TY - JOUR
T1 - Plasma contains ultrashort single-stranded DNA in addition to nucleosomal cell-free DNA
AU - Cheng, Jordan
AU - Morselli, Marco
AU - Huang, Wei Lun
AU - Heo, You Jeong
AU - Pinheiro-Ferreira, Thalyta
AU - Li, Feng
AU - Wei, Fang
AU - Chia, David
AU - Kim, Yong
AU - He, Hua Jun
AU - Cole, Kenneth D.
AU - Su, Wu Chou
AU - Pellegrini, Matteo
AU - Wong, David T.W.
N1 - Funding Information:
This work was supported by NIH grants UH2/UH3 CA206126, UH2/UH3 TR000923, UO1 CA233370, R21 CA239052, Spectrum Solutions 20212918 (DTWW), and the Canadian Institute of Health Research Doctoral Foreign Study Award, Tobacco Related Disease Research Program (TRDRP) Predoctoral Fellowship, Jonsson Comprehensive Cancer Center Predoctoral Fellowship, NCI F99CA26498-01, and UL1TR001881 (JC). Conceptualization, J.C. M.M. M.P. and D.T.W.W.; Data Curation, J.C. M.M. W.H. and T.P.; Formal Analysis, J.C. M.M. and Y.H.; Funding Acquisition, J.C. and D.T.W.W.; Investigation, J.C. M.M. M.P. and D.T.W.W.; Methodology, J.C. M.M. M.P. and D.T.W.W.; Project Administration, M.P. and D.T.W.W.; Resources, D.T.W.W; Software, J.C. and M.M.; Supervision, M.P. and D.T.W.W.; Visualization, J.C. Y.H. Y.K. and M.M.; Writing—Original Draft, J.C. and M.M.; Writing—Review and Editing, J.C. M.M. W.H. Y.H. T.P. F.L. F.W. D.C. Y.K. H.J. K.C. W.S. M.P. and D.T.W.W. All authors have read and agreed to the submitted version of the manuscript. David Wong is a consultant to GSK, Mars-Wrigley, and Colgate Palmolive and has equity in RNAmeTRIX and Liquid Diagnostics LLC. Patents regarding the extraction and sequencing of ultrashort single-stranded DNA have been filed.
Funding Information:
This work was supported by NIH grants UH2/UH3 CA206126 , UH2/UH3 TR000923 , UO1 CA233370 , R21 CA239052 , Spectrum Solutions 20212918 (DTWW), and the Canadian Institute of Health Research Doctoral Foreign Study Award, Tobacco Related Disease Research Program (TRDRP) Predoctoral Fellowship, Jonsson Comprehensive Cancer Center Predoctoral Fellowship, NCI F99CA26498-01 , and UL1TR001881 (JC).
Publisher Copyright:
© 2022
PY - 2022/7/15
Y1 - 2022/7/15
N2 - 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.
AB - 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.
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U2 - 10.1016/j.isci.2022.104554
DO - 10.1016/j.isci.2022.104554
M3 - Article
AN - SCOPUS:85133330129
SN - 2589-0042
VL - 25
JO - iScience
JF - iScience
IS - 7
M1 - 104554
ER -