{"entity": "journal", "iuid": "24f11bc130ac40fbb99165c4f174ddd9", "timestamp": "2026-06-08T06:02:08.728Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Epigenomics.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Epigenomics"}}, "title": "Epigenomics", "issn": "1750-1911", "issn-l": "1750-192X", "publications_count": 5, "publications": [{"entity": "publication", "iuid": "9458971190ee41e099e40121d1866819", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9458971190ee41e099e40121d1866819"}}, "title": "Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.", "authors": [{"family": "J\u00f6nsson", "given": "Josefine", "initials": "J", "orcid": "0000-0003-0709-2828", "researcher": {"href": "https://publications.scilifelab.se/researcher/9a4b2eb9eef5496eb27e76fc9fca120a.json"}}, {"family": "Perfilyev", "given": "Alexander", "initials": "A"}, {"family": "Kugelberg", "given": "Unn", "initials": "U"}, {"family": "Skog", "given": "Signe", "initials": "S"}, {"family": "Lindstr\u00f6m", "given": "Axel", "initials": "A"}, {"family": "Ruhrmann", "given": "Sabrina", "initials": "S"}, {"family": "Ofori", "given": "Jones K", "initials": "JK"}, {"family": "Bacos", "given": "Karl", "initials": "K"}, {"family": "R\u00f6nn", "given": "Tina", "initials": "T"}, {"family": "\u00d6st", "given": "Anita", "initials": "A"}, {"family": "Ling", "given": "Charlotte", "initials": "C", "orcid": "0000-0003-0587-7154", "researcher": {"href": "https://publications.scilifelab.se/researcher/dd7c1ea934034c4db99f31a5a9b04691.json"}}], "type": "journal article", "published": "2025-02-00", "journal": {"title": "Epigenomics", "issn": "1750-192X", "volume": "17", "issue": "2", "pages": "89-104", "issn-l": null}, "abstract": "Dietary factors may regulate the epigenome. We aimed to explore whether a diet intervention, including excess sugar, affects the methylome in human sperm, and to describe the sperm methylome. We used Whole Genome Bisulfite Sequencing (WGBS) to analyze DNA methylation in sperm taken at three time points from 15 males during a diet intervention; i) at baseline, ii) after one week on a standardized diet, and iii) after an additional week on a high-sugar diet providing 150% of their estimated total energy expenditure.\n\nWe identified seven nominal diet-associated differentially methylated regions in sperm (p < 0.05). The diet was nominally associated with methylation of 143 sites linked to fertility (e.g. AHRR, GNAS, and HDAC4), 313 sites in imprinted genes (e.g. GLIS3, PEG10, PEG3, and SNURF), and 42 sites in top 1%-expressed genes (e.g. CHD2) (p < 0.05). In sperm, 3'UTRs and introns had the highest levels of methylation, while 5'UTRs and CpG islands had the lowest levels. Non-expressed genes in human sperm were hypomethylated in exons compared with transcribed genes.\n\nIn human sperm, DNA methylation levels were linked to gene expression, and excess sugar had modest effects on methylation on imprinted and highly expressed genes, and genes affecting fertility.", "doi": "10.1080/17501911.2024.2439782", "pmid": "39707713", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "NGI Short read": "Service"}, "xrefs": [], "notes": [], "created": "2025-02-03T07:41:54.349Z", "modified": "2025-02-03T07:41:54.880Z"}, {"entity": "publication", "iuid": "033b5a0bde204450b47ca9e89437b1fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/033b5a0bde204450b47ca9e89437b1fe"}}, "title": "Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.", "authors": [{"family": "Ek", "given": "Weronica E", "initials": "WE"}, {"family": "Ahsan", "given": "Muhammad", "initials": "M"}, {"family": "Rask-Andersen", "given": "Mathias", "initials": "M"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}], "type": "journal article", "published": "2017-04-00", "journal": {"volume": "9", "issn": "1750-192X", "issue": "4", "pages": "407-418", "title": "Epigenomics", "issn-l": null}, "abstract": "Epigenetic mechanisms are critical for normal immune development and epigenetic alterations might therefore be possible contributors to immune diseases. To investigate if DNA methylation in whole blood is associated with total and allergen-specific IgE levels.\n\nWe performed an epigenome-wide association study to investigate the association between DNA methylation and IgE level, allergen-specific IgE and self-reported immune diseases and allergies in 728 individuals.\n\nWe identified and replicated 15 CpG sites associated with IgE, mapping to biologically relevant genes, including ACOT7, ILR5A, KCNH2, PRG2 and EPX. A total of 331 loci were associated with allergen-specific IgE, but none of these CpG sites were associated with self-reported allergies and immune diseases.\n\nThis study shows that IgE levels are associated with DNA methylation levels at numerous CpG sites, which might provide new leads for investigating the links between IgE and allergic inflammation.", "doi": "10.2217/epi-2016-0158", "pmid": "28322575", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-10-25T15:18:20.445Z", "modified": "2024-01-16T13:48:48.187Z"}, {"entity": "publication", "iuid": "145267903a5e40b9867d5b9851f29d63", "links": {"self": {"href": "https://publications.scilifelab.se/publication/145267903a5e40b9867d5b9851f29d63.json"}, "display": {"href": "https://publications.scilifelab.se/publication/145267903a5e40b9867d5b9851f29d63"}}, "title": "DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.", "authors": [{"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Busche", "given": "Stephan", "initials": "S"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Sinnett", "given": "Daniel", "initials": "D"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2016-10-00", "journal": {"volume": "8", "issn": "1750-192X", "issue": "10", "pages": "1367-1387", "title": "Epigenomics", "issn-l": null}, "abstract": "To identify regions of aberrant DNA methylation in acute lymphoblastic leukemia (ALL) cells of different subtypes on a genome-wide scale.\n\nWhole-genome bisulfite sequencing (WGBS) was used to determine the DNA methylation levels in cells from four pediatric ALL patients of different subtypes. The findings were confirmed by 450k DNA methylation arrays in a large patient set.\n\nCompared with mature B or T cells WGBS detected on average 82,000 differentially methylated regions per patient. Differentially methylated regions are enriched to CpG poor regions, active enhancers and transcriptional start sites. We also identified approximately 8000 CpG islands with variable intermediate DNA methylation that seems to occur as a result of stochastic de novo methylation.\n\nWGBS provides an unbiased view and novel insights into the DNA methylome of ALL cells.", "doi": "10.2217/epi-2016-0052", "pmid": "27552300", "labels": {"National Genomics Infrastructure": "Technology development", "NGI Uppsala (SNP&SEQ Technology Platform)": "Technology development", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-03T13:00:27.830Z", "modified": "2024-01-16T13:48:49.431Z"}, {"entity": "publication", "iuid": "4459a54010c74509b02e375cad6671b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4459a54010c74509b02e375cad6671b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4459a54010c74509b02e375cad6671b5"}}, "title": "Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature.", "authors": [{"family": "Vymetalkova", "given": "Veronika", "initials": "V"}, {"family": "Vodicka", "given": "Pavel", "initials": "P"}, {"family": "Pardini", "given": "Barbara", "initials": "B"}, {"family": "Rosa", "given": "Fabio", "initials": "F"}, {"family": "Levy", "given": "Miroslav", "initials": "M"}, {"family": "Schneiderova", "given": "Michaela", "initials": "M"}, {"family": "Liska", "given": "Vaclav", "initials": "V"}, {"family": "Vodickova", "given": "Ludmila", "initials": "L"}, {"family": "Nilsson", "given": "Torbj\u00f6rn K", "initials": "TK"}, {"family": "Farkas", "given": "Sanja A", "initials": "SA"}], "type": "journal article", "published": "2016-09-00", "journal": {"volume": "8", "issn": "1750-192X", "issue": "9", "pages": "1193-1207", "title": "Epigenomics", "issn-l": null}, "abstract": "The aim of the present study is to address a genome-wide search for novel methylation biomarkers in the rectal cancer (RC), as only scarce information on methylation profile is available.\n\nWe analyzed methylation status in 25 pairs of RC and adjacent healthy mucosa using the Illumina Human Methylation 450 BeadChip.\n\nWe found significantly aberrant methylation in 33 genes. After validation of our results by pyrosequencing, we found a good agreement with our findings. The BPIL3 and HBBP1 genes resulted hypomethylated in RC, whereas TIFPI2, ADHFE1, FLI1 and TLX1 were hypermethylated. An external validation by TCGA datasets confirmed the results.\n\nOur study, with external validation, has demonstrated the feasibility of using specific methylated DNA signatures for developing biomarkers in RC.", "doi": "10.2217/epi-2016-0044", "pmid": "27529132", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [], "notes": [], "created": "2017-05-08T07:59:20.630Z", "modified": "2020-01-21T13:56:01.934Z"}, {"entity": "publication", "iuid": "34242cd550aa44afa65061ee6ac77f16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34242cd550aa44afa65061ee6ac77f16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34242cd550aa44afa65061ee6ac77f16"}}, "title": "DNA methylation changes in genes frequently mutated in sporadic colorectal cancer and in the DNA repair and Wnt/\u03b2-catenin signaling pathway genes.", "authors": [{"family": "Farkas", "given": "Sanja A", "initials": "SA"}, {"family": "Vymetalkova", "given": "Veronika", "initials": "V"}, {"family": "Vodickova", "given": "Ludmila", "initials": "L"}, {"family": "Vodicka", "given": "Pavel", "initials": "P"}, {"family": "Nilsson", "given": "Torbj\u00f6rn K", "initials": "TK"}], "type": "journal article", "published": "2014-04-00", "journal": {"volume": "6", "issn": "1750-192X", "issue": "2", "pages": "179-191", "title": "Epigenomics", "issn-l": null}, "abstract": "The onset and progression of colorectal cancer (CRC) involves a cascade of genetic and/or epigenetic events. The aim of the present study was to address the DNA methylation status of genes relevant in colorectal carcinogenesis and its progression, such as genes frequently mutated in CRC, genes involved in the DNA repair and Wnt signaling pathway.\n\nWe analyzed methylation status in totally 160 genes in 12 paired colorectal tumors and adjacent healthy mucosal tissues using the Illumina Infinium Human Methylation 450 BeadChip.\n\nWe found significantly aberrant methylation in 23 genes (NEIL1, NEIL3, DCLRE1C, NHEJ1, GTF2H5, CCNH, CTNNB1, DKK2, DKK3, FZD5 LRP5, TLE3, WNT2, WNT3A, WNT6, TCF7L1, CASP8, EDNRB1, GPC6, KIAA1804, MYO1B, SMAD2 and TTN). External validation by mRNA expression showed a good agreement between hypermethylation in cancer and down-regulated mRNA expression of the genes EDNRB1, GPC6 and SMAD2, and between hypomethylation and up-regulated mRNA expression of the CASP8 and DCLRE1C genes.\n\nAberrant methylation of the DCLRE1C and GPC6 genes are presented here for the first time and are therefore of special interest for further validation as novel candidate biomarker genes in CRC, and merit further validation with specific assays.", "doi": "10.2217/epi.14.7", "pmid": "24811787", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:37.173Z", "modified": "2020-01-21T13:56:01.494Z"}], "created": "2017-05-09T09:12:17.305Z", "modified": "2020-11-27T13:14:06.806Z"}