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
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.
