Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA

• Published in: Nucleic acids research Vol. 52; no. 11; p. e50
• Main Authors: Cheng, Jordan C, Swarup, Neeti, Morselli, Marco, Huang, Wei-Lun, Aziz, Mohammad, Caggiano, Christa, Kordi, Misagh, Patel, Abhijit A, Chia, David, Kim, Yong, Li, Feng, Wei, Fang, Zaitlen, Noah, Krysan, Kostyantyn, Dubinett, Steve, Pellegrini, Matteo, Wong, David T W
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 24.06.2024
• Subjects: 5-Methylcytosine - metabolism; Cell-Free Nucleic Acids - blood; Cell-Free Nucleic Acids - genetics; CpG Islands; DNA Methylation; DNA, Single-Stranded - blood; DNA, Single-Stranded - genetics; DNA, Single-Stranded - metabolism; Humans; Lung Neoplasms - blood; Lung Neoplasms - genetics; Methods; Promoter Regions, Genetic; Sequence Analysis, DNA - methods; Sulfites - chemistry; Whole Genome Sequencing - methods
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkae276

Whole-genome bisulfite sequencing (BS-Seq) measures cytosine methylation changes at single-base resolution and can be used to profile cell-free DNA (cfDNA). In plasma, ultrashort single-stranded cfDNA (uscfDNA, ∼50 nt) has been identified together with 167 bp double-stranded mononucleosomal cell-free DNA (mncfDNA). However, the methylation profile of uscfDNA has not been described. Conventional BS-Seq workflows may not be helpful because bisulfite conversion degrades larger DNA into smaller fragments, leading to erroneous categorization as uscfDNA. We describe the '5mCAdpBS-Seq' workflow in which pre-methylated 5mC (5-methylcytosine) single-stranded adapters are ligated to heat-denatured cfDNA before bisulfite conversion. This method retains only DNA fragments that are unaltered by bisulfite treatment, resulting in less biased uscfDNA methylation analysis. Using 5mCAdpBS-Seq, uscfDNA had lower levels of DNA methylation (∼15%) compared to mncfDNA and was enriched in promoters and CpG islands. Hypomethylated uscfDNA fragments were enriched in upstream transcription start sites (TSSs), and the intensity of enrichment was correlated with expressed genes of hemopoietic cells. Using tissue-of-origin deconvolution, we inferred that uscfDNA is derived primarily from eosinophils, neutrophils, and monocytes. As proof-of-principle, we show that characteristics of the methylation profile of uscfDNA can distinguish non-small cell lung carcinoma from non-cancer samples. The 5mCAdpBS-Seq workflow is recommended for any cfDNA methylation-based investigations.