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Yu J, Zhang H, Han P, Jiang X, Li J, Li B, Yang S, He C, Mao S, Dang Y, Xiang X. Circle-seq based method for eccDNA synthesis and its application as a canonical promoter independent vector for robust microRNA overexpression. Comput Struct Biotechnol J 2024; 23:358-368. [PMID: 38223344 PMCID: PMC10788182 DOI: 10.1016/j.csbj.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/05/2023] [Accepted: 12/15/2023] [Indexed: 01/16/2024] Open
Abstract
Extrachromosomal circular DNA (eccDNA) has recently gained increasing attention due to its significant role in cancer and other pathophysiologic states. The majority of circular DNAs detected by Circle-seq are small-size eccDNAs with enigmatic functions. One major technical hurdle is to synthesize eccDNA for functional identification. Here, we describe CAES (Circle-seq based Artificial EccDNA Synthesis), a promising and reliable method for artificial eccDNA synthesis. Eight eccDNAs carrying different microRNA genes (eccMIR) found in gastric cancer tissues, ranging from 329 bp to 2189 bp in size, were created utilizing the CAES method. Exonuclease V and single restriction-endonuclease digestion identified the circular structure of synthetic eccDNAs. The DNA circularization efficiency afforded by CAES ranged from 15.6% to 31.1%, which was negatively correlated with the eccDNA length. In addition, we demonstrated that CAES-synthesized eccMIRs can express both miRNA-3p and - 5p molecules efficiently independent of a canonical promoter in human cell lines. Further assays proved that these eccMIRs were functional as they were able to repress the luciferase gene containing a miRNA-target sequence in the 3'UTR as well as the endogenous mRNA targets. Finally, kinetics study revealed that eccDNA exhibited a decay rate similar to the standard plasmids and linear DNA in cultured cells. Together, this study offers a rapid and convenient method for Circle-seq users to synthesize artificial eccDNAs. It also demonstrates the promising potential of eccMIR as a bacterial DNA-free vector for safe and robust miRNA overexpression in both basic research and therapeutic applications.
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Affiliation(s)
- Jiaying Yu
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Haoran Zhang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Peng Han
- Department of Biology, University of Copenhagen, Copenhagen 2200, Denmark
| | - Xianming Jiang
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jing Li
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Bo Li
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Shaohua Yang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
| | - Chunxiao He
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Shuang Mao
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yonghui Dang
- College of Medicine and Forensics, Xi'an Jiaotong University Health Science Center, Xi'an 710061, China
| | - Xi Xiang
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, the Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
- Guangdong Provincial Key Laboratory of Digestive Cancer Research, Guangdong–Hong Kong–Macau University Joint Laboratory of Digestive Cancer Research, Digestive Diseases Center, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518107, China
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Zhang C, Du Q, Zhou X, Qu T, Liu Y, Ma K, Shen Z, Wang Q, Zhang Z, Zhang R. Differential expression and analysis of extrachromosomal circular DNAs as serum biomarkers in pulmonary arterial hypertension. Respir Res 2024; 25:181. [PMID: 38664836 PMCID: PMC11046951 DOI: 10.1186/s12931-024-02808-z] [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: 10/29/2023] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Extrachromosomal circular DNAs (eccDNAs) have been reported to play a key role in the occurrence and development of various diseases. However, the characterization and role of eccDNAs in pulmonary arterial hypertension (PAH) remain unclear. METHODS In the discovery cohort, we first explored eccDNA expression profiles by Circle-sequencing analysis. The candidate eccDNAs were validated by routine polymerase chain reaction (PCR), TOPO-TA cloning and Sanger sequencing. In the validation cohort, 30 patients with PAH and 10 healthy controls were recruited for qPCR amplification to detect the candidate eccDNAs. Datas at the baseline were collected, including clinical background, biochemical variables, echocardiography and hemodynamic factors. Receiver operating characteristic curve was used to investigate the diagnostic effect of the eccDNA. RESULTS We identified a total of 21,741 eccDNAs in plasma samples of 3 IPAH patients and 3 individuals in good health, and the expression frequency, GC content, length distribution, and genome distribution of the eccDNAs were thoroughly characterized and analyzed. In the validation cohort, 687 eccDNAs were differentially expressed in patients with IPAH compared with healthy controls (screening threshold: |FC|≥2 and P < 0.05). Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that the specific eccDNAs in IPAH were significantly enriched in calcium channel activity, the mitogen-activated protein kinase pathway, and the wnt signaling pathway. Verification queue found that the expression of eccDNA-chr2:131208878-131,424,362 in PAH was considerably higher than that in healthy controls and exhibited a high level of accuracy in predicting PAH with a sensitivity of 86.67% and a specificity of 90%. Furthermore, correlation analysis disclosed a significant association between serum eccDNA-chr2:131208878-131,424,362 and mean pulmonary artery pressure (mPAP) (r = 0.396, P = 0.03), 6 min walking distance (6MWD) (r = -0.399, P = 0.029), N-terminal pro-B-type natriuretic peptide (NT-proBNP) (r = 0.685, P < 0.001) and cardiac index (CI) (r = - 0.419, P = 0.021). CONCLUSIONS This is the first study to identify and characterize eccDNAs in patients with PAH. We revealed that serum eccDNA-chr2:131208878-131,424,362 is significantly overexpressed and can be used in the diagnosis of PAH, indicating its potential as a novel non-invasive biomarker.
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Affiliation(s)
- Chun Zhang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Qiang Du
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Xiao Zhou
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Tianyu Qu
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Yingying Liu
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Kai Ma
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Ziling Shen
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Qun Wang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China
| | - Zaikui Zhang
- Center of Pathology and Clinical Laboratory, Sir Run Run Hospital, Nanjing Medical University, Nanjing, 210000, People's Republic of China
| | - Ruifeng Zhang
- Department of Respiratory Medicine, Zhongda Hospital of Southeast University, Dingjiaqiao 87, Nanjing City, Jiangsu Province, 210000, People's Republic of China.
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Xiang X, Pan X, Lv W, Chen S, Li J, Zhang H, Liao Y, Yu J, Li J, Dang Y, You Z, Wang L, Chen W, Han P, Tang J. Identification and functional analysis of circulating extrachromosomal circular DNA in schizophrenia implicate its negative effect on the disorder. Clin Transl Med 2023; 13:e1488. [PMID: 37997514 PMCID: PMC10667620 DOI: 10.1002/ctm2.1488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 11/06/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023] Open
Affiliation(s)
- Xi Xiang
- Scientific Research CenterThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - Xiaoguang Pan
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Wei Lv
- College of Life SciencesUniversity of Chinese Academy of ScienceBeijingChina
| | - Shanshan Chen
- Department of PsychiatrySir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Jinguang Li
- Research Center for Mental Health and NeuroscienceWuhan Mental Health CenterWuhanChina
| | - Haoran Zhang
- College of Medicine and ForensicsXi'an Jiaotong University Health Science CenterXi'anChina
| | - Yanhui Liao
- Department of PsychiatrySir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Jiaying Yu
- Scientific Research CenterThe Seventh Affiliated Hospital of Sun Yat‐sen UniversityShenzhenChina
| | - Jing Li
- College of Medicine and ForensicsXi'an Jiaotong University Health Science CenterXi'anChina
| | - Yonghui Dang
- College of Medicine and ForensicsXi'an Jiaotong University Health Science CenterXi'anChina
| | - Zifan You
- Department of PsychiatrySir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Liangliang Wang
- Department of PsychiatrySir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Wei Chen
- Department of PsychiatrySir Run Run Shaw Hospital, Zhejiang University School of MedicineHangzhouChina
| | - Peng Han
- Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jinsong Tang
- Department of PsychiatrySir Run Run Shaw HospitalSchool of MedicineKey Laboratory of Medical Neurobiology of Zhejiang ProvinceHangzhouChina
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Di Vincenzo F, Yadid Y, Petito V, Emoli V, Masi L, Gerovska D, Araúzo-Bravo MJ, Gasbarrini A, Regenberg B, Scaldaferri F. Circular and Circulating DNA in Inflammatory Bowel Disease: From Pathogenesis to Potential Molecular Therapies. Cells 2023; 12:1953. [PMID: 37566032 PMCID: PMC10417561 DOI: 10.3390/cells12151953] [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: 06/19/2023] [Revised: 07/15/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023] Open
Abstract
Inflammatory bowel diseases (IBD), including Crohn's Disease (CD) and Ulcerative Colitis (UC) are chronic multifactorial disorders which affect the gastrointestinal tract with variable extent. Despite extensive research, their etiology and exact pathogenesis are still unknown. Cell-free DNAs (cfDNAs) are defined as any DNA fragments which are free from the origin cell and able to circulate into the bloodstream with or without microvescicles. CfDNAs are now being increasingly studied in different human diseases, like cancer or inflammatory diseases. However, to date it is unclear how IBD etiology is linked to cfDNAs in plasma. Extrachromosomal circular DNA (eccDNA) are non-plasmidic, nuclear, circular and closed DNA molecules found in all eukaryotes tested. CfDNAs appear to play an important role in autoimmune diseases, inflammatory processes, and cancer; recently, interest has also grown in IBD, and their role in the pathogenesis of IBD has been suggested. We now suggest that eccDNAs also play a role in IBD. In this review, we have comprehensively collected available knowledge in literature regarding cfDNA, eccDNA, and structures involving them such as neutrophil extracellular traps and exosomes, and their role in IBD. Finally, we focused on old and novel potential molecular therapies and drug delivery systems, such as nanoparticles, for IBD treatment.
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Affiliation(s)
- Federica Di Vincenzo
- IBD Unit, Centro di Malattie dell’Apparato Digerente (CeMAD), Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.D.V.); (L.M.); (A.G.); (F.S.)
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (Y.Y.); (V.E.)
| | - Ylenia Yadid
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (Y.Y.); (V.E.)
| | - Valentina Petito
- IBD Unit, Centro di Malattie dell’Apparato Digerente (CeMAD), Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.D.V.); (L.M.); (A.G.); (F.S.)
| | - Valeria Emoli
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (Y.Y.); (V.E.)
| | - Letizia Masi
- IBD Unit, Centro di Malattie dell’Apparato Digerente (CeMAD), Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.D.V.); (L.M.); (A.G.); (F.S.)
| | - Daniela Gerovska
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (M.J.A.-B.)
| | - Marcos Jesus Araúzo-Bravo
- Computational Biology and Systems Biomedicine, Biodonostia Health Research Institute, Calle Doctor Begiristain s/n, 20014 San Sebastian, Spain; (D.G.); (M.J.A.-B.)
- IKERBASQUE, Basque Foundation for Science, Calle María Díaz Harokoa 3, 48013 Bilbao, Spain
- Department of Cell Biology and Histology, Faculty of Medicine and Nursing, University of Basque Country (UPV/EHU), 48940 Leioa, Spain
| | - Antonio Gasbarrini
- IBD Unit, Centro di Malattie dell’Apparato Digerente (CeMAD), Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.D.V.); (L.M.); (A.G.); (F.S.)
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (Y.Y.); (V.E.)
| | - Birgitte Regenberg
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Universitetsparken 13, Room 426, DK-2100 Copenhagen, Denmark;
| | - Franco Scaldaferri
- IBD Unit, Centro di Malattie dell’Apparato Digerente (CeMAD), Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario “A. Gemelli” IRCCS, 00168 Rome, Italy; (F.D.V.); (L.M.); (A.G.); (F.S.)
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (Y.Y.); (V.E.)
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