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

doi:10.1016/j.isci.2022.104554

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

iScience. 2022 Jun 8;25(7):104554. doi: 10.1016/j.isci.2022.104554. eCollection 2022 Jul 15.

Authors

Affiliations

¹ School of Dentistry, University of California, Los Angeles, CA 90095, USA.
² Department of Molecular, Cellular & Developmental Biology, University of California, Los Angeles, CA 90095, USA.
³ Center of Applied Nanomedicine, National Cheng Kung University, Tainan 704, Taiwan.
⁴ The Samsung Advanced Institute for Health Sciences & Technology (SAIHST), Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 06355, Republic of Korea.
⁵ Department of Pathology, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
⁶ Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.

Abstract

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.

Keywords: Biological sciences; Biological sciences research methodologies; Biology experimental methods; Cell biology; Molecular biology; Molecular biology experimental approach.

Abstract

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