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Cases without a genomic alteration in the <jats:italic>FOXF1<\/jats:italic> locus have been described as well. The mechanisms responsible for <jats:italic>FOXF1<\/jats:italic> haploinsufficiency and the cause of ACD\/MPV in patients without a genomic <jats:italic>FOXF1<\/jats:italic> variant are poorly understood, complicating the search for potential therapeutic targets for ACD\/MPV. To investigate the contribution of aberrant DNA methylation, genome wide methylation patterns of ACD\/MPV lung tissues were compared with methylation patterns of control lung tissues using the recently developed technique Methylated DNA sequencing (MeD-seq).\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Eight ACD\/MPV lung tissue samples and three control samples were sequenced and their mutual comparison resulted in identification of 319 differentially methylated regions (DMRs) genome wide, involving 115 protein coding genes. The potentially upregulated genes were significantly enriched in developmental signalling pathways, whereas potentially downregulated genes were mainly enriched in O-linked glycosylation. In patients with a large maternal deletion encompassing the 60\u00a0kb <jats:italic>FOXF1<\/jats:italic> enhancer, DNA methylation patterns in this <jats:italic>FOXF1<\/jats:italic> enhancer were not significantly different compared to controls. However, two hypermethylated regions were detected in the 60\u00a0kb <jats:italic>FOXF1<\/jats:italic> enhancer of patients harbouring a <jats:italic>FOXF1<\/jats:italic> point mutation. Lastly, a large hypermethylated region overlapping the first <jats:italic>FOXF1<\/jats:italic> exon was found in one of the ACD\/MPV patients without a known pathogenic <jats:italic>FOXF1<\/jats:italic> variation.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This is the first study providing genome wide methylation data on lung tissue of ACD\/MPV patients. DNA methylation analyses in the <jats:italic>FOXF1<\/jats:italic> locus excludes maternal imprinting of the 60\u00a0kb <jats:italic>FOXF1<\/jats:italic> enhancer. Hypermethylation at the 60\u00a0kb <jats:italic>FOXF1<\/jats:italic> enhancer might contribute to <jats:italic>FOXF1<\/jats:italic> haploinsufficiency caused by heterozygous mutations in the <jats:italic>FOXF1<\/jats:italic> coding region. Interestingly, DNA methylation analyses of patients without a genomic <jats:italic>FOXF1<\/jats:italic> variant suggest that abnormal hypermethylation of exon 1 might play a role in some ACD\/MPV in patients.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s13148-021-01134-1","type":"journal-article","created":{"date-parts":[[2021,7,29]],"date-time":"2021-07-29T12:04:02Z","timestamp":1627560242000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Genome wide DNA methylation analysis of alveolar capillary dysplasia lung tissue reveals aberrant methylation of genes involved in development including the FOXF1 locus"],"prefix":"10.1186","volume":"13","author":[{"given":"Evelien","family":"Slot","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ruben","family":"Boers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joachim","family":"Boers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Wilfred F. 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