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

Research output: Contribution to journalJournal articlepeer-review

Standard

Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. / Lv, Wei; Pan, Xiaoguang; Han, Peng; Wang, Ziyu; Feng, Weijia; Xing, Xue; Wang, Qingqing; Qu, Kunli; Zeng, Yuchen; Zhang, Cailin; Xu, Zhe; Li, Yi; Zheng, Tianyu; Lin, Ling; Liu, Chengxun; Liu, Xuemei; Li, Hanbo; Henriksen, Rasmus Amund; Bolund, Lars; Lin, Lin; Jin, Xin; Yang, Huanming; Zhang, Xiuqing; Yin, Tailang; Regenberg, Birgitte; He, Fan; Luo, Yonglun.

In: Clinical and Translational Medicine, Vol. 12, No. 4, e817, 2022.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Lv, W, Pan, X, Han, P, Wang, Z, Feng, W, Xing, X, Wang, Q, Qu, K, Zeng, Y, Zhang, C, Xu, Z, Li, Y, Zheng, T, Lin, L, Liu, C, Liu, X, Li, H, Henriksen, RA, Bolund, L, Lin, L, Jin, X, Yang, H, Zhang, X, Yin, T, Regenberg, B, He, F & Luo, Y 2022, 'Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs', Clinical and Translational Medicine, vol. 12, no. 4, e817. https://doi.org/10.1002/ctm2.817

APA

Lv, W., Pan, X., Han, P., Wang, Z., Feng, W., Xing, X., Wang, Q., Qu, K., Zeng, Y., Zhang, C., Xu, Z., Li, Y., Zheng, T., Lin, L., Liu, C., Liu, X., Li, H., Henriksen, R. A., Bolund, L., ... Luo, Y. (2022). Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. Clinical and Translational Medicine, 12(4), [e817]. https://doi.org/10.1002/ctm2.817

Vancouver

Lv W, Pan X, Han P, Wang Z, Feng W, Xing X et al. Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. Clinical and Translational Medicine. 2022;12(4). e817. https://doi.org/10.1002/ctm2.817

Author

Lv, Wei ; Pan, Xiaoguang ; Han, Peng ; Wang, Ziyu ; Feng, Weijia ; Xing, Xue ; Wang, Qingqing ; Qu, Kunli ; Zeng, Yuchen ; Zhang, Cailin ; Xu, Zhe ; Li, Yi ; Zheng, Tianyu ; Lin, Ling ; Liu, Chengxun ; Liu, Xuemei ; Li, Hanbo ; Henriksen, Rasmus Amund ; Bolund, Lars ; Lin, Lin ; Jin, Xin ; Yang, Huanming ; Zhang, Xiuqing ; Yin, Tailang ; Regenberg, Birgitte ; He, Fan ; Luo, Yonglun. / Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs. In: Clinical and Translational Medicine. 2022 ; Vol. 12, No. 4.

Bibtex

@article{dcace027eb0446e7bee2a9421c3c8713,
title = "Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs",
abstract = "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.",
keywords = "Biomarkers, DNA, DNA, Circular/genetics, Female, Genomics, Humans, Male, Renal Insufficiency, Chronic/diagnosis",
author = "Wei Lv and Xiaoguang Pan and Peng Han and Ziyu Wang and Weijia Feng and Xue Xing and Qingqing Wang and Kunli Qu and Yuchen Zeng and Cailin Zhang and Zhe Xu and Yi Li and Tianyu Zheng and Ling Lin and Chengxun Liu and Xuemei Liu and Hanbo Li and Henriksen, {Rasmus Amund} and Lars Bolund and Lin Lin and Xin Jin and Huanming Yang and Xiuqing Zhang and Tailang Yin and Birgitte Regenberg and Fan He and Yonglun Luo",
note = "{\textcopyright} 2022 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.",
year = "2022",
doi = "10.1002/ctm2.817",
language = "English",
volume = "12",
journal = "Clinical and Translational Medicine",
issn = "2001-1326",
publisher = "SpringerOpen",
number = "4",

}

RIS

TY - JOUR

T1 - Circle-Seq reveals genomic and disease-specific hallmarks in urinary cell-free extrachromosomal circular DNAs

AU - Lv, Wei

AU - Pan, Xiaoguang

AU - Han, Peng

AU - Wang, Ziyu

AU - Feng, Weijia

AU - Xing, Xue

AU - Wang, Qingqing

AU - Qu, Kunli

AU - Zeng, Yuchen

AU - Zhang, Cailin

AU - Xu, Zhe

AU - Li, Yi

AU - Zheng, Tianyu

AU - Lin, Ling

AU - Liu, Chengxun

AU - Liu, Xuemei

AU - Li, Hanbo

AU - Henriksen, Rasmus Amund

AU - Bolund, Lars

AU - Lin, Lin

AU - Jin, Xin

AU - Yang, Huanming

AU - Zhang, Xiuqing

AU - Yin, Tailang

AU - Regenberg, Birgitte

AU - He, Fan

AU - Luo, Yonglun

N1 - © 2022 The Authors. Clinical and Translational Medicine published by John Wiley & Sons Australia, Ltd on behalf of Shanghai Institute of Clinical Bioinformatics.

PY - 2022

Y1 - 2022

N2 - 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.

AB - 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.

KW - Biomarkers

KW - DNA

KW - DNA, Circular/genetics

KW - Female

KW - Genomics

KW - Humans

KW - Male

KW - Renal Insufficiency, Chronic/diagnosis

U2 - 10.1002/ctm2.817

DO - 10.1002/ctm2.817

M3 - Journal article

C2 - 35474296

VL - 12

JO - Clinical and Translational Medicine

JF - Clinical and Translational Medicine

SN - 2001-1326

IS - 4

M1 - e817

ER -

ID: 307748262