{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:28:11Z","timestamp":1785407291903,"version":"3.56.0"},"posted":{"date-parts":[[2025,9,20]]},"group-title":"Genomics","reference-count":47,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T00:00:00Z","timestamp":1758326400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"award":["R37CA259359"],"award-info":[{"award-number":["R37CA259359"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]},{"award":["R00GM140251"],"award-info":[{"award-number":["R00GM140251"]}],"id":[{"id":"https:\/\/ror.org\/04q48ey07","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,9,23]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>DNA methylation is altered in all cancers, but the mechanisms responsible for these changes are not well understood. Using data from 100 primary samples, we show that regions with intermediate methylation in normal hematopoietic cells are hotspots for stable, clonal epimutations in acute myeloid leukemia. Analysis of hematopoietic stem cell clones demonstrated that intermediate methylation at epimutation hotspots reflects random allele-specific methylation and expression at the single cell level, representing a previously unrecognized form of somatically acquired imprinting. We identified somatically imprinted regions in other tissues and show they are epimutation hotspots in other cancer types. This demonstrates that random allele-specific methylation is both a general property of normal cells, and a vulnerability that renders them susceptible to cooperating events and clonal selection during cancer.<\/jats:p>","DOI":"10.1101\/2025.09.18.677221","type":"posted-content","created":{"date-parts":[[2025,9,20]],"date-time":"2025-09-20T14:55:14Z","timestamp":1758380114000},"source":"Crossref","is-referenced-by-count":0,"title":["Intermediately Methylated Regions in Normal Cells Are Epimutation Hotspots in Cancer"],"prefix":"10.64898","author":[{"given":"Mohamed","family":"Mahgoub","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haley","family":"Abel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nidhi","family":"Davarapalli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Heidi","family":"Struthers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emilee","family":"Kotnik","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brittany","family":"Johnson","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christopher","family":"Markovic","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Catrina","family":"Fronick","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Robert","family":"Fulton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3438-3938","authenticated-orcid":false,"given":"Michael P.","family":"Meers","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5314-3043","authenticated-orcid":false,"given":"David H.","family":"Spencer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025092518450706000_2025.09.18.677221v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/301089a0"},{"key":"2025092518450706000_2025.09.18.677221v2.2","doi-asserted-by":"publisher","DOI":"10.1016\/S0006-291X(83)80115-6"},{"key":"2025092518450706000_2025.09.18.677221v2.3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/11.19.6883"},{"key":"2025092518450706000_2025.09.18.677221v2.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2017.01.021"},{"key":"2025092518450706000_2025.09.18.677221v2.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41375-021-01476-y"},{"key":"2025092518450706000_2025.09.18.677221v2.6","doi-asserted-by":"publisher","DOI":"10.1158\/2159-8290.CD-16-1032"},{"key":"2025092518450706000_2025.09.18.677221v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/nature26000"},{"key":"2025092518450706000_2025.09.18.677221v2.8","doi-asserted-by":"crossref","unstructured":"C. Koelsche , D. Schrimpf , D. Stichel , M. Sill , F. Sahm , D. E. Reuss , M. Blattner , B. Worst , C. E. Heilig , K. Beck , P. Horak , S. Kreutzfeldt , E. Paff , S. Stark , P. Johann , F. Selt , J. Ecker , D. Sturm , K. W. Pajtler , A. Reinhardt , A. K. Wefers , P. Sievers , A. Ebrahimi , A. Suwala , F. Fern\u00e1ndez-Klett , B. Casalini , A. Korshunov , V. Hovestadt , F. K. F. Kommoss , M. Kriegsmann , M. Schick , M. Bewerunge-Hudler , T. Milde , O. Witt , A. E. Kulozik , M. Kool , L. Romero-P\u00e9rez , T. G. P. Gr\u00fcnewald , T. Kirchner , W. Wick , M. Platten , A. Unterberg , M. Uhl , A. Abdollahi , J. Debus , B. Lehner , C. Thomas , M. Hasselblatt , W. Paulus , C. Hartmann , O. Staszewski , M. Prinz , J. Hench , S. Frank , Y. M. H. Versleijen-Jonkers , M. E. Weidema , T. Mentzel , K. Griewank , E. de \u00c1lava , J. D. Mart\u00edn , M. A. I. Gastearena , K. T.-E. Chang , S. Y. Y. Low , A. Cuevas-Bourdier , M. Mittelbronn , M. Mynarek , S. Rutkowski , U. Sch\u00fcller , V. F. Mautner , J. Schittenhelm , J. Serrano , M. Snuderl , R. B\u00fcttner , T. Klingebiel , R. Buslei , M. Gessler , P. Wesseling , W. N. M. Dinjens , S. Brandner , Z. Jaunmuktane , I. Lyskj\u00e6r , P. Schirmacher , A. Stenzinger , B. Brors , H. Glimm , C. Heining , O. M. Tirado , M. S\u00e1inz-Jaspeado , J. Mora , J. Alonso , X. G. del Muro , S. Moran , M. Esteller , J. K. Benhamida , M. Ladanyi , E. Wardelmann , C. Antonescu , A. Flanagan , U. Dirksen , P. Hohenberger , D. Baumhoer , W. Hartmann , C. Vokuhl , U. Flucke , I. Petersen , G. Mechtersheimer , D. Capper , D. T. W. Jones , S. Fr\u00f6hling , S. M. Pfister , A. von Deimling , Sarcoma classification by DNA methylation profiling. Nat. Commun. 12, 498 (2021).","DOI":"10.1038\/s41467-020-20603-4"},{"key":"2025092518450706000_2025.09.18.677221v2.9","doi-asserted-by":"crossref","unstructured":"B. Giacopelli , M. Wang , A. Cleary , Y.-Z. Wu , A. R. Schultz , M. Schmutz , J. S. Blachly , A.-K. Eisfeld , B. Mundy-Bosse , S. Vosberg , P. A. Greif , R. Claus , L. Bullinger , R. Garzon , K. R. Coombes , C. D. Bloomfield , B. J. Druker , J. W. Tyner , J. C. Byrd , C. C. Oakes , DNA methylation epitypes highlight underlying developmental and disease pathways in acute myeloid leukemia. Genome Res 31, gr.269233.120 (2021).","DOI":"10.1101\/gr.269233.120"},{"key":"2025092518450706000_2025.09.18.677221v2.10","doi-asserted-by":"publisher","DOI":"10.1016\/S1535-6108(02)00061-2"},{"key":"2025092518450706000_2025.09.18.677221v2.11","doi-asserted-by":"publisher","DOI":"10.1038\/nrc4001"},{"key":"2025092518450706000_2025.09.18.677221v2.12","doi-asserted-by":"crossref","first-page":"573","DOI":"10.1038\/ng0507-573b","article-title":"Heritable germline epimutations in humans","volume":"39","year":"2007","journal-title":"Nat. Genet"},{"key":"2025092518450706000_2025.09.18.677221v2.13","first-page":"2174","article-title":"O. behalf of the I. C. I. Consortium","volume":"161","year":"2013","journal-title":"Targeted methylation testing of a patient cohort broadens the epigenetic and clinical description of imprinting disorders. Am. J. M\u00e9d. Genet. Part A"},{"key":"2025092518450706000_2025.09.18.677221v2.14","doi-asserted-by":"publisher","DOI":"10.1086\/367926"},{"key":"2025092518450706000_2025.09.18.677221v2.15","doi-asserted-by":"crossref","unstructured":"M. P. Hitchins , R. L. Ward , Constitutional (germline) MLH1 epimutation as an aetiological mechanism for hereditary non-polyposis colorectal cancer. J. M\u00e9d. Genet. 46, 793 (2009).","DOI":"10.1136\/jmg.2009.068122"},{"key":"2025092518450706000_2025.09.18.677221v2.16","doi-asserted-by":"publisher","DOI":"10.1038\/ng1342"},{"key":"2025092518450706000_2025.09.18.677221v2.17","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1182\/blood.2020009244","article-title":"Allele-specific expression of GATA2 due to epigenetic dysregulation in CEBPA double-mutant AML","volume":"138","year":"2021","journal-title":"Blood"},{"key":"2025092518450706000_2025.09.18.677221v2.18","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/8.4.661"},{"key":"2025092518450706000_2025.09.18.677221v2.19","unstructured":"K. O\u2019Neill , E. Pleasance , J. Fan , V. Akbari , G. Chang , K. Dixon , V. Csizmok , S. MacLennan , V. Porter , A. Galbraith , C. J. Grisdale , L. Culibrk , J. H. Dupuis , R. Corbett , J. Hopkins , R. Bowlby , P. Pandoh , D. E. Smailus , D. Cheng , T. Wong , C. Frey , Y. Shen , L. F. Paulin , F. J. Sedlazeck , J. M. T. Nelson , E. Chuah , K. L. Mungall , R. A. Moore , R. Coope , A. J. Mungall , M. K. McConechy , L. M. Williamson , K. A. Schrader , S. Yip , M. A. Marra , J. Laskin , S. J. M. Jones , Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes. medRxiv, 2024.02.20.24302959 (2024)."},{"key":"2025092518450706000_2025.09.18.677221v2.20","doi-asserted-by":"publisher","DOI":"10.1126\/science.1148910"},{"key":"2025092518450706000_2025.09.18.677221v2.21","doi-asserted-by":"crossref","unstructured":"O. Stewart , C. Gruber , H. E. Randolph , R. Patel , M. Ramba , E. Calzoni , L. H. Huang , J. Levy , S. Buta , A. Lee , C. Sazeides , Z. Prue , D. P. H. van Konijnenburg , I. K. Chinn , L. A. Pedroza , J. R. Lupski , E. G. Schmitt , M. A. Cooper , A. Puel , X. Peng , S. Boisson-Dupuis , J. Bustamante , S. Okada , M. Martin-Fernandez , J. S. Orange , J.-L. Casanova , J. D. Milner , D. Bogunovic , Monoallelic expression can govern penetrance of inborn errors of immunity. Nature, 1\u201312 (2025).","DOI":"10.1038\/s41586-024-08346-4"},{"key":"2025092518450706000_2025.09.18.677221v2.22","doi-asserted-by":"publisher","DOI":"10.1038\/s41375-018-0134-9"},{"key":"2025092518450706000_2025.09.18.677221v2.23","doi-asserted-by":"crossref","first-page":"5330","DOI":"10.1038\/s41467-021-25630-3","article-title":"Locus specific epigenetic modalities of random allelic expression imbalance","volume":"12","year":"2021","journal-title":"Nat. Commun"},{"key":"2025092518450706000_2025.09.18.677221v2.24","doi-asserted-by":"publisher","DOI":"10.1126\/science.1245316"},{"key":"2025092518450706000_2025.09.18.677221v2.25","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2010.03.017"},{"key":"2025092518450706000_2025.09.18.677221v2.26","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1301689"},{"key":"2025092518450706000_2025.09.18.677221v2.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccell.2015.07.012"},{"key":"2025092518450706000_2025.09.18.677221v2.28","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa1402121"},{"key":"2025092518450706000_2025.09.18.677221v2.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.ccr.2009.11.020"},{"key":"2025092518450706000_2025.09.18.677221v2.30","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2017.124"},{"key":"2025092518450706000_2025.09.18.677221v2.31","doi-asserted-by":"publisher","DOI":"10.1038\/ncomms7363"},{"key":"2025092518450706000_2025.09.18.677221v2.32","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btac650"},{"key":"2025092518450706000_2025.09.18.677221v2.33","doi-asserted-by":"publisher","DOI":"10.1101\/gr.278146.123"},{"key":"2025092518450706000_2025.09.18.677221v2.34","doi-asserted-by":"publisher","DOI":"10.1038\/ng.3805"},{"key":"2025092518450706000_2025.09.18.677221v2.35","doi-asserted-by":"publisher","DOI":"10.1126\/science.aaz1646"},{"key":"2025092518450706000_2025.09.18.677221v2.36","first-page":"e2200559","article-title":"Persistent Molecular Disease in Adult Patients With AML Evaluated With Whole-Exome and Targeted Error-Corrected DNA Sequencing. JCO Precis","volume":"7","year":"2023","journal-title":"Oncol"},{"key":"2025092518450706000_2025.09.18.677221v2.37","doi-asserted-by":"publisher","DOI":"10.1182\/blood-2010-07-298331"},{"key":"2025092518450706000_2025.09.18.677221v2.38","doi-asserted-by":"publisher","DOI":"10.1126\/science.6844925"},{"key":"2025092518450706000_2025.09.18.677221v2.39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-57433-1"},{"key":"2025092518450706000_2025.09.18.677221v2.40","doi-asserted-by":"crossref","unstructured":"N. Loyfer , J. Magenheim , A. Peretz , G. Cann , J. Bredno , A. Klochendler , I. Fox-Fisher , S. Shabi-Porat , M. Hecht , T. Pelet , J. Moss , Z. Drawshy , H. Amini , P. Moradi , S. Nagaraju , D. Bauman , D. Shveiky , S. Porat , U. Dior , G. Rivkin , O. Or , N. Hirshoren , E. Carmon , A. Pikarsky , A. Khalaileh , G. Zamir , R. Grinbaum , M. A. Gazala , I. Mizrahi , N. Shussman , A. Korach , O. Wald , U. Izhar , E. Erez , V. Yutkin , Y. Samet , D. R. Golinkin , K. L. Spalding , H. Druid , P. Arner , A. M. J. Shapiro , M. Grompe , A. Aravanis , O. Venn , A. Jamshidi , R. Shemer , Y. Dor , B. Glaser , T. Kaplan , A DNA methylation atlas of normal human cell types. Nature, 1\u2013 10 (2023).","DOI":"10.1038\/s41586-022-05580-6"},{"key":"2025092518450706000_2025.09.18.677221v2.41","unstructured":"K. O\u2019Neill , E. Pleasance , J. Fan , V. Akbari , G. Chang , K. Dixon , V. Csizmok , S. MacLennan , V. Porter , A. Galbraith , C. J. Grisdale , L. Culibrk , J. H. Dupuis , R. Corbett , J. Hopkins , R. Bowlby , P. Pandoh , D. E. Smailus , D. Cheng , T. Wong , C. Frey , Y. Shen , E. Lewis , L. F. Paulin , F. J. Sedlazeck , J. M. T. Nelson , E. Chuah , K. L. Mungall , R. A. Moore , R. Coope , A. J. Mungall , M. K. McConechy , L. M. Williamson , K. A. Schrader , S. Yip , M. A. Marra , J. Laskin , S. J. M. Jones , Long-read sequencing of an advanced cancer cohort resolves rearrangements, unravels haplotypes, and reveals methylation landscapes. Cell Genom. 4, 100674 (2024)."},{"key":"2025092518450706000_2025.09.18.677221v2.42","doi-asserted-by":"crossref","unstructured":"Z. Zhang , Y. Hong , S. Zhang , X. Zhu , L. Liu , X. Liao , H. Gu , H. Fang , J. Shi , Toward the DNA methylation haplotype map of 11 common solid cancers. Cell Rep. 44, 116197 (2025).","DOI":"10.1016\/j.celrep.2025.116197"},{"key":"2025092518450706000_2025.09.18.677221v2.43","doi-asserted-by":"crossref","unstructured":"A. L. Costa , D. Doncevic , Y. Wu , L. Yang , K. H. Man , A.-S. Spreng , H. Winter , M. N. C. Fletcher , B. Radlwimmer , C. Herrmann , A new IDH-independent hypermethylation phenotype is associated with astrocyte-like cell state in glioblastoma. Genome Biol. 26, 192 (2025).","DOI":"10.1186\/s13059-025-03670-y"},{"key":"2025092518450706000_2025.09.18.677221v2.44","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-20225-w"},{"key":"2025092518450706000_2025.09.18.677221v2.45","doi-asserted-by":"publisher","DOI":"10.1038\/nature14248"},{"key":"2025092518450706000_2025.09.18.677221v2.46","doi-asserted-by":"crossref","unstructured":"M. Chen , R. Fu , Y. Chen , L. Li , S.-W. Wang , High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations. Nat. Methods, 1\u201311 (2025).","DOI":"10.1038\/s41592-024-02567-1"},{"key":"2025092518450706000_2025.09.18.677221v2.47","doi-asserted-by":"crossref","first-page":"478","DOI":"10.1038\/s41586-025-09041-8","article-title":"Clonal tracing with somatic epimutations reveals dynamics of blood ageing","volume":"643","year":"2025","journal-title":"Nature"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.09.18.677221","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T09:35:48Z","timestamp":1768469748000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.09.18.677221"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,20]]},"references-count":47,"URL":"https:\/\/doi.org\/10.1101\/2025.09.18.677221","relation":{},"subject":[],"published":{"date-parts":[[2025,9,20]]},"subtype":"preprint"}}