{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T04:45:40Z","timestamp":1791002740697,"version":"4.1.0"},"reference-count":56,"publisher":"Wiley","issue":"3","license":[{"start":{"date-parts":[[2024,11,26]],"date-time":"2024-11-26T00:00:00Z","timestamp":1732579200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Eur J Clin Investigation"],"published-print":{"date-parts":[[2025,3]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Placental\u2010originated cell\u2010free DNA (cfDNA) provides unique opportunities to study (epi)genetic placental programming remotely, but studies investigating the cfDNA methylome are scarce and usually technologically challenging. Methylated DNA sequencing (MeD\u2010seq) is well compatible with low cfDNA concentrations and has a high genome\u2010wide coverage. We therefore aim to investigate the feasibility of genome\u2010wide methylation profiling of first trimester maternal cfDNA using MeD\u2010seq, by identifying placental\u2010specific methylation marks in cfDNA.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We collected cfDNA from nonpregnant controls (female <jats:italic>n<\/jats:italic>\u2009=\u20096, male <jats:italic>n<\/jats:italic>\u2009=\u200912) and pregnant women (<jats:italic>n<\/jats:italic>\u2009=\u200910), first trimester placentas (<jats:italic>n<\/jats:italic>\u2009=\u200910), and paired preconceptional and first trimester buffy coats (total <jats:italic>n<\/jats:italic>\u2009=\u200920). Differentially methylated regions (DMRs) were identified between pregnant and nonpregnant women. We investigated placental\u2010specific markers in maternal cfDNA, including <jats:italic>RASSF1<\/jats:italic> promoter and Y\u2010chromosomal methylation, and studied overlap with placental and buffy coat DNA methylation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We identified 436 DMRs between cfDNA from pregnant and nonpregnant women, which were validated using male cfDNA. <jats:italic>RASSF1<\/jats:italic> promoter methylation was higher in maternal cfDNA (fold change 2.87, unpaired <jats:italic>t<\/jats:italic>\u2010test <jats:italic>p<\/jats:italic>\u2009&lt;\u2009.0001). Differential methylation of Y\u2010chromosomal sequences could determine fetal sex. DMRs in maternal cfDNA showed large overlap with DNA methylation of these regions in placentas and buffy coats. Sixteen DMRs in maternal cfDNA were specifically found only in placentas. These novel potential placental\u2010specific DMRs were more prominent than <jats:italic>RASSF1<\/jats:italic>.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>MeD\u2010seq can detect (novel) genome\u2010wide placental DNA methylation marks and determine fetal sex in maternal cfDNA. Our results indicate a placental and immune\u2010cell contribution to the pregnancy\u2010specific cfDNA methylation signature. This study supports future research into maternal cfDNA methylation.<\/jats:p><\/jats:sec>","DOI":"10.1111\/eci.14363","type":"journal-article","created":{"date-parts":[[2024,11,26]],"date-time":"2024-11-26T17:10:06Z","timestamp":1732641006000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Genome\u2010wide methylation profiling of maternal cell\u2010free <scp>DNA<\/scp> using methylated <scp>DNA<\/scp> sequencing (<scp>MeD<\/scp>\u2010seq) indicates a placental and immune\u2010cell signature"],"prefix":"10.1111","volume":"55","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5476-037X","authenticated-orcid":false,"given":"Marjolein M.","family":"van Vliet","sequence":"first","affiliation":[{"name":"Department of Obstetrics and Gynaecology Erasmus MC  Rotterdam The Netherlands"},{"name":"Department of Developmental Biology Erasmus MC  Rotterdam The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruben G.","family":"Boers","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology Erasmus MC  Rotterdam The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joachim B.","family":"Boers","sequence":"additional","affiliation":[{"name":"Department of Developmental Biology Erasmus MC  Rotterdam The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olivier J. M.","family":"Sch\u00e4ffers","sequence":"additional","affiliation":[{"name":"Department of Obstetrics and Gynaecology Erasmus MC  Rotterdam The Netherlands"},{"name":"Department of Developmental Biology Erasmus MC  Rotterdam The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lotte E.","family":"van der Meeren","sequence":"additional","affiliation":[{"name":"Department of Pathology Erasmus Medical Centre Rotterdam  Rotterdam The Netherlands"},{"name":"Department of Pathology Leiden University Medical Center  Leiden The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4353-5756","authenticated-orcid":false,"given":"R\u00e9gine P. 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