Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA

Jordan Cheng; Marco Morselli; Wei-Lun Huang; You Jeong Heo; Thalyta Pinheiro-Ferreira; Feng Li; Fang Wei; David Chia; Yong Kim; Hua-Jun He; Kenneth D. Cole; Wu-Chou Su; Matteo Pellegrini; David T.W. Wong

iScience (Jul 2022)

Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA

Jordan Cheng,
Marco Morselli,
Wei-Lun Huang,
You Jeong Heo,
Thalyta Pinheiro-Ferreira,
Feng Li,
Fang Wei,
David Chia,
Yong Kim,
Hua-Jun He,
Kenneth D. Cole,
Wu-Chou Su,
Matteo Pellegrini,
David T.W. Wong

Affiliations

Jordan Cheng: School of Dentistry, University of California, Los Angeles, CA 90095, USA
Marco Morselli: Department of Molecular, Cellular & Developmental Biology, University of California, Los Angeles, CA 90095, USA
Wei-Lun Huang: Center of Applied Nanomedicine, National Cheng Kung University, Tainan 704, Taiwan
You Jeong Heo: School of Dentistry, University of California, Los Angeles, CA 90095, USA; The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea
Thalyta Pinheiro-Ferreira: School of Dentistry, University of California, Los Angeles, CA 90095, USA
Feng Li: School of Dentistry, University of California, Los Angeles, CA 90095, USA
Fang Wei: School of Dentistry, University of California, Los Angeles, CA 90095, USA
David Chia: Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
Yong Kim: School of Dentistry, University of California, Los Angeles, CA 90095, USA
Hua-Jun He: Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
Kenneth D. Cole: Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
Wu-Chou Su: Center of Applied Nanomedicine, National Cheng Kung University, Tainan 704, Taiwan
Matteo Pellegrini: Department of Molecular, Cellular & Developmental Biology, University of California, Los Angeles, CA 90095, USA; Corresponding author
David T.W. Wong: School of Dentistry, University of California, Los Angeles, CA 90095, USA; Corresponding author

Journal volume & issue: Vol. 25, no. 7
p. 104554

Abstract

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Summary: Plasma cell-free DNA is being widely explored as a biomarker for clinical screening. Currently, methods are optimized for the extraction and detection of double-stranded mononucleosomal cell-free DNA of ∼160bp in length. We introduce uscfDNA-seq, a single-stranded cell-free DNA next-generation sequencing pipeline, which bypasses previous limitations to reveal a population of ultrashort single-stranded cell-free DNA in human plasma. This species has a modal size of 50nt and is distinctly separate from mononucleosomal cell-free DNA. Treatment with single-stranded and double-stranded specific nucleases suggests that ultrashort cell-free DNA is primarily single-stranded. It is distributed evenly across chromosomes and has a similar distribution profile over functional elements as the genome, albeit with an enrichment over promoters, exons, and introns, which may be suggestive of a terminal state of genome degradation. The examination of this cfDNA species could reveal new features of cell death pathways or it can be used for cell-free DNA biomarker discovery.

Published in iScience

ISSN: 2589-0042 (Online)
Publisher: Elsevier
Country of publisher: United States
LCC subjects: Science
Website: http://www.cell.com/iscience/home

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