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Tsiakanikas P, Athanasopoulou K, Darioti IA, Agiassoti VT, Theocharis S, Scorilas A, Adamopoulos PG. Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies. Life (Basel) 2024; 14:922. [PMID: 39202666 PMCID: PMC11355349 DOI: 10.3390/life14080922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/13/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a form of a circular double-stranded DNA that exists independently of conventional chromosomes. eccDNA exhibits a broad and random distribution across eukaryotic cells and has been associated with tumor-related properties due to its ability to harbor the complete gene information of oncogenes. The complex and multifaceted mechanisms underlying eccDNA formation include pathways such as DNA damage repair, breakage-fusion-bridge (BFB) mechanisms, chromothripsis, and cell apoptosis. Of note, eccDNA plays a pivotal role in tumor development, genetic heterogeneity, and therapeutic resistance. The high copy number and transcriptional activity of oncogenes carried by eccDNA contribute to the accelerated growth of tumors. Notably, the amplification of oncogenes on eccDNA is implicated in the malignant progression of cancer cells. The improvement of high-throughput sequencing techniques has greatly enhanced our knowledge of eccDNA by allowing for a detailed examination of its genetic structures and functions. However, we still lack a comprehensive and efficient annotation for eccDNA, while challenges persist in the study and understanding of the functional role of eccDNA, emphasizing the need for the development of robust methodologies. The potential clinical applications of eccDNA, such as its role as a measurable biomarker or therapeutic target in diseases, particularly within the spectrum of human malignancies, is a promising field for future research. In conclusion, eccDNA represents a quite dynamic and multifunctional genetic entity with far-reaching implications in cancer pathogenesis and beyond. Further research is essential to unravel the molecular pathways of eccDNA formation, elucidate its functional roles, and explore its clinical applications. Addressing these aspects is crucial for advancing our understanding of genomic instability and developing novel strategies for tailored therapeutics, especially in cancer.
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Affiliation(s)
- Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Ioanna A. Darioti
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Vasiliki Taxiarchoula Agiassoti
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Stamatis Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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Purshouse K, Pollard SM, Bickmore WA. Imaging extrachromosomal DNA (ecDNA) in cancer. Histochem Cell Biol 2024; 162:53-64. [PMID: 38625562 PMCID: PMC7616135 DOI: 10.1007/s00418-024-02280-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/19/2024] [Indexed: 04/17/2024]
Abstract
Extrachromosomal DNA (ecDNA) are circular regions of DNA that are found in many cancers. They are an important means of oncogene amplification, and correlate with treatment resistance and poor prognosis. Consequently, there is great interest in exploring and targeting ecDNA vulnerabilities as potential new therapeutic targets for cancer treatment. However, the biological significance of ecDNA and their associated regulatory control remains unclear. Light microscopy has been a central tool in the identification and characterisation of ecDNA. In this review we describe the different cellular models available to study ecDNA, and the imaging tools used to characterise ecDNA and their regulation. The insights gained from quantitative imaging are discussed in comparison with genome sequencing and computational approaches. We suggest that there is a crucial need for ongoing innovation using imaging if we are to achieve a full understanding of the dynamic regulation and organisation of ecDNA and their role in tumourigenesis.
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Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- Centre for Regenerative Medicine, Institute for Regeneration and Repair & Cancer Research UK Scotland Centre, University of Edinburgh, Edinburgh, UK
- Edinburgh Cancer Research UK Centre, University of Edinburgh, Edinburgh, UK
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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3
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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4
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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Wu N, Wei L, Zhu Z, Liu Q, Li K, Mao F, Qiao J, Zhao X. Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction. Protein Cell 2024; 15:6-20. [PMID: 37233789 PMCID: PMC10762679 DOI: 10.1093/procel/pwad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.
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Affiliation(s)
- Ning Wu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
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6
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Ren S, Wu D, Shen X, Wu Q, Li C, Xiong H, Xiong Z, Gong R, Liu Z, Wang W, Chen J. Deciphering the role of extrachromosomal circular DNA in adipose stem cells from old and young donors. Stem Cell Res Ther 2023; 14:341. [PMID: 38017497 PMCID: PMC10683086 DOI: 10.1186/s13287-023-03575-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 11/16/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND The functional impairment of adipose stem cells (ASCs) during aging limits their clinical transformation. Studies have shown that extrachromosomal circular DNAs (eccDNAs) are associated with tumor progression and cell aging, but the roles of eccDNAs in ASCs remain unknown. METHOD We conducted Circle sequencing (Circle-seq) to identify eccDNAs in ASCs isolated from young and old donors. The differentially expressed eccDNAs were calculated, annotated and validated via polymerase chain reaction. RESULTS Thousands of eccDNAs were identified and comprehensively characterized. Most of them were GC-rich, < 1000 base pairs in size, and were enriched on chromosome 19 and 17 with a high density of Alu elements and genes, 2 kb upstream/downstream of genes and satellites. In total, 3025 eccDNAs were differentially expressed among the two ASC groups. Conjoint analysis of the Circle-seq results and previous RNA-seq results revealed that 73 eccDNAs and 55 genes exhibited the same differential expression between the two groups. KEGG and GO analyses revealed that genes encoding differentially expressed eccDNAs were enriched for cell adhesion, cellular senescence and TGF-β receptor signaling pathway. We also found that aged ASCs exhibited loss of eccDNAs, including CAMK2G (chr10: 75577899-75578176), TRABD2B (chr1: 48305638-48307008) and TRABD2B (chr1: 48305425-48307091). CONCLUSION In this study, we elucidated the first eccDNA profile relating to ASCs and demonstrated that three eccDNAs are lost in aged ASCs, which may be potential biomarkers of stem cell aging and valuable targets for stem cell rejuvenation.
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Affiliation(s)
- Sen Ren
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Du Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Xiaoyong Shen
- Hospital of Stomatology Wuhan University, Wuhan, 430079, China
| | - Qian Wu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Chengcheng Li
- Department of Hand Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Hewei Xiong
- Department of Emergency Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Zhongwei Xiong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Rui Gong
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Zheng Liu
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Wei Wang
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
| | - Jincao Chen
- Department of Neurosurgery, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China.
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7
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Rose JC, Wong ITL, Daniel B, Jones MG, Yost KE, Hung KL, Curtis EJ, Mischel PS, Chang HY. Disparate pathways for extrachromosomal DNA biogenesis and genomic DNA repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.22.563489. [PMID: 37961138 PMCID: PMC10634728 DOI: 10.1101/2023.10.22.563489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Oncogene amplification on extrachromosomal DNA (ecDNA) is a pervasive driver event in cancer, yet our understanding of how ecDNA forms is limited. Here, we couple a CRISPR-based method for induction of ecDNA with extensive characterization of newly formed ecDNA to examine ecDNA biogenesis. We find that DNA circularization is efficient, irrespective of 3D genome context, with formation of a 1 Mb and 1.8 Mb ecDNA both reaching 15%. We show non-homologous end joining and microhomology mediated end joining both contribute to ecDNA formation, while inhibition of DNA-PKcs and ATM have opposing impacts on ecDNA formation. EcDNA and the corresponding chromosomal excision scar form at significantly different rates and respond differently to DNA-PKcs and ATM inhibition. Taken together, our results support a model of ecDNA formation in which double strand break ends dissociate from their legitimate ligation partners prior to joining of illegitimate ends to form the ecDNA and excision scar.
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Affiliation(s)
- John C Rose
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ivy Tsz-Lo Wong
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Bence Daniel
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew G Jones
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Kathryn E Yost
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - King L Hung
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Ellis J Curtis
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Paul S Mischel
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
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8
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Zivanovic A, Miller J, Munro S, Knutson T, Li Y, Passow C, Simonaitis P, Lynch M, Oseth L, Zhao S, Feng F, Wikström P, Corey E, Morrissey C, Henzler C, Raphael B, Dehm S. Co-evolution of AR gene copy number and structural complexity in endocrine therapy resistant prostate cancer. NAR Cancer 2023; 5:zcad045. [PMID: 37636316 PMCID: PMC10448862 DOI: 10.1093/narcan/zcad045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/17/2023] [Accepted: 08/09/2023] [Indexed: 08/29/2023] Open
Abstract
Androgen receptor (AR) inhibition is standard of care for advanced prostate cancer (PC). However, efficacy is limited by progression to castration-resistant PC (CRPC), usually due to AR re-activation via mechanisms that include AR amplification and structural rearrangement. These two classes of AR alterations often co-occur in CRPC tumors, but it is unclear whether this reflects intercellular or intracellular heterogeneity of AR. Resolving this is important for developing new therapies and predictive biomarkers. Here, we analyzed 41 CRPC tumors and 6 patient-derived xenografts (PDXs) using linked-read DNA-sequencing, and identified 7 tumors that developed complex, multiply-rearranged AR gene structures in conjunction with very high AR copy number. Analysis of PDX models by optical genome mapping and fluorescence in situ hybridization showed that AR residing on extrachromosomal DNA (ecDNA) was an underlying mechanism, and was associated with elevated levels and diversity of AR expression. This study identifies co-evolution of AR gene copy number and structural complexity via ecDNA as a mechanism associated with endocrine therapy resistance.
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Affiliation(s)
- Andrej Zivanovic
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Jeffrey T Miller
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Sarah A Munro
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Todd P Knutson
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Yingming Li
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Courtney N Passow
- University of Minnesota Genomics Center, University of Minnesota, Minneapolis, MN, USA
| | - Pijus Simonaitis
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Molly Lynch
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - LeAnn Oseth
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin-Madison, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, USA
- William S. Middleton Memorial Veterans Hospital, Madison, Madison, WI, USA
| | - Felix Y Feng
- Departments of Radiation Oncology, Urology, and Medicine, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California at San Francisco, San Francisco, CA, USA
| | - Pernilla Wikström
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, WA, USA
| | - Christine Henzler
- Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin J Raphael
- Department of Computer Science, Princeton University, Princeton, NJ, USA
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Department of Urology, University of Minnesota, Minneapolis, MN, USA
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9
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dos Santos CR, Hansen LB, Rojas-Triana M, Johansen AZ, Perez-Moreno M, Regenberg B. Variation of extrachromosomal circular DNA in cancer cell lines. Comput Struct Biotechnol J 2023; 21:4207-4214. [PMID: 37705597 PMCID: PMC10495552 DOI: 10.1016/j.csbj.2023.08.027] [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: 05/03/2023] [Revised: 08/26/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023] Open
Abstract
The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro growth of cancer cell lines, questioning the reproducibility of studies utilizing cancer cell line models. Here, we conducted a comprehensive analysis of eccDNA variability in seven cancer cell lines (MCA3D, PDV, HaCa4, CarC, MIA-PaCa-2, AsPC-1, and PC-3). We compared the content of unique eccDNAs between triplicates of each cell line and found that the number of unique eccDNA is specific to each cell line, while the eccDNA sequence content varied greatly among triplicates (∼ 0-1% eccDNA coordinate commonality). In the PC-3 cell line, we found that the large eccDNA (ecDNA) with MYC is present in high-copy number in an NCI cell line isolate but not present in ATCC isolates. Together, these results reveal that the sequence content of eccDNA is highly variable in cancer cell lines. This highlights the importance of testing cancer cell lines before use, and to enrich for subclones in cell lines with the desired eccDNA to get relatively pure population for studying the role of eccDNA in cancer.
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Affiliation(s)
| | | | - Monica Rojas-Triana
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Astrid Zedlitz Johansen
- Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, DK-2730 Herlev, Denmark
| | - Mirna Perez-Moreno
- Cell biology and Physiology, Department of Biology, University of Copenhagen, Denmark
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
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Conte M, Matteuzzi T, Esposito A, Chiariello AM, Bianco S, Vercellone F, Nicodemi M. Phase separation of ecDNA aggregates establishes in-trans contact domains boosting selective MYC regulatory interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.17.549291. [PMID: 37503084 PMCID: PMC10370113 DOI: 10.1101/2023.07.17.549291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Extrachromosomal DNAs (ecDNAs) are found in the nucleus of an array of human cancer cells where they can form clusters that were associated to oncogene overexpression, as they carry genes and cis-regulatory elements. Yet, the mechanisms of aggregation and gene amplification beyond copy-number effects remain mostly unclear. Here, we investigate, at the single molecule level, MYC-harboring ecDNAs of COLO320-DM colorectal cancer cells by use of a minimal polymer model of the interactions of ecDNA BRD4 binding sites and BRD4 molecules. We find that BRD4 induces ecDNAs phase separation, resulting in the self-assembly of clusters whose predicted structure is validated against HiChIP data (Hung et al., 2021). Clusters establish in-trans associated contact domains (I-TADs) enriched, beyond copy number, in regulatory contacts among specific ecDNA regions, encompassing its PVT1-MYC fusions but not its other canonical MYC copy. That explains why the fusions originate most of ecDNA MYC transcripts (Hung et al., 2021), and shows that ecDNA clustering per se is important but not sufficient to amplify oncogene expression beyond copy-number, reconciling opposite views on the role of clusters (Hung et al., 2021; Zhu et al., 2021; Purshouse et al. 2022). Regulatory contacts become strongly enriched as soon as half a dozen ecDNAs aggregate, then saturate because of steric hindrance, highlighting that even cells with few ecDNAs can experience pathogenic MYC upregulations. To help drug design and therapeutic applications, with the model we dissect the effects of JQ1, a BET inhibitor. We find that JQ1 reverses ecDNA phase separation hence abolishing I-TADs and extra regulatory contacts, explaining how in COLO320-DM cells it reduces MYC transcription (Hung et al., 2021).
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Affiliation(s)
- Mattia Conte
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Tommaso Matteuzzi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea Esposito
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Andrea M. Chiariello
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Simona Bianco
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Francesca Vercellone
- DIETI, Università di Napoli Federico II, Via Claudio 21, 80125 Naples, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
| | - Mario Nicodemi
- Dipartimento di Fisica, Università di Napoli Federico II, and INFN Napoli, Complesso Universitario di Monte Sant’Angelo, 80126 Naples, Italy
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11
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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12
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Bianconi A, Palmieri G, Aruta G, Monticelli M, Zeppa P, Tartara F, Melcarne A, Garbossa D, Cofano F. Updates in Glioblastoma Immunotherapy: An Overview of the Current Clinical and Translational Scenario. Biomedicines 2023; 11:1520. [PMID: 37371615 DOI: 10.3390/biomedicines11061520] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 05/21/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
Glioblastoma (GBM) is the most common and aggressive central nervous system tumor, requiring multimodal management. Due to its malignant behavior and infiltrative growth pattern, GBM is one of the most difficult tumors to treat and gross total resection is still considered to be the first crucial step. The deep understanding of GBM microenvironment and the possibility of manipulating the patient's innate and adaptive immune system to fight the neoplasm represent the base of immunotherapeutic strategies that currently express the future for the fight against GBM. Despite the immunotherapeutic approach having been successfully adopted in several solid and haematologic neoplasms, immune resistance and the immunosuppressive environment make the use of these strategies challenging in GBM treatment. We describe the most recent updates regarding new therapeutic strategies that target the immune system, immune checkpoint inhibitors, chimeric antigen receptor T cell therapy, peptide and oncolytic vaccines, and the relevant mechanism of immune resistance. However, no significant results have yet been obtained in studies targeting single molecules/pathways. The future direction of GBM therapy will include a combined approach that, in contrast to the inescapable current treatment modality of maximal resection followed by chemo- and radiotherapy, may combine a multifaceted immunotherapy treatment with the dual goals of directly killing tumor cells and activating the innate and adaptive immune response.
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Affiliation(s)
- Andrea Bianconi
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | | | - Gelsomina Aruta
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Matteo Monticelli
- UOC Neurochirurgia, Dipartimento di Medicina Traslazionale e per la Romagna, Università degli Studi di Ferrara, 44121 Ferrara, Italy
| | - Pietro Zeppa
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Fulvio Tartara
- Headache Science and Neurorehabilitation Center, IRCCS Mondino Foundation, Department of Brain and Behavioral Sciences, University of Pavia, 27100 Pavia, Italy
| | - Antonio Melcarne
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Diego Garbossa
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
| | - Fabio Cofano
- Neurosurgery, Department of Neurosciences, University of Turin, 10126 Turin, Italy
- Humanitas Gradenigo, 10100 Turin, Italy
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13
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Yang Y, Yang Y, Huang H, Song T, Mao S, Liu D, Zhang L, Li W. PLCG2 can exist in eccDNA and contribute to the metastasis of non-small cell lung cancer by regulating mitochondrial respiration. Cell Death Dis 2023; 14:257. [PMID: 37031207 PMCID: PMC10082821 DOI: 10.1038/s41419-023-05755-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 03/14/2023] [Accepted: 03/17/2023] [Indexed: 04/10/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) participate in tumorigenesis and tumor progression. However, the role and mechanism of eccDNAs have yet to be elucidated in non-small cell lung cancer (NSCLC). In our research, three surgically matched NSCLC tissue samples, NSCLC cell lines (H1299, A549, and H460), and a normal lung cell line (MRC-5) were used as study objects. High-throughput eccDNA sequencing and bioinformatics analysis were performed to study the distribution pattern and level of eccDNA expression. The upregulated candidate eccDNA-encoding PLCG2 was validated by routine PCR. Plasmid transfection, RNA interference, qRT‒PCR and western blotting experiments were used to verify the expression level of PLCG2. Our results showed that the chromosome distribution, length distribution, and genomic annotation of the eccDNAs were comparable between the NSCLC and normal groups. Nevertheless, there were no significant differences in eccDNAs between NSCLC tissues and matched normal lung tissues. The eccDNA derived from PLCG2 was upregulated in NSCLC cells. TCGA analysis and immunohistochemistry showed that PLCG2 was highly expressed in lung cancer tissues and tended to be associated with poor outcome. We also demonstrated that PLCG2 can promote metastasis through the regulation of mitochondrial respiration. These results suggested that PLCG2 identified by eccDNA sequencing acts as an oncogene and might be a new biomarker for NSCLC diagnosis and prognosis evaluation.
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Affiliation(s)
- Yongfeng Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Ying Yang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Hong Huang
- Institute of Clinical Pathology, Key Laboratory of Transplantation Engineering and Immunology, Ministry of Health, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Tingting Song
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Shengqiang Mao
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China
| | - Dan Liu
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
| | - Li Zhang
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Institute of Respiratory Health, Center of Precision Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan Province, China.
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14
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Walentynowicz KA, Engelhardt D, Cristea S, Yadav S, Onubogu U, Salatino R, Maerken M, Vincentelli C, Jhaveri A, Geisberg J, McDonald TO, Michor F, Janiszewska M. Single-cell heterogeneity of EGFR and CDK4 co-amplification is linked to immune infiltration in glioblastoma. Cell Rep 2023; 42:112235. [PMID: 36920905 PMCID: PMC10114292 DOI: 10.1016/j.celrep.2023.112235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/20/2022] [Accepted: 02/23/2023] [Indexed: 03/15/2023] Open
Abstract
Glioblastoma (GBM) is the most aggressive brain tumor, with a median survival of ∼15 months. Targeted approaches have not been successful in this tumor type due to the large extent of intratumor heterogeneity. Mosaic amplification of oncogenes suggests that multiple genetically distinct clones are present in each tumor. To uncover the relationships between genetically diverse subpopulations of GBM cells and their native tumor microenvironment, we employ highly multiplexed spatial protein profiling coupled with single-cell spatial mapping of fluorescence in situ hybridization (FISH) for EGFR, CDK4, and PDGFRA. Single-cell FISH analysis of a total of 35,843 single nuclei reveals that tumors in which amplifications of EGFR and CDK4 more frequently co-occur in the same cell exhibit higher infiltration of CD163+ immunosuppressive macrophages. Our results suggest that high-throughput assessment of genomic alterations at the single-cell level could provide a measure for predicting the immune state of GBM.
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Affiliation(s)
- Kacper A Walentynowicz
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Dalit Engelhardt
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Simona Cristea
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Department of Medical Oncology, Harvard Medical School, Boston, MA, USA
| | - Shreya Yadav
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | - Ugoma Onubogu
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Roberto Salatino
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA
| | - Melanie Maerken
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA
| | | | - Aashna Jhaveri
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jacob Geisberg
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Thomas O McDonald
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Franziska Michor
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; The Broad Institute of MIT and Harvard, Cambridge, MA, USA; The Ludwig Center at Harvard, Boston, MA, USA.
| | - Michalina Janiszewska
- Department of Molecular Medicine, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation and Technologies, Jupiter, FL, USA; Department of Molecular Medicine, Scripps Research, Jupiter, FL, USA; The Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, La Jolla, CA, USA.
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15
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Chen Y, Qiu Q, She J, Yu J. Extrachromosomal circular DNA in colorectal cancer: biogenesis, function and potential as therapeutic target. Oncogene 2023; 42:941-951. [PMID: 36859558 PMCID: PMC10038807 DOI: 10.1038/s41388-023-02640-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 03/03/2023]
Abstract
Extrachromosomal circular DNA (ecDNA) has gained renewed interest since its discovery more than half a century ago, emerging as critical driver of tumor evolution. ecDNA is highly prevalent in many types of cancers, including colorectal cancer (CRC), which is one of the most deadly cancers worldwide. ecDNAs play an essential role in regulating oncogene expression, intratumor heterogeneity, and resistance to therapy independently of canonical chromosomal alterations in CRC. Furthermore, the existence of ecDNAs is attributed to the patient's prognosis, since ecDNA-based oncogene amplification adversely affects clinical outcomes. Recent understanding of ecDNA put an extra layer of complexity in the pathogenesis of CRC. In this review, we will discuss the current understanding on mechanisms of biogenesis, and distinctive features of ecDNA in CRC. In addition, we will examine how ecDNAs mediate oncogene overexpression, gene regulation, and topological interactions with active chromatin, which facilitates genetic heterogeneity, accelerates CRC malignancy, and enhances rapid adaptation to therapy resistance. Finally, we will discuss the potential diagnostic and therapeutic implications of ecDNAs in CRC.
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Affiliation(s)
- Yinnan Chen
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Quanpeng Qiu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China
| | - Junjun She
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
| | - Jun Yu
- Center for Gut Microbiome Research, Med-X Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Department of High Talent, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, China.
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China.
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16
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Purshouse K, Friman ET, Boyle S, Dewari PS, Grant V, Hamdan A, Morrison GM, Brennan PM, Beentjes SV, Pollard SM, Bickmore WA. Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells. eLife 2022; 11:e80207. [PMID: 36476408 PMCID: PMC9728993 DOI: 10.7554/elife.80207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 10/21/2022] [Indexed: 12/12/2022] Open
Abstract
Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size, and chromatin accessibility facilitate clustering of ecDNA and colocalization with transcriptional hubs, and that this underpins their elevated transcriptional activity. Here, we use super-resolution imaging and quantitative image analysis to evaluate GBM stem cells harbouring distinct ecDNA species (EGFR, CDK4, PDGFRA). We find no evidence that ecDNA routinely cluster with one another or closely interact with transcriptional hubs. Cells with EGFR-containing ecDNA have increased EGFR transcriptional output, but transcription per gene copy is similar in ecDNA compared to the endogenous chromosomal locus. These data suggest that it is the increased copy number of oncogene-harbouring ecDNA that primarily drives high levels of oncogene transcription, rather than specific interactions of ecDNA with each other or with high concentrations of the transcriptional machinery.
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Affiliation(s)
- Karin Purshouse
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Elias T Friman
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
| | - Shelagh Boyle
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
| | - Pooran Singh Dewari
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Vivien Grant
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Alhafidz Hamdan
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Gillian M Morrison
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Paul M Brennan
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
- Centre for Clinical Brain Sciences, University of EdinburghEdinburghUnited Kingdom
| | - Sjoerd V Beentjes
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
- School of Mathematics, University of EdinburghEdinburghUnited Kingdom
| | - Steven M Pollard
- Centre for Regenerative Medicine and Cancer Research UK Edinburgh Centre, Institute for Regeneration and Repair, The University of EdinburghEdinburghUnited Kingdom
| | - Wendy A Bickmore
- MRC Human Genetics Unit, Institute of Genetics and Cancer, The University of EdinburghEdinburghUnited Kingdom
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17
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Lin B, Ziebro J, Smithberger E, Skinner KR, Zhao E, Cloughesy TF, Binder ZA, O’Rourke DM, Nathanson DA, Furnari FB, Miller CR. EGFR, the Lazarus target for precision oncology in glioblastoma. Neuro Oncol 2022; 24:2035-2062. [PMID: 36125064 PMCID: PMC9713527 DOI: 10.1093/neuonc/noac204] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The Lazarus effect is a rare condition that happens when someone seemingly dead shows signs of life. The epidermal growth factor receptor (EGFR) represents a target in the fatal neoplasm glioblastoma (GBM) that through a series of negative clinical trials has prompted a vocal subset of the neuro-oncology community to declare this target dead. However, an argument can be made that the core tenets of precision oncology were overlooked in the initial clinical enthusiasm over EGFR as a therapeutic target in GBM. Namely, the wrong drugs were tested on the wrong patients at the wrong time. Furthermore, new insights into the biology of EGFR in GBM vis-à-vis other EGFR-driven neoplasms, such as non-small cell lung cancer, and development of novel GBM-specific EGFR therapeutics resurrects this target for future studies. Here, we will examine the distinct EGFR biology in GBM, how it exacerbates the challenge of treating a CNS neoplasm, how these unique challenges have influenced past and present EGFR-targeted therapeutic design and clinical trials, and what adjustments are needed to therapeutically exploit EGFR in this devastating disease.
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Affiliation(s)
- Benjamin Lin
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Julia Ziebro
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Erin Smithberger
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Pathobiology and Translational Sciences Program, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Kasey R Skinner
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Neurosciences Curriculum, School of Medicine, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eva Zhao
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Timothy F Cloughesy
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Zev A Binder
- Department of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Donald M O’Rourke
- Department of Neurosurgery and Glioblastoma Translational Center of Excellence, Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Frank B Furnari
- Department of Medicine, Division of Regenerative Medicine, University of California, San Diego, San Diego, California, USA
- Ludwig Cancer Research, San Diego, California, USA
| | - C Ryan Miller
- Department of Pathology, Division of Neuropathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
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18
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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19
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Dewdney B, Ursich L, Fletcher EV, Johns TG. Anoctamins and Calcium Signalling: An Obstacle to EGFR Targeted Therapy in Glioblastoma? Cancers (Basel) 2022; 14:cancers14235932. [PMID: 36497413 PMCID: PMC9740065 DOI: 10.3390/cancers14235932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Glioblastoma is the most common form of high-grade glioma in adults and has a poor survival rate with very limited treatment options. There have been no significant advancements in glioblastoma treatment in over 30 years. Epidermal growth factor receptor is upregulated in most glioblastoma tumours and, therefore, has been a drug target in recent targeted therapy clinical trials. However, while many inhibitors and antibodies for epidermal growth factor receptor have demonstrated promising anti-tumour effects in preclinical models, they have failed to improve outcomes for glioblastoma patients in clinical trials. This is likely due to the highly plastic nature of glioblastoma tumours, which results in therapeutic resistance. Ion channels are instrumental in the development of many cancers and may regulate cellular plasticity in glioblastoma. This review will explore the potential involvement of a class of calcium-activated chloride channels called anoctamins in brain cancer. We will also discuss the integrated role of calcium channels and anoctamins in regulating calcium-mediated signalling pathways, such as epidermal growth factor signalling, to promote brain cancer cell growth and migration.
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Affiliation(s)
- Brittany Dewdney
- Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia
- Correspondence: ; Tel.: +61-8-6319-1023
| | - Lauren Ursich
- Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia
| | - Emily V. Fletcher
- Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia
| | - Terrance G. Johns
- Cancer Centre, Telethon Kids Institute, Perth, WA 6009, Australia
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia
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20
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Wu M, Rai K. Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics. Comput Struct Biotechnol J 2022; 20:6011-6022. [PMID: 36382182 PMCID: PMC9647416 DOI: 10.1016/j.csbj.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Since the advent of sequencing technologies in the 1990s, researchers have focused on the association between aberrations in chromosomal DNA and disease. However, not all forms of the DNA are linear and chromosomal. Extrachromosomal circular DNAs (eccDNAs) are double-stranded, closed-circled DNA constructs free from the chromosome that reside in the nuclei. Although widely overlooked, the eccDNAs have recently gained attention for their potential roles in physiological response, intratumoral heterogeneity and cancer therapeutics. In this review, we summarize the history, classifications, biogenesis, and highlight recent progresses on the emerging topic of eccDNAs and comment on their potential application as biomarkers in clinical settings.
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Affiliation(s)
- Manrong Wu
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kunal Rai
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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21
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Extrachromosomal circular DNA: biogenesis, structure, functions and diseases. Signal Transduct Target Ther 2022; 7:342. [PMID: 36184613 PMCID: PMC9527254 DOI: 10.1038/s41392-022-01176-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.
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22
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Ilić M, Zaalberg IC, Raaijmakers JA, Medema RH. Life of double minutes: generation, maintenance, and elimination. Chromosoma 2022; 131:107-125. [PMID: 35487993 PMCID: PMC9470669 DOI: 10.1007/s00412-022-00773-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 12/20/2022]
Abstract
Advances in genome sequencing have revealed a type of extrachromosomal DNA, historically named double minutes (also referred to as ecDNA), to be common in a wide range of cancer types, but not in healthy tissues. These cancer-associated circular DNA molecules contain one or a few genes that are amplified when double minutes accumulate. Double minutes harbor oncogenes or drug resistance genes that contribute to tumor aggressiveness through copy number amplification in combination with favorable epigenetic properties. Unequal distribution of double minutes over daughter cells contributes to intratumoral heterogeneity, thereby increasing tumor adaptability. In this review, we discuss various models delineating the mechanism of generation of double minutes. Furthermore, we highlight how double minutes are maintained, how they evolve, and discuss possible mechanisms driving their elimination.
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Affiliation(s)
- Mila Ilić
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Irene C Zaalberg
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
- Center for Molecular Medicine, University Medical Center Utrecht, Utrecht University, Universiteitsweg, 100, 3584, CG Utrecht, The Netherlands
| | - Jonne A Raaijmakers
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - René H Medema
- Division of Cell Biology, Oncode Institute, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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23
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Zhu Y, Gong L, Wei CL. Guilt by association: EcDNA as a mobile transactivator in cancer. Trends Cancer 2022; 8:747-758. [PMID: 35753910 PMCID: PMC9388558 DOI: 10.1016/j.trecan.2022.04.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/10/2022] [Accepted: 04/28/2022] [Indexed: 10/17/2022]
Abstract
Extrachromosomal DNA (ecDNA), first described in the 1960s, is emerging as a prevalent but poorly characterized oncogenic alteration in cancer. ecDNA is a reservoir for oncogene amplification and is associated with an aggressive tumor phenotype and poor patient outcome. Despite the long-held knowledge of its existence, little is known about how ecDNA affects tumor cell behavior. Recent data reveal that ecDNA hubs are mobile transcriptional enhancers which can transactivate gene expression through chromatin interactions. Given its prevalence, structural complexity, and unequal segregation into daughter cells, ecDNA can offer selective growth advantages, contribute to intratumor heterogeneity (ITH), and accelerate tumor evolution. Future technology development is expected to transform the current paradigm for studying ecDNA and lead to therapeutic strategies targeting ecDNA vulnerabilities.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; International Institutes of Medicine, The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang 322000, China
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA; Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang 311121, China
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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24
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Dubois F, Sidiropoulos N, Weischenfeldt J, Beroukhim R. Structural variations in cancer and the 3D genome. Nat Rev Cancer 2022; 22:533-546. [PMID: 35764888 PMCID: PMC10423586 DOI: 10.1038/s41568-022-00488-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/18/2022] [Indexed: 12/21/2022]
Abstract
Structural variations (SVs) affect more of the cancer genome than any other type of somatic genetic alteration but difficulties in detecting and interpreting them have limited our understanding. Clinical cancer sequencing also increasingly aims to detect SVs, leading to a widespread necessity to interpret their biological and clinical relevance. Recently, analyses of large whole-genome sequencing data sets revealed features that impact rates of SVs across the genome in different cancers. A striking feature has been the extent to which, in both their generation and their influence on the selective fitness of cancer cells, SVs are more specific to individual cancer types than other genetic alterations such as single-nucleotide variants. This Perspective discusses how the folding of the 3D genome, and differences in its folding across cell types, affect observed SV rates in different cancer types as well as how SVs can impact cancer cell fitness.
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Affiliation(s)
- Frank Dubois
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Nikos Sidiropoulos
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- The Finsen Laboratory, Rigshospitalet, Copenhagen, Denmark.
- Department of Urology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Rameen Beroukhim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of and Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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25
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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26
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Arrey G, Keating ST, Regenberg B. A unifying model for extrachromosomal circular DNA load in eukaryotic cells. Semin Cell Dev Biol 2022; 128:40-50. [PMID: 35292190 DOI: 10.1016/j.semcdb.2022.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/06/2023]
Abstract
Extrachromosomal circular DNA (eccDNA) with exons and whole genes are common features of eukaryotic cells. Work from especially tumours and the yeast Saccharomyces cerevisiae has revealed that eccDNA can provide large selective advantages and disadvantages. Besides the phenotypic effect due to expression of an eccDNA fragment, eccDNA is different from other mutations in that it is released from 1:1 segregation during cell division. This means that eccDNA can quickly change copy number, pickup secondary mutations and reintegrate into a chromosome to establish substantial genetic variation that could not have evolved via canonical mechanisms. We propose a unifying 5-factor model for conceptualizing the eccDNA load of a eukaryotic cell, emphasizing formation, replication, segregation, selection and elimination. We suggest that the magnitude of these sequential events and their interactions determine the copy number of eccDNA in mitotically dividing cells. We believe that our model will provide a coherent framework for eccDNA research, to understand its biology and the factors that can be manipulated to modulate eccDNA load in eukaryotic cells.
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Affiliation(s)
- Gerard Arrey
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Samuel T Keating
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark
| | - Birgitte Regenberg
- Section for Ecology and Evolution, University of Copenhagen, Copenhagen, Denmark.
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27
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Wu P, Liu Y, Zhou R, Liu L, Zeng H, Xiong F, Zhang S, Gong Z, Zhang W, Guo C, Wang F, Zhou M, Zu X, Zeng Z, Li Y, Li G, Huang H, Xiong W. Extrachromosomal Circular DNA: A New Target in Cancer. Front Oncol 2022; 12:814504. [PMID: 35494014 PMCID: PMC9046939 DOI: 10.3389/fonc.2022.814504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 03/17/2022] [Indexed: 12/12/2022] Open
Abstract
Genomic instability and amplification are intrinsically important traits determining the development and heterogeneity of tumors. The role of extrachromosomal circular DNA (eccDNA) in tumors has recently been highlighted. EccDNAs are unique genetic materials located off the chromosomal DNA. They have been detected in a variety of tumors. This review analyzes the mechanisms involved in the formation of eccDNAs and their genetic characteristics. In addition, the high-copy number and transcriptional levels of oncogenes located in eccDNA molecules contribute to the acceleration of tumor evolution and drug resistance and drive the development of genetic heterogeneity. Understanding the specific genomic forms of eccDNAs and characterizing their potential functions will provide new strategies for tumor therapy. Further research may yield new targets and molecular markers for the early diagnosis and treatment of human cancer.
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Affiliation(s)
- Pan Wu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Yuhang Liu
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Ruijia Zhou
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Lingyun Liu
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Hongli Zeng
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Fang Xiong
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Shanshan Zhang
- Department of Stomatology, Xiangya Hospital, Central South University, Changsha, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wenling Zhang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Ming Zhou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Xuyu Zu
- Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, China
| | - Zhaoyang Zeng
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - Yong Li
- Department of Medicine, Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States
| | - Guiyuan Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
| | - He Huang
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: He Huang, ; Wei Xiong,
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, China
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: He Huang, ; Wei Xiong,
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28
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Noer JB, Hørsdal OK, Xiang X, Luo Y, Regenberg B. Extrachromosomal circular DNA in cancer: history, current knowledge, and methods. Trends Genet 2022; 38:766-781. [PMID: 35277298 DOI: 10.1016/j.tig.2022.02.007] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 02/10/2022] [Accepted: 02/11/2022] [Indexed: 12/12/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) is a closed-circle, nuclear, nonplasmid DNA molecule found in all tested eukaryotes. eccDNA plays important roles in cancer pathogenesis, evolution of tumor heterogeneity, and therapeutic resistance. It is known under many names, including very large cancer-specific circular extrachromosomal DNA (ecDNA), which carries oncogenes and is often amplified in cancer cells. Our understanding of eccDNA has historically been limited and fragmented. To provide better a context of new and previous research on eccDNA, in this review we give an overview of the various names given to eccDNA at different times. We describe the different mechanisms for formation of eccDNA and the methods used to study eccDNA thus far. Finally, we explore the potential clinical value of eccDNA.
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Affiliation(s)
- Julie B Noer
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Oskar K Hørsdal
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Xi Xiang
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China
| | - Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus, Denmark; Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Shenzhen, Qingdao, China; Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark.
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29
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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: 44] [Impact Index Per Article: 22.0] [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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30
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Robert M, Crasta K. Breaking the vicious circle: Extrachromosomal circular DNA as an emerging player in tumour evolution. Semin Cell Dev Biol 2021; 123:140-150. [PMID: 34857471 DOI: 10.1016/j.semcdb.2021.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 12/16/2022]
Abstract
Extrachromosomal circular DNA (ecDNA) or double minutes have gained renewed interest since its discovery more than five decades ago, emerging as potent drivers of tumour evolution. This has largely been motivated by recent discovery that the tumour-exclusive ecDNA are highly prevalent in almost all cancers unlike previously thought. EcDNAs contribute to elevated oncogene expression, intratumoural heterogeneity, tumour adaptation and therapy resistance independently of canonical chromosomal alterations. Importantly, ecDNAs play a critical role in patient survival as ecDNA-based oncogene amplification adversely affects clinical outcome to a significantly greater extent than intrachromosomal amplification. Chromothripsis, a major driver of ecDNA biogenesis and gene amplification, is a mutational process characterised by chromosomal shattering and localised complex genome rearrangement. Chemotherapeutic drugs can lead to chromothriptic rearrangements and therapy resistance. In this review, we examine how ecDNAs mediate oncogene overexpression, facilitate accelerated tumour malignancy and enhance rapid adaptation independently of linear chromosomes. We delve into discoveries pertaining to mechanisms of biogenesis, distinctive features of ecDNA, gene regulation and topological interactions with active chromatin. We also discuss the critical role of chromothripsis in engendering ecDNA amplification and evolution. One envisions that insights into ecDNA biology not only hold importance for the cancer genome and tumour evolutionary dynamics, but could also inform prognostication and clinical intervention, particularly for cancers characterised by high oncogene amplification.
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Affiliation(s)
- Matius Robert
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore
| | - Karen Crasta
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Healthy Longevity Translational Research Program, National University of Singapore, Singapore; NUS Centre for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Agency for Science, Technology & Research (A⁎STAR), Institute of Molecular and Cell Biology, Singapore.
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31
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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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32
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Cao X, Wang S, Ge L, Zhang W, Huang J, Sun W. Extrachromosomal Circular DNA: Category, Biogenesis, Recognition, and Functions. Front Vet Sci 2021; 8:693641. [PMID: 34568472 PMCID: PMC8458813 DOI: 10.3389/fvets.2021.693641] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 12/17/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA), existing as double-stranded circular DNA, is derived and free from chromosomes. It is common in eukaryotes but has a strong heterogeneity in count, length, and origin. It has been demonstrated that eccDNA could function in telomere and rDNA maintenance, aging, drug resistance, tumorigenesis, and phenotypic variations of plants and animals. Here we review the current knowledge about eccDNA in category, biogenesis, recognition, and functions. We also provide perspectives on the potential implications of eccDNA in life science.
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Affiliation(s)
- Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Shan Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinlin Huang
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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33
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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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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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35
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Shiras A, Mondal A. Extrachromosomal DNA: Redefining the pathogenesis of glioblastoma. Biochim Biophys Acta Rev Cancer 2021; 1876:188551. [PMID: 33892052 DOI: 10.1016/j.bbcan.2021.188551] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/30/2021] [Accepted: 04/16/2021] [Indexed: 12/19/2022]
Abstract
Glioblastoma is an incurable most prevalent primary malignant brain tumor in adults. Surgery followed by radiotherapy with concomitant chemotherapy is the standard of care in patients with glioblastoma. Although, prognosis remains poor with a median survival in the range of 12-15 months. Over the decades of research has identified the gene mutation, angiogenesis, cell signaling for the development novel therapeutics. However, recent understanding on extrachromosomal DNA (ecDNA) put extra-layer of complexity in glioblastoma pathogenesis. These ecDNAs are present in significantly higher copy number in the nucleus of the cancer cells and contains several oncogenes which are instrumental for intra-tumoral genetic heterogeneity, accelerated tumor evolution and therapy resistance. In this review, we will discuss the current understanding on biogenesis, disease progression and potential therapeutic implications of ecDNAs in glioblastoma.
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Affiliation(s)
- Anjali Shiras
- Lab-03, Old Building, National Centre for Cell Science, Pune, India
| | - Abir Mondal
- Department of Life Sciences, Shiv Nadar University, India.
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36
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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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37
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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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38
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汪 雨, 叶 凡, 张 霄, 邹 睿, 王 明, 俞 锴, 崔 诗. [Amplification of Extrachromosomal Oncogene and Tumorigenesis and Development]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2020; 23:1101-1107. [PMID: 33357318 PMCID: PMC7786228 DOI: 10.3779/j.issn.1009-3419.2020.101.48] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/16/2020] [Accepted: 09/20/2020] [Indexed: 11/05/2022]
Abstract
Extrachromosomal DNA (ecDNA) is a small segment of circular DNA located outside the chromosome, which has the function of self-replication. Recently, amplification of oncogenes on ecDNA has been proved to be a common phenomenon in tumor cells, and has some characteristics worth studying, such as correlation with patients' poor prognosis. Multiple chromosomal events are involved in the formation of ecDNA, and its amplification can directly increase the number of DNA copies of extra-chromosomal oncogenes and accelerate the generation and development of tumors. Moreover, the segregation pattern of unequal transmission of parental ecDNA cells to offspring not only increases tumor heterogeneity, but also enhances tumor adaptation to environment and response to therapy. This article reviews the current status and potential significance of ecDNA in tumor cells.
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Affiliation(s)
- 雨彤 汪
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 凡 叶
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 霄 张
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 睿涵 邹
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 明远 王
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 锴 俞
- 211166 南京,南京医科大学第一临床医学院Nanjing Medical University, Nanjing 211166, China
| | - 诗允 崔
- 210029 南京,南京医科大学第一附属医院肿瘤科Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, China
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39
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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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40
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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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41
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Alaei-Mahabadi B, Elliott K, Larsson E. Systematic investigation of promoter substitutions resulting from somatic intrachromosomal structural alterations in diverse human cancers. Sci Rep 2020; 10:18176. [PMID: 33097743 PMCID: PMC7584658 DOI: 10.1038/s41598-020-74420-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 09/10/2020] [Indexed: 11/21/2022] Open
Abstract
One of the ways in which genes can become activated in tumors is by somatic structural genomic rearrangements leading to promoter swapping events, typically in the context of gene fusions that cause a weak promoter to be substituted for a strong promoter. While identifiable by whole genome sequencing, limited availability of this type of data has prohibited comprehensive study of the phenomenon. Here, we leveraged the fact that copy number alterations (CNAs) arise as a result of structural alterations in DNA, and that they may therefore be informative of gene rearrangements, to pinpoint recurrent promoter swapping at a previously intractable scale. CNA data from nearly 9500 human tumors was combined with transcriptomic sequencing data to identify several cases of recurrent activating intrachromosomal promoter substitution events, either involving proper gene fusions or juxtaposition of strong promoters to gene upstream regions. Our computational screen demonstrates that a combination of CNA and expression data can be useful for identifying novel fusion events with potential driver roles in large cancer cohorts.
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Affiliation(s)
- Babak Alaei-Mahabadi
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Kerryn Elliott
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden
| | - Erik Larsson
- Department Of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30, Gothenburg, Sweden.
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42
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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: 31] [Impact Index Per Article: 7.8] [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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43
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Tanaka H, Watanabe T. Mechanisms Underlying Recurrent Genomic Amplification in Human Cancers. Trends Cancer 2020; 6:462-477. [PMID: 32383436 PMCID: PMC7285850 DOI: 10.1016/j.trecan.2020.02.019] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/17/2022]
Abstract
Focal copy-number increases (genomic amplification) pinpoint oncogenic driver genes and therapeutic targets in cancer genomes. With the advent of genomic technologies, recurrent genomic amplification has been mapped throughout the genome. Recurrent amplification could be solely due to positive selection for the tumor-promoting effects of amplified gene products. Alternatively, recurrence could result from the susceptibility of the loci to amplification. Distinguishing between these possibilities requires a full understanding of the amplification mechanisms. Two mechanisms, the formation of double minute (DM) chromosomes and breakage-fusion-bridge (BFB) cycles, have been repeatedly linked to genomic amplification, and the impact of both mechanisms has been confirmed in cancer genomics data. We review the details of these mechanisms and discuss the mechanisms underlying recurrence.
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Affiliation(s)
- Hisashi Tanaka
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Biomedical Sciences, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA.
| | - Takaaki Watanabe
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA 90046, USA; Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
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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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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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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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Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro Oncol 2019; 20:873-884. [PMID: 29432615 PMCID: PMC6280138 DOI: 10.1093/neuonc/noy020] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Adult diffuse gliomas are a diverse group of brain neoplasms that inflict a high emotional toll on patients and their families. The Cancer Genome Atlas and similar projects have provided a comprehensive understanding of the somatic alterations and molecular subtypes of glioma at diagnosis. However, gliomas undergo significant cellular and molecular evolution during disease progression. We review the current knowledge on the genomic and epigenetic abnormalities in primary tumors and after disease recurrence, highlight the gaps in the literature, and elaborate on the need for a new multi-institutional effort to bridge these knowledge gaps and how the Glioma Longitudinal Analysis Consortium (GLASS) aims to systemically catalog the longitudinal changes in gliomas. The GLASS initiative will provide essential insights into the evolution of glioma toward a lethal phenotype, with the potential to reveal targetable vulnerabilities and, ultimately, improved outcomes for a patient population in need.
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Koga T, Li B, Figueroa JM, Ren B, Chen CC, Carter BS, Furnari FB. Mapping of genomic EGFRvIII deletions in glioblastoma: insight into rearrangement mechanisms and biomarker development. Neuro Oncol 2019; 20:1310-1320. [PMID: 29660021 DOI: 10.1093/neuonc/noy058] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Epidermal growth factor receptor (EGFR) variant III (vIII) is the most common oncogenic rearrangement in glioblastoma (GBM), generated by deletion of exons 2 to 7 of EGFR. The proximal breakpoints occur in variable positions within the 123-kb intron 1, presenting significant challenges in terms of polymerase chain reaction (PCR)-based mapping. Molecular mechanisms underlying these deletions remain unclear. Methods We determined the presence of EGFRvIII and its breakpoints for 29 GBM samples using quantitative PCR, arrayed PCR mapping, Sanger sequencing, and whole genome sequencing (WGS). Patient-specific breakpoint PCR was performed on tumors, plasma, and cerebrospinal fluid (CSF) samples. The breakpoint sequences and single nucleotide polymorphisms (SNPs) were analyzed to elucidate the underlying biogenic mechanism. Results PCR mapping and WGS independently unveiled 8 EGFRvIII breakpoints in 6 tumors. Patient-specific primers yielded EGFRvIII PCR amplicons in matched tumors and in cell-free DNA (cfDNA) from a CSF sample, but not in cfDNA or extracellular-vesicle DNA from plasma. The breakpoint analysis revealed nucleotide insertions in 4 samples, an insertion of a region outside of the EGFR locus in 1, microhomologies in 3, as well as a duplication or an inversion accompanied by microhomologies in 2, suggestive of distinct DNA repair mechanisms. In the GBM samples that harbored distinct breakpoints, the SNP compositions of EGFRvIII and amplified non-vIII EGFR were identical, suggesting that these rearrangements arose from amplified non-vIII EGFR. Conclusion Our approach efficiently "fingerprints" each sample's EGFRvIII breakpoints. Breakpoint sequence analyses suggest that independent breakpoints arose from precursor amplified non-vIII EGFR through different DNA repair mechanisms.
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Affiliation(s)
- Tomoyuki Koga
- Ludwig Cancer Research, University of California San Diego, La Jolla, California
| | - Bin Li
- Ludwig Cancer Research, University of California San Diego, La Jolla, California
| | - Javier M Figueroa
- Department of Neurosurgery, University of California San Diego, La Jolla, California
| | - Bing Ren
- Ludwig Cancer Research, University of California San Diego, La Jolla, California
| | - Clark C Chen
- Department of Neurosurgery, University of California San Diego, La Jolla, California.,Department of Neurosurgery, University of Minnesota, Minneapolis, Minnesota
| | - Bob S Carter
- Department of Neurosurgery, University of California San Diego, La Jolla, California.,Department of Neurosurgery, Harvard Medical School, Boston, Massachusetts
| | - Frank B Furnari
- Ludwig Cancer Research, University of California San Diego, La Jolla, California
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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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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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