{"entity": "publication", "iuid": "9779940ec8694f7b85936f39d787c714", "timestamp": "2026-09-24T14:46:17.778Z", "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"}