{"entity": "researcher", "timestamp": "2026-09-24T15:35:54.045Z", "family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "affiliations": ["Division of Oncology, Department of Clinical Sciences, Lund and CREATE Health Strategic Center for Translational Cancer Research, Lund University, Lund, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/8119afcc89de4612af587fc5f9894414.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/8119afcc89de4612af587fc5f9894414"}}, "publications": [{"entity": "publication", "iuid": "0ee00aff002c4776a25adbbe84433352", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0ee00aff002c4776a25adbbe84433352.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0ee00aff002c4776a25adbbe84433352"}}, "title": "The DNA methylation landscape of primary triple-negative breast cancer.", "authors": [{"family": "Aine", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0851-5952", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9782fed0f6f241b081264c3c0c2fef7f.json"}}, {"family": "Nacer", "given": "Deborah F", "initials": "DF", "orcid": "0000-0002-7117-1371", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/994ff56cdd4d4afb80e9c6a254fee95f.json"}}, {"family": "Arbajian", "given": "Elsa", "initials": "E", "orcid": "0000-0002-1484-0073", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c0d09ac22874c21aa25050058393812.json"}}, {"family": "Veerla", "given": "Srinivas", "initials": "S", "orcid": "0000-0001-7328-6239", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/44e47d0d4dd34428902bb18ffaa5e33a.json"}}, {"family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8119afcc89de4612af587fc5f9894414.json"}}, {"family": "H\u00e4kkinen", "given": "Jari", "initials": "J", "orcid": "0000-0002-8466-9179", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c5bfa55b9ef54c97a884078a80ec9c8f.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8acb3ba52a54c7a82f2a096516a8e05.json"}}, {"family": "Rosengren", "given": "Frida", "initials": "F"}, {"family": "Vallon-Christersson", "given": "Johan", "initials": "J", "orcid": "0000-0002-2195-0385", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5a79aa63d75d4ffbb4228bc7c3e16ac4.json"}}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5", "orcid": "0000-0002-5793-132X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/42b9688e2b634ae5b40b28b2ff23f9ee.json"}}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c7e552718d34d09a9a11aa54e90e37c.json"}}], "type": "journal article", "published": "2025-03-28", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "3041", "issn-l": "2041-1723"}, "abstract": "Triple-negative breast cancer (TNBC) is a clinically challenging and molecularly heterogenous breast cancer subgroup. Here, we investigate the DNA methylation landscape of TNBC. By analyzing tumor methylome profiles and accounting for the genomic context of CpG methylation, we divide TNBC into two epigenetic subtypes corresponding to a Basal and a non-Basal group, in which characteristic transcriptional patterns are correlated with DNA methylation of distal regulatory elements and epigenetic regulation of key steroid response genes and developmental transcription factors. Further subdivision of the Basal and non-Basal subtypes identifies subgroups transcending genetic and proposed TNBC mRNA subtypes, demonstrating widely differing immunological microenvironments, putative epigenetically-mediated immune evasion strategies, and a specific metabolic gene network in older patients that may be epigenetically regulated. Our study attempts to target the epigenetic backbone of TNBC, an approach that may inform future studies regarding tumor origins and the role of the microenvironment in shaping the cancer epigenome.", "doi": "10.1038/s41467-025-58158-x", "pmid": "40155623", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11953470"}, {"db": "pii", "key": "10.1038/s41467-025-58158-x"}], "notes": [], "created": "2026-09-23T09:06:28.629Z", "modified": "2026-09-23T09:06:29.016Z"}, {"entity": "publication", "iuid": "9779940ec8694f7b85936f39d787c714", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9779940ec8694f7b85936f39d787c714.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9779940ec8694f7b85936f39d787c714"}}, "title": "Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms.", "authors": [{"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Arslan", "given": "Taner", "initials": "T", "orcid": "0000-0002-2388-1811", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4fcf442970d44f5dac8736fbd96ba550.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Pan", "given": "Yanbo", "initials": "Y", "orcid": "0000-0001-9442-7782", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/51c4acd7c38841d7b259026d6311d88b.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Berkovska", "given": "Olena", "initials": "O", "orcid": "0000-0002-8811-0591", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/887be29288744e6c860e1e00a2501dce.json"}}, {"family": "Umer", "given": "Husen M", "initials": "HM"}, {"family": "Mermelekas", "given": "Georgios", "initials": "G"}, {"family": "Pirmoradian", "given": "Mohammad", "initials": "M"}, {"family": "J\u00f6nsson", "given": "Mats", "initials": "M"}, {"family": "Brunnstr\u00f6m", "given": "Hans", "initials": "H", "orcid": "0000-0001-7402-138X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1b51d0768d1a4c31bba8cf898f962a09.json"}}, {"family": "Brustugun", "given": "Odd Terje", "initials": "OT"}, {"family": "Purohit", "given": "Krishna Pinganksha", "initials": "KP"}, {"family": "Cunningham", "given": "Richard", "initials": "R"}, {"family": "Foroughi Asl", "given": "Hassan", "initials": "H"}, {"family": "Isaksson", "given": "Sofi", "initials": "S"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Aine", "given": "Mattias", "initials": "M", "orcid": "0000-0002-0851-5952", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9782fed0f6f241b081264c3c0c2fef7f.json"}}, {"family": "Karlsson", "given": "Anna", "initials": "A", "orcid": "0000-0001-6974-5965", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8119afcc89de4612af587fc5f9894414.json"}}, {"family": "Kotevska", "given": "Marija", "initials": "M"}, {"family": "Gram Hansen", "given": "Carsten", "initials": "C"}, {"family": "Drageset Haakensen", "given": "Vilde", "initials": "V"}, {"family": "Helland", "given": "\u00c5slaug", "initials": "\u00c5"}, {"family": "Tamborero", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8acb3ba52a54c7a82f2a096516a8e05.json"}}, {"family": "Branca", "given": "Rui M", "initials": "RM"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J", "orcid": "0000-0001-5254-5115", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3c7e552718d34d09a9a11aa54e90e37c.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}], "type": "journal article", "published": "2021-11-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "2", "issue": "11", "pages": "1224-1242", "issn-l": null}, "abstract": "Despite major advancements in lung cancer treatment, long-term survival is still rare, and a deeper understanding of molecular phenotypes would allow the identification of specific cancer dependencies and immune evasion mechanisms. Here we performed in-depth mass spectrometry (MS)-based proteogenomic analysis of 141 tumors representing all major histologies of non-small cell lung cancer (NSCLC). We identified six distinct proteome subtypes with striking differences in immune cell composition and subtype-specific expression of immune checkpoints. Unexpectedly, high neoantigen burden was linked to global hypomethylation and complex neoantigens mapped to genomic regions, such as endogenous retroviral elements and introns, in immune-cold subtypes. Further, we linked immune evasion with LAG3 via STK11 mutation-dependent HNF1A activation and FGL1 expression. Finally, we develop a data-independent acquisition MS-based NSCLC subtype classification method, validate it in an independent cohort of 208 NSCLC cases and demonstrate its clinical utility by analyzing an additional cohort of 84 late-stage NSCLC biopsy samples.", "doi": "10.1038/s43018-021-00259-9", "pmid": "34870237", "labels": [], "xrefs": [{"db": "mid", "key": "EMS133264"}, {"db": "pmc", "key": "PMC7612062"}, {"db": "pii", "key": "10.1038/s43018-021-00259-9"}], "notes": [], "created": "2026-09-23T07:36:20.274Z", "modified": "2026-09-23T07:36:20.545Z"}]}