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

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  • Wei Lv
  • Ziyu Wang
  • Xue Xing
  • Qingqing Wang
  • Yuchen Zeng
  • Cailin Zhang
  • Zhe Xu
  • Yi Li
  • Tianyu Zheng
  • Ling Lin
  • Chengxun Liu
  • Xuemei Liu
  • Hanbo Li
  • Lars Bolund
  • Lin Lin
  • Xin Jin
  • Huanming Yang
  • Xiuqing Zhang
  • Tailang Yin
  • Fan He
  • Yonglun Luo

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.

Original languageEnglish
Article numbere817
JournalClinical and Translational Medicine
Issue number4
Number of pages16
Publication statusPublished - 2022

Bibliographical note

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

    Research areas

  • Biomarkers, DNA, DNA, Circular/genetics, Female, Genomics, Humans, Male, Renal Insufficiency, Chronic/diagnosis

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