tumors carrying such variants.
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Affiliation(s)
- Ke Xu
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Liang Ding
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ti-Cheng Chang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ying Shao
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jason Chiang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Heather Mulder
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shuoguo Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Tim I Shaw
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ji Wen
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Laura Hover
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - Clay McLeod
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yong-Dong Wang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - John Easton
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Michael Rusch
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - James Dalton
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - James R Downing
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA
| | - David W Ellison
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
| | - Jinghui Zhang
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Suzanne J Baker
- Department of Developmental Neurobiology, St. Jude Children's Research Hospital, 262 Danny Thomas Pl, Memphis, TN, 38105, USA.
| | - Gang Wu
- Department of Computational Biology, St. Jude Children's Research Hospital, MS1135, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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