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Yu J, Zhang H, Han P, Jiang X, Li J, Li B, Yang S, He C, Mao S, Dang Y, Xiang X. Circle-seq based method for eccDNA synthesis and its application as a canonical promoter independent vector for robust microRNA overexpression. Comput Struct Biotechnol J 2024; 23:358-368. [PMID: 38223344 PMCID: PMC10788182 DOI: 10.1016/j.csbj.2023.12.019] [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: 10/11/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) has recently gained increasing attention due to its significant role in cancer and other pathophysiologic states. The majority of circular DNAs detected by Circle-seq are small-size eccDNAs with enigmatic functions. One major technical hurdle is to synthesize eccDNA for functional identification. Here, we describe CAES (Circle-seq based Artificial EccDNA Synthesis), a promising and reliable method for artificial eccDNA synthesis. Eight eccDNAs carrying different microRNA genes (eccMIR) found in gastric cancer tissues, ranging from 329 bp to 2189 bp in size, were created utilizing the CAES method. Exonuclease V and single restriction-endonuclease digestion identified the circular structure of synthetic eccDNAs. The DNA circularization efficiency afforded by CAES ranged from 15.6% to 31.1%, which was negatively correlated with the eccDNA length. In addition, we demonstrated that CAES-synthesized eccMIRs can express both miRNA-3p and - 5p molecules efficiently independent of a canonical promoter in human cell lines. Further assays proved that these eccMIRs were functional as they were able to repress the luciferase gene containing a miRNA-target sequence in the 3'UTR as well as the endogenous mRNA targets. Finally, kinetics study revealed that eccDNA exhibited a decay rate similar to the standard plasmids and linear DNA in cultured cells. Together, this study offers a rapid and convenient method for Circle-seq users to synthesize artificial eccDNAs. It also demonstrates the promising potential of eccMIR as a bacterial DNA-free vector for safe and robust miRNA overexpression in both basic research and therapeutic applications.
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Affiliation(s)
- Jiaying Yu
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Haoran Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Peng Han
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xianming Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jing Li
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bo Li
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Shaohua Yang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Chunxiao He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Shuang Mao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yonghui Dang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xi Xiang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
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Li F, Ming W, Lu W, Wang Y, Dong X, Bai Y. Bioinformatics advances in eccDNA identification and analysis. Oncogene 2024; 43:3021-3036. [PMID: 39209966 DOI: 10.1038/s41388-024-03138-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 08/09/2024] [Accepted: 08/16/2024] [Indexed: 09/04/2024]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are a unique class of chromosome-originating circular DNA molecules, which are closely linked to oncogene amplification. Due to recent technological advances, particularly in high-throughput sequencing technology, bioinformatics methods based on sequencing data have become primary approaches for eccDNA identification and functional analysis. Currently, eccDNA-relevant databases incorporate previously identified eccDNA and provide thorough functional annotations and predictions, thereby serving as a valuable resource for eccDNA research. In this review, we collected around 20 available eccDNA-associated bioinformatics tools, including identification tools and annotation databases, and summarized their properties and capabilities. We evaluated some of the eccDNA detection methods in simulated data to offer recommendations for future eccDNA detection. We also discussed the current limitations and prospects of bioinformatics methodologies in eccDNA research.
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Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, PR China.
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China
| | - Xianjun Dong
- Adams Center of Parkinson's Disease Research, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
- Department of Neurology, Yale School of Medicine, Yale University, 100 College St, New Haven, CT, 06511, USA.
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, PR China.
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Yao Y, Wang Q, Jiang W, Li H, Li X, Zi T, Qin X, Zhao Y, Wu D, Wu G. Extrachromosomal circular DNA-related SPOCK1 contributes to development and enzalutamide resistance of prostate cancer by regulating epithelial mesenchymal transition. Heliyon 2024; 10:e37075. [PMID: 39328548 PMCID: PMC11425131 DOI: 10.1016/j.heliyon.2024.e37075] [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: 01/30/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Prostate cancer is a significant contributor to cancer-related mortality, and the tumor typically develops into castration-resistant prostate cancer (CRPC). Hence, few effective clinical strategies are available to patients with advanced disease. Extrachromosomal circular DNA (eccDNA) is a type of circular DNA originating from the chromosomes but is likely independent of them. Because of its unique structural characteristics, eccDNA has extensive applications as a new biomarker for cancer prevention and treatment. Circle-seq obtains a comprehensive picture of the overall landscape of eccDNA sizes and content in cell populations. In this study, we used Circle-seq and studied the distribution pattern and expression level of eccDNA in prostate cancer. We confirmed that eccDNA is derived from every human chromosome and has sequences from all known types of genomic structures, revealing it is a common mutational element in prostate cancer. We also identified an eccDNA-related gene SPOCK1 that promotes drug resistance, proliferation, and metastasis of many cancers through the epithelial-mesenchymal transition (EMT) mechanism. The SPOCK1-associated eccDNA was highly upregulated in various groups of sequencing results, and SPOCK1 was highly expressed in prostate cancer tissues and cells. Therefore, SPOCK1 exists as eccDNA in prostate cancer and encourages its development and drug resistance via the EMT mechanism. Our results suggest that upregulated genes in the form of eccDNA are oncogenes in prostate cancer and play a pivotal role in carcinogenesis.
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Affiliation(s)
- Yicong Yao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qinghua Wang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Wei Jiang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Haopeng Li
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xilei Li
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Tong Zi
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xin Qin
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yan Zhao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Denglong Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Gang Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
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Fessler J, Ting S, Yi H, Haase S, Chen J, Gulec S, Wang Y, Smyers N, Goble K, Cannon D, Mehta A, Ford C, Brunk E. CytoCellDB: a comprehensive resource for exploring extrachromosomal DNA in cancer cell lines. NAR Cancer 2024; 6:zcae035. [PMID: 39091515 PMCID: PMC11292414 DOI: 10.1093/narcan/zcae035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/31/2024] [Accepted: 07/24/2024] [Indexed: 08/04/2024] Open
Abstract
Recently, the cancer community has gained a heightened awareness of the roles of extrachromosomal DNA (ecDNA) in cancer proliferation, drug resistance and epigenetic remodeling. However, a hindrance to studying ecDNA is the lack of available cancer model systems that express ecDNA. Increasing our awareness of which model systems express ecDNA will advance our understanding of fundamental ecDNA biology and unlock a wealth of potential targeting strategies for ecDNA-driven cancers. To bridge this gap, we created CytoCellDB, a resource that provides karyotype annotations for cell lines within the Cancer Dependency Map (DepMap) and the Cancer Cell Line Encyclopedia (CCLE). We identify 139 cell lines that express ecDNA, a 200% increase from what is currently known. We expanded the total number of cancer cell lines with ecDNA annotations to 577, which is a 400% increase, covering 31% of cell lines in CCLE/DepMap. We experimentally validate several cell lines that we predict express ecDNA or homogeneous staining regions (HSRs). We demonstrate that CytoCellDB can be used to characterize aneuploidy alongside other molecular phenotypes, (gene essentialities, drug sensitivities, gene expression). We anticipate that CytoCellDB will advance cytogenomics research as well as provide insights into strategies for developing therapeutics that overcome ecDNA-driven drug resistance.
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Affiliation(s)
- Jacob Fessler
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Stephanie Ting
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Hong Yi
- Renaissance Computing Institute (RENCI), University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Santiago Haase
- Integrative Program for Biological and Genome Sciences (IBGS), University of North Carolina, Chapel Hill, USA
| | - Jingting Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Saygin Gulec
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Yue Wang
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Nathan Smyers
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Kohen Goble
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Danielle Cannon
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Aarav Mehta
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
| | - Christina Ford
- Integrative Program for Biological and Genome Sciences (IBGS), University of North Carolina, Chapel Hill, USA
| | - Elizabeth Brunk
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
- Integrative Program for Biological and Genome Sciences (IBGS), University of North Carolina, Chapel Hill, USA
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
- Computational Medicine Program, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516, USA
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Fang J, Ying L, Ma Z, Yang Y, Zhu R, Su D. The distribution of the extrachromosomal DNA molecules in early lung cancer. Sci Prog 2024; 107:368504241276771. [PMID: 39228317 PMCID: PMC11375654 DOI: 10.1177/00368504241276771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Lung cancer (LC) is a highly lethal cancer worldwide. Research on the distribution and nature of extrachromosomal DNA molecules (EcDNAm) in early LC is scarce. In this study, after removing linear DNA and mitochondrial circular DNA, EcDNAm were extracted from two paired LC tissue samples and amplified using rolling circle amplification. High throughput extrachromosomal DNA (EcDNA) or RNA sequencing and bioinformatics analysis were subsequently utilized to explore the distribution and nature of the EcDNAm. Additionally, to elucidate the role of oncogenes with large EcDNAm sizes, gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed. The RNA sequencing results revealed significant differences in certain genes between tumors and corresponding normal samples. At the same time, slight distinctions were observed between relapsed and non-relapsed tumor samples. The nature of the EcDNAm was compared between LC samples and matched normal samples. There was a tendency for the number of EcDNAm with longer size (EcDNA) and its containing driver oncogenes to be higher in cancer samples. Enrichment analysis of the cancer samples revealed enrichment in biological processes, such as positive regulation of protein localization, axon development, and in-utero embryonic development. This study highlights the universal distribution and characteristics of EcDNAm in early LC. Moreover, our work fills the investigation of the EcDNAm gap and future studies should focus on the application of EcDNA as a potential biomarker in patients with early LC.
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Affiliation(s)
- Jianfei Fang
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Lisha Ying
- Zhejiang Cancer Institute, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Zhengxiao Ma
- Postgraduate Training Base Alliance of Wenzhou Medical University (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
| | - Ying Yang
- The Second Clinical Medical College, Zhejiang Chinese Medicine University, Hangzhou, Zhejiang, China
| | - Rui Zhu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Dan Su
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
- Postgraduate Training Base Alliance of Wenzhou Medical University (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
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6
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Li Z, Qian D. Extrachromosomal circular DNA (eccDNA): from carcinogenesis to drug resistance. Clin Exp Med 2024; 24:83. [PMID: 38662139 PMCID: PMC11045593 DOI: 10.1007/s10238-024-01348-6] [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: 12/15/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) is a circular form of DNA that exists outside of the chromosome. Although it has only been a few decades since its discovery, in recent years, it has been found to have a close relationship with cancer, which has attracted widespread attention from researchers. Thus far, under the persistent research of researchers from all over the world, eccDNA has been found to play an important role in a variety of tumors, including breast cancer, lung cancer, ovarian cancer, etc. Herein, we review the sources of eccDNA, classifications, and the mechanisms responsible for their biogenesis. In addition, we introduce the relationship between eccDNA and various cancers and the role of eccDNA in the generation and evolution of cancer. Finally, we summarize the research significance and importance of eccDNA in cancer, and highlight new prospects for the application of eccDNA in the future detection and treatment of cancer.
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Affiliation(s)
- Zhaoxing Li
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Daohai Qian
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China.
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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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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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Wu N, Wei L, Zhu Z, Liu Q, Li K, Mao F, Qiao J, Zhao X. Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction. Protein Cell 2024; 15:6-20. [PMID: 37233789 PMCID: PMC10762679 DOI: 10.1093/procel/pwad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.
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Affiliation(s)
- Ning Wu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
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10
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Lu W, Li F, Ouyang Y, Jiang Y, Zhang W, Bai Y. A comprehensive analysis of library preparation methods shows high heterogeneity of extrachromosomal circular DNA but distinct chromosomal amount levels reflecting different cell states. Analyst 2023; 149:148-160. [PMID: 37987554 DOI: 10.1039/d3an01300f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Extrachromosomal circular DNA (eccDNA) was discovered several decades ago, but little is known about its function. With the development of sequencing technology, several library preparation methods have been developed to elucidate the biogenesis and function of eccDNA. However, different treatment methods have certain biases that can lead to their erroneous interpretation. To address these issues, we compared the performance of different library preparation methods. Our investigation revealed that the utilization of rolling-circle amplification (RCA) and restriction enzyme linearization of mitochondrial DNA (mtDNA) significantly enhanced the efficiency of enriching extrachromosomal circular DNA (eccDNA). However, it also introduced certain biases, such as an unclear peak in ∼160-200 bp periodicity and the absence of a typical motif pattern. Furthermore, given that RCA can lead to a disproportionate change in copy numbers, eccDNA quantification using split and discordant reads should be avoided. Analysis of the genomic and elements distribution of the overall population of eccDNA molecules revealed a high correlation between the replicates, and provided a possible stability signature for eccDNA, which could potentially reflect different cell lines or cell states. However, we found only a few eccDNA with identical junction sites in each replicate, showing a high degree of heterogeneity of eccDNA. The emergence of different motif patterns flanking junctional sites in eccDNAs of varying sizes suggests the involvement of multiple potential mechanisms in eccDNA generation. This study comprehensively compares and discusses various essential approaches for eccDNA library preparation, offering valuable insights and practical advice to researchers involved in characterizing eccDNA.
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Affiliation(s)
- Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Yunfei Ouyang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
| | - Yali Jiang
- The Friendship Hospital of Ili Kazakh Autonomous Prefecture, Ili & Jiangsu Joint Institute of Health, Yining, Xinjiang Uygur Autonomous Region, 835000, China
| | - Weizhong Zhang
- Department of Ophthalmology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu, 210096, China.
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11
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Zhao X, Zhao H, Liu Y, Guo Z. Methods, bioinformatics tools and databases in ecDNA research: An overview. Comput Biol Med 2023; 167:107680. [PMID: 37976817 DOI: 10.1016/j.compbiomed.2023.107680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/25/2023] [Accepted: 11/06/2023] [Indexed: 11/19/2023]
Abstract
Extrachromosomal DNA (ecDNA), derived from chromosomes, is a cancer-specific circular DNA molecule. EcDNA drives tumor initiation and progression, which is associated with poor clinical outcomes and drug resistance in a wide range of cancers. Although ecDNA was first discovered in 1965, tremendous technological revolutions in recent years have provided crucial new insights into its key biological functions and regulatory mechanisms. Here, we provide a thorough overview of the methods, bioinformatics tools, and database resources used in ecDNA research, mainly focusing on their performance, strengths, and limitations. This study can provide important reference for selecting the most appropriate method in ecDNA research. Furthermore, we offer suggestions for the current bioinformatics analysis of ecDNA and provide an outlook to the future research.
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Affiliation(s)
- Xinyu Zhao
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Huan Zhao
- Key Laboratory of Marine Bio-resource Restoration and Habitat Reparation, Dalian Ocean University, Dalian, 116023, China
| | - Yupeng Liu
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China
| | - Zhiyun Guo
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, 610031, China.
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12
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Wang Q, Zhang J, Liu Z, Duan Y, Li C. Integrative approaches based on genomic techniques in the functional studies on enhancers. Brief Bioinform 2023; 25:bbad442. [PMID: 38048082 PMCID: PMC10694556 DOI: 10.1093/bib/bbad442] [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: 08/28/2023] [Revised: 10/22/2023] [Accepted: 11/08/2023] [Indexed: 12/05/2023] Open
Abstract
With the development of sequencing technology and the dramatic drop in sequencing cost, the functions of noncoding genes are being characterized in a wide variety of fields (e.g. biomedicine). Enhancers are noncoding DNA elements with vital transcription regulation functions. Tens of thousands of enhancers have been identified in the human genome; however, the location, function, target genes and regulatory mechanisms of most enhancers have not been elucidated thus far. As high-throughput sequencing techniques have leapt forwards, omics approaches have been extensively employed in enhancer research. Multidimensional genomic data integration enables the full exploration of the data and provides novel perspectives for screening, identification and characterization of the function and regulatory mechanisms of unknown enhancers. However, multidimensional genomic data are still difficult to integrate genome wide due to complex varieties, massive amounts, high rarity, etc. To facilitate the appropriate methods for studying enhancers with high efficacy, we delineate the principles, data processing modes and progress of various omics approaches to study enhancers and summarize the applications of traditional machine learning and deep learning in multi-omics integration in the enhancer field. In addition, the challenges encountered during the integration of multiple omics data are addressed. Overall, this review provides a comprehensive foundation for enhancer analysis.
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Affiliation(s)
- Qilin Wang
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Junyou Zhang
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Zhaoshuo Liu
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Yingying Duan
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
| | - Chunyan Li
- School of Engineering Medicine, Beihang University, Beijing 100191, China
- School of Biological Science and Medical Engineering, Beihang University, Beijing 100191, China
- Key Laboratory of Big Data-Based Precision Medicine (Ministry of Industry and Information Technology), Beihang University, Beijing 100191, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing 100191, China
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13
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Guo T, Chen GQ, Li XF, Wang M, Liu KM, Yang XY, Liu SC, Feng YL, Liu PY, Lin H, Xie AY. Small extrachromosomal circular DNA harboring targeted tumor suppressor gene mutations supports intratumor heterogeneity in mouse liver cancer induced by multiplexed CRISPR/Cas9. Genome Med 2023; 15:80. [PMID: 37803452 PMCID: PMC10557318 DOI: 10.1186/s13073-023-01230-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/08/2023] [Indexed: 10/08/2023] Open
Abstract
BACKGROUND Primary liver cancer has significant intratumor genetic heterogeneity (IGH), which drives cancer evolution and prevents effective cancer treatment. CRISPR/Cas9-induced mouse liver cancer models can be used to elucidate how IGH is developed. However, as CRISPR/Cas9 could induce chromothripsis and extrachromosomal DNA in cells in addition to targeted mutations, we wondered whether this effect contributes to the development of IGH in CRISPR/Cas9-induced mouse liver cancer. METHODS CRISPR/Cas9-based targeted somatic multiplex-mutagenesis was used to target 34 tumor suppressor genes (TSGs) for induction of primary liver tumors in mice. Target site mutations in tumor cells were analyzed and compared between single-cell clones and their subclones, between different time points of cell proliferation, and between parental clones and single-cell clones derived from mouse subcutaneous allografts. Genomic instability and generation of extrachromosomal circular DNA (eccDNA) was explored as a potential mechanism underlying the oscillation of target site mutations in these liver tumor cells. RESULTS After efficiently inducing autochthonous liver tumors in mice within 30-60 days, analyses of CRISPR/Cas9-induced tumors and single-cell clones derived from tumor nodules revealed multiplexed and heterogeneous mutations at target sites. Many target sites frequently displayed more than two types of allelic variations with varying frequencies in single-cell clones, indicating increased copy number of these target sites. The types and frequencies of targeted TSG mutations continued to change at some target sites between single-cell clones and their subclones. Even the proliferation of a subclone in cell culture and in mouse subcutaneous graft altered the types and frequencies of targeted TSG mutations in the absence of continuing CRISPR/Cas9 genome editing, indicating a new source outside primary chromosomes for the development of IGH in these liver tumors. Karyotyping of tumor cells revealed genomic instability in these cells manifested by high levels of micronuclei and chromosomal aberrations including chromosomal fragments and chromosomal breaks. Sequencing analysis further demonstrated the generation of eccDNA harboring targeted TSG mutations in these tumor cells. CONCLUSIONS Small eccDNAs carrying TSG mutations may serve as an important source supporting intratumor heterogeneity and tumor evolution in mouse liver cancer induced by multiplexed CRISPR/Cas9.
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Affiliation(s)
- Tao Guo
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Guo-Qiao Chen
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Xu-Fan Li
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Meng Wang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Kun-Ming Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Xiao-Ying Yang
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Si-Cheng Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Yi-Li Feng
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China
| | - Peng-Yuan Liu
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China.
| | - Hui Lin
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
| | - An-Yong Xie
- Innovation Center for Minimally Invasive Technique and Device, Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 3 East Qingchun Rd, Hangzhou, Zhejiang, 310019, P. R. China.
- Institute of Translational Medicine, Zhejiang University School of Medicine and Zhejiang University Cancer Center, 268 Kai Xuan Rd, Hangzhou, Zhejiang, 310029, P. R. China.
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14
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Fu W, MacGregor DR, Comont D, Saski CA. Sequence Characterization of Extra-Chromosomal Circular DNA Content in Multiple Blackgrass ( Alopecurus myosuroides) Populations. Genes (Basel) 2023; 14:1905. [PMID: 37895254 PMCID: PMC10606437 DOI: 10.3390/genes14101905] [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: 09/15/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Alopecurus myosuroides (blackgrass) is a problematic weed of Western European winter wheat, and its success is largely due to widespread multiple-herbicide resistance. Previous analysis of F2 seed families derived from two distinct blackgrass populations exhibiting equivalent non-target site resistance (NTSR) phenotypes shows resistance is polygenic and evolves from standing genetic variation. Using a CIDER-seq pipeline, we show that herbicide-resistant (HR) and herbicide-sensitive (HS) F3 plants from these F2 seed families as well as the parent populations they were derived from carry extra-chromosomal circular DNA (eccDNA). We identify the similarities and differences in the coding structures within and between resistant and sensitive populations. Although the numbers and size of detected eccDNAs varied between the populations, comparisons between the HR and HS blackgrass populations identified shared and unique coding content, predicted genes, and functional protein domains. These include genes related to herbicide detoxification such as Cytochrome P450s, ATP-binding cassette transporters, and glutathione transferases including AmGSTF1. eccDNA content was mapped to the A. myosuroides reference genome, revealing genomic regions at the distal end of chromosome 5 and the near center of chromosomes 1 and 7 as regions with a high number of mapped eccDNA gene density. Mapping to 15 known herbicide-resistant QTL regions showed that the eccDNA coding sequences matched twelve, with four QTL matching HS coding sequences; only one region contained HR coding sequences. These findings establish that, like other pernicious weeds, blackgrass has eccDNAs that contain homologs of chromosomal genes, and these may contribute genetic heterogeneity and evolutionary innovation to rapidly adapt to abiotic stresses, including herbicide treatment.
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Affiliation(s)
- Wangfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Dana R. MacGregor
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - David Comont
- Rothamsted Research, Protecting Crops and the Environment, Harpenden, Hertfordshire AL5 2JQ, UK; (D.R.M.); (D.C.)
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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15
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Li F, Ming W, Lu W, Wang Y, Li X, Dong X, Bai Y. FLED: a full-length eccDNA detector for long-reads sequencing data. Brief Bioinform 2023; 24:bbad388. [PMID: 37930031 PMCID: PMC10632013 DOI: 10.1093/bib/bbad388] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/24/2023] [Accepted: 09/30/2023] [Indexed: 11/07/2023] Open
Abstract
Reconstructing the full-length sequence of extrachromosomal circular DNA (eccDNA) from short sequencing reads has proved challenging given the similarity of eccDNAs and their corresponding linear DNAs. Previous sequencing methods were unable to achieve high-throughput detection of full-length eccDNAs. Herein, a novel algorithm was developed, called Full-Length eccDNA Detection (FLED), to reconstruct the sequence of eccDNAs based on the strategy that combined rolling circle amplification and nanopore long-reads sequencing technology. Seven human epithelial and cancer cell line samples were analyzed by FLED and over 5000 full-length eccDNAs were identified per sample. The structures of identified eccDNAs were validated by both Polymerase Chain Reaction (PCR) and Sanger sequencing. Compared to other published nanopore-based eccDNA detectors, FLED exhibited higher sensitivity. In cancer cell lines, the genes overlapped with eccDNA regions were enriched in cancer-related pathways and cis-regulatory elements can be predicted in the upstream or downstream of intact genes on eccDNA molecules, and the expressions of these cancer-related genes were dysregulated in tumor cell lines, indicating the regulatory potency of eccDNAs in biological processes. The proposed method takes advantage of nanopore long reads and enables unbiased reconstruction of full-length eccDNA sequences. FLED is implemented using Python3 which is freely available on GitHub (https://github.com/FuyuLi/FLED).
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Affiliation(s)
- Fuyu Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Wenlong Ming
- Institute for AI in Medicine, School of Artificial Intelligence, Nanjing University of Information Science and Technology, Nanjing, 210044, P. R. China
| | - Wenxiang Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Ying Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xiaohan Li
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
| | - Xianjun Dong
- Genomics and Bioinformatics Hub, Brigham and Women's Hospital, Boston, MA 02115, USA
- Precision Neurology Program, Brigham and Women's Hospital, Boston, MA 02115, USA
- Department of Neurology, Harvard Medical School, Boston, MA 02115, USA
| | - Yunfei Bai
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, P. R. China
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16
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Luo X, Zhang L, Cui J, An Q, Li H, Zhang Z, Sun G, Huang W, Li Y, Li C, Jia W, Zou L, Zhao G, Xiao F. Small extrachromosomal circular DNAs as biomarkers for multi-cancer diagnosis and monitoring. Clin Transl Med 2023; 13:e1393. [PMID: 37649244 PMCID: PMC10468585 DOI: 10.1002/ctm2.1393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Small extrachromosomal circular DNAs (eccDNAs) have the potential to be cancer biomarkers. However, the formation mechanisms and functions of small eccDNAs selected in carcinogenesis are not clear, and whether the small eccDNA profile in the plasma of cancer patients represents that in cancer tissues remains to be elucidated. METHODS A novel sequencing workflow based on the nanopore sequencing platform was used to sequence naturally existing full-length small eccDNAs in tissues and plasma collected from 25 cancer patients (including prostate cancer, hepatocellular carcinoma and colorectal cancer), and from an independent validation cohort (including 7 cancer plasma and 14 healthy plasma). RESULTS Compared with those in non-cancer tissues, small eccDNAs detected in cancer tissues had a significantly larger number and size (P = 0.040 and 2.2e-16, respectively), along with more even distribution and different formation mechanisms. Although small eccDNAs had different general characteristics and genomic annotation between cancer tissues and the paired plasma, they had similar formation mechanisms and cancer-related functions. Small eccDNAs originated from some specific genes had great multi-cancer diagnostic value in tissues (AUC ≥ 0.8) and plasma (AUC > 0.9), especially increasing the accuracy of multi-cancer prediction of CEA/CA19-9 levels. The high multi-cancer diagnostic value of small eccDNAs originated from ALK&ETV6 could be extrapolated from tissues (AUC = 0.804) to plasma and showed high positive predictive value (100%) and negative predictive value (82.35%) in a validation cohort. CONCLUSIONS As independent and stable circular DNA molecules, small eccDNAs in both tissues and plasma can be used as ideal biomarkers for cost-effective multi-cancer diagnosis and monitoring.
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Affiliation(s)
- Xuanmei Luo
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Lili Zhang
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Jian Cui
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Qi An
- Department of General SurgeryBeijing HospitalBeijingChina
| | - Hexin Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Zaifeng Zhang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gaoyuan Sun
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Wei Huang
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Yifei Li
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Chang Li
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Wenzhuo Jia
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Lihui Zou
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
| | - Gang Zhao
- Department of General SurgeryBeijing HospitalBeijingChina
- National Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
| | - Fei Xiao
- Peking University Fifth School of Clinical MedicineBeijing HospitalNational Center of GerontologyBeijingChina
- The Key Laboratory of GeriatricsBeijing Institute of GeriatricsInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing HospitalNational Center of Gerontology of National Health CommissionBeijingChina
- Clinical BiobankBeijing HospitalNational Center of GerontologyNational Health CommissionInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijingChina
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17
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dos Santos CR, Hansen LB, Rojas-Triana M, Johansen AZ, Perez-Moreno M, Regenberg B. Variation of extrachromosomal circular DNA in cancer cell lines. Comput Struct Biotechnol J 2023; 21:4207-4214. [PMID: 37705597 PMCID: PMC10495552 DOI: 10.1016/j.csbj.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 08/26/2023] [Accepted: 08/26/2023] [Indexed: 09/15/2023] Open
Abstract
The presence of oncogene carrying eccDNAs is strongly associated with carcinogenesis and poor patient survival. Tumour biopsies and in vitro cancer cell lines are frequently utilized as models to investigate the role of eccDNA in cancer. However, eccDNAs are often lost during the in vitro growth of cancer cell lines, questioning the reproducibility of studies utilizing cancer cell line models. Here, we conducted a comprehensive analysis of eccDNA variability in seven cancer cell lines (MCA3D, PDV, HaCa4, CarC, MIA-PaCa-2, AsPC-1, and PC-3). We compared the content of unique eccDNAs between triplicates of each cell line and found that the number of unique eccDNA is specific to each cell line, while the eccDNA sequence content varied greatly among triplicates (∼ 0-1% eccDNA coordinate commonality). In the PC-3 cell line, we found that the large eccDNA (ecDNA) with MYC is present in high-copy number in an NCI cell line isolate but not present in ATCC isolates. Together, these results reveal that the sequence content of eccDNA is highly variable in cancer cell lines. This highlights the importance of testing cancer cell lines before use, and to enrich for subclones in cell lines with the desired eccDNA to get relatively pure population for studying the role of eccDNA in cancer.
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Affiliation(s)
| | | | - Monica Rojas-Triana
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
| | - Astrid Zedlitz Johansen
- Department of Oncology, Copenhagen University Hospital, Herlev and Gentofte, DK-2730 Herlev, Denmark
| | - Mirna Perez-Moreno
- Cell biology and Physiology, Department of Biology, University of Copenhagen, Denmark
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
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18
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Peng Y, Li Y, Zhang W, ShangGuan Y, Xie T, Wang K, Qiu J, Pu W, Hu B, Zhang X, Yin L, Tang D, Dai Y. The characteristics of extrachromosomal circular DNA in patients with end-stage renal disease. Eur J Med Res 2023; 28:134. [PMID: 36967395 PMCID: PMC10041755 DOI: 10.1186/s40001-023-01064-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/15/2023] [Indexed: 03/28/2023] Open
Abstract
BACKGROUND End-stage renal disease (ESRD) is the final stage of chronic kidney disease (CKD). In addition to the structurally intact chromosome genomic DNA, there is a double-stranded circular DNA called extrachromosomal circular DNA (eccDNA), which is thought to be involved in the epigenetic regulation of human disease. However, the features of eccDNA in ESRD patients are barely known. In this study, we identified eccDNA from ESRD patients and healthy people, as well as revealed the characteristics of eccDNA in patients with ESRD. METHODS Using the high-throughput Circle-Sequencing technique, we examined the eccDNA in peripheral blood mononuclear cells (PBMCs) from healthy people (NC) (n = 12) and ESRD patients (n = 16). We analyzed the length distribution, genome elements, and motifs feature of eccDNA in ESRD patients. Then, after identifying the specific eccDNA in ESRD patients, we explored the potential functions of the target genes of the specific eccDNA. Finally, we investigated the probable hub eccDNA using algorithms. RESULTS In total, 14,431 and 11,324 eccDNAs were found in the ESRD and NC groups, respectively, with sizes ranging from 0.01 kb to 60 kb at most. Additionally, the ESRD group had a greater distribution of eccDNA on chromosomes 4, 11, 13, and 20. In two groups, we also discovered several motifs of specific eccDNAs. Furthermore, we identified 13,715 specific eccDNAs in the ESRD group and 10,585 specific eccDNAs in the NC group, both of which were largely annotated as mRNA catalog. Pathway studies using Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) showed that the specific eccDNA in ESRD was markedly enriched in cell junction and communication pathways. Furthermore, we identified potentially 20 hub eccDNA-targeting genes from all ESRD-specific eccDNA-targeting genes. Also, we found that 39 eccDNA-targeting genes were associated with ESRD, and some of these eccDNAs may be related to the pathogenesis of ESRD. CONCLUSIONS Our findings revealed the characteristics of eccDNA in ESRD patients and discovered potentially hub and ESRD-relevant eccDNA-targeting genes, suggesting a novel probable mechanism of ESRD.
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Affiliation(s)
- Yue Peng
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Yixi Li
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Wei Zhang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Yu ShangGuan
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Ting Xie
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Kang Wang
- Key Renal Laboratory of Shenzhen, Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, 518020, Guangdong, China
| | - Jing Qiu
- Key Renal Laboratory of Shenzhen, Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, 518020, Guangdong, China
| | - Wenjun Pu
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China
| | - Biying Hu
- Institute of Nephrology and Blood Purification, The First Affiliated Hospital of Jinan University, Jinan University, Guangzhou, China
| | - Xinzhou Zhang
- Key Renal Laboratory of Shenzhen, Department of Nephrology, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, Shenzhen, 518020, Guangdong, China
| | - Lianghong Yin
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China.
- Guangzhou Enttxs Medical Products Co., Ltd. P.R. Guangzhou, Guangzhou, China.
| | - Donge Tang
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China.
| | - Yong Dai
- Clinical Medical Research Center, Guangdong Provincial Engineering Research Center of Autoimmune Disease Precision Medicine, Shenzhen Engineering Research Center of Autoimmune Disease, The Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Jinan University, Shenzhen, China.
- Department of Pathology, The 924th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Guangxi Key Laboratory of Metabolic Diseases Research, Guilin, 541002, Guangxi, China.
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19
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Wang Y, Wang M, Zhang Y. Purification, full-length sequencing and genomic origin mapping of eccDNA. Nat Protoc 2023; 18:683-699. [PMID: 36517607 DOI: 10.1038/s41596-022-00783-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 09/23/2022] [Indexed: 12/23/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) was discovered more than half a century ago. However, its biogenesis and function have just begun to be elucidated. One hurdle that has prevented our understanding of eccDNA is the difficulty in obtaining pure eccDNA from cells. The current eccDNA purification methods mainly rely on depleting linear DNAs by exonuclease digestion after obtaining crude circles by alkaline lysis. Owing to eccDNA's low abundance and heterogeneous size, the current purification methods are not efficient in obtaining pure eccDNA. Here we describe a new three-step eccDNA purification (3SEP) procedure that adds a step to recover circular DNA, but not linear DNA that escape from the exonuclease digestion, whereby 3SEP results in eccDNA preparations with high purity and reproducibility. Additionally, we developed a full-length eccDNA sequencing technique by combining rolling-circle amplification with Nanopore sequencing. Accordingly, we developed a full-length eccDNA caller (Flec) to call the consensus sequence of multiple tandem copies of eccDNA contained within the debranched rolling-circle amplification product and map the consensus to its genomic origin. Collectively, our protocol will facilitate eccDNA identification and characterization, and has the potential for diagnostic and clinical applications. For a well-trained molecular biologist, it takes ~1-2 d to purify eccDNAs, another 5-6 d to carry out Nanopore library preparation and sequencing, and 1-5 d for an experienced bioinformatic scientist to analyze the data.
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Affiliation(s)
- Yuangao Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Meng Wang
- Howard Hughes Medical Institute, Boston, MA, USA.,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA
| | - Yi Zhang
- Howard Hughes Medical Institute, Boston, MA, USA. .,Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA, USA. .,Department of Genetics, Boston, MA, USA. .,Harvard Stem Cell Institute WAB-149G, Boston, MA, USA.
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20
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Gerovska D, Araúzo-Bravo MJ. Skeletal Muscles of Sedentary and Physically Active Aged People Have Distinctive Genic Extrachromosomal Circular DNA Profiles. Int J Mol Sci 2023; 24:ijms24032736. [PMID: 36769072 PMCID: PMC9917053 DOI: 10.3390/ijms24032736] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/19/2023] [Accepted: 01/26/2023] [Indexed: 02/04/2023] Open
Abstract
To bring new extrachromosomal circular DNA (eccDNA) enrichment technologies closer to the clinic, specifically for screening, early diagnosis, and monitoring of diseases or lifestyle conditions, it is paramount to identify the differential pattern of the genic eccDNA signal between two states. Current studies using short-read sequenced purified eccDNA data are based on absolute numbers of unique eccDNAs per sample or per gene, length distributions, or standard methods for RNA-seq differential analysis. Previous analyses of RNA-seq data found significant transcriptomics difference between sedentary and active life style skeletal muscle (SkM) in young people but very few in old. The first attempt using circulomics data from SkM and blood of aged lifelong sedentary and physically active males found no difference at eccDNA level. To improve the capability of finding differences between circulomics data groups, we designed a computational method to identify Differentially Produced per Gene Circles (DPpGCs) from short-read sequenced purified eccDNA data based on the circular junction, split-read signal, of the eccDNA, and implemented it into a software tool DifCir in Matlab. We employed DifCir to find to the distinctive features of the influence of the physical activity or inactivity in the aged SkM that would have remained undetected by transcriptomics methods. We mapped the data from tissue from SkM and blood from two groups of aged lifelong sedentary and physically active males using Circle_finder and subsequent merging and filtering, to find the number and length distribution of the unique eccDNA. Next, we used DifCir to find up-DPpGCs in the SkM of the sedentary and active groups. We assessed the functional enrichment of the DPpGCs using Disease Gene Network and Gene Set Enrichment Analysis. To find genes that produce eccDNA in a group without comparison with another group, we introduced a method to find Common PpGCs (CPpGCs) and used it to find CPpGCs in the SkM of the sedentary and active group. Finally, we found the eccDNA that carries whole genes. We discovered that the eccDNA in the SkM of the sedentary group is not statistically different from that of physically active aged men in terms of number and length distribution of eccDNA. In contrast, with DifCir we found distinctive gene-associated eccDNA fingerprints. We identified statistically significant up-DPpGCs in the two groups, with the top up-DPpGCs shed by the genes AGBL4, RNF213, DNAH7, MED13, and WWTR1 in the sedentary group, and ZBTB7C, TBCD, ITPR2, and DDX11-AS1 in the active group. The up-DPpGCs in both groups carry mostly gene fragments rather than whole genes. Though the subtle transcriptomics difference, we found RYR1 to be both transcriptionally up-regulated and up-DPpGCs gene in sedentary SkM. DifCir emphasizes the high sensitivity of the circulome compared to the transcriptome to detect the molecular fingerprints of exercise in aged SkM. It allows efficient identification of gene hotspots that excise more eccDNA in a health state or disease compared to a control condition.
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Affiliation(s)
- Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
| | - Marcos J. Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain
- Basque Foundation for Science, IKERBASQUE, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- CIBER of Frailty and Healthy Aging (CIBERfes), 28029 Madrid, Spain
- Max Planck Institute for Molecular Biomedicine, Computational Biology and Bioinformatics, Röntgenstr. 20, 48149 Münster, Germany
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
- Correspondence: (D.G.); (M.J.A.-B.)
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21
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Guo J, Zhang Z, Li Q, Chang X, Liu X. TeCD: The eccDNA Collection Database for extrachromosomal circular DNA. BMC Genomics 2023; 24:47. [PMID: 36707765 PMCID: PMC9881285 DOI: 10.1186/s12864-023-09135-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 01/13/2023] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA) is a kind of DNA that widely exists in eukaryotic cells. Studies in recent years have shown that eccDNA is often enriched during tumors and aging, and participates in the development of cell physiological activities in a special way, so people have paid more and more attention to the eccDNA, and it has also become a critical new topic in modern biological research. DESCRIPTION We built a database to collect eccDNA, including animals, plants and fungi, and provide researchers with an eccDNA retrieval platform. The collected eccDNAs were processed in a uniform format and classified according to the species to which it belongs and the chromosome of the source. Each eccDNA record contained sequence length, start and end sites on the corresponding chromosome, order of the bases, genomic elements such as genes and transposons, and other information in the respective sequencing experiment. All the data were stored into the TeCD (The eccDNA Collection Database) and the BLAST (Basic Local Alignment Search Tool) sequence alignment function was also added into the database for analyzing the potential eccDNA sequences. CONCLUSION We built TeCD, a platform for users to search and obtain eccDNA data, and analyzed the possible potential functions of eccDNA. These findings may provide a basis and direction for researchers to further explore the biological significance of eccDNA in the future.
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Affiliation(s)
- Jing Guo
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
| | - Ze Zhang
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Qingcui Li
- grid.410726.60000 0004 1797 8419School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China
| | - Xiao Chang
- grid.464226.00000 0004 1760 7263Institute of Statistics and Applied Mathematics, Anhui University of Finance & Economics, Bengbu, 233030 China
| | - Xiaoping Liu
- grid.410726.60000 0004 1797 8419Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.410726.60000 0004 1797 8419Key Laboratory of Systems Health Science of Zhejiang Province, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, 310013 China ,grid.27255.370000 0004 1761 1174School of Mathematics and Statistics, Shandong University, Weihai, 264209 Shandong China
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22
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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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23
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Chen Z, Qi Y, He J, Xu C, Ge Q, Zhuo W, Si J, Chen S. Distribution and characterization of extrachromosomal circular DNA in colorectal cancer. MOLECULAR BIOMEDICINE 2022; 3:38. [PMID: 36459282 PMCID: PMC9718908 DOI: 10.1186/s43556-022-00104-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 11/09/2022] [Indexed: 12/05/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) has been shown to play an important role in the amplification of tumor genes and the maintenance of intra-tumor genetic heterogeneity, although its complex functional mechanism still remains to be elucidated. As the top three common malignancies in the world, colorectal cancer (CRC) has been threatening human life and health, whose tumorigenesis and development may have elusive connection with eccDNAs. Here, we described the extensive distribution of eccDNAs in the CRC tissues using Circle-seq, which range in size from hundreds to thousands of base pairs (bp). The distribution in tumor tissues had aggregation and tendency compared with random in tumor-adjacent tissues, accompanied with smaller and more regular circle lengths. After sequencing and restoring, we found that the shedding sites of eccDNAs in CRC had similar tendency in chromosome distribution, and focused on tumor-associated genes. Meanwhile, we combined RNA sequencing to explore the correlation of eccDNA differential expression in the gene transcription and signaling pathways, confirming a connection between eccDNA and RNA somewhere. Subsequently, we validated eccDNAs in CRC cell lines and the potential consistency of the junction sites of eccDNAs in CRC tissues and cell lines. Using fragments of the cationic amino acid transporter SLC7A1 to synthesize eccDNAs, we discovered the role of eccDNAs in different regions within the gene.
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Affiliation(s)
- Zhehang Chen
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Yadong Qi
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Jiamin He
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Chaochao Xu
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China
| | - Qiwei Ge
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.412465.0Department of Gastroenterology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, Zhejiang, Province China
| | - Wei Zhuo
- grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XDepartment of Cell Biology and Department of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianmin Si
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, China
| | - Shujie Chen
- grid.13402.340000 0004 1759 700XDepartment of Gastroenterology, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, Zhejiang, Province China ,grid.13402.340000 0004 1759 700XInstitute of Gastroenterology, Zhejiang University, Hangzhou, China ,grid.13402.340000 0004 1759 700XCancer Center, Zhejiang University, Hangzhou, China
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24
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Wu M, Rai K. Demystifying extrachromosomal DNA circles: Categories, biogenesis, and cancer therapeutics. Comput Struct Biotechnol J 2022; 20:6011-6022. [PMID: 36382182 PMCID: PMC9647416 DOI: 10.1016/j.csbj.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Since the advent of sequencing technologies in the 1990s, researchers have focused on the association between aberrations in chromosomal DNA and disease. However, not all forms of the DNA are linear and chromosomal. Extrachromosomal circular DNAs (eccDNAs) are double-stranded, closed-circled DNA constructs free from the chromosome that reside in the nuclei. Although widely overlooked, the eccDNAs have recently gained attention for their potential roles in physiological response, intratumoral heterogeneity and cancer therapeutics. In this review, we summarize the history, classifications, biogenesis, and highlight recent progresses on the emerging topic of eccDNAs and comment on their potential application as biomarkers in clinical settings.
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Affiliation(s)
- Manrong Wu
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kunal Rai
- Graduate Program in Quantitative and Computational Biosciences, Baylor College of Medicine, Houston, TX, USA
- Department of Genomic Medicine, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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25
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Zhao Y, Yu L, Zhang S, Su X, Zhou X. Extrachromosomal circular DNA: Current status and future prospects. eLife 2022; 11:81412. [PMID: 36256570 PMCID: PMC9578701 DOI: 10.7554/elife.81412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a double-stranded DNA molecule found in various organisms, including humans. In the past few decades, the research on eccDNA has mainly focused on cancers and their associated diseases. Advancements in modern omics technologies have reinvigorated research on eccDNA and shed light on the role of these molecules in a range of diseases and normal cell phenotypes. In this review, we first summarize the formation of eccDNA and its modes of action in eukaryotic cells. We then outline eccDNA as a disease biomarker and reveal its regulatory mechanism. We finally discuss the future prospects of eccDNA, including basic research and clinical application. Thus, with the deepening of understanding and exploration of eccDNAs, they hold great promise in future biomedical research and clinical translational application.
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Affiliation(s)
- Yiheng Zhao
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Linchan Yu
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Shuchen Zhang
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiangyu Su
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiang Zhou
- Department of Cardiology, The Second Affiliated Hospital of Soochow University, Suzhou, China
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26
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Extrachromosomal circular DNA: biogenesis, structure, functions and diseases. Signal Transduct Target Ther 2022; 7:342. [PMID: 36184613 PMCID: PMC9527254 DOI: 10.1038/s41392-022-01176-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/14/2022] [Accepted: 09/01/2022] [Indexed: 11/08/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA), ranging in size from tens to millions of base pairs, is independent of conventional chromosomes. Recently, eccDNAs have been considered an unanticipated major source of somatic rearrangements, contributing to genomic remodeling through chimeric circularization and reintegration of circular DNA into the linear genome. In addition, the origin of eccDNA is considered to be associated with essential chromatin-related events, including the formation of super-enhancers and DNA repair machineries. Moreover, our understanding of the properties and functions of eccDNA has continuously and greatly expanded. Emerging investigations demonstrate that eccDNAs serve as multifunctional molecules in various organisms during diversified biological processes, such as epigenetic remodeling, telomere trimming, and the regulation of canonical signaling pathways. Importantly, its special distribution potentiates eccDNA as a measurable biomarker in many diseases, especially cancers. The loss of eccDNA homeostasis facilitates tumor initiation, malignant progression, and heterogeneous evolution in many cancers. An in-depth understanding of eccDNA provides novel insights for precision cancer treatment. In this review, we summarized the discovery history of eccDNA, discussed the biogenesis, characteristics, and functions of eccDNA. Moreover, we emphasized the role of eccDNA during tumor pathogenesis and malignant evolution. Therapeutically, we summarized potential clinical applications that target aberrant eccDNA in multiple diseases.
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27
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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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28
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Lv W, Pan X, Han P, Wang Z, Feng W, Xing X, Wang Q, Qu K, Zeng Y, Zhang C, Xu Z, Li Y, Zheng T, Lin L, Liu C, Liu X, Li H, Henriksen RA, Bolund L, Lin L, Jin X, Yang H, Zhang X, Yin T, Regenberg B, He F, Luo Y. Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. Clin Transl Med 2022; 12:e817. [PMID: 35474296 PMCID: PMC9042798 DOI: 10.1002/ctm2.817] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/08/2022] [Accepted: 03/29/2022] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine. METHODS Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq. RESULTS Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA. CONCLUSIONS This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring.
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Affiliation(s)
- Wei Lv
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiaoguang Pan
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Peng Han
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ziyu Wang
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Department of Biochemistry and Molecular Biology, School of Basic Medicine, Qingdao University, Qingdao, Shandong, China
| | - Weijia Feng
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xue Xing
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qingqing Wang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Kunli Qu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Yuchen Zeng
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,College of Life Sciences, Tianjin University, Tianjin, China
| | - Cailin Zhang
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhe Xu
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Yi Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China
| | - Tianyu Zheng
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Ling Lin
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Chengxun Liu
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Xuemei Liu
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Hanbo Li
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China
| | - Rasmus Amund Henriksen
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Section for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Lars Bolund
- Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Lin Lin
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
| | - Xin Jin
- BGI-Shenzhen, Shenzhen, China
| | - Huanming Yang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,Guangdong Provincial Academician Workstation of BGI Synthetic Genomics, BGI-Shenzhen, Shenzhen, China
| | - Xiuqing Zhang
- College of Life Sciences, University of Chinese Academy of Science, Beijing, China.,IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,BGI-Shenzhen, Shenzhen, China
| | - Tailang Yin
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Fan He
- Department of Nephrology, Tongji Hospital Affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yonglun Luo
- IBMC-BGI Center, the Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China.,Lars Bolund Institute of Regenerative Medicine, Qingdao-Europe Advanced Institute for Life Sciences, BGI-Qingdao, Qingdao, China.,BGI-Shenzhen, Shenzhen, China.,Department of Biomedicine, Aarhus University, Aarhus, Denmark.,Steno Diabetes Center Aarhus, Aarhus University Hospital, Aarhus, Denmark
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29
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Cen Y, Fang Y, Ren Y, Hong S, Lu W, Xu J. Global characterization of extrachromosomal circular DNAs in advanced high grade serous ovarian cancer. Cell Death Dis 2022; 13:342. [PMID: 35418185 PMCID: PMC9007969 DOI: 10.1038/s41419-022-04807-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 03/21/2022] [Accepted: 03/30/2022] [Indexed: 01/02/2023]
Abstract
High grade serous ovarian cancer (HGSOC) is the most aggressive subtype of ovarian cancer and HGSOC patients often appear with metastasis, leading to the poor prognosis. Up to date, the extrachromosomal circular DNAs (eccDNAs) have been shown to be involved in cancer genome remodeling but the roles of eccDNAs in metastatic HGSOC are still not clear. Here we explored eccDNA profiles in HGSOC by Circle-Sequencing analysis using four pairs of primary and metastatic tissues of HGSOC patients. Within the differentially expressed eccDNAs screened out by our analysis, eight candidates were validated by outward PCR and qRT-PCR analysis. Among them, DNMT1circle10302690-10302961 was further confirmed by FISH assay and BaseScope assay, as the most significantly down-regulated eccDNA in metastatic tumors of HGSOC. Lower expression of DNMT1circle10302690-10302961 in both primary and metastatic tumors was associated with worse prognosis of HGSOC. Taken together, our finding firstly demonstrated the eccDNAs landscape of primary and metastatic tissues of HGSOC. The eccDNA DNMT1circle10302690-10302961 can be considered as a potential biomarker or a therapeutically clinical target of HGSOC metastasis and prognosis.
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Affiliation(s)
- Yixuan Cen
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Yifeng Fang
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, 310016, China
| | - Yan Ren
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China
| | - Shiyuan Hong
- Institute of Life Sciences, Chongqing Medical University, Chongqing, 400016, China.
| | - Weiguo Lu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China. .,Cancer Center, Zhejiang University, Hangzhou, 310058, China.
| | - Junfen Xu
- Women's Reproductive Health Laboratory of Zhejiang Province; Women's Hospital; School of Medicine, Zhejiang University, Hangzhou, 310006, China. .,Department of Gynecologic Oncology, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
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30
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Zhao X, Shi L, Ruan S, Bi W, Chen Y, Chen L, Liu Y, Li M, Qiao J, Mao F. CircleBase: an integrated resource and analysis platform for human eccDNAs. Nucleic Acids Res 2022; 50:D72-D82. [PMID: 34792166 PMCID: PMC8728191 DOI: 10.1093/nar/gkab1104] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/22/2022] Open
Abstract
Rapid advances in high-throughput sequencing technologies have led to the discovery of thousands of extrachromosomal circular DNAs (eccDNAs) in the human genome. Loss-of-function experiments are difficult to conduct on circular and linear chromosomes, as they usually overlap. Hence, it is challenging to interpret the molecular functions of eccDNAs. Here, we present CircleBase (http://circlebase.maolab.org), an integrated resource and analysis platform used to curate and interpret eccDNAs in multiple cell types. CircleBase identifies putative functional eccDNAs by incorporating sequencing datasets, computational predictions, and manual annotations. It classifies them into six sections including targeting genes, epigenetic regulations, regulatory elements, chromatin accessibility, chromatin interactions, and genetic variants. The eccDNA targeting and regulatory networks are displayed by informative visualization tools and then prioritized. Functional enrichment analyses revealed that the top-ranked cancer cell eccDNAs were enriched in oncogenic pathways such as the Ras and PI3K-Akt signaling pathways. In contrast, eccDNAs from healthy individuals were not significantly enriched. CircleBase provides a user-friendly interface for searching, browsing, and analyzing eccDNAs in various cell/tissue types. Thus, it is useful to screen for potential functional eccDNAs and interpret their molecular mechanisms in human cancers and other diseases.
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Affiliation(s)
- Xiaolu Zhao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing, China
| | - Leisheng Shi
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shasha Ruan
- Department of Clinical Oncology, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
- The First Clinical College of Wuhan University, Wuhan, Hubei, China
| | - Wenjian Bi
- Department of Medical Genetics, School of Basic Medical Sciences, Peking University, Beijing, China
| | - Yifan Chen
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
- Biobank, Peking University Third Hospital, Beijing, China
| | - Lin Chen
- State Key Laboratory of Natural and Biomimetic Drugs, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Yifan Liu
- Department of Biochemistry & Molecular Medicine, University of Southern California Keck School of Medicine, Los Angeles, CA, USA
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology (Peking University Third Hospital), Beijing, China
- Beijing Advanced Innovation Center for Genomics, Beijing, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing, China
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31
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Feng W, Arrey G, Zole E, lv W, Liang X, Han P, Mohiyuddin M, Pilegaard H, Regenberg B. Targeted removal of mitochondrial DNA from mouse and human extrachromosomal circular DNA with CRISPR-Cas9. Comput Struct Biotechnol J 2022; 20:3059-3067. [PMID: 35782732 PMCID: PMC9233219 DOI: 10.1016/j.csbj.2022.06.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 06/12/2022] [Indexed: 11/12/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is common in eukaryotic cells. Amplification of oncogenes on large eccDNA (ecDNA) can drive biological processes such as tumorigenesis, and identification of eccDNA by sequencing after removal of chromosomal DNA is therefore important for understanding their impact on the expressed phenotype. However, the circular mitochondrial DNA (mtDNA) might challenge the detection of eccDNA because the average somatic cell has hundreds of copies of mtDNA. Here we show that 61.2–99.5% of reads from eccDNA-enriched samples correspond to mtDNA in mouse tissues. We have developed a method to selectively remove mtDNA from total circular DNA by CRISPR/Cas9 guided cleavage of mtDNA with one single-guide RNA (sgRNA) or two sgRNAs followed by exonuclease degradation of the linearized mtDNA. Sequencing revealed that mtDNA reads were 85.9% ± 12.6% removed from eccDNA of 9 investigated mouse tissues. CRISPR/Cas9 cleavage also efficiently removed mtDNA from a human HeLa cell line and colorectal cancer samples. We identified up to 14 times more, and also larger eccDNA in CRISPR/Cas9 treated colorectal cancer samples than in untreated samples. We foresee that the method can be applied to effectively remove mtDNA from any eukaryotic species to obtain higher eccDNA yields.
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32
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Zhao XK, Xing P, Song X, Zhao M, Zhao L, Dang Y, Lei LL, Xu RH, Han WL, Wang PP, Yang MM, Hu JF, Zhong K, Zhou FY, Han XN, Meng CL, Ji JJ, Chen X, Wang LD. Focal amplifications are associated with chromothripsis events and diverse prognoses in gastric cardia adenocarcinoma. Nat Commun 2021; 12:6489. [PMID: 34764264 PMCID: PMC8586158 DOI: 10.1038/s41467-021-26745-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 10/21/2021] [Indexed: 01/24/2023] Open
Abstract
The role of focal amplifications and extrachromosomal DNA (ecDNA) is unknown in gastric cardia adenocarcinoma (GCA). Here, we identify frequent focal amplifications and ecDNAs in Chinese GCA patient samples, and find focal amplifications in the GCA cohort are associated with the chromothripsis process and may be induced by accumulated DNA damage due to local dietary habits. We observe diverse correlations between the presence of oncogene focal amplifications and prognosis, where ERBB2 focal amplifications positively correlate with prognosis and EGFR focal amplifications negatively correlate with prognosis. Large-scale ERBB2 immunohistochemistry results from 1668 GCA patients show survival probability of ERBB2 positive patients is lower than that of ERBB2 negative patients when their surviving time is under 2 years, however, the tendency is opposite when their surviving time is longer than 2 years. Our observations indicate that the ERBB2 focal amplifications may represent a good prognostic marker in GCA patients.
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Affiliation(s)
- Xue-Ke Zhao
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Xin Song
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Miao Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Linxuan Zhao
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Yonglong Dang
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden
| | - Ling-Ling Lei
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Rui-Hua Xu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Wen-Li Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Pan-Pan Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Miao-Miao Yang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Jing-Feng Hu
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Kan Zhong
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Fu-You Zhou
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Xue-Na Han
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Chao-Long Meng
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Jia-Jia Ji
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, 75108, Uppsala, Sweden.
| | - Li-Dong Wang
- State Key Laboratory of Esophageal Cancer Prevention & Treatment and Henan Key, Laboratory for Esophageal Cancer Research of The First Affiliated Hospital, Zhengzhou University, 450052, Zhengzhou, Henan, PR China.
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33
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DNA Repair Inhibition Leads to Active Export of Repetitive Sequences to the Cytoplasm Triggering an Inflammatory Response. J Neurosci 2021; 41:9286-9307. [PMID: 34593604 DOI: 10.1523/jneurosci.0845-21.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 07/25/2021] [Accepted: 09/01/2021] [Indexed: 01/02/2023] Open
Abstract
Adult-onset neurodegenerative diseases are often accompanied by evidence of a chronic inflammation that includes activation of microglial cells and altered levels of brain cytokines. Aspects of this response are likely secondary reactions to neurodegeneration, but for many illnesses the inflammation may itself be an early and even causative disease event. In such cases, the inflammation is referred to as "sterile" as it occurs in the absence of an actual bacterial or viral pathogen. A potent trigger of sterile inflammation in CNS microglia has been shown to be the presence of DNA in the cytoplasm (cytoDNA) induced either by direct DNA damage or by inhibited DNA repair. We have shown that cytoDNA comes from the cell nucleus as a result of insufficient DNA damage repair. Using wild-type and Atm -/- mouse microglia, we extend these observations here by showing that its genomic origins are not random, but rather are heavily biased toward transcriptionally inactive, intergenic regions, in particular repetitive elements and AT-rich sequences. Once released from the genome, in both males and females, we show that cytoDNA is actively exported to the cytoplasm by a CRM1-dependent mechanism. In the cytoplasm, it is degraded either by a cytosolic exonuclease, Trex1, or an autophagy pathway that ends with degradation in the lysosome. Blocking the accumulation of cytoDNA prevents the emergence of the sterile inflammation reaction. These findings offer new insights into the emergence of sterile inflammation and offer novel approaches that may be of use in combatting a wide range of neurodegenerative conditions.SIGNIFICANCE STATEMENT Sterile inflammation describes a state where the defenses of the immune system are activated in the absence of a true pathogen. A potent trigger of this unorthodox response is the presence of DNA in the cytoplasm, which immune cells interpret as an invading virus or pathogen. We show that when DNA damage increases, fragments of the cell's own genome are actively exported to the cytoplasm where they are normally degraded. If this degradation is incomplete an immune reaction is triggered. Both age and stress increase DNA damage, and as age-related neurodegenerative diseases are frequently accompanied by a chronic low-level inflammation, strategies that reduce the induction of cytoplasmic DNA or speed its clearance become attractive therapeutic targets.
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34
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Ling X, Han Y, Meng J, Zhong B, Chen J, Zhang H, Qin J, Pang J, Liu L. Small extrachromosomal circular DNA (eccDNA): major functions in evolution and cancer. Mol Cancer 2021; 20:113. [PMID: 34479546 PMCID: PMC8414719 DOI: 10.1186/s12943-021-01413-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 08/22/2021] [Indexed: 12/13/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) refers to a type of circular DNA that originate from but are likely independent of chromosomes. Due to technological advancements, eccDNAs have recently emerged as multifunctional molecules with numerous characteristics. The unique topological structure and genetic characteristics of eccDNAs shed new light on the monitoring, early diagnosis, treatment, and prediction of cancer. EccDNAs are commonly observed in both normal and cancer cells and function via different mechanisms in the stress response to exogenous and endogenous stimuli, aging, and carcinogenesis and in drug resistance during cancer treatment. The structural diversity of eccDNAs contributes to the function and numerical diversity of eccDNAs and thereby endows eccDNAs with powerful roles in evolution and in cancer initiation and progression by driving genetic plasticity and heterogeneity from extrachromosomal sites, which has been an ignored function in evolution in recent decades. EccDNAs show great potential in cancer, and we summarize the features, biogenesis, evaluated functions, functional mechanisms, related methods, and clinical utility of eccDNAs with a focus on their role in evolution and cancer.
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Affiliation(s)
- Xiaoxuan Ling
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Yali Han
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jinxue Meng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Bohuan Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jialong Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - He Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jiheng Qin
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Jing Pang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China
| | - Linhua Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China. .,Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P.R. China.
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35
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Chen W, Weng Z, Xie Z, Xie Y, Zhang C, Chen Z, Ruan F, Wang J, Sun Y, Fang Y, Guo M, Tong Y, Li Y, Tang C. Sequencing of methylase-accessible regions in integral circular extrachromosomal DNA reveals differences in chromatin structure. Epigenetics Chromatin 2021; 14:40. [PMID: 34425889 PMCID: PMC8383416 DOI: 10.1186/s13072-021-00416-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 08/11/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although extrachromosomal DNA (ecDNA) has been intensively studied for several decades, the mechanisms underlying its tumorigenic effects have been revealed only recently. In most conventional sequencing studies, the high-throughput short-read sequencing largely ignores the epigenetic status of most ecDNA regions except for the junctional areas. METHODS Here, we developed a method of sequencing enzyme-accessible chromatin in circular DNA (CCDA-seq) based on the use of methylase to label open chromatin without fragmentation and exonuclease to enrich ecDNA sequencing depth, followed by long-read nanopore sequencing. RESULTS Using CCDA-seq, we observed significantly different patterns in nucleosome/regulator binding to ecDNA at a single-molecule resolution. CONCLUSIONS These results deepen the understanding of ecDNA regulatory mechanisms.
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Affiliation(s)
- Weitian Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhe Weng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhe Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
- Department of Biology, Cell Biology and Physiology, University of Copenhagen 13, 2100, Copenhagen, Denmark
| | - Yeming Xie
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chen Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Zhichao Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | | | - Juan Wang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yuxin Sun
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yitong Fang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Mei Guo
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yiqin Tong
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yaning Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Chong Tang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.
- Nantong University, Nantong, 226000, China.
- Nephrosis Precision Medicine Innovation Center, University of Beihua School of Medicine, Jilin City, 132011, China.
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36
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Ain Q, Schmeer C, Wengerodt D, Witte OW, Kretz A. Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration. Int J Mol Sci 2020; 21:E2477. [PMID: 32252492 PMCID: PMC7177960 DOI: 10.3390/ijms21072477] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 12/13/2022] Open
Abstract
Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.
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Affiliation(s)
- Quratul Ain
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (Q.A.); (C.S.); (D.W.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
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