{"entity": "researcher", "timestamp": "2026-07-13T09:59:20.391Z", "family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "affiliations": ["https://ror.org/026vcq606 Royal Institute of Technology - KTH, School of Chemistry, Biotechnology and Health, Science for Life Laboratory, Stockholm, Sweden artemy.zhigulev@scilifelab.se."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e"}}, "publications": [{"entity": "publication", "iuid": "87bf60ec792f4e9caf54376f46b3ad5f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/87bf60ec792f4e9caf54376f46b3ad5f"}}, "title": "Rare regulatory mutations disrupt mesenchymal molecular programs driving endocardial cushion formation in bicuspid aortic valve.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Buyan", "given": "Andrey", "initials": "A", "orcid": "0000-0001-9105-4028", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed79c4583ae342a5ae931e39f7e282a7.json"}}, {"family": "L\u00e1z\u00e1r", "given": "Enik\u0151", "initials": "E", "orcid": "0000-0001-8664-7531", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd94abaf66dd407da5056c04174fc62d.json"}}, {"family": "Gryzunov", "given": "Nikita", "initials": "N", "orcid": "0009-0000-0782-8650", "researcher": {"href": "https://publications.scilifelab.se/researcher/6bb53aa525ff4269936724c077b2d387.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Mauron", "given": "Rapha\u00ebl", "initials": "R", "orcid": "0009-0004-0909-3554", "researcher": {"href": "https://publications.scilifelab.se/researcher/fa0b2662f1bc40b682ff6923c797877e.json"}}, {"family": "Nozdrin", "given": "Vladimir", "initials": "V", "orcid": "0009-0004-3053-1387", "researcher": {"href": "https://publications.scilifelab.se/researcher/456249fbb9ef48cebc32cc15fe39a35b.json"}}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S"}, {"family": "Petersson Sj\u00f6gren", "given": "Madeleine", "initials": "M"}, {"family": "Schwochow", "given": "Doreen", "initials": "D"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A", "orcid": "0000-0002-3427-9455", "researcher": {"href": "https://publications.scilifelab.se/researcher/9096109f1be94b7197fd249c4193c9d7.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Kulakovskiy", "given": "Ivan V", "initials": "IV", "orcid": "0000-0002-6554-8128", "researcher": {"href": "https://publications.scilifelab.se/researcher/41163cb5ec5d44668f9c6f06edb379ab.json"}}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2026-04-18", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "17", "issue": "1", "issn-l": "2041-1723"}, "abstract": "Bicuspid aortic valve, a prevalent congenital malformation, predisposes individuals to severe complications. Although the condition exhibits substantial heritability, known protein-coding and common regulatory mutations explain a minority of cases. To assess the contribution of rare regulatory variants, here we integrate high-resolution three-dimensional genome organization profiling with matched whole-genome sequencing from eight individuals with bicuspid aortic valves and eight with standard tricuspid aortic valves. In bicuspid aortic valve patients, mutation-driven chromatin rewiring affected 1.8-fold more valve development genes than in healthy individuals. Genome-wide in silico analyses show that rare regulatory mutations disrupt the transcriptomes of mesenchymal cell populations necessary for endocardial cushion formation. We identify 198 candidate genes associated with bicuspid aortic valve, revealing pronounced heterogeneity and complex interplay between coding and regulatory mutations. Collectively, our findings establish rare regulatory mutations as contributors to the heritability of bicuspid aortic valve and underscore the need to elucidate their mechanistic roles in disease pathogenesis.", "doi": "10.1038/s41467-026-71758-5", "pmid": "41997951", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC13090386"}, {"db": "pii", "key": "10.1038/s41467-026-71758-5"}], "notes": [], "created": "2026-05-11T11:41:45.495Z", "modified": "2026-05-11T11:41:46.015Z"}, {"entity": "publication", "iuid": "33f838f6e3d2497fa4b6fd9a71cd282a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33f838f6e3d2497fa4b6fd9a71cd282a"}}, "title": "An endothelial regulatory module links blood pressure regulation with elite athletic performance.", "authors": [{"family": "Fegraeus", "given": "Kim", "initials": "K", "orcid": "0000-0002-6428-3420", "researcher": {"href": "https://publications.scilifelab.se/researcher/f232e1deee984344a57c88f550020e61.json"}}, {"family": "Rosengren", "given": "Maria K", "initials": "MK", "orcid": "0000-0003-0144-7034", "researcher": {"href": "https://publications.scilifelab.se/researcher/2b771ed57d3e4c409c2a208173945786.json"}}, {"family": "Naboulsi", "given": "Rakan", "initials": "R", "orcid": "0000-0002-3610-4341", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae740ff060a5499fa477891138e95117.json"}}, {"family": "Orlando", "given": "Ludovic", "initials": "L"}, {"family": "\u00c5brink", "given": "Magnus", "initials": "M", "orcid": "0000-0002-1335-3927", "researcher": {"href": "https://publications.scilifelab.se/researcher/50a91636c1064a0c944f7d794ba6ec72.json"}}, {"family": "Jouni", "given": "Ahmad", "initials": "A"}, {"family": "Velie", "given": "Brandon D", "initials": "BD"}, {"family": "Raine", "given": "Amanda", "initials": "A"}, {"family": "Egner", "given": "Beate", "initials": "B"}, {"family": "Mattsson", "given": "C Mikael", "initials": "CM", "orcid": "0000-0002-0642-4838", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ca360922eb047129f945ec3ca5f59e3.json"}}, {"family": "L\u00e5ng", "given": "Karin", "initials": "K"}, {"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Bj\u00f6rck", "given": "Hanna M", "initials": "HM", "orcid": "0000-0002-9155-3609", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d162f3de0f941e0a91387357892d656.json"}}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Andersson", "given": "G\u00f6ran", "initials": "G", "orcid": "0000-0001-5131-3144", "researcher": {"href": "https://publications.scilifelab.se/researcher/39ce81c314db47c8ad63c3ed38dffcb3.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS", "orcid": "0000-0002-0850-230X", "researcher": {"href": "https://publications.scilifelab.se/researcher/86acdca0104c4552880d5a7cb5ac6565.json"}}, {"family": "Lindgren", "given": "Gabriella", "initials": "G", "orcid": "0000-0001-6046-9669", "researcher": {"href": "https://publications.scilifelab.se/researcher/a050dea8e99c47fabac28c14fe4daabb.json"}}], "type": "journal article", "published": "2024-06-00", "journal": {"title": "PLoS Genet.", "issn": "1553-7404", "volume": "20", "issue": "6", "pages": "e1011285", "issn-l": "1553-7390"}, "abstract": "The control of transcription is crucial for homeostasis in mammals. A previous selective sweep analysis of horse racing performance revealed a 19.6 kb candidate regulatory region 50 kb downstream of the Endothelin3 (EDN3) gene. Here, the region was narrowed to a 5.5 kb span of 14 SNVs, with elite and sub-elite haplotypes analyzed for association to racing performance, blood pressure and plasma levels of EDN3 in Coldblooded trotters and Standardbreds. Comparative analysis of human HiCap data identified the span as an enhancer cluster active in endothelial cells, interacting with genes relevant to blood pressure regulation. Coldblooded trotters with the sub-elite haplotype had significantly higher blood pressure compared to horses with the elite performing haplotype during exercise. Alleles within the elite haplotype were part of the standing variation in pre-domestication horses, and have risen in frequency during the era of breed development and selection. These results advance our understanding of the molecular genetics of athletic performance and vascular traits in both horses and humans.", "doi": "10.1371/journal.pgen.1011285", "pmid": "38885195", "labels": {"NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "NGI Short read": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC11182536"}, {"db": "pii", "key": "PGENETICS-D-23-00898"}], "notes": [], "created": "2024-10-21T11:19:11.160Z", "modified": "2024-11-25T10:31:46.138Z"}, {"entity": "publication", "iuid": "b65e656b7fd14984a6c8a44d2edb0795", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b65e656b7fd14984a6c8a44d2edb0795.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b65e656b7fd14984a6c8a44d2edb0795"}}, "title": "Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.", "authors": [{"family": "Zhigulev", "given": "Artemy", "initials": "A", "orcid": "0000-0001-9251-1059", "researcher": {"href": "https://publications.scilifelab.se/researcher/81a7e8bb937744b5a18ed42d4f2dea5e.json"}}, {"family": "Norberg", "given": "Zandra", "initials": "Z"}, {"family": "Cordier", "given": "Julie", "initials": "J"}, {"family": "Spalinskas", "given": "Rapolas", "initials": "R", "orcid": "0000-0002-1648-6426", "researcher": {"href": "https://publications.scilifelab.se/researcher/18ca0b7337b849a49861aedf2971067e.json"}}, {"family": "Bassereh", "given": "Hassan", "initials": "H", "orcid": "0000-0002-9202-3765", "researcher": {"href": "https://publications.scilifelab.se/researcher/83cc119164de497f95b65f8ad11cac79.json"}}, {"family": "Bj\u00f6rn", "given": "Niclas", "initials": "N"}, {"family": "Pradhananga", "given": "Sailendra", "initials": "S", "orcid": "0000-0002-0834-3169", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1917cb059924a779ac38e3023778461.json"}}, {"family": "Gr\u00e9en", "given": "Henrik", "initials": "H", "orcid": "0000-0002-8015-5728", "researcher": {"href": "https://publications.scilifelab.se/researcher/0d92037931f64b70b8d4bf78dab628b4.json"}}, {"family": "Sahl\u00e9n", "given": "Pelin", "initials": "P", "orcid": "0000-0001-6943-9618", "researcher": {"href": "https://publications.scilifelab.se/researcher/d032e807335049b2ac8a5e2398dd48e7.json"}}], "type": "journal article", "published": "2024-03-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "7", "issue": "3", "issn-l": "2575-1077"}, "abstract": "Non-small cell lung cancer is often diagnosed at advanced stages, and many patients are still treated with classical chemotherapy. The unselective nature of chemotherapy often results in severe myelosuppression. Previous studies showed that protein-coding mutations could not fully explain the predisposition to myelosuppression. Here, we investigate the possible role of enhancer mutations in myelosuppression susceptibility. We produced transcriptome and promoter-interaction maps (using HiCap) of three blood stem-like cell lines treated with carboplatin or gemcitabine. Taking advantage of publicly available enhancer datasets, we validated HiCap results in silico and in living cells using epigenetic CRISPR technology. We also developed a network approach for interactome analysis and detection of differentially interacting genes. Differential interaction analysis provided additional information on relevant genes and pathways for myelosuppression compared with differential gene expression analysis at the bulk level. Moreover, we showed that enhancers of differentially interacting genes are highly enriched for variants associated with differing levels of myelosuppression. Altogether, our work represents a prominent example of integrative transcriptome and gene regulatory datasets analysis for the functional annotation of noncoding mutations.", "doi": "10.26508/lsa.202302244", "pmid": "38228368", "labels": {"NGI Short read": "Service", "NGI Stockholm (Genomics Production)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pmc", "key": "PMC10796589"}, {"db": "pii", "key": "7/3/e202302244"}], "notes": [], "created": "2024-03-18T09:44:22.332Z", "modified": "2025-02-28T14:23:45.768Z"}]}