{"entity": "researcher", "timestamp": "2026-08-11T13:52:35.012Z", "family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "affiliations": ["Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden."], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956"}}, "publications": [{"entity": "publication", "iuid": "a820631626024f32811c8031777bf540", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a820631626024f32811c8031777bf540"}}, "title": "Combinatorial DNMTs and EZH2 inhibition reprograms the H3K27me3 and DNAme-mediated onco-epigenome to suppress multiple myeloma proliferation.", "authors": [{"family": "Atienza P\u00e1rraga", "given": "Alba", "initials": "A"}, {"family": "Nylund", "given": "Patrick", "initials": "P", "orcid": "0000-0002-1274-4010", "researcher": {"href": "https://publications.scilifelab.se/researcher/683976ea3c094b198998dabb0d433f4b.json"}}, {"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Garrido-Zabala", "given": "Berta", "initials": "B"}, {"family": "Tziola", "given": "Stefania Iliana", "initials": "SI"}, {"family": "Vasquez", "given": "Louella", "initials": "L", "orcid": "0000-0002-5758-6036", "researcher": {"href": "https://publications.scilifelab.se/researcher/0479eadb09d44ece8523730e1e0fd0b1.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications.scilifelab.se/researcher/a69051a0275c442c8c0d5621b4000929.json"}}, {"family": "Raykova", "given": "Doroteya", "initials": "D", "orcid": "0000-0001-6452-2199", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a81c40491e349178167f148f2351875.json"}}, {"family": "Skaftason", "given": "Aron", "initials": "A"}, {"family": "Ma", "given": "Anqi", "initials": "A", "orcid": "0000-0002-9293-4753", "researcher": {"href": "https://publications.scilifelab.se/researcher/67c70ee5b7bd4136a74d7605ec7b1614.json"}}, {"family": "Jin", "given": "Jian", "initials": "J", "orcid": "0000-0002-3774-1609", "researcher": {"href": "https://publications.scilifelab.se/researcher/ed488bfe2c024a6b874b3b964ce80b97.json"}}, {"family": "Mart\u00edn-Subero", "given": "Jos\u00e9 Ignacio", "initials": "JI", "orcid": "0000-0001-8809-5195", "researcher": {"href": "https://publications.scilifelab.se/researcher/06ccbd6b7051490fb2764ce9da7a418e.json"}}, {"family": "\u00d6berg", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-3609-1197", "researcher": {"href": "https://publications.scilifelab.se/researcher/c68243c8cc754cdb8b380db120f3b771.json"}}, {"family": "De Bruyne", "given": "Elke", "initials": "E", "orcid": "0000-0003-4012-4617", "researcher": {"href": "https://publications.scilifelab.se/researcher/e2715df4e920432c9723d8fdf4ff897b.json"}}, {"family": "Komorowski", "given": "Jan", "initials": "J", "orcid": "0000-0002-0766-8789", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2d1190dfa864e4089c58c864857b114.json"}}, {"family": "Jernberg Wiklund", "given": "Helena", "initials": "H"}, {"family": "Kalushkova", "given": "Antonia", "initials": "A", "orcid": "0000-0003-4535-506X", "researcher": {"href": "https://publications.scilifelab.se/researcher/df89c7522b7b4af3b3cef8555380fe8c.json"}}], "type": "journal article", "published": "2025-08-27", "journal": {"title": "Sci Rep", "issn": "2045-2322", "issn-l": "2045-2322", "volume": "15", "issue": "1", "pages": "31568"}, "abstract": "Comprehensive epigenomic studies in multiple myeloma (MM) that unravel the connections between major epigenetic regulators, their intertwined collaboration and the potential of combinatorial targeting remain limited. Utilizing ChIP-seq, ATAC-seq, RNA-seq, and DNA methylation (DNAme) data, we generated whole-genome chromatin annotations from normal plasma cells and MM patients, revealing epigenomic re-configuration affecting downstream genes involved in tumour growth and survival. Primary MM samples showed global DNA hypomethylation but site-specific hypermethylation was observed at transcription start sites, promoters, and enhancers. Moreover, increased deposition of H3K27me3 was observed in clinically relevant functional chromatin clusters. Combined EZH2 and DNMTs inhibition resulted in extensive epigenomic alterations activating apoptosis and cell cycle genes, leading to increased G2/M arrest and apoptosis in MM cell lines. Our findings provide novel insights into the role of epigenetic gene silencing in MM tumorigenesis and the interplay between the Polycomb repressive complex 2 and DNAme.\r\n\r\nThe online version contains supplementary material available at 10.1038/s41598-025-17093-z.", "doi": "10.1038/s41598-025-17093-z", "pmid": "40866476", "labels": {"NGI Short read": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "National Genomics Infrastructure": "Service", "Bioinformatics (NBIS)": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Bioinformatics Support, Infrastructure and Training": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC12391466"}, {"db": "pii", "key": "10.1038/s41598-025-17093-z"}], "notes": [], "created": "2025-09-08T07:11:30.283Z", "modified": "2025-10-06T12:40:33.288Z"}, {"entity": "publication", "iuid": "62ecd11c1f8b43f984f8802df9da6dbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/62ecd11c1f8b43f984f8802df9da6dbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/62ecd11c1f8b43f984f8802df9da6dbb"}}, "title": "Single nucleus transcriptomics data integration recapitulates the major cell types in human liver.", "authors": [{"family": "Diamanti", "given": "Klev", "initials": "K", "orcid": "0000-0002-4922-8415", "researcher": {"href": "https://publications.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Inda D\u00edaz", "given": "Juan Salvador", "initials": "JS", "orcid": "0000-0002-3735-8300", "researcher": {"href": "https://publications.scilifelab.se/researcher/40b6bd806d874198a7509500bddfd939.json"}}, {"family": "Raine", "given": "Amanda", "initials": "A", "orcid": "0000-0002-2775-6516", "researcher": {"href": "https://publications.scilifelab.se/researcher/a97b7df8379f42f0a412fb7c234a6c70.json"}}, {"family": "Pan", "given": "Gang", "initials": "G", "orcid": "0000-0003-4243-1821", "researcher": {"href": "https://publications.scilifelab.se/researcher/e956246a20aa4ed3a67c084a4c1e5289.json"}}, {"family": "Wadelius", "given": "Claes", "initials": "C", "orcid": "0000-0002-2033-7829", "researcher": {"href": "https://publications.scilifelab.se/researcher/2ec5ca1122024da4893b61e329a5ece5.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M", "orcid": "0000-0003-1143-1431", "researcher": {"href": "https://publications.scilifelab.se/researcher/e35211c06385459baee12101121d2a15.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Hepatol Res", "issn": "1386-6346", "issn-l": null, "volume": "51", "issue": "2", "pages": "233-238"}, "abstract": "The aim of this study was to explore the benefits of data integration from different platforms for single nucleus transcriptomics profiling to characterize cell populations in human liver.\n\nWe generated single-nucleus RNA sequencing data from Chromium 10X Genomics and Drop-seq for a human liver sample. We utilized state of the art bioinformatics tools to undertake a rigorous quality control and to integrate the data into a common space summarizing the gene expression variation from the respective platforms, while accounting for known and unknown confounding factors.\n\nAnalysis of single nuclei transcriptomes from both 10X and Drop-seq allowed identification of the major liver cell types, while the integrated set obtained enough statistical power to separate a small population of inactive hepatic stellate cells that was not characterized in either of the platforms.\n\nIntegration of droplet-based single nucleus transcriptomics data enabled identification of a small cluster of inactive hepatic stellate cells that highlights the potential of our approach. We suggest single-nucleus RNA sequencing integrative approaches could be utilized to design larger and cost-effective studies.", "doi": "10.1111/hepr.13585", "pmid": "33119937", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [], "notes": [], "created": "2020-12-08T23:37:37.148Z", "modified": "2024-01-16T13:48:40.820Z"}, {"entity": "publication", "iuid": "aadffd1889e544f1b9aa22c5a6ca91ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aadffd1889e544f1b9aa22c5a6ca91ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aadffd1889e544f1b9aa22c5a6ca91ac"}}, "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.scilifelab.se/researcher/b71560391b294bb5a344b9c6cabfc956.json"}}, {"family": "Cavalli", "given": "Marco", "initials": "M"}, {"family": "Pan", "given": "Gang", "initials": "G"}, {"family": "Pereira", "given": "Maria J", "initials": "MJ", "orcid": "0000-0001-5498-3899", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee6367673ade411a885a20ecefdac3c1.json"}}, {"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"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal-article", "published": "2019-12-00", "journal": {"volume": "9", "issn": "2045-2322", "issue": "1", "pages": "9653", "title": "Sci Rep", "issn-l": "2045-2322"}, "abstract": "Type 2 diabetes (T2D) mellitus is a complex metabolic disease commonly caused by insulin resistance in several tissues. We performed a matched two-dimensional metabolic screening in tissue samples from 43 multi-organ donors. The intra-individual analysis was assessed across five key metabolic tissues (serum, visceral adipose tissue, liver, pancreatic islets and skeletal muscle), and the inter-individual across three different groups reflecting T2D progression. We identified 92 metabolites differing significantly between non-diabetes and T2D subjects. In diabetes cases, carnitines were significantly higher in liver, while lysophosphatidylcholines were significantly lower in muscle and serum. We tracked the primary tissue of origin for multiple metabolites whose alterations were reflected in serum. An investigation of three major stages spanning from controls, to pre-diabetes and to overt T2D indicated that a subset of lysophosphatidylcholines was significantly lower in the muscle of pre-diabetes subjects. Moreover, glycodeoxycholic acid was significantly higher in liver of pre-diabetes subjects while additional increase in T2D was insignificant. We confirmed many previously reported findings and substantially expanded on them with altered markers for early and overt T2D. Overall, the analysis of this unique dataset can increase the understanding of the metabolic interplay between organs in the development of T2D.", "doi": "10.1038/s41598-019-45906-5", "pmid": "31273253", "labels": {"Bioinformatics Support for Computational Resources": "Service", "Swedish Metabolomics Centre": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s41598-019-45906-5"}, {"db": "pmc", "key": "PMC6609645"}], "notes": [], "created": "2020-01-07T15:53:12.510Z", "modified": "2025-10-17T13:03:17.098Z"}]}