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1
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Mao X, Rao G, Li G, Chen S. Insights into Extrachromosomal DNA in Cancer: Biogenesis, Methodologies, Functions, and Therapeutic Potential. Adv Biol (Weinh) 2025; 9:e2400433. [PMID: 39945006 DOI: 10.1002/adbi.202400433] [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: 07/25/2024] [Revised: 02/01/2025] [Indexed: 03/17/2025]
Abstract
Originating from, but independent of, linear chromosomes, extrachromosomal DNA (ecDNA) exists in a more active state of transcription and autonomous replication. It plays a crucial role in the development of malignancies and therapy resistance. Since its discovery in eukaryotic cells more than half a century ago, the biological characteristics and functions of ecDNA have remained unclear due to limitations in detection methods. However, recent advancements in research tools have transformed ecDNA research. It is believed that ecDNA exhibits greater activity in the abnormal amplification of oncogenes, thereby driving cancer progression through their overexpression. Notably, compared to linear DNA, ecDNA can also function as a genomic element with regulatory roles, including both trans- and cis-acting functions. Its critical roles in tumorigenesis, evolution, progression, and drug resistance in malignant tumors are increasingly recognized. This review provides a comprehensive summary of the evolutionary context of ecDNA and highlights significant progress in understanding its biological functions and potential applications as a therapeutic target in malignant tumors.
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Affiliation(s)
- Xudong Mao
- Department of Urology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
| | - Guocheng Rao
- Department of Endocrinology & Metabolism, Daepartment of Biotherapy, Center for Diabetes and Metabolism Research, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610000, P. R. China
| | - Gonghui Li
- Department of Urology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
| | - Shihan Chen
- Department of Endocrinology, The Affiliated Sir Run Run Shaw Hospital, College of Medicine, Zhejiang University, Hangzhou, 310000, P. R. China
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Wang Z, Yu J, Zhu W, Hong X, Xu Z, Mao S, Huang L, Han P, He C, Song C, Xiang X. Unveiling the mysteries of extrachromosomal circular DNA: from generation to clinical relevance in human cancers and health. Mol Cancer 2024; 23:276. [PMID: 39707444 DOI: 10.1186/s12943-024-02187-5] [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: 09/24/2024] [Accepted: 11/26/2024] [Indexed: 12/23/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are a type of circular DNAs originating from but independent of chromosomal DNAs. Nowadays, with the rapid development of sequencing and bioinformatics, the accuracy of eccDNAs detection has significantly improved. This advancement has consequently enhanced the feasibility of exploring the biological characteristics and functions of eccDNAs. This review elucidates the potential mechanisms of eccDNA generation, the existing methods for their detection and analysis, and their basic features. Furthermore, it focuses on the biological functions of eccDNAs in regulating gene expression under both physiological and pathological conditions. Additionally, the review summarizes the clinical implications of eccDNAs in human cancers and health.
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Affiliation(s)
- Zilong Wang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaying Yu
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Wenli Zhu
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Xiaoning Hong
- Clinical Big Data Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Zhen Xu
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Shuang Mao
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Lei Huang
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Peng Han
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China
- Department of Biology, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Chunxiao He
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Changze Song
- Department of Andrology, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
| | - Xi Xiang
- Scientific Research Center, The Seventh Affiliated Hospital, Sun Yat-Sen University, Shenzhen, 518107, China.
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Trasser M, Bohl-Viallefond G, Barragán-Borrero V, Diezma-Navas L, Loncsek L, Nordborg M, Marí-Ordóñez A. PTGS is dispensable for the initiation of epigenetic silencing of an active transposon in Arabidopsis. EMBO Rep 2024; 25:5780-5809. [PMID: 39511423 PMCID: PMC11624286 DOI: 10.1038/s44319-024-00304-5] [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: 05/27/2024] [Revised: 10/09/2024] [Accepted: 10/21/2024] [Indexed: 11/15/2024] Open
Abstract
Transposable elements (TEs) are repressed in plants through transcriptional gene silencing (TGS), maintained epigenetic silencing marks such as DNA methylation. However, the mechanisms by which silencing is first installed remain poorly understood in plants. Small interfering (si)RNAs and post-transcriptional gene silencing (PTGS) are believed to mediate the initiation of TGS by guiding the first deposition of DNA methylation. To determine how this silencing installation works, we took advantage of ÉVADÉ (EVD), an endogenous retroelement in Arabidopsis, able to recapitulate true de novo silencing with a sequence of PTGS followed by a TGS. To test whether PTGS is required for TGS, we introduce active EVD into RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6) mutants, an essential PTGS component. EVD activity and silencing are monitored across several generations. In the absence of PTGS, silencing of EVD is still achieved through installation of RNA-directed DNA methylation (RdDM). Our study shows that PTGS is dispensable for de novo EVD silencing. Although we cannot rule out that PTGS might facilitate TGS, or control TE activity, initiation of epigenetic silencing can take place in its absence.
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Affiliation(s)
- Marieke Trasser
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA
| | - Grégoire Bohl-Viallefond
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
| | - Verónica Barragán-Borrero
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
| | - Laura Diezma-Navas
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
| | - Lukas Loncsek
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
| | - Magnus Nordborg
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria
| | - Arturo Marí-Ordóñez
- Gregor Mendel Institute of Molecular Plant Biology (GMI) of the Austrian Academy of Sciences, Vienna, 1030, Austria.
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Ling X, Jiao Q, Lin D, Chen J, Han Y, Meng J, Zhong B, Zhang H, Zhang G, Zhu F, Qin J, Ruan Y, Liu L. Extrachromosomal circular DNA containing DTX1 promotes cell growth in hydroquinone-induced malignantly transformed cells by regulating the transcription of DTX1. BMC Cancer 2024; 24:1448. [PMID: 39587541 PMCID: PMC11587744 DOI: 10.1186/s12885-024-13177-7] [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: 12/25/2023] [Accepted: 11/09/2024] [Indexed: 11/27/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNA (eccDNA), a novel class of DNA with a circular topological structure, is present in a variety of cancer cells and tissues and may play broad roles in processes ranging from aging to cancer cell heterogeneity through multiple mechanisms. EccDNA has been characterized by profile, structure and function in several prominent studies but its effect on hydroquinone (HQ)-induced malignantly transformed cells (TK6-HQ) is still elusive. METHODS Circle-seq was applied to determine the eccDNA counts and characteristics of TK6-HQ cells. DNA-fluorescence in situ hybridization was used to measure the abundance of eccDNA_DTX1. Differential gene expression analysis was carried out by RNA-seq. Gene expression was quantified by wertern blot and qPCR. Decircularization of eccDNA_DTX1 was achieved by CRISPR/Cas9. Tumorigenicity was evaluated by xenograft assay in BALB/c nude mice. RESULTS In this study, we characterized the structure of eccDNAs and the function of DTX1-containing eccDNA (eccDNA_DTX1) in TK6-HQ cells. A total of 669,179 eccDNAs were identified, including 901 eccDNAs with different counts. Most of the eccDNAs were < 1000 bp in length and were enriched in four periodic peaks starting at 186 bp with an interval of ~ 180 bp. The genomic distribution of eccDNAs confirmed that eccDNAs could be observed across all chromosomes and had greater enrichment on chromosomes 17, 19, 20, and 22, with abundant Alu repeat elements, introns and CpG islands. By combining the results of the integrated circle-seq analysis of eccDNAs with those from the RNA-seq analysis (differentially expressed genes, 1064 upregulated and 427 downregulated), the authors showed that the transcription of 20 potential coding genes might be driven by eccDNAs. Finally, the knockdown of eccDNA_DTX1 by CRISPR/Cas9 inhibited the growth of TK6-HQ cells in vitro and in vivo by inhibiting the transcription of DTX1 and promoting ferroptosis, and ferroptosis inhibior, Ferrostatin-1, abrogated the proliferation inhibition of eccDNA_DTX1 knockdown. CONCLUSIONS EccDNA_DTX1 promotes cell growth in hydroquinone-induced malignantly transformed cells by regulating the transcription of DTX1 and ferroptosis. This study profiles eccDNA characteristics and defines the role and mechanism of eccDNA_DTX1 for the first time, shedding new light on the relationship between eccDNAs and carcinogenesis.
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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
| | - Qunfang Jiao
- 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
| | - Daifan Lin
- 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
| | - 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
| | - 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
| | - Gongda Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P. R. China
| | - Fangling Zhu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, 523808, P. R. China
| | - Jiheng Qin
- Guangdong Provincial Key Laboratory of Medical Immunology and Molecular Diagnostics, Guangdong Meidical University, Dongguan, 523808, P.R. China
| | - Yongdui Ruan
- The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan, 523722, 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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Gao X, Liu K, Luo S, Tang M, Liu N, Jiang C, Fang J, Li S, Hou Y, Guo C, Qu K. Comparative analysis of methodologies for detecting extrachromosomal circular DNA. Nat Commun 2024; 15:9208. [PMID: 39448595 PMCID: PMC11502736 DOI: 10.1038/s41467-024-53496-8] [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: 12/07/2023] [Accepted: 10/14/2024] [Indexed: 10/26/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is crucial in oncogene amplification, gene transcription regulation, and intratumor heterogeneity. While various analysis pipelines and experimental methods have been developed for eccDNA identification, their detection efficiencies have not been systematically assessed. To address this, we evaluate the performance of 7 analysis pipelines using seven simulated datasets, in terms of accuracy, identity, duplication rate, and computational resource consumption. We also compare the eccDNA detection efficiency of 7 experimental methods through twenty-one real sequencing datasets. Here, we show that Circle-Map and Circle_finder (bwa-mem-samblaster) outperform the other short-read pipelines. However, Circle_finder (bwa-mem-samblaster) exhibits notable redundancy in its outcomes. CReSIL is the most effective pipeline for eccDNA detection in long-read sequencing data at depths higher than 10X. Moreover, long-read sequencing-based Circle-Seq shows superior efficiency in detecting copy number-amplified eccDNA over 10 kb in length. These results offer valuable insights for researchers in choosing the suitable methods for eccDNA research.
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Affiliation(s)
- Xuyuan Gao
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Ke Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Songwen Luo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Meifang Tang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Nianping Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chen Jiang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Jingwen Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang, China
| | - Shouzhen Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Yanbing Hou
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chuang Guo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- School of Pharmacy, Bengbu Medical University, Bengbu, China.
- Department of Rheumatology and Immunology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China.
- School of Biomedical Engineering, Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 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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Yuan XQ, Zhou N, Song SJ, Xie YX, Chen SQ, Yang TF, Peng X, Zhang CY, Zhu YH, Peng L. Decoding the genomic enigma: Approaches to studying extrachromosomal circular DNA. Heliyon 2024; 10:e36659. [PMID: 39263178 PMCID: PMC11388731 DOI: 10.1016/j.heliyon.2024.e36659] [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: 02/21/2024] [Revised: 08/19/2024] [Accepted: 08/20/2024] [Indexed: 09/13/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a pervasive yet enigmatic component of the eukaryotic genome, exists autonomously from its chromosomal counterparts. Ubiquitous in eukaryotes, eccDNA plays a critical role in the orchestration of cellular processes and the etiology of diseases, particularly cancers. However, the full scope of its influence on health and disease remains elusive, presenting a rich vein of research yet to be mined. Unraveling the complexities of eccDNA necessitates a distillation of methodologies - from biogenesis to functional analysis - a landscape we overview in this study with precision and clarity. Here, we systematically outline cutting-edge methodologies from high-throughput sequencing and bioinformatics to experimental validations, showcasing the intricate world of eccDNAs. We combed through a treasure trove of auxiliary research resources and analytical tools. Moreover, we chart a course for future inquiry, illuminating the horizon with potential groundbreaking strategies for designing eccDNA research projects and pioneering new methodological frontiers.
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Affiliation(s)
- Xiao-Qing Yuan
- Guangdong Provincial Key Laboratory of Cancer Pathogenesis and Precision Diagnosis and Treatment, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, 516621, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Nan Zhou
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510370, China
| | - Shi-Jian Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Yi-Xia Xie
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Shui-Qin Chen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Teng-Fei Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Xian Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
- Puai Medical College, Shaoyang University, Shaoyang, 422100, China
| | - Chao-Yang Zhang
- Research Unit Analytical Pathology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, 85764, Germany
| | - Ying-Hua Zhu
- Department of Genetic Medicine, Dongguan Children's Hospital Affiliated to Guangdong Medical University, Dongguan, 523325, China
| | - Li Peng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
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8
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Gumińska N, Hałakuc P, Zakryś B, Milanowski R. Circular extrachromosomal DNA in Euglena gracilis under normal and stress conditions. Protist 2024; 175:126033. [PMID: 38574508 DOI: 10.1016/j.protis.2024.126033] [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: 11/30/2023] [Revised: 03/10/2024] [Accepted: 03/27/2024] [Indexed: 04/06/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) enhances genomic plasticity, augmenting its coding and regulatory potential. Advances in high-throughput sequencing have enabled the investigation of these structural variants. Although eccDNAs have been investigated in numerous taxa, they remained understudied in euglenids. Therefore, we examined eccDNAs predicted from Illumina sequencing data of Euglena gracilis Z SAG 1224-5/25, grown under optimal photoperiod and exposed to UV irradiation. We identified approximately 1000 unique eccDNA candidates, about 20% of which were shared across conditions. We also observed a significant enrichment of mitochondrially encoded eccDNA in the UV-irradiated sample. Furthermore, we found that the heterogeneity of eccDNA was reduced in UV-exposed samples compared to cells that were grown in optimal conditions. Hence, eccDNA appears to play a role in the response to oxidative stress in Euglena, as it does in other studied organisms. In addition to contributing to the understanding of Euglena genomes, our results contribute to the validation of bioinformatics pipelines on a large, non-model genome.
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Affiliation(s)
- Natalia Gumińska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland; Laboratory of RNA Biology, International Institute of Molecular and Cell Biology in Warsaw, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland.
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Bożena Zakryś
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland
| | - Rafał Milanowski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, 101 Żwirki i Wigury Street, 02-089 Warsaw, Poland.
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Zhou L, Tang W, Ye B, Zou L. Characterization, biogenesis model, and current bioinformatics of human extrachromosomal circular DNA. Front Genet 2024; 15:1385150. [PMID: 38746056 PMCID: PMC11092383 DOI: 10.3389/fgene.2024.1385150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Human extrachromosomal circular DNA, or eccDNA, has been the topic of extensive investigation in the last decade due to its prominent regulatory role in the development of disorders including cancer. With the rapid advancement of experimental, sequencing and computational technology, millions of eccDNA records are now accessible. Unfortunately, the literature and databases only provide snippets of this information, preventing us from fully understanding eccDNAs. Researchers frequently struggle with the process of selecting algorithms and tools to examine eccDNAs of interest. To explain the underlying formation mechanisms of the five basic classes of eccDNAs, we categorized their characteristics and functions and summarized eight biogenesis theories. Most significantly, we created a clear procedure to help in the selection of suitable techniques and tools and thoroughly examined the most recent experimental and bioinformatics methodologies and data resources for identifying, measuring and analyzing eccDNA sequences. In conclusion, we highlighted the current obstacles and prospective paths for eccDNA research, specifically discussing their probable uses in molecular diagnostics and clinical prediction, with an emphasis on the potential contribution of novel computational strategies.
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Affiliation(s)
- Lina Zhou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Wenyi Tang
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Bo Ye
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
| | - Lingyun Zou
- School of Medicine, Chongqing University, Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing University Central Hospital, Chongqing University, Chongqing, China
- School of Medicine, Jinan University, Guangzhou, Guangdong, China
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10
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Schmidt N, Sielemann K, Breitenbach S, Fuchs J, Pucker B, Weisshaar B, Holtgräwe D, Heitkam T. Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:171-190. [PMID: 38128038 DOI: 10.1111/tpj.16599] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/05/2023] [Accepted: 12/08/2023] [Indexed: 12/23/2023]
Abstract
Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.
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Affiliation(s)
- Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Katharina Sielemann
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
- Graduate School DILS, Bielefeld Institute for Bioinformatics Infrastructure (BIBI), Bielefeld University, 33615, Bielefeld, Germany
| | - Sarah Breitenbach
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
| | - Jörg Fuchs
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Stadt Seeland, Germany
| | - Boas Pucker
- Plant Biotechnology and Bioinformatics, Institute of Plant Biology & Braunschweig Integrated Centre of Systems Biology (BRICS), TU Braunschweig, 38106, Braunschweig, Germany
| | - Bernd Weisshaar
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Daniela Holtgräwe
- Genetics and Genomics of Plants, Center for Biotechnology (CeBiTec) & Faculty of Biology, Bielefeld University, 33615, Bielefeld, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, 01069, Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Graz, Austria
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11
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Yan X, Mischel P, Chang H. Extrachromosomal DNA in cancer. Nat Rev Cancer 2024; 24:261-273. [PMID: 38409389 DOI: 10.1038/s41568-024-00669-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/18/2024] [Indexed: 02/28/2024]
Abstract
Extrachromosomal DNA (ecDNA) has recently been recognized as a major contributor to cancer pathogenesis that is identified in most cancer types and is associated with poor outcomes. When it was discovered over 60 years ago, ecDNA was considered to be rare, and its impact on tumour biology was not well understood. The application of modern imaging and computational techniques has yielded powerful new insights into the importance of ecDNA in cancer. The non-chromosomal inheritance of ecDNA during cell division results in high oncogene copy number, intra-tumoural genetic heterogeneity and rapid tumour evolution that contributes to treatment resistance and shorter patient survival. In addition, the circular architecture of ecDNA results in altered patterns of gene regulation that drive elevated oncogene expression, potentially enabling the remodelling of tumour genomes. The generation of clusters of ecDNAs, termed ecDNA hubs, results in interactions between enhancers and promoters in trans, yielding a new paradigm in oncogenic transcription. In this Review, we highlight the rapid advancements in ecDNA research, providing new insights into ecDNA biogenesis, maintenance and transcription and its role in promoting tumour heterogeneity. To conclude, we delve into a set of unanswered questions whose answers will pave the way for the development of ecDNA targeted therapeutic approaches.
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Affiliation(s)
- Xiaowei Yan
- Department of Dermatology, Stanford University, Stanford, CA, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA
| | - Paul Mischel
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.
- Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| | - Howard Chang
- Department of Dermatology, Stanford University, Stanford, CA, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.
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12
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Li D, Qian X, Wang Y, Yin Y, Sun H, Zhao H, Wu J, Qiu L. Molecular characterization and functional roles of circulating cell-free extrachromosomal circular DNA. Clin Chim Acta 2024; 556:117822. [PMID: 38325714 DOI: 10.1016/j.cca.2024.117822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Circular DNA segments isolated from chromosomes are known as extrachromosomal circular DNA (eccDNA). Its distinct structure and characteristics, along with the variations observed in different disease states, makes it a promising biomarker. Recent studies have revealed the presence of eccDNAs in body fluids, indicating their involvement in various biological functions. This finding opens up avenues for utilizing eccDNAs as convenient and real-time biomarkers for disease diagnosis, treatment monitoring, and prognosis assessment through noninvasive analysis of body fluids. In this comprehensive review, we focused on elucidating the size profiles, potential mechanisms of formation and clearance, detection methods, and potential clinical applications of eccDNAs. We aimed to provide a valuable reference resource for future research in this field.
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Affiliation(s)
- Dandan Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Xia Qian
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yingjie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yicong Yin
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Huishan Sun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Jie Wu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Ling Qiu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
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13
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Garcia S, Kovarik A, Maiwald S, Mann L, Schmidt N, Pascual-Díaz JP, Vitales D, Weber B, Heitkam T. The Dynamic Interplay Between Ribosomal DNA and Transposable Elements: A Perspective From Genomics and Cytogenetics. Mol Biol Evol 2024; 41:msae025. [PMID: 38306580 PMCID: PMC10946416 DOI: 10.1093/molbev/msae025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 01/29/2024] [Indexed: 02/04/2024] Open
Abstract
Although both are salient features of genomes, at first glance ribosomal DNAs and transposable elements are genetic elements with not much in common: whereas ribosomal DNAs are mainly viewed as housekeeping genes that uphold all prime genome functions, transposable elements are generally portrayed as selfish and disruptive. These opposing characteristics are also mirrored in other attributes: organization in tandem (ribosomal DNAs) versus organization in a dispersed manner (transposable elements); evolution in a concerted manner (ribosomal DNAs) versus evolution by diversification (transposable elements); and activity that prolongs genomic stability (ribosomal DNAs) versus activity that shortens it (transposable elements). Re-visiting relevant instances in which ribosomal DNA-transposable element interactions have been reported, we note that both repeat types share at least four structural and functional hallmarks: (1) they are repetitive DNAs that shape genomes in evolutionary timescales, (2) they exchange structural motifs and can enter co-evolution processes, (3) they are tightly controlled genomic stress sensors playing key roles in senescence/aging, and (4) they share common epigenetic marks such as DNA methylation and histone modification. Here, we give an overview of the structural, functional, and evolutionary characteristics of both ribosomal DNAs and transposable elements, discuss their roles and interactions, and highlight trends and future directions as we move forward in understanding ribosomal DNA-transposable element associations.
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Affiliation(s)
- Sònia Garcia
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
| | - Ales Kovarik
- Institute of Biophysics, Academy of Sciences of the Czech Republic, 61265 Brno, Czech Republic
| | - Sophie Maiwald
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | | | - Daniel Vitales
- Institut Botànic de Barcelona (IBB), CSIC-CMCNB, 08038 Barcelona, Catalonia, Spain
- Laboratori de Botànica–Unitat Associada CSIC, Facultat de Farmàcia i Ciències de l’Alimentació, Universitat de Barcelona, 08028 Barcelona, Catalonia, Spain
| | - Beatrice Weber
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069 Dresden, Germany
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, A-8010 Graz, Austria
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14
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Mann L, Balasch K, Schmidt N, Heitkam T. High-fidelity (repeat) consensus sequences from short reads using combined read clustering and assembly. BMC Genomics 2024; 25:109. [PMID: 38267856 PMCID: PMC10809544 DOI: 10.1186/s12864-023-09948-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/28/2023] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Despite the many cheap and fast ways to generate genomic data, good and exact genome assembly is still a problem, with especially the repeats being vastly underrepresented and often misassembled. As short reads in low coverage are already sufficient to represent the repeat landscape of any given genome, many read cluster algorithms were brought forward that provide repeat identification and classification. But how can trustworthy, reliable and representative repeat consensuses be derived from unassembled genomes? RESULTS Here, we combine methods from repeat identification and genome assembly to derive these robust consensuses. We test several use cases, such as (1) consensus building from clustered short reads of non-model genomes, (2) from genome-wide amplification setups, and (3) specific repeat-centred questions, such as the linked vs. unlinked arrangement of ribosomal genes. In all our use cases, the derived consensuses are robust and representative. To evaluate overall performance, we compare our high-fidelity repeat consensuses to RepeatExplorer2-derived contigs and check, if they represent real transposable elements as found in long reads. Our results demonstrate that it is possible to generate useful, reliable and trustworthy consensuses from short reads by a combination from read cluster and genome assembly methods in an automatable way. CONCLUSION We anticipate that our workflow opens the way towards more efficient and less manual repeat characterization and annotation, benefitting all genome studies, but especially those of non-model organisms.
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Affiliation(s)
- Ludwig Mann
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Kristin Balasch
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Nicola Schmidt
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, D-01069, Dresden, Germany.
- Institute of Biology, NAWI Graz, Karl-Franzens-Universität, Graz, A-8010, Austria.
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15
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Fang M, Fang J, Luo S, Liu K, Yu Q, Yang J, Zhou Y, Li Z, Sun R, Guo C, Qu K. eccDNA-pipe: an integrated pipeline for identification, analysis and visualization of extrachromosomal circular DNA from high-throughput sequencing data. Brief Bioinform 2024; 25:bbae034. [PMID: 38349061 PMCID: PMC10862650 DOI: 10.1093/bib/bbae034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 02/15/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is currently attracting considerable attention from researchers due to its significant impact on tumor biogenesis. High-throughput sequencing (HTS) methods for eccDNA identification are continually evolving. However, an efficient pipeline for the integrative and comprehensive analysis of eccDNA obtained from HTS data is still lacking. Here, we introduce eccDNA-pipe, an accessible software package that offers a user-friendly pipeline for conducting eccDNA analysis starting from raw sequencing data. This dataset includes data from various sequencing techniques such as whole-genome sequencing (WGS), Circle-seq and Circulome-seq, obtained through short-read sequencing or long-read sequencing. eccDNA-pipe presents a comprehensive solution for both upstream and downstream analysis, encompassing quality control and eccDNA identification in upstream analysis and downstream tasks such as eccDNA length distribution analysis, differential analysis of genes enriched with eccDNA and visualization of eccDNA structures. Notably, eccDNA-pipe automatically generates high-quality publication-ready plots. In summary, eccDNA-pipe provides a comprehensive and user-friendly pipeline for customized analysis of eccDNA research.
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Affiliation(s)
- Minghao Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
| | - Jingwen Fang
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
| | - Songwen Luo
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ke Liu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Qiaoni Yu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Jiaxuan Yang
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Youyang Zhou
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Zongkai Li
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ruoming Sun
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Chuang Guo
- Department of Rheumatology and Immunology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230021, China
- School of Pharmacy, Bengbu Medical University, Bengbu, 233030, China
| | - Kun Qu
- Department of Oncology, The First Affiliated Hospital of USTC, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Advanced Technology, University of Science and Technology of China, Hefei, 230027, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, 230088, China
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou, 215123, China
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16
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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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17
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Smalheiser NR. Mobile circular DNAs regulating memory and communication in CNS neurons. Front Mol Neurosci 2023; 16:1304667. [PMID: 38125007 PMCID: PMC10730651 DOI: 10.3389/fnmol.2023.1304667] [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: 09/29/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
Stimuli that stimulate neurons elicit transcription of immediate-early genes, a process which requires local sites of chromosomal DNA to form double-strand breaks (DSBs) generated by topoisomerase IIb within a few minutes, followed by repair within a few hours. Wakefulness, exploring a novel environment, and contextual fear conditioning also elicit turn-on of synaptic genes requiring DSBs and repair. It has been reported (in non-neuronal cells) that extrachromosomal circular DNA can form at DSBs as the sites are repaired. I propose that activated neurons may generate extrachromosomal circular DNAs during repair at DSB sites, thus creating long-lasting "markers" of that activity pattern which contain sequences from their sites of origin and which regulate long-term gene expression. Although the population of extrachromosomal DNAs is diverse and overall associated with pathology, a subclass of small circular DNAs ("microDNAs," ∼100-400 bases long), largely derives from unique genomic sequences and has attractive features to act as stable, mobile circular DNAs to regulate gene expression in a sequence-specific manner. Circular DNAs can be templates for the transcription of RNAs, particularly small inhibitory siRNAs, circular RNAs and other non-coding RNAs that interact with microRNAs. These may regulate translation and transcription of other genes involved in synaptic plasticity, learning and memory. Another possible fate for mobile DNAs is to be inserted stably into chromosomes after new DSB sites are generated in response to subsequent activation events. Thus, the insertions of mobile DNAs into activity-induced genes may tend to inactivate them and aid in homeostatic regulation to avoid over-excitation, as well as providing a "counter" for a neuron's activation history. Moreover, activated neurons release secretory exosomes that can be transferred to recipient cells to regulate their gene expression. Mobile DNAs may be packaged into exosomes, released in an activity-dependent manner, and transferred to recipient cells, where they may be templates for regulatory RNAs and possibly incorporated into chromosomes. Finally, aging and neurodegenerative diseases (including Alzheimer's disease) are also associated with an increase in DSBs in neurons. It will become important in the future to assess how pathology-associated DSBs may relate to activity-induced mobile DNAs, and whether the latter may potentially contribute to pathogenesis.
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Affiliation(s)
- Neil R. Smalheiser
- Department of Psychiatry, University of Illinois College of Medicine, Chicago, IL, United States
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18
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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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19
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Wu S, Tao T, Zhang L, Zhu X, Zhou X. Extrachromosomal DNA (ecDNA): Unveiling its role in cancer progression and implications for early detection. Heliyon 2023; 9:e21327. [PMID: 38027570 PMCID: PMC10643110 DOI: 10.1016/j.heliyon.2023.e21327] [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: 05/25/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Extrachromosomal DNA (ecDNA) is a special class of circular DNA in eukaryotes, which is independent of conventional chromosomes. These circular molecules play important roles in biology, especially in cancer biology. The emergence of sequencing technologies such as CCDA-seq and Amplicon Architect has led to a progressive unraveling of the mystery of ecDNA. Consequently, insights into its function and potential applications have begun to surface. Among these studies, the most noteworthy research pertains to cancer-related investigations into ecDNA. Numerous studies have underscored the significance of ecDNA in the pathogenesis of cancer and its role in accelerating cancer evolution. This review provides an overview of the source, structure, and function of ecDNA, while compiling recent advancements in ecDNA in the field of cancer. Nonetheless, further research is imperative to determine its effectiveness and specificity as a biomarker for early cancer detection.
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Affiliation(s)
- Shuhong Wu
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Lin Zhang
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
| | - Xiao Zhu
- Computational Systems Biology Lab (CSBL), The Marine Biomedical Research Institute, Guangdong Medical University, Zhanjiang, China
- Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou Medical College, Hangzhou, China
| | - Xiaorong Zhou
- Department of Immunology, School of Medicine, Nantong University, Nantong, China
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20
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Hu J, Zhang Z, Xiao S, Cao Y, Chen Y, Weng J, Jiang H, Li W, Chen JY, Liu C. Microhomology-mediated circular DNA formation from oligonucleosomal fragments during spermatogenesis. eLife 2023; 12:RP87115. [PMID: 37847146 PMCID: PMC10581685 DOI: 10.7554/elife.87115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023] Open
Abstract
The landscape of extrachromosomal circular DNA (eccDNA) during mammalian spermatogenesis, as well as the biogenesis mechanism, remains to be explored. Here, we revealed widespread eccDNA formation in human sperms and mouse spermatogenesis. We noted that germline eccDNAs are derived from oligonucleosomal DNA fragmentation in cells likely undergoing cell death, providing a potential new way for quality assessment of human sperms. Interestingly, small-sized eccDNAs are associated with euchromatin, while large-sized ones are preferentially generated from heterochromatin. By comparing sperm eccDNAs with meiotic recombination hotspots and structural variations, we found that they are barely associated with de novo germline deletions. We further developed a bioinformatics pipeline to achieve nucleotide-resolution eccDNA detection even with the presence of microhomologous sequences that interfere with precise breakpoint identification. Empowered by our method, we provided strong evidence to show that microhomology-mediated end joining is the major eccDNA biogenesis mechanism. Together, our results shed light on eccDNA biogenesis mechanism in mammalian germline cells.
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Affiliation(s)
- Jun Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing UniversityNanjingChina
| | - Zhe Zhang
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Sai Xiao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
| | - Yalei Cao
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Yinghong Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
| | - Jiaming Weng
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
| | - Hui Jiang
- Department of Urology, Department of Reproductive Medicine Center, Peking University Third HospitalBeijingChina
- Department of Urology, Peking University First Hospital Institute of UrologyBeijingChina
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of ScienceBeijingChina
| | - Jia-Yu Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Department of Andrology, Nanjing Drum Tower Hospital, Nanjing UniversityNanjingChina
- Nanchuang (Jiangsu) Institute of Chemistry and HealthNanjingChina
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical UniversityGuangzhouChina
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Stem Cell and Regenerative Medicine Innovation Institute, Chinese Academy of ScienceBeijingChina
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21
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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22
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Cui Y, Zhang LJ, Li J, Xu YJ, Liu MY. Diagnostic value of circular free DNA for colorectal cancer detection. World J Gastrointest Oncol 2023; 15:1086-1095. [PMID: 37389117 PMCID: PMC10302987 DOI: 10.4251/wjgo.v15.i6.1086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 03/29/2023] [Accepted: 05/17/2023] [Indexed: 06/14/2023] Open
Abstract
BACKGROUND Minimally invasive or noninvasive, sensitive and accurate detection of colorectal cancer (CRC) is urgently needed in clinical practice.
AIM To identify a noninvasive, sensitive and accurate circular free DNA marker detected by digital polymerase chain reaction (dPCR) for the early diagnosis of clinical CRC.
METHODS A total of 195 healthy control (HC) individuals and 101 CRC patients (38 in the early CRC group and 63 in the advanced CRC group) were enrolled to establish the diagnostic model. In addition, 100 HC individuals and 62 patients with CRC (30 early CRC and 32 advanced CRC groups) were included separately to validate the model. CAMK1D was dPCR. Binary logistic regression analysis was used to establish a diagnostic model including CAMK1D and CEA.
RESULTS To differentiate between the 195 HCs and 101 CRC patients (38 early CRC and 63 advanced CRC patients), the common biomarkers CEA and CAMK1D were used alone or in combination to evaluate their diagnostic value. The area under the curves (AUCs) of CEA and CAMK1D were 0.773 (0.711, 0.834) and 0.935 (0.907, 0.964), respectively. When CEA and CAMK1D were analyzed together, the AUC was 0.964 (0.945, 0.982). In differentiating between the HC and early CRC groups, the AUC was 0.978 (0.960, 0.995), and the sensitivity and specificity were 88.90% and 90.80%, respectively. In differentiating between the HC and advanced CRC groups, the AUC was 0.956 (0.930, 0.981), and the sensitivity and specificity were 81.30% and 95.90%, respectively. After building the diagnostic model containing CEA and CAMK1D, the AUC of the CEA and CAMK1D joint model was 0.906 (0.858, 0.954) for the validation group. In differentiating between the HC and early CRC groups, the AUC was 0.909 (0.844, 0.973), and the sensitivity and specificity were 93.00% and 83.30%, respectively. In differentiating between the HC and advanced CRC groups, the AUC was 0.904 (0.849, 0.959), and the sensitivity and specificity were 93.00% and 75.00%, respectively.
CONCLUSION We built a diagnostic model including CEA and CAMK1D for differentiating between HC individuals and CRC patients. Compared with the common biomarker CEA alone, the diagnostic model exhibited significant improvement.
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Affiliation(s)
- Yao Cui
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University People's Hospital, Zhengzhou 450003, Henan Province, China
| | - Lu-Jin Zhang
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University People's Hospital, Zhengzhou 450003, Henan Province, China
| | - Jian Li
- Department of General Surgery, Henan Tumor Hospital, The Affiliated Tumor Hospital of Zhengzhou University, Zhengzhou 450000, Henan Province, China
| | - Yu-Jie Xu
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University People's Hospital, Zhengzhou 450003, Henan Province, China
| | - Ming-Yue Liu
- Department of Oncology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University, Henan University People's Hospital, Zhengzhou 450003, Henan Province, China
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23
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Merkulov P, Egorova E, Kirov I. Composition and Structure of Arabidopsis thaliana Extrachromosomal Circular DNAs Revealed by Nanopore Sequencing. PLANTS (BASEL, SWITZERLAND) 2023; 12:2178. [PMID: 37299157 PMCID: PMC10255303 DOI: 10.3390/plants12112178] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 05/19/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023]
Abstract
Extrachromosomal circular DNAs (eccDNAs) are enigmatic DNA molecules that have been detected in a range of organisms. In plants, eccDNAs have various genomic origins and may be derived from transposable elements. The structures of individual eccDNA molecules and their dynamics in response to stress are poorly understood. In this study, we showed that nanopore sequencing is a useful tool for the detection and structural analysis of eccDNA molecules. Applying nanopore sequencing to the eccDNA molecules of epigenetically stressed Arabidopsis plants grown under various stress treatments (heat, abscisic acid, and flagellin), we showed that TE-derived eccDNA quantity and structure vary dramatically between individual TEs. Epigenetic stress alone did not cause eccDNA up-regulation, whereas its combination with heat stress triggered the generation of full-length and various truncated eccDNAs of the ONSEN element. We showed that the ratio between full-length and truncated eccDNAs is TE- and condition-dependent. Our work paves the way for further elucidation of the structural features of eccDNAs and their connections with various biological processes, such as eccDNA transcription and eccDNA-mediated TE silencing.
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Affiliation(s)
- Pavel Merkulov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia;
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ekaterina Egorova
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
| | - Ilya Kirov
- Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia;
- All-Russia Research Institute of Agricultural Biotechnology, 127550 Moscow, Russia;
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24
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Jiang R, Yang M, Zhang S, Huang M. Advances in sequencing-based studies of microDNA and ecDNA: Databases, identification methods, and integration with single-cell analysis. Comput Struct Biotechnol J 2023; 21:3073-3080. [PMID: 37273851 PMCID: PMC10238454 DOI: 10.1016/j.csbj.2023.05.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/06/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a class of circular DNA molecules that originate from genomic DNA but are separate from chromosomes. They are common in various organisms, with sizes ranging from a few hundred to millions of base pairs. A special type of large extrachromosomal DNA (ecDNA) is prevalent in cancer cells. Research on ecDNA has significantly contributed to our comprehension of cancer development, progression, evolution, and drug resistance. The use of next-generation (NGS) and third-generation sequencing (TGS) techniques to identify eccDNAs throughout the genome has become a trend in current research. Here, we briefly review current advances in the biological mechanisms and applications of two distinct types of eccDNAs: microDNA and ecDNA. In addition to presenting available identification tools based on sequencing data, we summarize the most recent efforts to integrate ecDNA with single-cell analysis and put forth suggestions to promote the process.
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Affiliation(s)
| | | | - Shufan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou 215123, China
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25
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Mokhtar MM, Alsamman AM, El Allali A. PlantLTRdb: An interactive database for 195 plant species LTR-retrotransposons. FRONTIERS IN PLANT SCIENCE 2023; 14:1134627. [PMID: 36950350 PMCID: PMC10025401 DOI: 10.3389/fpls.2023.1134627] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/16/2023] [Indexed: 05/29/2023]
Abstract
LTR-retrotransposons (LTR-RTs) are a large group of transposable elements that replicate through an RNA intermediate and alter genome structure. The activities of LTR-RTs in plant genomes provide helpful information about genome evolution and gene function. LTR-RTs near or within genes can directly alter gene function. This work introduces PlantLTRdb, an intact LTR-RT database for 195 plant species. Using homology- and de novo structure-based methods, a total of 150.18 Gbp representing 3,079,469 pseudomolecules/scaffolds were analyzed to identify, characterize, annotate LTR-RTs, estimate insertion ages, detect LTR-RT-gene chimeras, and determine nearby genes. Accordingly, 520,194 intact LTR-RTs were discovered, including 29,462 autonomous and 490,732 nonautonomous LTR-RTs. The autonomous LTR-RTs included 10,286 Gypsy and 19,176 Copia, while the nonautonomous were divided into 224,906 Gypsy, 218,414 Copia, 1,768 BARE-2, 3,147 TR-GAG and 4,2497 unknown. Analysis of the identified LTR-RTs located within genes showed that a total of 36,236 LTR-RTs were LTR-RT-gene chimeras and 11,619 LTR-RTs were within pseudo-genes. In addition, 50,026 genes are within 1 kbp of LTR-RTs, and 250,587 had a distance of 1 to 10 kbp from LTR-RTs. PlantLTRdb allows researchers to search, visualize, BLAST and analyze plant LTR-RTs. PlantLTRdb can contribute to the understanding of structural variations, genome organization, functional genomics, and the development of LTR-RT target markers for molecular plant breeding. PlantLTRdb is available at https://bioinformatics.um6p.ma/PlantLTRdb.
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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: 3.0] [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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Kang J, Dai Y, Li J, Fan H, Zhao Z. Investigating cellular heterogeneity at the single-cell level by the flexible and mobile extrachromosomal circular DNA. Comput Struct Biotechnol J 2023; 21:1115-1121. [PMID: 36789262 PMCID: PMC9900259 DOI: 10.1016/j.csbj.2023.01.025] [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: 09/22/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a special class of DNA derived from linear chromosomes. It coexists independently with linear chromosomes in the nucleus. eccDNA has been identified in multiple organisms, including Homo sapiens, and has been shown to play important roles relevant to tumor progression and drug resistance. To date, computational tools developed for eccDNA detection are only applicable to bulk tissue. Investigating eccDNA at the single-cell level using a computational approach will elucidate the heterogeneous and cell-type-specific landscape of eccDNA within cellular context. Here, we performed the first eccDNA analysis at the single-cell level using data generated by single-cell Assay for Transposase-Accessible Chromatin with sequencing (scATAC-seq) in adult and pediatric glioblastoma (GBM) samples. Glioblastoma multiforme (GBM) is an aggressive tumor of the central nervous system with a poor prognosis. Our analysis provides an overview of cellular origins, genomic distribution, as well as the differential regulations between linear and circular genome under disease- and cell-type-specific conditions across the open chromatin regions in GBM. We focused on some eccDNA elements that are potential mobile enhancers acting in a trans-regulation manner. In summary, this pilot study revealed novel eccDNA features in the cellular context of brain tumor, supporting the strong need for eccDNA investigation at the single-cell level.
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Affiliation(s)
- Jiajinlong Kang
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yulin Dai
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jinze Li
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Department of Epidemiology, Human Genetics, and Environment Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Huihui Fan
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Department of Neurology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA,Correspondence to: Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA.
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA,Department of Epidemiology, Human Genetics, and Environment Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA,Correspondence to: Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, 7000 Fannin St. Suite 600, Houston, TX 77030, USA.
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28
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Bajus M, Macko-Podgórni A, Grzebelus D, Baránek M. A review of strategies used to identify transposition events in plant genomes. FRONTIERS IN PLANT SCIENCE 2022; 13:1080993. [PMID: 36531345 PMCID: PMC9751208 DOI: 10.3389/fpls.2022.1080993] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Transposable elements (TEs) were initially considered redundant and dubbed 'junk DNA'. However, more recently they were recognized as an essential element of genome plasticity. In nature, they frequently become active upon exposition of the host to stress conditions. Even though most transposition events are neutral or even deleterious, occasionally they may happen to be beneficial, resulting in genetic novelty providing better fitness to the host. Hence, TE mobilization may promote adaptability and, in the long run, act as a significant evolutionary force. There are many examples of TE insertions resulting in increased tolerance to stresses or in novel features of crops which are appealing to the consumer. Possibly, TE-driven de novo variability could be utilized for crop improvement. However, in order to systematically study the mechanisms of TE/host interactions, it is necessary to have suitable tools to globally monitor any ongoing TE mobilization. With the development of novel potent technologies, new high-throughput strategies for studying TE dynamics are emerging. Here, we present currently available methods applied to monitor the activity of TEs in plants. We divide them on the basis of their operational principles, the position of target molecules in the process of transposition and their ability to capture real cases of actively transposing elements. Their possible theoretical and practical drawbacks are also discussed. Finally, conceivable strategies and combinations of methods resulting in an improved performance are proposed.
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Affiliation(s)
- Marko Bajus
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
| | - Alicja Macko-Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, Poland
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, Poland
| | - Miroslav Baránek
- Mendeleum—Institute of Genetics, Faculty of Horticulture, Mendel University in Brno, Lednice, Czechia
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29
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Wanchai V, Jenjaroenpun P, Leangapichart T, Arrey G, Burnham CM, Tümmler MC, Delgado-Calle J, Regenberg B, Nookaew I. CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences. Brief Bioinform 2022; 23:bbac422. [PMID: 36198068 PMCID: PMC10144670 DOI: 10.1093/bib/bbac422] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 12/14/2022] Open
Abstract
Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.
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Affiliation(s)
- Visanu Wanchai
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Piroon Jenjaroenpun
- Division of Bioinformatics and Data Management for Research, Research Group and Research Network Division, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thongpan Leangapichart
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Gerard Arrey
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Charles M Burnham
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Maria C Tümmler
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jesus Delgado-Calle
- Department of Physiology and Cell Biology, College of Medicine, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Birgitte Regenberg
- Ecology and Evolution, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
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Zhu Y, Liu Z, Guo Y, Li S, Qu Y, Dai L, Chen Y, Ning W, Zhang H, Ma L. Whole-genome sequencing of extrachromosomal circular DNA of cerebrospinal fluid of medulloblastoma. Front Oncol 2022; 12:934159. [PMID: 36452490 PMCID: PMC9703567 DOI: 10.3389/fonc.2022.934159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 10/12/2022] [Indexed: 03/22/2024] Open
Abstract
BACKGROUND Medulloblastoma (MB) is a malignant tumor associated with a poor prognosis in part due to a lack of effective detection methods. Extrachromosomal circular DNA (eccDNA) has been associated with multiple tumors. Nonetheless, little is currently known on eccDNA in MB. METHODS Genomic features of eccDNAs were identified in MB tissues and matched cerebrospinal fluid (CSF) and compared with corresponding normal samples using Circle map. The nucleotides on both sides of the eccDNAs' breakpoint were analyzed to understand the mechanisms of eccDNA formation. Bioinformatics analysis combined with the Gene Expression Omnibus (GEO) database identified features of eccDNA-related genes in MB. Lasso Cox regression model, univariate and multivariate Cox regression analysis, time-dependent ROC, and Kaplan-Meier curve were used to assess the potential diagnostic and prognostic value of the hub genes. RESULTS EccDNA was profiled in matched tumor and CSF samples from MB patients, and control, eccDNA-related genes enriched in MB were identified. The distribution of eccDNAs in the genome was closely related to gene density and the mechanism of eccDNA formation was evaluated. EccDNAs in CSF exhibited similar distribution with matched MB tissues but were differentially expressed between tumor and normal. Ten hub genes prominent in both the eccDNA dataset and the GEO database were selected to classify MB patients to either high- or low-risk groups, and a prognostic nomogram was thus established. CONCLUSIONS This study provides preliminary evidence of the characteristics and formation mechanism of eccDNAs in MB and CSF. Importantly, eccDNA-associated hub genes in CSF could be used as diagnostic and prognostic biomarkers for MB.
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Affiliation(s)
- Yi Zhu
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Zhihui Liu
- Department of Obstetrics and Gynecology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- Chinese Academy of Sciences (CAS) Key Laboratory of Infection and Immunity, Institute of biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lin Dai
- Department of Neurosurgery, Binzhou Medical University Hospital, Binzhou, China
| | - Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
- Department of Neurosurgery, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
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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: 18] [Impact Index Per Article: 6.0] [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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Peng H, Mirouze M, Bucher E. Extrachromosomal circular DNA: A neglected nucleic acid molecule in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102263. [PMID: 35872391 DOI: 10.1016/j.pbi.2022.102263] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/15/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Throughout the years, most plant genomic studies were focused on nuclear chromosomes. Extrachromosomal circular DNA (eccDNA) has largely been neglected for decades since its discovery in 1965. While initial research showed that eccDNAs can originate from highly repetitive sequences, recent findings show that many regions of the genome can contribute to the eccDNA pool. Currently, the biological functions of eccDNAs, if any, are a mystery but recent studies have indicated that they can be regulated by different genomic loci and contribute to stress response and adaptation. In this review, we outline current relevant technological developments facilitating eccDNA identification and the latest discoveries about eccDNAs in plants. Finally, we explore the probable functions and future research directions that could be undertaken with respect to different eccDNA sources.
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Affiliation(s)
- Haoran Peng
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland; Department of Botany and Plant Biology, Section of Biology, Faculty of Science, University of Geneva, 1211, Geneva, Switzerland
| | - Marie Mirouze
- Institut de Recherche pour le Développement (IRD), EMR269 MANGO, Université de Perpignan, 66860 Perpignan, France; Laboratory of Plant Genome and Development, Université de Perpignan, 66860, Perpignan, France.
| | - Etienne Bucher
- Crop Genome Dynamics Group, Agroscope Changins, 1260, Nyon, Switzerland.
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Kwolek K, Kędzierska P, Hankiewicz M, Mirouze M, Panaud O, Grzebelus D, Macko‐Podgórni A. Diverse and mobile: eccDNA-based identification of carrot low-copy-number LTR retrotransposons active in callus cultures. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1811-1828. [PMID: 35426957 PMCID: PMC9324142 DOI: 10.1111/tpj.15773] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/15/2022] [Accepted: 03/29/2022] [Indexed: 05/28/2023]
Abstract
Long terminal repeat retrotransposons (LTR-RTs) are mobilized via an RNA intermediate using a 'copy and paste' mechanism, and account for the majority of repetitive DNA in plant genomes. As a side effect of mobilization, the formation of LTR-RT-derived extrachromosomal circular DNAs (eccDNAs) occurs. Thus, high-throughput sequencing of eccDNA can be used to identify active LTR-RTs in plant genomes. Despite the release of a reference genome assembly, carrot LTR-RTs have not yet been thoroughly characterized. LTR-RTs are abundant and diverse in the carrot genome. We identified 5976 carrot LTR-RTs, 2053 and 1660 of which were attributed to Copia and Gypsy superfamilies, respectively. They were further classified into lineages, families and subfamilies. More diverse LTR-RT lineages, i.e. lineages comprising many low-copy-number subfamilies, were more frequently associated with genic regions. Certain LTR-RT lineages have been recently active in Daucus carota. In particular, low-copy-number LTR-RT subfamilies, e.g. those belonging to the DcAle lineage, have significantly contributed to carrot genome diversity as a result of continuing activity. We utilized eccDNA sequencing to identify and characterize two DcAle subfamilies, Alex1 and Alex3, active in carrot callus. We documented 14 and 32 de novo insertions of Alex1 and Alex3, respectively, which were positioned in non-repetitive regions.
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Affiliation(s)
- Kornelia Kwolek
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Patrycja Kędzierska
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Magdalena Hankiewicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Marie Mirouze
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
- IRD, EMR IRD‐CNRS‐UPVD ‘MANGO’Université de PerpignanPerpignanFrance
| | - Olivier Panaud
- Laboratoire Génome et Développement des Plantes, UMR 5096 CNRS/UPVDUniversité de PerpignanVia Domitia, 52 Avenue Paul Alduy66 860Perpignan CedexFrance
| | - Dariusz Grzebelus
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
| | - Alicja Macko‐Podgórni
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and HorticultureUniversity of Agriculture in Krakow31 120KrakowPoland
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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: 0.7] [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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