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Qiu GH, Fu M, Zheng X, Huang C. Protection of the genome and the central exome by peripheral non-coding DNA against DNA damage in health, ageing and age-related diseases. Biol Rev Camb Philos Soc 2025; 100:508-529. [PMID: 39327815 DOI: 10.1111/brv.13151] [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: 09/26/2023] [Revised: 09/15/2024] [Accepted: 09/18/2024] [Indexed: 09/28/2024]
Abstract
DNA in eukaryotic genomes is under constant assault from both exogenous and endogenous sources, leading to DNA damage, which is considered a major molecular driver of ageing. Fortunately, the genome and the central exome are safeguarded against these attacks by abundant peripheral non-coding DNA. Non-coding DNA codes for small non-coding RNAs that inactivate foreign nucleic acids in the cytoplasm and physically blocks these attacks in the nucleus. Damage to non-coding DNA produced during such blockage is removed in the form of extrachromosomal circular DNA (eccDNA) through nucleic pore complexes. Consequently, non-coding DNA serves as a line of defence for the exome against DNA damage. The total amount of non-coding DNA/heterochromatin declines with age, resulting in a decrease in both physical blockage and eccDNA exclusion, and thus an increase in the accumulation of DNA damage in the nucleus during ageing and in age-related diseases. Here, we summarize recent evidence supporting a protective role of non-coding DNA in healthy and pathological states and argue that DNA damage is the proximate cause of ageing and age-related genetic diseases. Strategies aimed at strengthening the protective role of non-coding DNA/heterochromatin could potentially offer better systematic protection for the dynamic genome and the exome against diverse assaults, reduce the burden of DNA damage to the exome, and thus slow ageing, counteract age-related genetic diseases and promote a healthier life for individuals.
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Affiliation(s)
- Guo-Hua Qiu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Mingjun Fu
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Xintian Zheng
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
| | - Cuiqin Huang
- College of Life Sciences, Longyan University, Longyan, 364012, People's Republic of China
- Fujian Provincial Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Engineering Research Center for the Prevention and Control of Animal-Origin Zoonosis, Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Fujian Province Universities, Longyan, People's Republic of China
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Ran XK, Zhao XF, Wei ZW, Pang HZ, Tang YF, Liu R, Wu TX, Liu XD. Circle-seq reveals that eccDNA may be a key blood biomarker for HBV-associated liver cancer. Front Genet 2025; 15:1454153. [PMID: 39850493 PMCID: PMC11754267 DOI: 10.3389/fgene.2024.1454153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 12/23/2024] [Indexed: 01/25/2025] Open
Abstract
INTRODUCTION Extrachromosomal circular DNA (eccDNA) regulates tumor occurrence and development. Relevant eccDNA profiles have been established for various types of cancer; however, the eccDNA expression profiles in the blood of patients with hepatocellular carcinoma (HCC) and liver cirrhosis (LC) remain unknown. The present study aimed to investigate the eccDNA expression profiles in the blood of patients with HCC and LC. METHODS Circle-seq was used to detect eccDNAs in the blood samples. Full transcript sequencing was used to analyze the RNA in the samples. Geno Ontology enrichment and Kyoto Encyclopedia of Genes and Genome pathway analyses were performed on differentially expressed eccDNA-related genes. The identified eccDNA is combined with mRNA to screen target genes using bioinformatics analysis. EccDNAs were confirmed through polymerase chain reaction and Sanger sequencing. RESULTS Overall, 103,235 eccDNAs were identified in HCC, whereas 67,110 eccDNAs were detected in LC. In total, 7,095 upregulated eccDNAs and 1,284 downregulated eccDNAs were identified. Following analysis of differential genes using bioinformatics, six candidate genes were screened out based on gene expression and cancer relevance. Experiments have verified that LAMA4 [circle112550019-112550510] and KANK1 [circle674459-674907] are real and expressed target genes, and their source genes are closely related to the survival time of patients with liver cancer. CONCLUSION Our research results revealed the main characteristics of eccDNAs in the blood of patients with HBV-related HCC and LC. It was found that eccDNAs were mainly less than 1,000 bp in length. Difference analysis showed that some eccDNAs had consistent and overlapping expressions with mRNAs. We found that LAMA4 [circle112550019-112550510] and KANK1 [circle674459-674907] are target genes related to HCC, and both of them may become potential biomarkers for the diagnosis and prognosis of HCC.
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Affiliation(s)
- Xiao K. Ran
- Graduate School, Guangxi University of Chinese Medicine, Nanning, China
| | - Xiao F. Zhao
- Hepatology Department, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Zhen W. Wei
- Hepatology Department, Nanning Fourth People’s Hospital, Nanning, China
| | - Hua Z. Pang
- Hepatology Department, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Yan F. Tang
- Hepatology Department, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Rong Liu
- Hepatology Department, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
| | - Tie X. Wu
- Graduate School, Guangxi University of Chinese Medicine, Nanning, China
| | - Xu D. Liu
- Hepatology Department, Ruikang Hospital Affiliated to Guangxi University of Chinese Medicine, Nanning, China
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Jiang J, Xia N, Yang M, Qiu P, Zhu W, Chen J, Zhu J. Identification and validation of glucose metabolism-related gene signature in endometrial cancer. BMC Cancer 2025; 25:30. [PMID: 39773448 PMCID: PMC11708096 DOI: 10.1186/s12885-024-13418-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2024] [Accepted: 12/31/2024] [Indexed: 01/11/2025] Open
Abstract
BACKGROUND Metabolic syndrome associated with glucose metabolism plays a pivotal role in tumorigenesis, potentially elevating the risk of endometrial cancer (EC). This study sought to establish a glucose metabolism-related gene (GMRG) signature linked to EC. METHODS Differential analysis was conducted to identify differentially expressed genes (DEGs) between EC and normal samples from the TCGA-EC dataset. Glucose metabolism-related DEGs (GMR-DEGs) were then derived by intersecting these DEGs with GMRGs. A prognostic signature for EC was developed through the Least Absolute Shrinkage and Selection Operator (LASSO) regression and univariate Cox analysis. Additionally, immune profiling and immunotherapy responsiveness were evaluated across two distinct risk subgroups, accompanied by a single-cell analysis of prognostic genes. The expression levels of these prognostic genes were quantified at both transcriptional and translational stages using reverse transcription quantitative PCR (RT-qPCR) and immunohistochemistry (IHC) in clinical samples. Furthermore, the functional significance of key genes was explored through in vitro assays. RESULTS 2,912 DEGs and 202 GMR-DEGs were identified between the EC and normal groups. Subsequently, six prognostic genes were derived, including ASRGL1, SLC38A3, SLC2A1, ALDH1B1, GAD1, and GLYATL1. EC patients were classified into high and low-risk subgroups based on the six genes. Independent prognostic analysis indicated that risk score and disease stage were significant independent prognostic factors. Single-cell analysis revealed that the six prognostic genes were highly expressed in ciliated and epithelial cells. Immune cell infiltration was generally lower in the high-risk group, where tumor purity was elevated. The expression levels of SLC38A3, SLC2A1, and ASRGL1 are higher in tumor samples by RT-qPCR, with IHC confirming increased SLC38A3 expression. Finally, SLC38A3 may function as oncogenes in EC, as revealed by the results of in vitro experiments. CONCLUSIONS In this study, we developed six novel prognostic genes in EC based on glycolysis, and corresponding prognostic models were developed. Notably, we identified SLC38A3 as the key gene, which offers valuable insights for further research into EC.
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Affiliation(s)
- Juan Jiang
- Department of Obstetrics and Gynecology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China
| | - Nan Xia
- Department of Pathology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China
| | - Mei Yang
- Advanced Molecular Pathology, Institute of Soochow University and SANO, Suzhou, China
| | - Ping Qiu
- Department of Obstetrics and Gynecology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China
| | - Wei Zhu
- Department of Obstetrics and Gynecology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China
| | - Jing Chen
- Department of Pathology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China
| | - Jiamei Zhu
- Department of Obstetrics and Gynecology, Jingjiang People's Hospital Affiliated to Yangzhou University, Taizhou, China.
- Advanced Molecular Pathology, Institute of Soochow University and SANO, Suzhou, China.
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Hu F, Qiu Z. Spotlight on the function and trends on extrachromosomal circular DNA (eccDNA): A bibliometric analysis from 2008 - 2023. Exp Cell Res 2025; 444:114318. [PMID: 39547353 DOI: 10.1016/j.yexcr.2024.114318] [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: 07/22/2024] [Revised: 09/28/2024] [Accepted: 10/31/2024] [Indexed: 11/17/2024]
Abstract
Extrachromosomal circular DNA (eccDNA),a type of circular DNA that has a nucleosomal structure, is widely distributed in eukaryotic chromosomes and has been found to modulate genome instability and plasticity, playing a role in regulating gene expression and genome evolution. To comprehensively outline the stages of eccDNA research development, including author collaborations, research topics and hotspots, and their temporal evolution trends, we conducted a bibliometric analysis of 242 publications related to eccDNA research published from 2008 to 2023 in the Web of Science Core Collection. The bibliometric analysis was performed using CiteSpace, the R package Bibliometrix, and VOSviewer. The USA, the University of California system, and Turner Km were found to be the most influential nation, organization, and author in this field, respectively. The exploration of Characterization and Diagnosis, Heterochromatin,Circ-Seq and Cancer Drug Resistance on eccDNA are the most concerned hotspots. EccDNA research has become a rapidly growing hotspot, receiving extensive attention from scholars in recent years. This study is the first to investigate the development and current challenges of eccDNA research through bibliometric analysis.The research on eccDNA has advanced from disorder to more intricate molecular functions. At present, the rapid growth of eccDNA studies in cancer has not been accompanied by an intuitive analysis of its evolutionary patterns. This review provides an overview of eccDNA's biological characteristics and functions, with a focus on its role in cancer research.
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Affiliation(s)
- Fan Hu
- Zhuhai Jingyuan Biomedical Technology Co., LTD, Zhuhai, Guangdong, 519000, People's Republic of China.
| | - Zhengqi Qiu
- Faculty of Medicine, Macau University of Science and Technology, Est. Seak Pai Van Praia Park, Rés-Do-Chão R, Coloane, Macao, 999078, People's Republic of China
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Yao Y, Wang Q, Jiang W, Li H, Li X, Zi T, Qin X, Zhao Y, Wu D, Wu G. Extrachromosomal circular DNA-related SPOCK1 contributes to development and enzalutamide resistance of prostate cancer by regulating epithelial mesenchymal transition. Heliyon 2024; 10:e37075. [PMID: 39328548 PMCID: PMC11425131 DOI: 10.1016/j.heliyon.2024.e37075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 08/26/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Prostate cancer is a significant contributor to cancer-related mortality, and the tumor typically develops into castration-resistant prostate cancer (CRPC). Hence, few effective clinical strategies are available to patients with advanced disease. Extrachromosomal circular DNA (eccDNA) is a type of circular DNA originating from the chromosomes but is likely independent of them. Because of its unique structural characteristics, eccDNA has extensive applications as a new biomarker for cancer prevention and treatment. Circle-seq obtains a comprehensive picture of the overall landscape of eccDNA sizes and content in cell populations. In this study, we used Circle-seq and studied the distribution pattern and expression level of eccDNA in prostate cancer. We confirmed that eccDNA is derived from every human chromosome and has sequences from all known types of genomic structures, revealing it is a common mutational element in prostate cancer. We also identified an eccDNA-related gene SPOCK1 that promotes drug resistance, proliferation, and metastasis of many cancers through the epithelial-mesenchymal transition (EMT) mechanism. The SPOCK1-associated eccDNA was highly upregulated in various groups of sequencing results, and SPOCK1 was highly expressed in prostate cancer tissues and cells. Therefore, SPOCK1 exists as eccDNA in prostate cancer and encourages its development and drug resistance via the EMT mechanism. Our results suggest that upregulated genes in the form of eccDNA are oncogenes in prostate cancer and play a pivotal role in carcinogenesis.
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Affiliation(s)
- Yicong Yao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Qinghua Wang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Wei Jiang
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Haopeng Li
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xilei Li
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Tong Zi
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xin Qin
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yan Zhao
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
- School of Medicine, Tongji University, Shanghai, 200092, China
| | - Denglong Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
| | - Gang Wu
- Department of Urology, Tongji Hospital, School of Medicine, Tongji University, Shanghai, 200065, China
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Tsiakanikas P, Athanasopoulou K, Darioti IA, Agiassoti VT, Theocharis S, Scorilas A, Adamopoulos PG. Beyond the Chromosome: Recent Developments in Decoding the Significance of Extrachromosomal Circular DNA (eccDNA) in Human Malignancies. Life (Basel) 2024; 14:922. [PMID: 39202666 PMCID: PMC11355349 DOI: 10.3390/life14080922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/13/2024] [Accepted: 07/23/2024] [Indexed: 09/03/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a form of a circular double-stranded DNA that exists independently of conventional chromosomes. eccDNA exhibits a broad and random distribution across eukaryotic cells and has been associated with tumor-related properties due to its ability to harbor the complete gene information of oncogenes. The complex and multifaceted mechanisms underlying eccDNA formation include pathways such as DNA damage repair, breakage-fusion-bridge (BFB) mechanisms, chromothripsis, and cell apoptosis. Of note, eccDNA plays a pivotal role in tumor development, genetic heterogeneity, and therapeutic resistance. The high copy number and transcriptional activity of oncogenes carried by eccDNA contribute to the accelerated growth of tumors. Notably, the amplification of oncogenes on eccDNA is implicated in the malignant progression of cancer cells. The improvement of high-throughput sequencing techniques has greatly enhanced our knowledge of eccDNA by allowing for a detailed examination of its genetic structures and functions. However, we still lack a comprehensive and efficient annotation for eccDNA, while challenges persist in the study and understanding of the functional role of eccDNA, emphasizing the need for the development of robust methodologies. The potential clinical applications of eccDNA, such as its role as a measurable biomarker or therapeutic target in diseases, particularly within the spectrum of human malignancies, is a promising field for future research. In conclusion, eccDNA represents a quite dynamic and multifunctional genetic entity with far-reaching implications in cancer pathogenesis and beyond. Further research is essential to unravel the molecular pathways of eccDNA formation, elucidate its functional roles, and explore its clinical applications. Addressing these aspects is crucial for advancing our understanding of genomic instability and developing novel strategies for tailored therapeutics, especially in cancer.
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Affiliation(s)
- Panagiotis Tsiakanikas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Konstantina Athanasopoulou
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Ioanna A. Darioti
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Vasiliki Taxiarchoula Agiassoti
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Stamatis Theocharis
- First Department of Pathology, Medical School, National and Kapodistrian University of Athens, 15772 Athens, Greece; (V.T.A.)
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panagiotis G. Adamopoulos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
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Kaur S, Mendonca P, Soliman KFA. The Anticancer Effects and Therapeutic Potential of Kaempferol in Triple-Negative Breast Cancer. Nutrients 2024; 16:2392. [PMID: 39125273 PMCID: PMC11314279 DOI: 10.3390/nu16152392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/16/2024] [Accepted: 07/21/2024] [Indexed: 08/12/2024] Open
Abstract
Breast cancer is the second-leading cause of cancer death among women in the United States. Triple-negative breast cancer (TNBC), a subtype of breast cancer, is an aggressive phenotype that lacks estrogen (ER), progesterone (PR), and human epidermal growth (HER-2) receptors, which is challenging to treat with standardized hormonal therapy. Kaempferol is a natural flavonoid with antioxidant, anti-inflammatory, neuroprotective, and anticancer effects. Besides anti-tumorigenic, antiproliferative, and apoptotic effects, kaempferol protects non-cancerous cells. Kaempferol showed anti-breast cancer effects by inducing DNA damage and increasing caspase 3, caspase 9, and pAMT expression, modifying ROS production by Nrf2 modulation, inducing apoptosis by increasing cleaved PARP and Bax and downregulating Bcl-2 expression, inducing cell cycle arrest at the G2/M phase; inhibiting immune evasion by modulating the JAK-STAT3 pathway; and inhibiting the angiogenic and metastatic potential of tumors by downregulating MMP-3 and MMP-9 levels. Kaempferol holds promise for boosting the efficacy of anticancer agents, complementing their effects, or reversing developed chemoresistance. Exploring novel TNBC molecular targets with kaempferol could elucidate its mechanisms and identify strategies to overcome limitations for clinical application. This review summarizes the latest research on kaempferol's potential as an anti-TNBC agent, highlighting promising but underexplored molecular pathways and delivery challenges that warrant further investigation to achieve successful clinical translation.
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Affiliation(s)
- Sukhmandeep Kaur
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL 32307, USA;
| | - Patricia Mendonca
- Department of Biology, College of Science and Technology, Florida A&M University, Tallahassee, FL 32307, USA
| | - Karam F. A. Soliman
- Division of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Institute of Public Health, Florida A&M University, Tallahassee, FL 32307, USA;
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8
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Li Z, Qian D. Extrachromosomal circular DNA (eccDNA): from carcinogenesis to drug resistance. Clin Exp Med 2024; 24:83. [PMID: 38662139 PMCID: PMC11045593 DOI: 10.1007/s10238-024-01348-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/03/2024] [Indexed: 04/26/2024]
Abstract
Extrachromosomal circular DNA (eccDNA) is a circular form of DNA that exists outside of the chromosome. Although it has only been a few decades since its discovery, in recent years, it has been found to have a close relationship with cancer, which has attracted widespread attention from researchers. Thus far, under the persistent research of researchers from all over the world, eccDNA has been found to play an important role in a variety of tumors, including breast cancer, lung cancer, ovarian cancer, etc. Herein, we review the sources of eccDNA, classifications, and the mechanisms responsible for their biogenesis. In addition, we introduce the relationship between eccDNA and various cancers and the role of eccDNA in the generation and evolution of cancer. Finally, we summarize the research significance and importance of eccDNA in cancer, and highlight new prospects for the application of eccDNA in the future detection and treatment of cancer.
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Affiliation(s)
- Zhaoxing Li
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China
| | - Daohai Qian
- Department of Hepatobiliary Surgery, Yijishan Hospital of Wannan Medical College, Wuhu, China.
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9
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Deng E, Fan X. Categorizing Extrachromosomal Circular DNA as Biomarkers in Serum of Cancer. Biomolecules 2024; 14:488. [PMID: 38672504 PMCID: PMC11048305 DOI: 10.3390/biom14040488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 04/07/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA), a double-stranded circular DNA molecule found in multiple organisms, has garnered an increasing amount of attention in recent years due to its close association with the initiation, malignant progression, and heterogeneous evolution of cancer. The presence of eccDNA in serum assists in non-invasive tumor diagnosis as a biomarker that can be assessed via liquid biopsies. Furthermore, the specific expression patterns of eccDNA provide new insights into personalized cancer therapy. EccDNA plays a pivotal role in tumorigenesis, development, diagnosis, and treatment. In this review, we comprehensively outline the research trajectory of eccDNA, discuss its role as a diagnostic and prognostic biomarker, and elucidate its regulatory mechanisms in cancer. In particular, we emphasize the potential application value of eccDNA in cancer diagnosis and treatment and anticipate the development of novel tumor diagnosis strategies based on serum eccDNA in the future.
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Affiliation(s)
- Enze Deng
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
| | - Xiaoying Fan
- Guangzhou National Laboratory, No. 9 XingDaoHuanBei Road, Guangzhou International Bio Island, Guangzhou 510005, China
- GMU-GIBH Joint School of Life Sciences, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510005, China
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10
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Zuo S, Li X, Yang Y, Zhou J, He Q. A Quick Method to Synthesize Extrachromosomal Circular DNA In Vitro. Molecules 2023; 28:molecules28104236. [PMID: 37241975 DOI: 10.3390/molecules28104236] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/29/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
Extrachromosomal circular DNA (eccDNA) is a special class of circular DNA in eukaryotes. Recent studies have suggested that eccDNA is the product of genomic instability and has important biological functions to regulate many downstream biological processes. While NGS (Next-Generation Sequencing)-based eccDNA sequencing has led to the identification of many eccDNAs in both healthy and diseased tissues, the specific biological functions of individual eccDNAs have yet to be clearly elucidated. Synthesizing eccDNAs longer than 1 kb with specific sequences remains a major challenge in the field, which has hindered our ability to fully understand their functions. Current methods for synthesizing eccDNAs primarily rely on chemical oligo synthesis, ligation, or the use of a specific gene editing and recombination systems. Therefore, these methods are often limited by the length of eccDNAs and are complex, expensive, as well as time-consuming. In this study, we introduce a novel method named QuickLAMA (Ligase-Assisted Minicircle Accumulation) for rapidly synthesizing eccDNAs up to 2.6 kb using a simple PCR and ligation approach. To validate the efficacy of our method, we synthesized three eccDNAs of varying lengths from cancer tissue and PC3 cells and confirmed successful circularization through sequencing and restriction enzyme digestion. Additional analyses have demonstrated that this method is highly efficient, cost-effective, and time-efficient, with good reproducibility. Using the method, a well-trained molecular biologist can synthesize and purify multiple eccDNAs within a single day, and it can be easily standardized and processed in a high-throughput manner, indicating the potential of the method to produce a wide range of desired eccDNAs and promote the translation of eccDNA research into clinical applications.
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Affiliation(s)
- Shanru Zuo
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha 410013, China
| | - Xueguang Li
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Yide Yang
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Junhua Zhou
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
| | - Quanyuan He
- The Key Laboratory of Model Animals and Stem Cell Biology in Hunan Province, School of Medicine, Hunan Normal University, Changsha 410013, China
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Luo J, Li Y, Zhang T, Xv T, Chen C, Li M, Qiu Q, Song Y, Wan S. Extrachromosomal circular DNA in cancer drug resistance and its potential clinical implications. Front Oncol 2023; 12:1092705. [PMID: 36793345 PMCID: PMC9923117 DOI: 10.3389/fonc.2022.1092705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/28/2022] [Indexed: 01/31/2023] Open
Abstract
Chemotherapy is widely used to treat patients with cancer. However, resistance to chemotherapeutic drugs remains a major clinical concern. The mechanisms of cancer drug resistance are extremely complex and involve such factors such as genomic instability, DNA repair, and chromothripsis. A recently emerging area of interest is extrachromosomal circular DNA (eccDNA), which forms owing to genomic instability and chromothripsis. eccDNA exists widely in physiologically healthy individuals but also arises during tumorigenesis and/or treatment as a drug resistance mechanism. In this review, we summarize the recent progress in research regarding the role of eccDNA in the development of cancer drug resistance as well as the mechanisms thereof. Furthermore, we discuss the clinical applications of eccDNA and propose some novel strategies for characterizing drug-resistant biomarkers and developing potential targeted cancer therapies.
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Affiliation(s)
- Juanjuan Luo
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China,China Medical University, Shenyang, China, Ganzhou, China
| | - Ying Li
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Tangxuan Zhang
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Tianhan Xv
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Chao Chen
- Department of Interventional Radiology, The People’s Hospital of Ganzhou City, Ganzhou, China
| | - Mengting Li
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Qixiang Qiu
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China
| | - Yusheng Song
- Department of Interventional Radiology, The People’s Hospital of Ganzhou City, Ganzhou, China,*Correspondence: Shaogui Wan, ; Yusheng Song,
| | - Shaogui Wan
- Center for Molecular Pathology, Department of Basic Medicine, Gannan Medical University, Ganzhou, China,China Medical University, Shenyang, China, Ganzhou, China,*Correspondence: Shaogui Wan, ; Yusheng Song,
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Sun H, Lu X, Zou L. EccBase: A high-quality database for exploration and characterization of extrachromosomal circular DNAs in cancer. Comput Struct Biotechnol J 2023; 21:2591-2601. [PMID: 37114214 PMCID: PMC10126927 DOI: 10.1016/j.csbj.2023.04.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 04/13/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) are widely observed in eukaryotes. Previous studies have demonstrated that eccDNAs are essential to cancer progression, and found that they can not only express in normal cells to regulate RNA, but also function differently in different tissues. It is of major interest to conduct computational or experiments assay to elucidate the mechanisms of eccDNA function, uncover key eccDNAs associated with diseases, and even develop related algorithms for liquid biopsy. Naturally, a comprehensive eccDNAs data resource is urgently needed to provide annotation and analysis more in-depth research. In this study, we constructed the eccBase (http://www.eccbase.net) in literature curation and database retrieval, which was the first database mainly collecting eccDNAs from Homo sapiens (n = 754,391) and Mus musculus (n = 481,381). Homo sapiens eccDNAs were taken from 50 kinds of cancer tissue and/or cell line, and 5 kinds of healthy tissues. The Mus musculus eccDNAs were sourced from 13 kinds of healthy tissue and/or cell line. We thoroughly annotated all eccDNA molecules in terms of basic information, genomic composition, regulatory elements, epigenetic modifications, and raw data. EccBase provided users with the ability to browse, search, download for targets of interest, as well as similarity alignment by the integrated BLAST. Further, comparative analysis suggested the cancer eccDNA is composed of nucleosomes and is prominently derived from the gene-dense regions. We also initially revealed that eccDNAs are strongly tissue-specific. In short, we have started a robust database for eccDNA resource utilization, which may facilitate studying the role of eccDNA in cancer development and therapy, cell function maintenance, and tissue differentiation.
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Affiliation(s)
- Haiyang Sun
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 300350 Tianjin, China
- Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, 518102 Shenzhen, China
| | - Xinyi Lu
- State Key Laboratory of Medicinal Chemical Biology, Nankai University, 300350 Tianjin, China
| | - Lingyun Zou
- Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing Key Laboratory of Emergency Medicine, Chongqing University Central Hospital, Chongqing University, 400014 Chongqing, China
- Shenzhen Baoan Women’s and Children’s Hospital, Jinan University, 518102 Shenzhen, China
- Corresponding author at: Department of Clinical Data Research, Chongqing Emergency Medical Center, Chongqing Key Laboratory of Emergency Medicine, Chongqing University Central Hospital, Chongqing University, 400014 Chongqing, China.
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