{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"medRxiv"}],"indexed":{"date-parts":[[2026,1,16]],"date-time":"2026-01-16T12:26:23Z","timestamp":1768566383654,"version":"3.49.0"},"posted":{"date-parts":[[2023,11,5]]},"group-title":"Genetic and Genomic Medicine","reference-count":17,"publisher":"openRxiv","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,12,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:sec>\n                  <jats:title>OBJECTIVE<\/jats:title>\n                  <jats:p>\n                    Van der Woude Syndrome (VWS) classically presents with combinations of lip pits (LP) and orofacial clefts, with marked phenotypic discordance even amongst individuals carrying the same mutation. Such discordance suggests a possible role for epigenetic factors as phenotypic modifiers. Both\n                    <jats:italic>IRF6<\/jats:italic>\n                    , causal for 70% of VWS cases, and\n                    <jats:italic>TP63<\/jats:italic>\n                    interact in a regulatory loop to coordinate epithelial proliferation and differentiation for palatogenesis. We hypothesize that differential DNA methylation (DNAm) in CpG sites within regulatory regions of\n                    <jats:italic>IRF6<\/jats:italic>\n                    and\n                    <jats:italic>TP63<\/jats:italic>\n                    are associated with VWS phenotypic discordance.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>METHODS<\/jats:title>\n                  <jats:p>\n                    We measured DNAm levels of CpG sites located in the promoter regions of\n                    <jats:italic>IRF6<\/jats:italic>\n                    and\n                    <jats:italic>TP63<\/jats:italic>\n                    and in an\n                    <jats:italic>IRF6<\/jats:italic>\n                    enhancer element (MCS9.7) in 83 individuals with VWS grouped within 5 phenotypes for primary analysis: 1=CL+\/-P+LP, 2=CL+\/-P, 3=CP+LP, 4=CP, 5=LP and 2 phenotypes for secondary analysis: 1=any cleft and LP, 2= any cleft without LP. DNA samples were bisulfite converted and pyrosequenced with target-specific primers. Methylation levels were compared amongst phenotypes.\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>RESULTS<\/jats:title>\n                  <jats:p>\n                    CpG sites in the\n                    <jats:italic>IRF6<\/jats:italic>\n                    promoter showed statistically significant differences in methylation among phenotypic groups in both analyses (P&lt;0.05). Individuals with any form of cleft (Groups 1-4) had significantly higher methylation levels than individuals with lip pits only (Group 5). In the secondary analysis, individuals in Group 1 (cleft+LP) had significantly higher methylation than Group 2 (cleft only).\n                  <\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>CONCLUSION<\/jats:title>\n                  <jats:p>\n                    Results indicated that hypermethylation of the\n                    <jats:italic>IRF6<\/jats:italic>\n                    promoter is associated with more severe phenotypes (any cleft +\/- lip pits); thus, possibly impacting an already genetically weakened\n                    <jats:italic>IRF6<\/jats:italic>\n                    protein and leading to a more severe phenotype.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2023.11.04.23298094","type":"posted-content","created":{"date-parts":[[2023,11,5]],"date-time":"2023-11-05T12:30:17Z","timestamp":1699187417000},"source":"Crossref","is-referenced-by-count":0,"title":["DNA methylation effects on Van der Woude Syndrome phenotypic variability"],"prefix":"10.64898","author":[{"given":"Amanda","family":"Seaberg","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5223-6846","authenticated-orcid":false,"given":"Waheed","family":"Awotoye","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fang","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lindsey","family":"Dunlay","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1229-5964","authenticated-orcid":false,"given":"Azeez","family":"Butali","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeff","family":"Murray","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lina","family":"Moreno-Uribe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2239-8120","authenticated-orcid":false,"given":"Aline","family":"Petrin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2023120817251156000_2023.11.04.23298094v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/gim.2012.141"},{"key":"2023120817251156000_2023.11.04.23298094v2.2","doi-asserted-by":"publisher","DOI":"10.1111\/cge.12675"},{"key":"2023120817251156000_2023.11.04.23298094v2.3","doi-asserted-by":"publisher","DOI":"10.1002\/mgg3.1355"},{"key":"2023120817251156000_2023.11.04.23298094v2.4","doi-asserted-by":"publisher","DOI":"10.3389\/fdmed.2023.1120948"},{"key":"2023120817251156000_2023.11.04.23298094v2.5","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2013.11.009"},{"key":"2023120817251156000_2023.11.04.23298094v2.6","doi-asserted-by":"publisher","DOI":"10.1155\/2014\/871460"},{"key":"2023120817251156000_2023.11.04.23298094v2.7","doi-asserted-by":"publisher","DOI":"10.1038\/ng985"},{"key":"2023120817251156000_2023.11.04.23298094v2.8","doi-asserted-by":"publisher","DOI":"10.1002\/ajmg.a.34022"},{"key":"2023120817251156000_2023.11.04.23298094v2.9","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1110931108"},{"key":"2023120817251156000_2023.11.04.23298094v2.10","doi-asserted-by":"publisher","DOI":"10.1172\/JCI42821"},{"key":"2023120817251156000_2023.11.04.23298094v2.11","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddt664"},{"key":"2023120817251156000_2023.11.04.23298094v2.12","doi-asserted-by":"publisher","DOI":"10.1093\/hmg\/ddp201"},{"key":"2023120817251156000_2023.11.04.23298094v2.13","doi-asserted-by":"publisher","DOI":"10.1038\/ng1894"},{"key":"2023120817251156000_2023.11.04.23298094v2.14","doi-asserted-by":"publisher","DOI":"10.1111\/j.1525-1470.2011.01575.x"},{"key":"2023120817251156000_2023.11.04.23298094v2.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.devcel.2011.08.005"},{"key":"2023120817251156000_2023.11.04.23298094v2.16","doi-asserted-by":"publisher","DOI":"10.1016\/j.tem.2009.12.007"},{"key":"2023120817251156000_2023.11.04.23298094v2.17","doi-asserted-by":"publisher","DOI":"10.1530\/REP-16-0376"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2023.11.04.23298094","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T19:44:29Z","timestamp":1768506269000},"score":1,"resource":{"primary":{"URL":"http:\/\/medrxiv.org\/lookup\/doi\/10.1101\/2023.11.04.23298094"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,11,5]]},"references-count":17,"URL":"https:\/\/doi.org\/10.1101\/2023.11.04.23298094","relation":{},"subject":[],"published":{"date-parts":[[2023,11,5]]},"subtype":"preprint"}}