Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs
文献类型：期刊论文
| 作者 | Lv, Wei1,2; Pan, Xiaoguang3; Han, Peng3,4; Wang, Ziyu3,5; Feng, Weijia4; Xing, Xue6; Wang, Qingqing1,7; Qu, Kunli3,4; Zeng, Yuchen2,8; Zhang, Cailin6 |
| 刊名 | CLINICAL AND TRANSLATIONAL MEDICINE
 |
| 出版日期 | 2022-04-01 |
| 卷号 | 12 |
| ISSN号 | 2001-1326 |
| 关键词 | cell-free DNA chronic kidney disease early diagnosis extrachromosomal circular DNA miRNA next generation sequencing noninvasive biomarkers |
| DOI | 10.1002/ctm2.817 |
| 通讯作者 | He, Fan(fhe@tjh.tjmu.edu.cn) ; Luo, Yonglun(alun@biomed.au.dk) |
| 英文摘要 | Background Extrachromosomal circular deoxyribonucleic acid (eccDNA) is evolving as a valuable biomarker, while little is known about its presence in urine. Methods Here, we report the discovery and analysis of urinary cell-free eccDNAs (ucf-eccDNAs) in healthy controls and patients with advanced chronic kidney disease (CKD) by Circle-Seq. Results Millions of unique ucf-eccDNAs were identified and comprehensively characterised. The ucf-eccDNAs are GC-rich. Most ucf-eccDNAs are less than 1000 bp and are enriched in four pronounced peaks at 207, 358, 553 and 732 bp. Analysis of the genomic distribution of ucf-eccDNAs shows that eccDNAs are found on all chromosomes but enriched on chromosomes 17, 19 and 20 with a high density of protein-coding genes, CpG islands, short interspersed transposable elements (SINEs) and simple repeat elements. Analysis of eccDNA junction sequences further suggests that microhomology and palindromic repeats might be involved in eccDNA formation. The ucf-eccDNAs in CKD patients are significantly higher than those in healthy controls. Moreover, eccDNA with miRNA genes is highly enriched in CKD ucf-eccDNA. Conclusions This work discovers and provides the first deep characterisation of ucf-eccDNAs and suggests ucf-eccDNA as a valuable noninnvasive biomarker for urogenital disorder diagnosis and monitoring. |
| WOS关键词 | MISMATCH REPAIR ; MICRORNAS ; PLASMA ; DIAGNOSIS ; MICRODNAS ; ORIGIN |
| 资助项目 | China National GeneBank ; Qingdao-Europe Advanced Institute for Life Sciences ; European Union[899417] |
| WOS研究方向 | Oncology ; Research & Experimental Medicine |
| 语种 | 英语 |
| 出版者 | JOHN WILEY & SONS LTD |
| WOS记录号 | WOS:000787537800001 |
| 资助机构 | China National GeneBank ; Qingdao-Europe Advanced Institute for Life Sciences ; European Union |
| 源URL | [http://ir.hfcas.ac.cn:8080/handle/334002/131478]  |
| 专题 | 中国科学院合肥物质科学研究院 |
| 通讯作者 | He, Fan; Luo, Yonglun |
| 作者单位 | 1.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China 2.Chinese Acad Sci, IBMC BGI Ctr, Canc Hosp, Univ Chinese Acad Sci,Zhejiang Canc Hosp,Inst Bas, Hangzhou 310022, Zhejiang, Peoples R China 3.BGI Qingdao, Qingdao Europe Adv Inst Life Sci, Lars Bolund Inst Regenerat Med, Qingdao, Peoples R China 4.Univ Copenhagen, Dept Biol, Ecol & Evolut, Copenhagen, Denmark 5.Qingdao Univ, Sch Basic Med, Dept Biochem & Mol Biol, Qingdao, Shandong, Peoples R China 6.Huazhong Univ Sci & Technol, Tongji Hosp, Dept Nephrol, Tongji Med Coll, Wuhan, Peoples R China 7.Chinese Acad Sci, Beijing Inst Life Sci, Beijing, Peoples R China 8.Tianjin Univ, Coll Life Sci, Tianjin, Peoples R China 9.Univ Copenhagen, GLOBE Inst, Sect GeoGenet, Copenhagen, Denmark 10.BGI Shenzhen, Shenzhen, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lv, Wei,Pan, Xiaoguang,Han, Peng,et al. Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs[J]. CLINICAL AND TRANSLATIONAL MEDICINE,2022,12. |
| APA | Lv, Wei.,Pan, Xiaoguang.,Han, Peng.,Wang, Ziyu.,Feng, Weijia.,...&Luo, Yonglun.(2022).Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs.CLINICAL AND TRANSLATIONAL MEDICINE,12. |
| MLA | Lv, Wei,et al."Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs".CLINICAL AND TRANSLATIONAL MEDICINE 12(2022). |
入库方式： OAI收割
来源：合肥物质科学研究院
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