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In plasma, ultrashort single-stranded cfDNA (uscfDNA, \u223c50 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 \u20185mCAdpBS-Seq\u2019 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 (\u223c15%) 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\u00a0genes\u00a0of 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.<\/jats:p>","DOI":"10.1093\/nar\/gkae276","type":"journal-article","created":{"date-parts":[[2024,5,27]],"date-time":"2024-05-27T00:02:13Z","timestamp":1716768133000},"page":"e50-e50","source":"Crossref","is-referenced-by-count":8,"title":["Single-stranded pre-methylated 5mC adapters uncover the methylation profile of plasma ultrashort Single-stranded cell-free DNA"],"prefix":"10.1093","volume":"52","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5352-4017","authenticated-orcid":false,"given":"Jordan C","family":"Cheng","sequence":"first","affiliation":[{"name":"School of Dentistry, University of California , Los Angeles , Los Angeles , CA\u00a0 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Neeti","family":"Swarup","sequence":"additional","affiliation":[{"name":"School of Dentistry, University of California , Los Angeles , Los Angeles , CA\u00a0 90095 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CA\u00a0 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yong","family":"Kim","sequence":"additional","affiliation":[{"name":"School of Dentistry, University of California , Los Angeles , Los Angeles , CA\u00a0 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Li","sequence":"additional","affiliation":[{"name":"School of Dentistry, University of California , Los Angeles , Los Angeles , CA\u00a0 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fang","family":"Wei","sequence":"additional","affiliation":[{"name":"School of Dentistry, University of California , Los Angeles , Los Angeles , CA\u00a0 90095 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noah","family":"Zaitlen","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine, University of California Los Angeles , Los Angeles , CA 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Genomics"},{"key":"2024112915041772900_B60","doi-asserted-by":"crossref","first-page":"1285","DOI":"10.1101\/gr.164418.113","article-title":"Nucleosome repositioning links DNA (de)methylation and differential CTCF binding during stem cell development","volume":"24","author":"Teif","year":"2014","journal-title":"Genome Res."},{"key":"2024112915041772900_B61","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1038\/nature16462","article-title":"Competition between DNA methylation and transcription factors determines binding of NRF1","volume":"528","author":"Domcke","year":"2015","journal-title":"Nature"},{"key":"2024112915041772900_B62","first-page":"473","article-title":"Quantitative characterization of tumor cell-free DNA shortening","volume":"21","author":"Guo","year":"2020","journal-title":"Bmc Genomics [Electronic Resource]"},{"key":"2024112915041772900_B63","doi-asserted-by":"crossref","first-page":"3885","DOI":"10.1038\/s41467-021-24198-2","article-title":"Promoter G-quadruplexes and transcription factors cooperate to shape the cell type-specific transcriptome","volume":"12","author":"Lago","year":"2021","journal-title":"Nat. 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Chem."},{"key":"2024112915041772900_B70","doi-asserted-by":"crossref","first-page":"2763","DOI":"10.3389\/fimmu.2018.02763","article-title":"Eosinophil extracellular traps and inflammatory pathologies\u2014untangling the web","volume":"9","author":"Mukherjee","year":"2018","journal-title":"Front. Immunol"},{"key":"2024112915041772900_B71","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1016\/j.alit.2020.09.002","article-title":"Eosinophils: cells known for over 140 years with broad and new functions","volume":"70","author":"Aoki","year":"2021","journal-title":"Allergol. Int."},{"key":"2024112915041772900_B72","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1073\/pnas.0710735105","article-title":"High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer","volume":"105","author":"Rauch","year":"2008","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2024112915041772900_B73","doi-asserted-by":"crossref","first-page":"296","DOI":"10.1139\/o05-036","article-title":"Causes and consequences of DNA hypomethylation in human cancer","volume":"83","author":"Hoffmann","year":"2005","journal-title":"Biochem. Cell Biol. Biochim. Biol. Cell."},{"key":"2024112915041772900_B74","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1016\/j.semcancer.2009.02.008","article-title":"DNA methylation patterns in lung carcinomas","volume":"19","author":"Pfeifer","year":"2009","journal-title":"Semin. Cancer Biol."},{"key":"2024112915041772900_B75","first-page":"1370","article-title":"Gene promoter hypermethylation in tumors and lymph nodes of stage I lung cancer patients","volume":"9","author":"Harden","year":"2003","journal-title":"Clin. 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Eng."},{"key":"2024112915041772900_B78","doi-asserted-by":"crossref","first-page":"7102","DOI":"10.1158\/0008-5472.CAN-04-1877","article-title":"Plakophilin 3 oncogene as prognostic marker and therapeutic target for lung cancer","volume":"65","author":"Furukawa","year":"2005","journal-title":"Cancer Res."},{"key":"2024112915041772900_B79","doi-asserted-by":"crossref","first-page":"441","DOI":"10.3892\/ol.2022.13561","article-title":"Cyclin B1 expression as an independent prognostic factor for lung adenocarcinoma and its potential pathways","volume":"24","author":"Li","year":"2022","journal-title":"Oncol. Lett."},{"key":"2024112915041772900_B80","doi-asserted-by":"crossref","first-page":"640","DOI":"10.1007\/s00535-022-01884-6","article-title":"Transcriptomic profiling on localized gastric cancer identified CPLX1 as a gene promoting malignant phenotype of gastric cancer and a predictor of recurrence after surgery and subsequent chemotherapy","volume":"57","author":"Tanaka","year":"2022","journal-title":"J. Gastroenterol."},{"key":"2024112915041772900_B81","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/j.gene.2017.10.020","article-title":"Characterization of germline mutations in familial lung cancer from the Chinese population","volume":"641","author":"Kanwal","year":"2018","journal-title":"Gene"},{"key":"2024112915041772900_B82","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1002\/ijc.29352","article-title":"Comprehensive characterization of the genomic alterations in human gastric cancer","volume":"137","author":"Cui","year":"2015","journal-title":"Int. J. 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Res."},{"key":"2024112915041772900_B84","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1186\/s13073-015-0228-1","article-title":"A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients","volume":"7","author":"Pongor","year":"2015","journal-title":"Genome Med"},{"key":"2024112915041772900_B85","doi-asserted-by":"crossref","first-page":"e21443","DOI":"10.1371\/journal.pone.0021443","article-title":"DNA methylation changes in Atypical adenomatous hyperplasia, adenocarcinoma In situ, and lung adenocarcinoma","volume":"6","author":"Selamat","year":"2011","journal-title":"PLoS One"},{"key":"2024112915041772900_B86","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.revmed.2005.02.013","article-title":"[Eosinophils and antitumour response]","volume":"26","author":"Costello","year":"2005","journal-title":"Rev. Med. 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