{"entity": "researcher", "timestamp": "2026-08-20T20:46:00.856Z", "family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91"}}, "publications": [{"entity": "publication", "iuid": "124441b2d26448a49a238d854fcc0d5c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/124441b2d26448a49a238d854fcc0d5c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/124441b2d26448a49a238d854fcc0d5c"}}, "title": "Functional annotation of noncoding mutations in cancer.", "authors": [{"family": "Umer", "given": "Husen M", "initials": "HM", "orcid": "0000-0003-3971-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/922625c410444833a263244d0313980e.json"}}, {"family": "Smolinska", "given": "Karolina", "initials": "K", "orcid": "0000-0003-0907-5298", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b491565d0ea04ceb897ce53f325781b3.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0003-0907-5298", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b491565d0ea04ceb897ce53f325781b3.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "journal article", "published": "2021-09-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "4", "issue": "9", "issn-l": null}, "abstract": "In a cancer genome, the noncoding sequence contains the vast majority of somatic mutations. While very few are expected to be cancer drivers, those affecting regulatory elements have the potential to have downstream effects on gene regulation that may contribute to cancer progression. To prioritize regulatory mutations, we screened somatic mutations in the Pan-Cancer Analysis of Whole Genomes cohort of 2,515 cancer genomes on individual bases to assess their potential regulatory roles in their respective cancer types. We found a highly significant enrichment of regulatory mutations associated with the deamination signature overlapping a CpG site in the CCAAT/Enhancer Binding Protein \u03b2 recognition sites in many cancer types. Overall, 5,749 mutated regulatory elements were identified in 1,844 tumor samples from 39 cohorts containing 11,962 candidate regulatory mutations. Our analysis indicated 20 or more regulatory mutations in 5.5% of the samples, and an overall average of six per tumor. Several recurrent elements were identified, and major cancer-related pathways were significantly enriched for genes nearby the mutated regulatory elements. Our results provide a detailed view of the role of regulatory elements in cancer genomes.", "doi": "10.26508/lsa.201900523", "pmid": "34282050", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8321657"}, {"db": "pii", "key": "4/9/e201900523"}], "notes": [], "created": "2026-08-20T13:03:53.335Z", "modified": "2026-08-20T13:03:53.475Z"}, {"entity": "publication", "iuid": "ea603904fe604e4191a2656a69ea8f0a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ea603904fe604e4191a2656a69ea8f0a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ea603904fe604e4191a2656a69ea8f0a"}}, "title": "Multifaceted regulation of hepatic lipid metabolism by YY1.", "authors": [{"family": "Pan", "given": "Gang", "initials": "G", "orcid": "0000-0003-4243-1821", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8322e7f4f5a842d0930a69a5e2eaf425.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K"}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Lara Guti\u00e9rrez", "given": "Ariadna", "initials": "A", "orcid": "0000-0003-3584-0627", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/690d77f4c483405c9035a675719b1d19.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "journal article", "published": "2021-07-00", "journal": {"title": "Life Sci. Alliance", "issn": "2575-1077", "volume": "4", "issue": "7", "issn-l": null}, "abstract": "Recent studies suggested that dysregulated YY1 plays a pivotal role in many liver diseases. To obtain a detailed view of genes and pathways regulated by YY1 in the liver, we carried out RNA sequencing in HepG2 cells after YY1 knockdown. A rigid set of 2,081 differentially expressed genes was identified by comparing the YY1-knockdown samples (n = 8) with the control samples (n = 14). YY1 knockdown significantly decreased the expression of several key transcription factors and their coactivators in lipid metabolism. This is illustrated by YY1 regulating PPARA expression through binding to its promoter and enhancer regions. Our study further suggest that down-regulation of the key transcription factors together with YY1 knockdown significantly decreased the cooperation between YY1 and these transcription factors at various regulatory regions, which are important in regulating the expression of genes in hepatic lipid metabolism. This was supported by the finding that the expression of SCD and ELOVL6, encoding key enzymes in lipogenesis, were regulated by the cooperation between YY1 and PPARA/RXRA complex over their promoters.", "doi": "10.26508/lsa.202000928", "pmid": "34099540", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8200296"}, {"db": "pii", "key": "4/7/e202000928"}], "notes": [], "created": "2026-08-20T13:03:55.696Z", "modified": "2026-08-20T13:03:55.828Z"}, {"entity": "publication", "iuid": "8561d6585bc748b3bff9999ab15c4e50", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8561d6585bc748b3bff9999ab15c4e50.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8561d6585bc748b3bff9999ab15c4e50"}}, "title": "Organ-specific metabolic pathways distinguish prediabetes, type 2 diabetes and normal tissues", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c3104b875f2e459093b1e468ba4af556.json"}}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/40667fda2aa5488aa45a95ce4e8a2c1f.json"}}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Castillejo-Lopez", "given": "Casimiro", "initials": "C"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Mundt", "given": "Filip", "initials": "F"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}, {"family": "Deshmukh", "given": "Atul Shahaji", "initials": "AS", "orcid": "0000-0002-2278-1843", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f87d7b0493d041ca9deb114573a99064.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M", "orcid": "0000-0003-1292-4799", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5dd80d7b355437f9ad1a29efa6814c0.json"}}, {"family": "Korsgren", "given": "Olle", "initials": "O", "orcid": "0000-0002-8524-9547", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f4f384eeb31a4b2dba5c9301bb34c156.json"}}, {"family": "Eriksson", "given": "Jan W", "initials": "JW", "orcid": "0000-0002-2639-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4ddd57ea228848ad9935c38e8b9b64e8.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "posted-content", "published": "2021-05-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.05.09.443296", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:08.047Z", "modified": "2026-08-20T10:04:08.243Z"}, {"entity": "publication", "iuid": "9c3e16b8b897461ab1f8bc81ff7e4db2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3e16b8b897461ab1f8bc81ff7e4db2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9c3e16b8b897461ab1f8bc81ff7e4db2"}}, "title": "Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type-2 diabetes", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8638ca04ea7f4ff8a191f3c6969b1394.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ"}, {"family": "Kumar", "given": "Chanchal", "initials": "C"}, {"family": "Skrtic", "given": "Stanko", "initials": "S"}, {"family": "Grabherr", "given": "Manfred", "initials": "M"}, {"family": "Ris\u00e9rus", "given": "Ulf", "initials": "U"}, {"family": "Eriksson", "given": "Jan W", "initials": "JW"}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1dffb9dd373741069230b4f80d7e1698.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f01aa16d2b3343e980a2f2a9eb93af91.json"}}], "type": "posted-content", "published": "2018-09-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/413203", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:11:07.526Z", "modified": "2026-08-20T11:11:07.597Z"}, {"entity": "publication", "iuid": "596c6842840d44b2a37aa630556f1a11", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/596c6842840d44b2a37aa630556f1a11.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/596c6842840d44b2a37aa630556f1a11"}}, "title": "Discovery and characterization of coding and non-coding driver mutations in more than 2,500 whole cancer genomes", "authors": [{"family": "Rheinbay", "given": "Esther", "initials": "E", "orcid": "0000-0002-5566-6729", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/527d460f24d445a09f64f054ac920fb3.json"}}, {"family": "Nielsen", "given": "Morten Muhlig", "initials": "MM", "orcid": 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