Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

doi:10.1002/ctm2.817

	Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs
	Lv, Wei 2,3; Pan, Xiaoguang 4; Han, Peng 4,5; Wang, Ziyu 4,6; Feng, Weijia 5; Xing, Xue 7; Wang, Qingqing 2,8; Qu, Kunli 4,5; Zeng, Yuchen 3,9; Zhang, Cailin 7
刊名	CLINICAL AND TRANSLATIONAL MEDICINE
	2022-04-01
卷号	12
关键词	cell-free DNA chronic kidney disease early diagnosis extrachromosomal circular DNA miRNA next generation sequencing noninvasive biomarkers
ISSN号	2001-1326
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.
资助项目	China National GeneBank ; Qingdao-Europe Advanced Institute for Life Sciences ; European Union[899417]
WOS关键词	MISMATCH REPAIR ; MICRORNAS ; PLASMA ; DIAGNOSIS ; MICRODNAS ; ORIGIN
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
内容类型	期刊论文
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.Aarhus Univ, Dept Biomed, Aarhus, Denmark 2.Univ Chinese Acad Sci, Coll Life Sci, Beijing, Peoples R China 3.Chinese Acad Sci, IBMC BGI Ctr, Canc Hosp, Univ Chinese Acad Sci,Zhejiang Canc Hosp,Inst Bas, Hangzhou 310022, Zhejiang, Peoples R China 4.BGI Qingdao, Qingdao Europe Adv Inst Life Sci, Lars Bolund Inst Regenerat Med, Qingdao, Peoples R China 5.Univ Copenhagen, Dept Biol, Ecol & Evolut, Copenhagen, Denmark 6.Qingdao Univ, Sch Basic Med, Dept Biochem & Mol Biol, Qingdao, Shandong, Peoples R China 7.Huazhong Univ Sci & Technol, Tongji Hosp, Dept Nephrol, Tongji Med Coll, Wuhan, Peoples R China 8.Chinese Acad Sci, Beijing Inst Life Sci, Beijing, Peoples R China 9.Tianjin Univ, Coll Life Sci, Tianjin, Peoples R China 10.Univ Copenhagen, GLOBE Inst, Sect GeoGenet, Copenhagen, Denmark
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).