1
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Zhang H, Liu B, Cheng J, Li Z, Jia M, Li M, Zhao L, Wang L, Xi Y. Characterization and integrated analysis of extrachromosomal DNA amplification in hematological malignancies. Neoplasia 2024; 56:101025. [PMID: 38996538 PMCID: PMC11301242 DOI: 10.1016/j.neo.2024.101025] [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: 02/27/2024] [Accepted: 07/03/2024] [Indexed: 07/14/2024]
Abstract
The study of extrachromosomal DNA (ecDNA), an element existing beyond classical chromosomes, contributes to creating a more comprehensive map of the cancer genome. In hematological malignancies, research on ecDNA has lacked comprehensive investigation into its frequency, structure, function, and mechanisms of formation. We re-analyzed WGS data from 208 hematological cancer samples across 11 types, focusing on ecDNA characteristics. Amplification of ecDNA was observed in 7 of these cancer types, with no instances found in normal blood cells. Patients with leukemia carrying ecDNA showed a low induction therapy remission rate (<30 %), a high relapse rate (75 %) among those who achieved complete remission, and a significantly lower survival rate compared to the general leukemia population, even those with complex chromosomal karyotypes. Among the 55 identified ecDNA amplicons, 268 genes were detected, of which 38 are known cancer-related genes exhibiting significantly increased copy numbers. By integrating RNA-Seq data, we discovered that the increased copy number, resulting in a higher amount of available DNA templates, indeed leads to the elevated expression of genes encoded on ecDNA. Additionally, through the integration of H3K4me3/H3K27ac chromatin immunoprecipitation sequencing, assay for transposase-accessible chromatin with sequencing, and high-throughput chromosome conformation capture data, we identified that ecDNA amplifications can also facilitate efficient, copy number-independent amplification of oncogenes. This process is linked to active histone modifications, improved chromatin accessibility, and enhancer hijacking, all of which are effects of ecDNA amplification. Mechanistically, chromothripsis and dysfunction of the DNA repair pathway can, to some extent, explain the origin of ecDNA.
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Affiliation(s)
- Hao Zhang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Bei Liu
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Juan Cheng
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Zijian Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Mingfeng Jia
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Ming Li
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Long Zhao
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Lina Wang
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yaming Xi
- Department of Hematology, The First Hospital of Lanzhou University, Lanzhou, Gansu 730000, China.
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2
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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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Meng XN, Ma JF, Liu YH, Li SQ, Wang X, Zhu J, Cai MD, Zhang HS, Song T, Xing S, Hou LQ, Guo H, Cui XB, Han J, Liu P, Ji GH, Sun WJ, Yu JC, Fu SB. Dynamic genomic changes in methotrexate-resistant human cancer cell lines beyond DHFR amplification suggest potential new targets for preventing drug resistance. Br J Cancer 2024; 130:1819-1827. [PMID: 38594370 PMCID: PMC11130306 DOI: 10.1038/s41416-024-02664-0] [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: 06/26/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Although DHFR gene amplification has long been known as a major mechanism for methotrexate (MTX) resistance in cancer, the early changes and detailed development of the resistance are not yet fully understood. METHODS We performed genomic, transcriptional and proteomic analyses of human colon cancer cells with sequentially increasing levels of MTX-resistance. RESULTS The genomic amplification evolved in three phases (pre-amplification, homogenously staining region (HSR) and extrachromosomal DNA (ecDNA)). We confirm that genomic amplification and increased expression of DHFR, with formation of HSRs and especially ecDNAs, is the major driver of resistance. However, DHFR did not play a detectable role in the early phase. In the late phase (ecDNA), increase in FAM151B protein level may also have an important role by decreasing sensitivity to MTX. In addition, although MSH3 and ZFYVE16 may be subject to different posttranscriptional regulations and therefore protein expressions are decreased in ecDNA stages compared to HSR stages, they still play important roles in MTX resistance. CONCLUSION The study provides a detailed evolutionary trajectory of MTX-resistance and identifies new targets, especially ecDNAs, which could help to prevent drug resistance. It also presents a proof-of-principal approach which could be applied to other cancer drug resistance studies.
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Affiliation(s)
- Xiang-Ning Meng
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jin-Fa Ma
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Yang-He Liu
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Si-Qing Li
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xu Wang
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jing Zhu
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Meng-Di Cai
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Hui-Shu Zhang
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Tiantian Song
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Shukai Xing
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Li-Qing Hou
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Huan Guo
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Xiao-Bo Cui
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jiang Han
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Peng Liu
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Guo-Hua Ji
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Wen-Jing Sun
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
| | - Jing-Cui Yu
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China
- Scientific Research Centre, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150081, China
| | - Song-Bin Fu
- Key laboratory of preservation of human genetic resources and disease control in China (Harbin Medical University), Ministry of Education, Harbin, 150081, China.
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, 150081, China.
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4
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Wu H, Liu S, Wu D, Zhou H, Wu G. Tumor extrachromosomal DNA: Biogenesis and recent advances in the field. Biomed Pharmacother 2024; 174:116588. [PMID: 38613997 DOI: 10.1016/j.biopha.2024.116588] [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: 02/09/2024] [Revised: 04/02/2024] [Accepted: 04/10/2024] [Indexed: 04/15/2024] Open
Abstract
Extrachromosomal DNA (ecDNA) is a self-replicating circular DNA originating from the chromosomal genome and exists outside the chromosome. It contains specific gene sequences and non-coding regions that regulate transcription. Recent studies have demonstrated that ecDNA is present in various malignant tumors. Malignant tumor development and poor prognosis may depend on ecDNA's distinctive ring structure, which assists in amplifying oncogenes. During cell division, an uneven distribution of ecDNA significantly enhances tumor cells' heterogeneity, allowing tumor cells to adapt to changes in the tumor microenvironment and making them more resistant to treatments. The application of ecDNA as a cancer biomarker and therapeutic target holds great potential. This article examines the latest advancements in this area and discusses the potential clinical applications of ecDNA.
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Affiliation(s)
- Haomin Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Shiqi Liu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Di Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Haonan Zhou
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China
| | - Gang Wu
- Department of General Surgery, the First Hospital of China Medical University, 155# Nanjing Street, Shenyang 110001, China.
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5
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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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6
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Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [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: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
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Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
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7
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Zhuang J, Zhang Y, Zhou C, Fan D, Huang T, Feng Q, Lu Y, Zhao Y, Zhao Q, Han B, Lu T. Dynamics of extrachromosomal circular DNA in rice. Nat Commun 2024; 15:2413. [PMID: 38499575 PMCID: PMC10948907 DOI: 10.1038/s41467-024-46691-0] [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: 08/07/2023] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
The genome's dynamic nature, exemplified by elements like extrachromosomal circular DNA (eccDNA), is crucial for biodiversity and adaptation. Yet, the role of eccDNA in plants, particularly rice, remains underexplored. Here, we identify 25,598 eccDNAs, unveiling the widespread presence of eccDNA across six rice tissues and revealing its formation as a universal and random process. Interestingly, we discover that direct repeats play a pivotal role in eccDNA formation, pointing to a unique origin mechanism. Despite eccDNA's prevalence in coding sequences, its impact on gene expression is minimal, implying its roles beyond gene regulation. We also observe the association between eccDNA's formation and minor chromosomal deletions, providing insights of its possible function in regulating genome stability. Further, we discover eccDNA specifically accumulated in rice leaves, which may be associated with DNA damage caused by environmental stressors like intense light. In summary, our research advances understanding of eccDNA's role in the genomic architecture and offers valuable insights for rice cultivation and breeding.
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Affiliation(s)
- Jundong Zhuang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Yaoxin Zhang
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, 100039, China
| | - Congcong Zhou
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Danlin Fan
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Tao Huang
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qi Feng
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yiqi Lu
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan Zhao
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qiang Zhao
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bin Han
- National Center for Gene Research, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Tingting Lu
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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8
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Bookey N, Drago P, Leung KY, Hughes L, MacCooey A, Ozaki M, Henry M, De Castro SCP, Doykov I, Heywood WE, Mills K, Murphy MM, Cavallé-Busquets P, Campbell S, Burtenshaw D, Meleady P, Cahill PA, Greene NDE, Parle-McDermott A. The Differential Translation Capabilities of the Human DHFR2 Gene Indicates a Developmental and Tissue-Specific Endogenous Protein of Low Abundance. Mol Cell Proteomics 2024; 23:100718. [PMID: 38224738 PMCID: PMC10884974 DOI: 10.1016/j.mcpro.2024.100718] [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: 12/08/2022] [Revised: 01/05/2024] [Accepted: 01/12/2024] [Indexed: 01/17/2024] Open
Abstract
A functional role has been ascribed to the human dihydrofolate reductase 2 (DHFR2) gene based on the enzymatic activity of recombinant versions of the predicted translated protein. However, the in vivo function is still unclear. The high amino acid sequence identity (92%) between DHFR2 and its parental homolog, DHFR, makes analysis of the endogenous protein challenging. This paper describes a targeted mass spectrometry proteomics approach in several human cell lines and tissue types to identify DHFR2-specific peptides as evidence of its translation. We show definitive evidence that the DHFR2 activity in the mitochondria is in fact mediated by DHFR, and not DHFR2. Analysis of Ribo-seq data and an experimental assessment of ribosome association using a sucrose cushion showed that the two main Ensembl annotated mRNA isoforms of DHFR2, 201 and 202, are differentially associated with the ribosome. This indicates a functional role at both the RNA and protein level. However, we were unable to detect DHFR2 protein at a detectable level in most cell types examined despite various RNA isoforms of DHFR2 being relatively abundant. We did detect a DHFR2-specific peptide in embryonic heart, indicating that the protein may have a specific role during embryogenesis. We propose that the main functionality of the DHFR2 gene in adult cells is likely to arise at the RNA level.
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Affiliation(s)
- Niamh Bookey
- School of Biotechnology, Dublin City University, Dublin, Ireland; DCU Life Sciences Institute, Dublin City University, Dublin, Ireland.
| | - Paola Drago
- School of Biotechnology, Dublin City University, Dublin, Ireland; DCU Life Sciences Institute, Dublin City University, Dublin, Ireland
| | - Kit-Yi Leung
- Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Linda Hughes
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Aoife MacCooey
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Mari Ozaki
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Michael Henry
- DCU Life Sciences Institute, Dublin City University, Dublin, Ireland
| | - Sandra C P De Castro
- Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ivan Doykov
- Translational Mass Spectrometry Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Wendy E Heywood
- Translational Mass Spectrometry Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Kevin Mills
- Translational Mass Spectrometry Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Michelle M Murphy
- Area of Preventive Medicine and Public Health, Department of Basic Medical Sciences, Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili, IISPV and CIBERobn (Instituto de Salud Carlos III), Reus, Spain
| | - Pere Cavallé-Busquets
- Area of Obstetrics, Hospital Universitari Sant Joan de Reus, IISPV and CIBERobn (Instituto de Salud Carlos III), Reus, Spain
| | - Susan Campbell
- Sheffield Hallam University, Department of Biosciences and Chemistry, Sheffield, UK
| | | | - Paula Meleady
- School of Biotechnology, Dublin City University, Dublin, Ireland; DCU Life Sciences Institute, Dublin City University, Dublin, Ireland
| | - Paul A Cahill
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Nicholas D E Greene
- Developmental Biology and Cancer Department, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Anne Parle-McDermott
- School of Biotechnology, Dublin City University, Dublin, Ireland; DCU Life Sciences Institute, Dublin City University, Dublin, Ireland.
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9
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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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10
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Dong Y, He Q, Chen X, Yang F, He L, Zheng Y. Extrachromosomal DNA (ecDNA) in cancer: mechanisms, functions, and clinical implications. Front Oncol 2023; 13:1194405. [PMID: 37448518 PMCID: PMC10338009 DOI: 10.3389/fonc.2023.1194405] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/05/2023] [Indexed: 07/15/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is circular DNA that plays an important role in the development and heterogeneity of cancer. The rapid evolution of methods to detect ecDNA, including microscopic and sequencing approaches, has greatly enhanced our knowledge of the role of ecDNA in cancer development and evolution. Here, we review the molecular characteristics, functions, mechanisms of formation, and detection methods of ecDNA, with a focus on the potential clinical implications of ecDNA in cancer. Specifically, we consider the role of ecDNA in acquired drug resistance, as a diagnostic and prognostic biomarker, and as a therapeutic target in the context of cancer. As the pathological and clinical significance of ecDNA continues to be explored, it is anticipated that ecDNA will have broad applications in the diagnosis, prognosis, and treatment of patients with cancer.
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Affiliation(s)
- Yucheng Dong
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Qi He
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xinyu Chen
- Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Fan Yang
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Li He
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Yongchang Zheng
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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11
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Sun H, Lu X, Zou L. EccBase: A high-quality database for exploration and characterization of extrachromosomal circular DNAs in cancer. Comput Struct Biotechnol J 2023; 21:2591-2601. [PMID: 37114214 PMCID: PMC10126927 DOI: 10.1016/j.csbj.2023.04.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are widely observed in eukaryotes. Previous studies have demonstrated that eccDNAs are essential to cancer progression, and found that they can not only express in normal cells to regulate RNA, but also function differently in different tissues. It is of major interest to conduct computational or experiments assay to elucidate the mechanisms of eccDNA function, uncover key eccDNAs associated with diseases, and even develop related algorithms for liquid biopsy. Naturally, a comprehensive eccDNAs data resource is urgently needed to provide annotation and analysis more in-depth research. In this study, we constructed the eccBase (http://www.eccbase.net) in literature curation and database retrieval, which was the first database mainly collecting eccDNAs from Homo sapiens (n = 754,391) and Mus musculus (n = 481,381). Homo sapiens eccDNAs were taken from 50 kinds of cancer tissue and/or cell line, and 5 kinds of healthy tissues. The Mus musculus eccDNAs were sourced from 13 kinds of healthy tissue and/or cell line. We thoroughly annotated all eccDNA molecules in terms of basic information, genomic composition, regulatory elements, epigenetic modifications, and raw data. EccBase provided users with the ability to browse, search, download for targets of interest, as well as similarity alignment by the integrated BLAST. Further, comparative analysis suggested the cancer eccDNA is composed of nucleosomes and is prominently derived from the gene-dense regions. We also initially revealed that eccDNAs are strongly tissue-specific. In short, we have started a robust database for eccDNA resource utilization, which may facilitate studying the role of eccDNA in cancer development and therapy, cell function maintenance, and tissue differentiation.
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Affiliation(s)
- Haiyang Sun
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 300350 Tianjin, China
- Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, 518102 Shenzhen, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 300350 Tianjin, China
| | - Lingyun Zou
- Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing Key Laboratory of Emergency Medicine, Chongqing University Central Hospital, Chongqing University, 400014 Chongqing, China
- Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, 518102 Shenzhen, China
- Corresponding author at: Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing Key Laboratory of Emergency Medicine, Chongqing University Central Hospital, Chongqing University, 400014 Chongqing, China.
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12
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Zhao L, Jiang Y, Lei X, Yang X. Amazing roles of extrachromosomal DNA in cancer progression. Biochim Biophys Acta Rev Cancer 2023; 1878:188843. [PMID: 36464200 DOI: 10.1016/j.bbcan.2022.188843] [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: 05/20/2022] [Revised: 11/20/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022]
Abstract
In cancers, extrachromosomal DNA (ecDNA) has gained renewed interest since its first discovery, presenting its roles in tumorigenesis. Because of the unique structure and genetic characteristics, extrachromosomal DNA shed new light on development, early diagnosis, treatment and prognosis of cancers. Occurs in cancer cells, extrachromosomal DNA, one dissociative circular extrachromosomal element, drives the amplification of oncogenes, promotes the transcription and lifts tumor heterogeneity to participate in tumorigenesis. Given its role act as messenger, extrachromosomal DNA is connected with drug resistance, tumor microenvironment, germline and aging. The diversity of space and time gives extrachromosomal DNA a crucial role in cancer progression that has been ignored for decades. Thus, in this review, we will focus on some unique information of extrachromosomal DNA and the regulation of oncogenes as well as its roles and possible mechanisms in tumorigenesis, which are of great significance for us to understand extrachromosomal DNA comprehensively in carcinogenic mechanism.
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Affiliation(s)
- Leilei Zhao
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China
| | - Yicun Jiang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China
| | - Xiaoyong Lei
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China
| | - Xiaoyan Yang
- School of Pharmaceutical Science, Hengyang Medical College, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, University of South China, 28 Western Changsheng Road, Hengyang, Hunan 421001, PR China.
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13
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Pecorino LT, Verhaak RG, Henssen A, Mischel PS. Extrachromosomal DNA (ecDNA): an origin of tumor heterogeneity, genomic remodeling, and drug resistance. Biochem Soc Trans 2022; 50:1911-1920. [PMID: 36355400 PMCID: PMC9788557 DOI: 10.1042/bst20221045] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 11/12/2022]
Abstract
The genome of cancer cells contains circular extrachromosomal DNA (ecDNA) elements not found in normal cells. Analysis of clinical samples reveal they are common in most cancers and their presence indicates poor prognosis. They often contain enhancers and driver oncogenes that are highly expressed. The circular ecDNA topology leads to an open chromatin conformation and generates new gene regulatory interactions, including with distal enhancers. The absence of centromeres leads to random distribution of ecDNAs during cell division and genes encoded on them are transmitted in a non-mendelian manner. ecDNA can integrate into and exit from chromosomal DNA. The numbers of specific ecDNAs can change in response to treatment. This dynamic ability to remodel the cancer genome challenges long-standing fundamentals, providing new insights into tumor heterogeneity, cancer genome remodeling, and drug resistance.
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Affiliation(s)
| | | | - Anton Henssen
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Paul S. Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford University, Stanford, CA, U.S.A
- Sarafan ChEM-H, Standford, CA, U.S.A
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14
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Use of ubiquitous chromatin opening elements (UCOE) as tools to maintain transgene expression in biotechnology. Comput Struct Biotechnol J 2022; 21:275-283. [PMID: 36582439 PMCID: PMC9764128 DOI: 10.1016/j.csbj.2022.11.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/28/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
Amongst the most important outputs of the biopharmaceutical industry are recombinant proteins, many of which are produced by integrating transgenes into the genomes of mammalian cells. However, expression is highly variable and can be unstable during prolonged culture. This is often due to epigenetic mechanisms silencing the transgenes. To combat this problem, vectors have been engineered to include ubiquitous chromatin opening elements (UCOEs) that protect against silencing. Here, we recount the evidence that UCOEs can modify chromatin environments and benefit biomanufacturing.
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15
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Yi E, Chamorro González R, Henssen AG, Verhaak RGW. Extrachromosomal DNA amplifications in cancer. Nat Rev Genet 2022; 23:760-771. [PMID: 35953594 PMCID: PMC9671848 DOI: 10.1038/s41576-022-00521-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2022] [Indexed: 12/19/2022]
Abstract
Extrachromosomal DNA (ecDNA) amplification is an important driver alteration in cancer. It has been observed in most cancer types and is associated with worse patient outcome. The functional impact of ecDNA has been linked to its unique properties, such as its circular structure that is associated with altered chromatinization and epigenetic regulatory landscape, as well as its ability to randomly segregate during cell division, which fuels intercellular copy number heterogeneity. Recent investigations suggest that ecDNA is structurally more complex than previously anticipated and that it localizes to specialized nuclear bodies (hubs) and can act in trans as an enhancer for genes on other ecDNAs or chromosomes. In this Review, we synthesize what is currently known about how ecDNA is generated and how its genetic and epigenetic architecture affects proto-oncogene deregulation in cancer. We discuss how recently identified ecDNA functions may impact oncogenesis but also serve as new therapeutic vulnerabilities in cancer.
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Affiliation(s)
- Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Rocío Chamorro González
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany
| | - Anton G Henssen
- Department of Paediatric Oncology/Hematology, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany.
- Max-Delbrück-Centrum für Molekulare Medizin (BIMSB/BIH), Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Neurosurgery, Amsterdam UMC, Amsterdam, the Netherlands.
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16
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Samanta A, Banerjee S, Maity TR, Jahnavi J, Datta S. Towards establishment of a plant-based model to assess the novel anti-cancerous lead molecule(s): An in silico, in vivo and in vitro assessment of some potential anti-cancerous drugs on Lathyrus sativus L. PROTOPLASMA 2022; 259:1455-1466. [PMID: 35195768 DOI: 10.1007/s00709-022-01745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/09/2022] [Indexed: 06/14/2023]
Abstract
The drug development process is one of the important aspects of medical biology. The classical lead identification strategy in the way of drug development based on animal cell is time-consuming, expensive and involving ethical issues. The following study aims to develop a novel plant-based screening of drugs. Study shows the efficacy of certain anti-cancerous drugs (Pemetrexed, 5-Fluorouracil, Methotrexate, Topotecan and Etoposide) on a plant-based (Lathyrus sativus L.) system. Two important characteristics of cancer cells were observed in the colchicine-treated polyploid cell and the callus, where the chromosome numbers were unusual and the division of cells were uncontrolled respectively. With increasing concentration, the drugs significantly reduced the mitotic index, ploidy level and callus growth. Increasing Pemetrexed concentration decreased the plant DHFR activity. A decrease in total RNA content was observed in 5-FU and Methotrexate with increasing concentrations of the drugs. Etoposide and Topotecan inhibited plant topoisomerase II and topoisomerase I activities, which was justified through plasmid nicking and comet assay, respectively. Molecular and biochemical study revealed similar results to the animal system. The in silico study had been done, and the structural similarity of drug binding domains of L. sativus and human beings had also been established. The binding site of the selected drugs to the domains of plant target proteins was also determined. Experimental results are significant in terms of the efficacy of known anti-cancerous drugs on the plant-based system. The proposed assay system is a cost-effective, convenient and less time-consuming process for primary screening of anti-cancerous lead molecules.
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Affiliation(s)
- Aveek Samanta
- Department of Botany, Prabhat Kumar College, Purba Medinipur, Contai, 721401, West Bengal, India
- Department of Biotechnology, Haldia Institute of Technology, Purba Medinipur, Haldia, 721657, West Bengal, India
| | - Saptadipa Banerjee
- Department of Biotechnology, Haldia Institute of Technology, Purba Medinipur, Haldia, 721657, West Bengal, India
| | - Tilak Raj Maity
- Department of Biotechnology, Haldia Institute of Technology, Purba Medinipur, Haldia, 721657, West Bengal, India
| | - Jangala Jahnavi
- Department of Biological Sciences, Birla Institute of Technology and Science, Pilani, 333031, Rajasthan, India
| | - Siraj Datta
- Department of Biotechnology, Haldia Institute of Technology, Purba Medinipur, Haldia, 721657, West Bengal, India.
- Subarnarekha Mahavidyalaya, Gopiballavpur, Jhargram, 721506, West Bengal, India.
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17
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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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18
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Li R, Wang Y, Li J, Zhou X. Extrachromosomal circular DNA (eccDNA): an emerging star in cancer. Biomark Res 2022; 10:53. [PMID: 35883211 PMCID: PMC9327165 DOI: 10.1186/s40364-022-00399-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/13/2022] [Indexed: 02/08/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is defined as a type of circular DNA that exists widely in nature and is independent of chromosomes. EccDNA has attracted the attention of researchers due to its broad, random distribution, complex biogenesis and tumor-relevant functions. EccDNA can carry complete gene information, especially the oncogenic driver genes that are often carried in tumors, with increased copy number and high transcriptional activity. The high overexpression of oncogenes by eccDNA leads to malignant growth of tumors. Regardless, the exact generation and functional mechanisms of eccDNA in disease progression are not yet clear. There is, however, an emerging body of evidence characterizing that eccDNA can be generated from multiple pathways, including DNA damage repair pathways, breakage-fusion-bridge (BFB) mechanisms, chromothripsis and cell apoptosis, and participates in the regulation of tumor progression with multiplex functions. This up-to-date review summarizes and discusses the origins, biogenesis and functions of eccDNA, including its contribution to the formation of oncogene instability and mutations, the heterogeneity and cellular senescence of tumor cells, and the proinflammatory response of tumors. We highlight the possible cancer-related applications of eccDNA, such as its potential use in the diagnosis, targeted therapy and prognostic assessment of cancer.
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Affiliation(s)
- Ruomeng Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.,State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Ying Wang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China
| | - Jing Li
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, Chinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and Management, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, 610041, PR China.
| | - Xikun Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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19
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Banerjee A, Rahman H, Prasad R, Golin J. How Fungal Multidrug Transporters Mediate Hyperresistance Through DNA Amplification and Mutation. Mol Microbiol 2022; 118:3-15. [PMID: 35611562 DOI: 10.1111/mmi.14947] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 11/30/2022]
Abstract
A significant portion of clinically observed antifungal resistance is mediated by ATP-binding cassette (ABC) and major facilitator superfamily (MFS) transport pumps that reside in the plasma membrane. We review the mechanisms responsible for this phenomenon. Hyperresistance is often brought about by several kinds of DNA amplification or by gain-of-function mutations in a variety of transcription factors. Both of these result in overexpression of ABC and MFS transporters. Recently, however, several additional modes of resistance have been observed. These include mutations in non-conserved nucleotides leading to altered mRNA stability and a mutation in yeast transporter Pdr5, which improves cooperativity between drug-binding sites.
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Affiliation(s)
- Atanu Banerjee
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India
| | - Hadiar Rahman
- Laboratory of Cell Biology, Center for Cancer Research, NCI, NIH, Bethesda, MD
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram, India.,Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India
| | - John Golin
- Department of Biology, Stern College, Yeshiva University, New York, NY
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20
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Hamdan A, Ewing A. Unravelling the tumour genome: the evolutionary and clinical impacts of structural variants in tumourigenesis. J Pathol 2022; 257:479-493. [PMID: 35355264 PMCID: PMC9321913 DOI: 10.1002/path.5901] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/16/2022] [Accepted: 03/28/2022] [Indexed: 11/15/2022]
Abstract
Structural variants (SVs) represent a major source of aberration in tumour genomes. Given the diversity in the size and type of SVs present in tumours, the accurate detection and interpretation of SVs in tumours is challenging. New classes of complex structural events in tumours are discovered frequently, and the definitions of the genomic consequences of complex events are constantly being refined. Detailed analyses of short‐read whole‐genome sequencing (WGS) data from large tumour cohorts facilitate the interrogation of SVs at orders of magnitude greater scale and depth. However, the inherent technical limitations of short‐read WGS prevent us from accurately detecting and investigating the impact of all the SVs present in tumours. The expanded use of long‐read WGS will be critical for improving the accuracy of SV detection, and in fully resolving complex SV events, both of which are crucial for determining the impact of SVs on tumour progression and clinical outcome. Despite the present limitations, we demonstrate that SVs play an important role in tumourigenesis. In particular, SVs contribute significantly to late‐stage tumour development and to intratumoural heterogeneity. The evolutionary trajectories of SVs represent a window into the clonal dynamics in tumours, a comprehensive understanding of which will be vital for influencing patient outcomes in the future. Recent findings have highlighted many clinical applications of SVs in cancer, from early detection to biomarkers for treatment response and prognosis. As the methods to detect and interpret SVs improve, elucidating the full breadth of the complex SV landscape and determining how these events modulate tumour evolution will improve our understanding of cancer biology and our ability to capitalise on the utility of SVs in the clinical management of cancer patients. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Alhafidz Hamdan
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ailith Ewing
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.,Cancer Research UK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
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21
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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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22
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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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23
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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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24
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Glenfield C, Innan H. Gene Duplication and Gene Fusion Are Important Drivers of Tumourigenesis during Cancer Evolution. Genes (Basel) 2021; 12:1376. [PMID: 34573358 PMCID: PMC8466788 DOI: 10.3390/genes12091376] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/27/2021] [Accepted: 08/29/2021] [Indexed: 02/07/2023] Open
Abstract
Chromosomal rearrangement and genome instability are common features of cancer cells in human. Consequently, gene duplication and gene fusion events are frequently observed in human malignancies and many of the products of these events are pathogenic, representing significant drivers of tumourigenesis and cancer evolution. In certain subsets of cancers duplicated and fused genes appear to be essential for initiation of tumour formation, and some even have the capability of transforming normal cells, highlighting the importance of understanding the events that result in their formation. The mechanisms that drive gene duplication and fusion are unregulated in cancer and they facilitate rapid evolution by selective forces akin to Darwinian survival of the fittest on a cellular level. In this review, we examine current knowledge of the landscape and prevalence of gene duplication and gene fusion in human cancers.
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Affiliation(s)
| | - Hideki Innan
- Department of Evolutionary Studies of Biosystems, SOKENDAI, The Graduate University for Advanced Studies, Shonan Village, Hayama, Kanagawar 240-0193, Japan;
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25
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Wang T, Zhang H, Zhou Y, Shi J. Extrachromosomal circular DNA: a new potential role in cancer progression. J Transl Med 2021; 19:257. [PMID: 34112178 PMCID: PMC8194206 DOI: 10.1186/s12967-021-02927-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is considered a circular DNA molecule that exists widely in nature and is independent of conventional chromosomes. eccDNA can be divided into small polydispersed circular DNA (spcDNA), telomeric circles (t-circles), microDNA, and extrachromosomal DNA (ecDNA) according to its size and sequence. Multiple studies have shown that eccDNA is the product of genomic instability, has rich and important biological functions, and is involved in the occurrence of many diseases, including cancer. In this review, we focus on the discovery history, formation process, characteristics, and physiological functions of eccDNAs; the potential functions of various eccDNAs in human cancer; and the research methods employed to study eccDNA.
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Affiliation(s)
- Tianyi Wang
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Haijian Zhang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Youlang Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China
| | - Jiahai Shi
- Nantong Key Laboratory of Translational Medicine in Cardiothoracic Diseases, and Research Institution of Translational Medicine in Cardiothoracic Diseases, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China. .,Department of Thoracic Surgery, Affiliated Hospital of Nantong University, No. 20, Xisi Road, Nantong, 226001, Jiangsu, China.
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26
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Abstract
Recent work from Zhu et al. (2021) reveals that extrachromosomal DNA circles harboring enhancers can serve as mobile regulatory elements that interact with chromosomal oncogenes, stimulating high-level gene activity and contributing to tumor heterogeneity and cancer progression.
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Affiliation(s)
- Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA.
| | - Benjamin J E Martin
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115, USA
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27
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Zhu Y, Gujar AD, Wong CH, Tjong H, Ngan CY, Gong L, Chen YA, Kim H, Liu J, Li M, Mil-Homens A, Maurya R, Kuhlberg C, Sun F, Yi E, deCarvalho AC, Ruan Y, Verhaak RGW, Wei CL. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Cancer Cell 2021; 39:694-707.e7. [PMID: 33836152 PMCID: PMC8119378 DOI: 10.1016/j.ccell.2021.03.006] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 11/05/2020] [Accepted: 03/12/2021] [Indexed: 12/13/2022]
Abstract
Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer.
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Affiliation(s)
- Yanfen Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chee-Hong Wong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Harianto Tjong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Liang Gong
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Yi-An Chen
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Meihong Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Adam Mil-Homens
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Chris Kuhlberg
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Fanyue Sun
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Ana C deCarvalho
- Department of Neurosurgery, Henry Ford Hospital, Detroit, MI 48202, USA
| | - Yijun Ruan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
| | - Chia-Lin Wei
- The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032, USA.
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28
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Shoshani O, Brunner SF, Yaeger R, Ly P, Nechemia-Arbely Y, Kim DH, Fang R, Castillon GA, Yu M, Li JSZ, Sun Y, Ellisman MH, Ren B, Campbell PJ, Cleveland DW. Chromothripsis drives the evolution of gene amplification in cancer. Nature 2021; 591:137-141. [PMID: 33361815 PMCID: PMC7933129 DOI: 10.1038/s41586-020-03064-z] [Citation(s) in RCA: 205] [Impact Index Per Article: 68.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 11/26/2020] [Indexed: 12/15/2022]
Abstract
Focal chromosomal amplification contributes to the initiation of cancer by mediating overexpression of oncogenes1-3, and to the development of cancer therapy resistance by increasing the expression of genes whose action diminishes the efficacy of anti-cancer drugs. Here we used whole-genome sequencing of clonal cell isolates that developed chemotherapeutic resistance to show that chromothripsis is a major driver of circular extrachromosomal DNA (ecDNA) amplification (also known as double minutes) through mechanisms that depend on poly(ADP-ribose) polymerases (PARP) and the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs). Longitudinal analyses revealed that a further increase in drug tolerance is achieved by structural evolution of ecDNAs through additional rounds of chromothripsis. In situ Hi-C sequencing showed that ecDNAs preferentially tether near chromosome ends, where they re-integrate when DNA damage is present. Intrachromosomal amplifications that formed initially under low-level drug selection underwent continuing breakage-fusion-bridge cycles, generating amplicons more than 100 megabases in length that became trapped within interphase bridges and then shattered, thereby producing micronuclei whose encapsulated ecDNAs are substrates for chromothripsis. We identified similar genome rearrangement profiles linked to localized gene amplification in human cancers with acquired drug resistance or oncogene amplifications. We propose that chromothripsis is a primary mechanism that accelerates genomic DNA rearrangement and amplification into ecDNA and enables rapid acquisition of tolerance to altered growth conditions.
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Affiliation(s)
- Ofer Shoshani
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | | | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Peter Ly
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yael Nechemia-Arbely
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dong Hyun Kim
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Rongxin Fang
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Guillaume A Castillon
- National Center for Microscopy and Imaging Research (NCMIR), University of California at San Diego, La Jolla, CA, USA
| | - Miao Yu
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Julia S Z Li
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ying Sun
- Department of Pediatrics, University of California at San Diego, La Jolla, CA, USA
| | - Mark H Ellisman
- National Center for Microscopy and Imaging Research (NCMIR), University of California at San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California at San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
| | - Bing Ren
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Peter J Campbell
- Wellcome Sanger Institute, Hinxton, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
| | - Don W Cleveland
- Ludwig Cancer Research, University of California at San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA.
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29
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Wu S, Bafna V, Mischel PS. Extrachromosomal DNA (ecDNA) in cancer pathogenesis. Curr Opin Genet Dev 2021; 66:78-82. [PMID: 33477016 DOI: 10.1016/j.gde.2021.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 12/19/2022]
Abstract
In cancer, oncogenes and surrounding regulatory regions can untether themselves from chromosomes, forming extrachromosomal DNA particles (ecDNAs). Because of their non-chromosomal inheritance, ecDNA drives high oncogene copy number and intratumoral genetic heterogeneity, endowing tumors with the ability to rapidly change their genomes, accelerating tumor evolution, and contributing to therapeutic resistance. Further, the circular topology of ecDNA leads to enhanced chromatin accessibility, altered gene regulation, and massive oncogene transcription, driving tumor growth and progression, and placing ecDNA at the interface of cancer genomics and epigenetics. Recent studies show that ecDNA is a common event in many of the most aggressive forms of cancer, potentially challenging our current precision oncology approaches. In this review, we discuss what is known about ecDNA and its biological and clinical impact, highlighting new research and suggesting the promise, and some of the challenges ahead for the field.
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Affiliation(s)
- Sihan Wu
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California at San Diego, La Jolla, CA, USA; Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA; Department of Pathology, University of California at San Diego, La Jolla, CA, USA.
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30
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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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31
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Abstract
Cancer Grand Challenges is a unique funding platform that dares global, multidisciplinary teams of researchers to come together, think differently, and tackle some of the toughest challenges in cancer research. Here, we discuss the nine intractable challenges currently open for application.
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32
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Choi G, Choy JH. Recent progress in layered double hydroxides as a cancer theranostic nanoplatform. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020; 13:e1679. [PMID: 33140557 DOI: 10.1002/wnan.1679] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 10/06/2020] [Accepted: 10/09/2020] [Indexed: 12/24/2022]
Abstract
Layered double hydroxide (LDH) has been a big challenge in exploring new hybrid materials by intercalating inorganic, organic, or bio molecules into their lamellar lattice, those which often showed dual functions from each other or new mutative properties. Recently, nano-bio convergence technology becomes one of the most extensively studied research fields in the view point of developing advanced drugs and diagnostic agents to fight against disease and eventually to improve the lives of human beings. Therefore, LDH as one of the nanomaterials have been intensively investigated not only as biocompatible drug delivery vehicle for cancer chemotherapy but also as diagnostic and imaging agents. In the present review, we have attempted to summarize theranostic functions of drug-LDH hybrid nanoparticles including their synthetic methods, physico-chemical and biological properties, and their unique mechanism overcoming drug resistance, and targeting properties based on in vitro and finally in vivo results. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > in vivo Nanodiagnostics and Imaging.
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Affiliation(s)
- Goeun Choi
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, Republic of Korea.,College of Science and Technology, Dankook University, Cheonan, Republic of Korea
| | - Jin-Ho Choy
- Intelligent Nanohybrid Materials Laboratory (INML), Institute of Tissue Regeneration Engineering (ITREN), Dankook University, Cheonan, Republic of Korea.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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33
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Kim H, Nguyen NP, Turner K, Wu S, Gujar AD, Luebeck J, Liu J, Deshpande V, Rajkumar U, Namburi S, Amin SB, Yi E, Menghi F, Schulte JH, Henssen AG, Chang HY, Beck CR, Mischel PS, Bafna V, Verhaak RGW. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat Genet 2020; 52:891-897. [PMID: 32807987 PMCID: PMC7484012 DOI: 10.1038/s41588-020-0678-2] [Citation(s) in RCA: 224] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 12/27/2022]
Abstract
Extrachromosomal DNA (ecDNA) amplification promotes intratumoral genetic heterogeneity and accelerated tumor evolution1-3; however, its frequency and clinical impact are unclear. Using computational analysis of whole-genome sequencing data from 3,212 cancer patients, we show that ecDNA amplification frequently occurs in most cancer types but not in blood or normal tissue. Oncogenes were highly enriched on amplified ecDNA, and the most common recurrent oncogene amplifications arose on ecDNA. EcDNA amplifications resulted in higher levels of oncogene transcription compared to copy number-matched linear DNA, coupled with enhanced chromatin accessibility, and more frequently resulted in transcript fusions. Patients whose cancers carried ecDNA had significantly shorter survival, even when controlled for tissue type, than patients whose cancers were not driven by ecDNA-based oncogene amplification. The results presented here demonstrate that ecDNA-based oncogene amplification is common in cancer, is different from chromosomal amplification and drives poor outcome for patients across many cancer types.
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Affiliation(s)
- Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Nam-Phuong Nguyen
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Boundless Bio, La Jolla, CA, USA
| | - Kristen Turner
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
- Boundless Bio, La Jolla, CA, USA
| | - Sihan Wu
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA
| | - Amit D Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jens Luebeck
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Bioinformatics & Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Jihe Liu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Viraj Deshpande
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
- Illumina, San Diego, CA, USA
| | - Utkrisht Rajkumar
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Sandeep Namburi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Francesca Menghi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Johannes H Schulte
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Anton G Henssen
- Department of Pediatric Hematology and Oncology, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- Experimental and Clinical Research Center, Max Delbrück Center for Molecular Medicine and Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
| | - Christine R Beck
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, Institute for Systems Genomics, University of Connecticut Health Center, Farmington, CT, USA
| | - Paul S Mischel
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
- Department of Pathology, University of California, San Diego, San Diego, CA, USA.
| | - Vineet Bafna
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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34
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Scotto L, Kinahan C, Casadei B, Mangone M, Douglass E, Murty VV, Marchi E, Ma H, George C, Montanari F, Califano A, O'Connor OA. Generation of pralatrexate resistant T-cell lymphoma lines reveals two patterns of acquired drug resistance that is overcome with epigenetic modifiers. Genes Chromosomes Cancer 2020; 59:639-651. [PMID: 32614991 PMCID: PMC7540375 DOI: 10.1002/gcc.22884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/26/2020] [Accepted: 06/27/2020] [Indexed: 12/14/2022] Open
Abstract
While pralatrexate (PDX) has been successfully developed for the treatment of T-cell lymphoma, the mechanistic basis for its T-cell selectivity and acquired resistance remains elusive. In an effort to potentially identify synergistic combinations that might circumnavigate or delay acquired PDX resistance, we generated resistant cells lines over a broad concentration range. PDX-resistant cell lines H9-12 and H9-200 were developed, each exhibiting an IC50 of 35 and over 1000 nM, respectively. These lines were established in vitro from parental H9 cells. Expression analysis of the proteins known to be important determinants of antifolate pharmacology revealed increase expression of dihydrofolate reductase (DHFR) due to gene amplification, and reduced folate carrier1 downregulation, as the putative mechanisms of resistance in H9-12 and H9-200 cells. Cross resistance was only seen with methotrexate but not with romidepsin, azacitidine (AZA), decitabine, gemcitabine, doxorubicin, or bortezomib. Resistance to PDX was reversed by pretreatment with hypomethylating agents in a concentration-dependent fashion. Comparison of gene expression profiles of parental and resistant cell lines confirmed markedly different patterns of gene expression, and identified the dual specificity phosphatase four (DUSP4) as one of the molecular target of PDX activity. Reduced STAT5 phosphorylation following exposure to PDX was observed in the H9 but not in the H9-12 and H9-200 cells. These data suggest that combination with hypomethylating agents could be potent, and that DUSP4 and STAT5 could represent putative biomarkers of PDX activity.
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Affiliation(s)
- Luigi Scotto
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Cristina Kinahan
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Beatrice Casadei
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Michael Mangone
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Eugene Douglass
- Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Vundavalli V Murty
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York, USA
| | - Enrica Marchi
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Helen Ma
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Changchun George
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Francesca Montanari
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA.,Division of Experimental Therapeutics, Columbia University Medical Center, New York, New York, USA
| | - Andrea Califano
- Department of Systems Biology, Columbia University Medical Center, New York, New York, USA
| | - Owen A O'Connor
- Center for Lymphoid Malignancies, Columbia University Medical Center, New York, New York, USA
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35
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Liao Z, Jiang W, Ye L, Li T, Yu X, Liu L. Classification of extrachromosomal circular DNA with a focus on the role of extrachromosomal DNA (ecDNA) in tumor heterogeneity and progression. Biochim Biophys Acta Rev Cancer 2020; 1874:188392. [PMID: 32735964 DOI: 10.1016/j.bbcan.2020.188392] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/26/2020] [Accepted: 07/10/2020] [Indexed: 02/08/2023]
Abstract
Although the eukaryotic genome is mainly comprised of linear chromosomal DNA, genes can also be found outside of chromosomes. The unconventional presence of extrachromosomal genes is usually found to be circular, and these structures are named extrachromosomal circular DNA (eccDNA), which are often observed in cancer cells. Various types of eccDNA including small polydispersed DNA (spcDNA), telomeric cirlces, microDNA, etc. have been discovered. Among these eccDNA, extrachromosomal DNA (ecDNA), which encompasses the full spectrum of large, gene-containing extrachromosomal particles, has regained great research interest due to recent technological advances such as next-generation sequencing and super-resolution microscopy. In this review, we summarize the different types of eccDNA and discuss the role of eccDNA, especially ecDNA in tumor heterogeneity and progression. Additionally, we discuss some possible future investigative directions related to ecDNA biogenesis and its clinical application.
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Affiliation(s)
- Zhenyu Liao
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wang Jiang
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Longyun Ye
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Tianjiao Li
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Liang Liu
- Department of Pancreatic Surgery, Shanghai Cancer Centre, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Shanghai Pancreatic Cancer Institute, Shanghai, China; Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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36
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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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37
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Clarke TL, Tang R, Chakraborty D, Van Rechem C, Ji F, Mishra S, Ma A, Kaniskan HÜ, Jin J, Lawrence MS, Sadreyev RI, Whetstine JR. Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification. Cancer Discov 2019; 10:306-325. [PMID: 31776131 DOI: 10.1158/2159-8290.cd-19-0463] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 10/29/2019] [Accepted: 11/25/2019] [Indexed: 11/16/2022]
Abstract
Acquired chromosomal DNA copy gains are a feature of many tumors; however, the mechanisms that underpin oncogene amplification are poorly understood. Recent studies have begun to uncover the importance of epigenetic states and histone lysine methyltransferases (KMT) and demethylases (KDM) in regulating transient site-specific DNA copy-number gains (TSSG). In this study, we reveal a critical interplay between a myriad of lysine methyltransferases and demethylases in modulating H3K4/9/27 methylation balance to control extrachromosomal amplification of the EGFR oncogene. This study further establishes that cellular signals (hypoxia and EGF) are able to directly promote EGFR amplification through modulation of the enzymes controlling EGFR copy gains. Moreover, we demonstrate that chemical inhibitors targeting specific KMTs and KDMs are able to promote or block extrachromosomal EGFR amplification, which identifies potential therapeutic strategies for controlling EGFR copy-number heterogeneity in cancer, and, in turn, drug response. SIGNIFICANCE: This study identifies a network of epigenetic factors and cellular signals that directly control EGFR DNA amplification. We demonstrate that chemical inhibitors targeting enzymes controlling this amplification can be used to rheostat EGFR copy number, which uncovers therapeutic opportunities for controlling EGFR DNA amplification heterogeneity and the associated drug response.This article is highlighted in the In This Issue feature, p. 161.
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Affiliation(s)
- Thomas L Clarke
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Ran Tang
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.,School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Damayanti Chakraborty
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Capucine Van Rechem
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Fei Ji
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts
| | - Sweta Mishra
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts
| | - Anqi Ma
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - H Ümit Kaniskan
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jian Jin
- Departments of Pharmacological Sciences and Oncological Sciences, Mount Sinai Center for Therapeutics Discovery, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, Charlestown, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Ruslan I Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts.,Massachusetts General Hospital, Department of Pathology, Harvard Medical School, Charlestown, Massachusetts
| | - Johnathan R Whetstine
- Department of Medicine, Massachusetts General Hospital Cancer Center and Harvard Medical School, Charlestown, Massachusetts.
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38
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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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39
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The Role of SVZ Stem Cells in Glioblastoma. Cancers (Basel) 2019; 11:cancers11040448. [PMID: 30934929 PMCID: PMC6521108 DOI: 10.3390/cancers11040448] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/22/2019] [Accepted: 03/26/2019] [Indexed: 12/27/2022] Open
Abstract
As most common primary brain cancer, glioblastoma is also the most aggressive and malignant form of cancer in the adult central nervous system. Glioblastomas are genetic and transcriptional heterogeneous tumors, which in spite of intensive research are poorly understood. Over the years conventional therapies failed to affect a cure, resulting in low survival rates of affected patients. To improve the clinical outcome, an important approach is to identify the cells of origin. One potential source for these are neural stem cells (NSCs) located in the subventricular zone, which is one of two niches in the adult nervous system where NSCs with the capacity of self-renewal and proliferation reside. These cells normally give rise to neuronal as well as glial progenitor cells. This review summarizes current findings about links between NSCs and cancer stem cells in glioblastoma and discusses current therapeutic approaches, which arise as a result of identifying the cell of origin in glioblastoma.
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40
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Mishra S, Van Rechem C, Pal S, Clarke TL, Chakraborty D, Mahan SD, Black JC, Murphy SE, Lawrence MS, Daniels DL, Whetstine JR. Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell 2018; 174:803-817.e16. [PMID: 30057114 PMCID: PMC6212369 DOI: 10.1016/j.cell.2018.06.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 04/02/2018] [Accepted: 06/08/2018] [Indexed: 12/28/2022]
Abstract
Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sangita Pal
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Thomas L Clarke
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Damayanti Chakraborty
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sarah D Mahan
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Sedona E Murphy
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Pathology, Harvard Medical School, 13th Street, Charlestown, MA 02129, USA; Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, MA 02142, USA
| | | | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA.
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41
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Patel NA, Anderson CR, Terkildsen SE, Davis RC, Pack LD, Bhargava S, Clarke HR. Antibody expression stability in CHO clonally derived cell lines and their subclones: Role of methylation in phenotypic and epigenetic heterogeneity. Biotechnol Prog 2018; 34:635-649. [DOI: 10.1002/btpr.2655] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 04/24/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Neha A. Patel
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
| | | | | | - Ray C. Davis
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
| | - Laura D. Pack
- Dept. of CMC Statistics; Seattle Genetics; Bothell WA 98021
| | - Swapnil Bhargava
- Dept. of Bioprocess Development; Seattle Genetics; Bothell WA 98021
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42
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Toffoli G, Viel A, Tumiotto L, Buttazzi P, Biscontin G, Boiocchi M. Sensitivity Pattern of Normal and Ha-Ras Transformed Nih3T3 Fibroblasts to Antineoplastic Drugs. TUMORI JOURNAL 2018; 75:423-8. [PMID: 2690431 DOI: 10.1177/030089168907500505] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ha-ras-transformed NIH3T3 fibroblasts were compared with the parental cell line to investigate the influence of the Ha-ras oncogene on cellular chemosensitivity to antineoplastic drugs. Four NIH3T3 cell clones independently transformed by the Ha-ras oncogene, activated by mutation or overexpression, were analyzed: 3 clones were obtained by transfection of NIH3T3 cells with a mutation-activated Ha-ras gene and 1 clone by transfection of a large copy number of the normal Ha-ras protooncogene. Chemosensitivity of the transformed clones and of the parental cell line was analyzed when cells were in the same condition of proliferative activity and cell cycle phase distribution. No significant differences in chemosensitivity were observed between transformed and untrans-formed cell lines to doxorubicin, VP-16, cis-platinum or mitomycin C. Therefore, data suggest that activated Ha-ras oncogenes have no role in sensitivity to these antineoplastic agents.
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Affiliation(s)
- G Toffoli
- Division of Experimental Oncology, Oncologic Reference Center, Aviano-Pordenone, Italy
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43
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Bugde P, Biswas R, Merien F, Lu J, Liu DX, Chen M, Zhou S, Li Y. The therapeutic potential of targeting ABC transporters to combat multi-drug resistance. Expert Opin Ther Targets 2017; 21:511-530. [DOI: 10.1080/14728222.2017.1310841] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Piyush Bugde
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Riya Biswas
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Fabrice Merien
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Science, AUT Roche Diagnostic Laboratory, Auckland University of Technology, Auckland, New Zealand
| | - Jun Lu
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Interprofessional Health Studies, Auckland University of Technology, Auckland, New Zealand
| | - Dong-Xu Liu
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Mingwei Chen
- Department of Respiratory Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Shufeng Zhou
- Department of Biotechnology and Bioengineering, College of Chemical Engineering, Huaqiao University, Xiamen, China
| | - Yan Li
- School of Science, Auckland University of Technology, Auckland, New Zealand
- School of Interprofessional Health Studies, Auckland University of Technology, Auckland, New Zealand
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44
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Marotta M, Onodera T, Johnson J, Budd GT, Watanabe T, Cui X, Giuliano AE, Niida A, Tanaka H. Palindromic amplification of the ERBB2 oncogene in primary HER2-positive breast tumors. Sci Rep 2017; 7:41921. [PMID: 28211519 PMCID: PMC5314454 DOI: 10.1038/srep41921] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 01/03/2017] [Indexed: 12/21/2022] Open
Abstract
Oncogene amplification confers a growth advantage to tumor cells for clonal expansion. There are several, recurrently amplified oncogenes throughout the human genome. However, it remains unclear whether this recurrent amplification is solely a manifestation of increased fitness resulting from random amplification mechanisms, or if a genomic locus-specific amplification mechanism plays a role. Here we show that the ERBB2 oncogene at 17q12 is susceptible to palindromic gene amplification, a mechanism characterized by the inverted (palindromic) duplication of genomic segments, in HER2-positive breast tumors. We applied two genomic approaches to investigate amplification mechanisms: sequencing of DNA libraries enriched with tumor-derived palindromic DNA (Genome-wide Analysis of Palindrome Formation) and whole genome sequencing (WGS). We observed significant enrichment of palindromic DNA within amplified ERBB2 genomic segments. Palindromic DNA was particularly enriched at amplification peaks and at boundaries between amplified and normal copy-number regions. Thus, palindromic gene amplification shaped the amplified ERBB2 locus. The enrichment of palindromic DNA throughout the amplified segments leads us to propose that the ERBB2 locus is amplified through the mechanism that repeatedly generates palindromic DNA, such as Breakage-Fusion-Bridge cycles. The genomic architecture surrounding ERBB2 in the normal genome, such as segmental duplications, could promote the locus-specific mechanism.
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Affiliation(s)
- Michael Marotta
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA
| | - Taku Onodera
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Jeffrey Johnson
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - G Thomas Budd
- Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Takaaki Watanabe
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA.,Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Xiaojiang Cui
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Armando E Giuliano
- Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
| | - Atsushi Niida
- Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Hisashi Tanaka
- Lerner Research Institute and Cleveland Clinic, Cleveland, OH, USA.,Department of Surgery, Cedars-Sinai Medical Center, West Hollywood, CA, USA
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45
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Nakano M, Fukami T, Gotoh S, Nakajima M. A-to-I RNA Editing Up-regulates Human Dihydrofolate Reductase in Breast Cancer. J Biol Chem 2017; 292:4873-4884. [PMID: 28188287 DOI: 10.1074/jbc.m117.775684] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 02/02/2017] [Indexed: 12/15/2022] Open
Abstract
Dihydrofolate reductase (DHFR) plays a key role in folate metabolism and is a target molecule of methotrexate. An increase in the cellular expression level of DHFR is one of the mechanisms of tumor resistance to methotrexate. The present study investigated the possibility that adenosine-to-inosine RNA editing, which causes nucleotide conversion by adenosine deaminase acting on RNA (ADAR) enzymes, might modulate DHFR expression. In human breast adenocarcinoma-derived MCF-7 cells, 26 RNA editing sites were identified in the 3'-UTR of DHFR. Knockdown of ADAR1 decreased the RNA editing levels of DHFR and resulted in a decrease in the DHFR mRNA and protein levels, indicating that ADAR1 up-regulates DHFR expression. Using a computational analysis, miR-25-3p and miR-125a-3p were predicted to bind to the non-edited 3'-UTR of DHFR but not to the edited sequence. The decrease in DHFR expression by the knockdown of ADAR1 was restored by transfection of antisense oligonucleotides for these miRNAs, suggesting that RNA editing mediated up-regulation of DHFR requires the function of these miRNAs. Interestingly, we observed that the knockdown of ADAR1 decreased cell viability and increased the sensitivity of MCF-7 cells to methotrexate. ADAR1 expression levels and the RNA editing levels in the 3'-UTR of DHFR in breast cancer tissues were higher than those in adjacent normal tissues. Collectively, the present study demonstrated that ADAR1 positively regulates the expression of DHFR by editing the miR-25-3p and miR-125a-3p binding sites in the 3'-UTR of DHFR, enhancing cellular proliferation and resistance to methotrexate.
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Affiliation(s)
- Masataka Nakano
- From the Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Tatsuki Fukami
- From the Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Saki Gotoh
- From the Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
| | - Miki Nakajima
- From the Drug Metabolism and Toxicology, Faculty of Pharmaceutical Sciences, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan
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46
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Horowitz M, Elstein D, Zimran A, Goker-Alpan O. New Directions in Gaucher Disease. Hum Mutat 2016; 37:1121-1136. [DOI: 10.1002/humu.23056] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 07/20/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Mia Horowitz
- Department of Cell Research and Immunology, Faculty of Life Sciences; Tel Aviv University; Ramat Aviv Israel
| | - Deborah Elstein
- Gaucher Clinic; Shaare Zedek Medical Center; Jerusalem Israel
| | - Ari Zimran
- Gaucher Clinic; Shaare Zedek Medical Center; Jerusalem Israel
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47
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Thierry A, Khanna V, Dujon B. Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast. G3 (BETHESDA, MD.) 2016; 6:1201-15. [PMID: 26945028 PMCID: PMC4856073 DOI: 10.1534/g3.115.024547] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 02/20/2016] [Indexed: 12/13/2022]
Abstract
Gene amplification has been observed in different organisms in response to environmental constraints, such as limited nutrients or exposure to a variety of toxic compounds, conferring them with specific phenotypic adaptations via increased expression levels. However, the presence of multiple gene copies in natural genomes has generally not been found in the absence of specific functional selection. Here, we show that the massive amplification of a chromosomal locus (up to 880 copies per cell) occurs in the absence of any direct selection, and is associated with low-order amplifications of flanking segments in complex chromosomal alterations. These results were obtained from mutants with restored phenotypes that spontaneously appeared from genetically engineered strains of the yeast Saccharomyces cerevisiae suffering from severe fitness reduction. Grossly extended chromosomes (macrotene) were formed, with complex structural alterations but sufficient stability to propagate unchanged over successive generations. Their detailed molecular analysis, including complete genome sequencing, identification of sequence breakpoints, and comparisons between mutants, revealed novel mechanisms causing their formation, whose combined action underlies the astonishing dynamics of eukaryotic chromosomes and their consequences.
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Affiliation(s)
- Agnès Thierry
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS (UMR3525), Sorbonne Universités, UPMC, Université Paris 06 (UFR927), F-75724 CEDEX 15, France
| | - Varun Khanna
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS (UMR3525), Sorbonne Universités, UPMC, Université Paris 06 (UFR927), F-75724 CEDEX 15, France
| | - Bernard Dujon
- Institut Pasteur, Unité de Génétique Moléculaire des Levures, CNRS (UMR3525), Sorbonne Universités, UPMC, Université Paris 06 (UFR927), F-75724 CEDEX 15, France
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48
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Zhang CZ, Pellman D. From Mutational Mechanisms in Single Cells to Mutational Patterns in Cancer Genomes. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:117-37. [PMID: 26968629 DOI: 10.1101/sqb.2015.80.027623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Analysis of mutations in thousands of cancer genomes has revealed many characteristic patterns of mutagenesis. The search for the molecular mechanisms underlying these mutational patterns has not only generated novel biological insight but also led to the development of new experimental strategies to study cell-to-cell variation and genome evolution. In this essay, we discuss recent progress in the study of mutational mechanisms with a particular emphasis on the analysis of mutagenesis at the single-cell level.
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Affiliation(s)
- Cheng-Zhong Zhang
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - David Pellman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215 Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142 Howard Hughes Medical Institute, Boston, Massachusetts 02115
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49
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Abstract
Chromosomal copy number changes are frequently associated with harmful consequences and are thought of as an underlying mechanism for the development of diseases. However, changes in copy number are observed during development and occur during normal biological processes. In this review, we highlight the causes and consequences of copy number changes in normal physiologic processes as well as cover their associations with cancer and acquired drug resistance. We discuss the permanent and transient nature of copy number gains and relate these observations to a new mechanism driving transient site-specific copy gains (TSSGs). Finally, we discuss implications of TSSGs in generating intratumoral heterogeneity and tumor evolution and how TSSGs can influence the therapeutic response in cancer.
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Affiliation(s)
- Sweta Mishra
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Charlestown, Massachusetts, USA
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50
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Corbin MV, Rockx DAP, Oostra AB, Joenje H, Dorsman JC. The iron-sulfur cluster assembly network component NARFL is a key element in the cellular defense against oxidative stress. Free Radic Biol Med 2015; 89:863-72. [PMID: 26456054 DOI: 10.1016/j.freeradbiomed.2015.08.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 08/05/2015] [Accepted: 08/29/2015] [Indexed: 10/22/2022]
Abstract
Aim of this study was to explore cellular changes associated with increased resistance to atmospheric oxygen using high-resolution DNA and RNA profiling combined with functional studies. Two independently selected oxygen-resistant substrains of HeLa cells (capable of proliferating at >80% O2, i.e. hyperoxia) were compared with their parental cells (adapted to growth at 20% O2, but unable to grow at >80% O2). A striking consistent alteration found to be associated with the oxygen-resistant state appeared to be an amplified and overexpressed region on chromosome 16p13.3 harboring 21 genes. The driver gene of this amplification was identified by functional studies as NARFL, which encodes a component of the cytosolic iron-sulfur cluster assembly system. In line with this result we found the cytosolic c-aconitase activity as well as the nuclear protein RTEL1, both Fe-S dependent proteins, to be protected by NARFL overexpression under hyperoxia. In addition, we observed a protective effect of NARFL against hyperoxia-induced loss of sister-chromatid cohesion. NARFL thus appeared to be a key factor in the cellular defense against hyperoxia-induced oxidative stress in human cells. Our findings suggest that new insight into age-related degenerative processes may come from studies that specifically address the involvement of iron-sulfur proteins.
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Affiliation(s)
- Monique V Corbin
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, 1081BT Amsterdam, The Netherlands.
| | - Davy A P Rockx
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, 1081BT Amsterdam, The Netherlands.
| | - Anneke B Oostra
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, 1081BT Amsterdam, The Netherlands.
| | - Hans Joenje
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, 1081BT Amsterdam, The Netherlands.
| | - Josephine C Dorsman
- Department of Clinical Genetics, Section Oncogenetics, VU University Medical Center, 1081BT Amsterdam, The Netherlands.
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