{"entity": "journal", "iuid": "65f55f69bd5e43c39c110a68aa020a24", "timestamp": "2026-07-17T08:51:17.548Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/Nat%20Cancer.json"}, "display": {"href": "https://publications.scilifelab.se/journal/Nat%20Cancer"}}, "title": "Nat Cancer", "issn": "2662-1347", "issn-l": null, "publications_count": 7, "publications": [{"entity": "publication", "iuid": "c2874ad4279747de98010159c6b2bbcc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2874ad4279747de98010159c6b2bbcc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2874ad4279747de98010159c6b2bbcc"}}, "title": "Aberrant expression of SLAMF6 constitutes a targetable immune escape mechanism in acute myeloid leukemia.", "authors": [{"family": "Sand\u00e9n", "given": "Carl", "initials": "C", "orcid": "0000-0002-8931-9565", "researcher": {"href": "https://publications.scilifelab.se/researcher/29207805704e4660b20eebc87efe5282.json"}}, {"family": "Landberg", "given": "Niklas", "initials": "N", "orcid": "0000-0001-6752-6507", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ad422be3ea44e419662d514ca40cbbe.json"}}, {"family": "Pe\u00f1a-Mart\u00ednez", "given": "Pablo", "initials": "P", "orcid": "0000-0002-0789-6431", "researcher": {"href": "https://publications.scilifelab.se/researcher/6d675e892dfc4334bb12051e004a7711.json"}}, {"family": "Thorsson", "given": "Hanna", "initials": "H", "orcid": "0000-0001-5393-2942", "researcher": {"href": "https://publications.scilifelab.se/researcher/7667559679a64a999d508ff7fa506782.json"}}, {"family": "Daga", "given": "Shruti", "initials": "S"}, {"family": "Puente-Moncada", "given": "Noelia", "initials": "N"}, {"family": "Rodriguez-Zabala", "given": "Maria", "initials": "M"}, {"family": "von Palffy", "given": "Sofia", "initials": "S"}, {"family": "Rissler", "given": "Marianne", "initials": "M"}, {"family": "Lazarevic", "given": "Vladimir", "initials": "V", "orcid": "0000-0002-1782-4423", "researcher": {"href": "https://publications.scilifelab.se/researcher/7113f0d0569247d4ac94b73ddc6ca74e.json"}}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Ohlin", "given": "Mats", "initials": "M", "orcid": "0000-0002-5105-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/fda1d1ed0b074a04a69b0c8b036dd001.json"}}, {"family": "Hyrenius-Wittsten", "given": "Axel", "initials": "A"}, {"family": "Orsmark-Pietras", "given": "Christina", "initials": "C", "orcid": "0000-0002-6533-0305", "researcher": {"href": "https://publications.scilifelab.se/researcher/66a38c96c9854fb18eb2420689d620e2.json"}}, {"family": "Lilljebj\u00f6rn", "given": "Henrik", "initials": "H", "orcid": "0000-0001-8703-1173", "researcher": {"href": "https://publications.scilifelab.se/researcher/b3a75300e8c346858ce8dd8f64ecae85.json"}}, {"family": "\u00c5gerstam", "given": "Helena", "initials": "H"}, {"family": "Fioretos", "given": "Thoas", "initials": "T", "orcid": "0000-0002-3235-6154", "researcher": {"href": "https://publications.scilifelab.se/researcher/35a5c1b6023345c6b1317c590bf80680.json"}}], "type": "journal article", "published": "2025-11-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "6", "issue": "11", "pages": "1821-1838", "issn-l": null}, "abstract": "Immunotherapy has shown limited success in acute myeloid leukemia (AML), indicating an incomplete understanding of the underlying immunoregulatory mechanisms. Here we identify an immune evasion mechanism present in 60% of AML cases, wherein primitive AML cells aberrantly express the lymphoid surface protein SLAMF6 (signaling lymphocyte activation molecule family member 6). Knockout of SLAMF6 in AML cells enables T cell activation and highly efficient killing of leukemia cells in coculture systems, demonstrating that SLAMF6 protects AML cells from recognition and elimination by the immune system in a mode analogous to the programmed cell death protein-ligand (PDL1/PD1) axis. Targeting SLAMF6 with an antibody against the SLAMF6 dimerization site inhibits the SLAMF6-SLAMF6 interaction and induces T cell activation and killing of AML cells both in vitro and in humanized in vivo models. In conclusion, we show that aberrant expression of SLAMF6 is a common and targetable immune escape mechanism that could pave the way for immunotherapy in AML.", "doi": "10.1038/s43018-025-01054-6", "pmid": "41044242", "labels": {"Clinical Genomics Lund": "Service", "Drug Discovery and Development": "Collaborative", "Structural Proteomics": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-025-01054-6"}, {"db": "pmc", "key": "PMC12643940"}], "notes": [], "created": "2025-11-05T18:37:31.700Z", "modified": "2025-11-26T16:29:09.833Z"}, {"entity": "publication", "iuid": "b6fc0f9d7a044833846df2ea3ca6b15b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b6fc0f9d7a044833846df2ea3ca6b15b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b6fc0f9d7a044833846df2ea3ca6b15b"}}, "title": "A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.", "authors": [{"family": "Giannakopoulou", "given": "Eirini", "initials": "E"}, {"family": "Lehander", "given": "Madeleine", "initials": "M"}, {"family": "Virding Culleton", "given": "Stina", "initials": "S"}, {"family": "Yang", "given": "Weiwen", "initials": "W"}, {"family": "Li", "given": "Yingqian", "initials": "Y"}, {"family": "Karpanen", "given": "Terhi", "initials": "T", "orcid": "0000-0002-2803-083X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ca6013dbea3045e798ce756d45b9777f.json"}}, {"family": "Yoshizato", "given": "Tetsuichi", "initials": "T"}, {"family": "Rustad", "given": "Even H", "initials": "EH"}, {"family": "Nielsen", "given": "Morten Milek", "initials": "MM"}, {"family": "Bollineni", "given": "Ravi Chand", "initials": "RC"}, {"family": "Tran", "given": "Trung T", "initials": "TT"}, {"family": "Delic-Sarac", "given": "Marina", "initials": "M"}, {"family": "Gjerdingen", "given": "Thea Johanne", "initials": "TJ"}, {"family": "Douvlataniotis", "given": "Karolos", "initials": "K"}, {"family": "Laos", "given": "Maarja", "initials": "M"}, {"family": "Ali", "given": "Muhammad", "initials": "M"}, {"family": "Hillen", "given": "Amy", "initials": "A", "orcid": "0000-0002-8567-1545", "researcher": {"href": "https://publications.scilifelab.se/researcher/fba7f6c5a2f04d71816a8381ede8a615.json"}}, {"family": "Mazzi", "given": "Stefania", "initials": "S"}, {"family": "Chin", "given": "Desmond Wai Loon", "initials": "DWL"}, {"family": "Mehta", "given": "Adi", "initials": "A"}, {"family": "Holm", "given": "Jeppe Sejer\u00f8", "initials": "JS"}, {"family": "Bentzen", "given": "Amalie Kai", "initials": "AK"}, {"family": "Bill", "given": "Marie", "initials": "M"}, {"family": "Griffioen", "given": "Marieke", "initials": "M", "orcid": "0000-0002-3001-4441", "researcher": {"href": "https://publications.scilifelab.se/researcher/1cb97023cdb84dd0aaecc659eca5d6a3.json"}}, {"family": "Gedde-Dahl", "given": "Tobias", "initials": "T"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Jacobsen", "given": "Sten Eirik W", "initials": "SEW", "orcid": "0000-0002-1362-3659", "researcher": {"href": "https://publications.scilifelab.se/researcher/648fc5e4f49e4330b095c26cd965cc98.json"}}, {"family": "Woll", "given": "Petter S", "initials": "PS", "orcid": "0000-0002-2340-2526", "researcher": {"href": "https://publications.scilifelab.se/researcher/77ae0c1d2cf5461894c6d0d80ed42f68.json"}}, {"family": "Olweus", "given": "Johanna", "initials": "J", "orcid": "0000-0002-1898-3100", "researcher": {"href": "https://publications.scilifelab.se/researcher/2bbcafcada6a4586948b50153464ec60.json"}}], "type": "journal article", "published": "2023-10-02", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "issn-l": null}, "abstract": "Acute myeloid leukemia (AML), the most frequent leukemia in adults, is driven by recurrent somatically acquired genetic lesions in a restricted number of genes. Treatment with tyrosine kinase inhibitors has demonstrated that targeting of prevalent FMS-related receptor tyrosine kinase 3 (FLT3) gain-of-function mutations can provide significant survival benefits for patients, although the efficacy of FLT3 inhibitors in eliminating FLT3-mutated clones is variable. We identified a T cell receptor (TCR) reactive to the recurrent D835Y driver mutation in the FLT3 tyrosine kinase domain (TCRFLT3D/Y). TCRFLT3D/Y-redirected T cells selectively eliminated primary human AML cells harboring the FLT3D835Y mutation in vitro and in vivo. TCRFLT3D/Y cells rejected both CD34+ and CD34- AML in mice engrafted with primary leukemia from patients, reaching minimal residual disease-negative levels, and eliminated primary CD34+ AML leukemia-propagating cells in vivo. Thus, T cells targeting a single shared mutation can provide efficient immunotherapy toward selective elimination of clonally involved primary AML cells in vivo.", "doi": "10.1038/s43018-023-00642-8", "pmid": "37783807", "labels": {"NGI Short read": "Service", "National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Production)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-023-00642-8"}], "notes": [], "created": "2023-10-19T13:55:47.476Z", "modified": "2023-10-19T13:55:47.704Z"}, {"entity": "publication", "iuid": "1a1d9f2b8c78456e97322487cf985e6d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1a1d9f2b8c78456e97322487cf985e6d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1a1d9f2b8c78456e97322487cf985e6d"}}, "title": "Author Correction: The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.", "authors": [{"family": "Tamborero", "given": "David", "initials": "D", "orcid": "0000-0002-7218-2806", "researcher": {"href": "https://publications.scilifelab.se/researcher/740d488afc204156b682b67589992023.json"}}, {"family": "Dienstmann", "given": "Rodrigo", "initials": "R"}, {"family": "Rachid", "given": "Maan Haj", "initials": "MH"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Lopez-Fernandez", "given": "Adria", "initials": "A", "orcid": "0000-0002-2844-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/959015b1815647edaee690c9d59b1913.json"}}, {"family": "Jonsson", "given": "Markus", "initials": "M"}, {"family": "Razzak", "given": "Ali", "initials": "A"}, {"family": "Bra\u00f1a", "given": "Irene", "initials": "I"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Yachnin", "given": "Jeffrey", "initials": "J"}, {"family": "Baird", "given": "Richard D", "initials": "RD", "orcid": "0000-0001-7071-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/11aa354bf2f74c4d8c31f3e0faf650db.json"}}, {"family": "Loriot", "given": "Yohann", "initials": "Y"}, {"family": "Massard", "given": "Christophe", "initials": "C"}, {"family": "Martin-Romano", "given": "Patricia", "initials": "P"}, {"family": "Opdam", "given": "Frans", "initials": "F"}, {"family": "Schlenk", "given": "Richard F", "initials": "RF"}, {"family": "Vernieri", "given": "Claudio", "initials": "C"}, {"family": "Masucci", "given": "Michele", "initials": "M"}, {"family": "Villalobos", "given": "Xenia", "initials": "X"}, {"family": "Chavarria", "given": "Elena", "initials": "E"}, {"family": "Cancer Core Europe consortium", "given": "", "initials": ""}, {"family": "Balma\u00f1a", "given": "Judith", "initials": "J", "orcid": "0000-0002-0762-6415", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bd06da8f9fa4d56bdc176d31695f78f.json"}}, {"family": "Apolone", "given": "Giovanni", "initials": "G"}, {"family": "Caldas", "given": "Carlos", "initials": "C", "orcid": "0000-0003-3547-1489", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cc09ee06f6c4391ba062ac65e85cb55.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Ernberg", "given": "Ingemar", "initials": "I", "orcid": "0000-0001-6518-1648", "researcher": {"href": "https://publications.scilifelab.se/researcher/1da842a1d09c4268840407774e351809.json"}}, {"family": "Fr\u00f6hling", "given": "Stefan", "initials": "S", "orcid": "0000-0001-7907-4595", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd46d3f4c2084ce7922ceb0220b09277.json"}}, {"family": "Garralda", "given": "Elena", "initials": "E"}, {"family": "Karlsson", "given": "Claes", "initials": "C"}, {"family": "Tabernero", "given": "Josep", "initials": "J", "orcid": "0000-0002-2495-8139", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9be0e16fc3f415e92754a6135bfc164.json"}}, {"family": "Voest", "given": "Emile", "initials": "E", "orcid": "0000-0001-8249-9586", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a8340e3b0445bea291f971e1c2c75e.json"}}, {"family": "Rodon", "given": "Jordi", "initials": "J"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "published erratum", "published": "2022-05-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "3", "issue": "5", "pages": "649", "issn-l": null}, "abstract": null, "doi": "10.1038/s43018-022-00378-x", "pmid": "35449310", "labels": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC9135626"}, {"db": "pii", "key": "10.1038/s43018-022-00378-x"}], "notes": [], "created": "2022-11-24T20:27:37.980Z", "modified": "2022-11-25T19:50:36.186Z"}, {"entity": "publication", "iuid": "2bcf23149f1f428991a34f8da5396b04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2bcf23149f1f428991a34f8da5396b04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2bcf23149f1f428991a34f8da5396b04"}}, "title": "The Molecular Tumor Board Portal supports clinical decisions and automated reporting for precision oncology.", "authors": [{"family": "Tamborero", "given": "David", "initials": "D", "orcid": "0000-0002-7218-2806", "researcher": {"href": "https://publications.scilifelab.se/researcher/740d488afc204156b682b67589992023.json"}}, {"family": "Dienstmann", "given": "Rodrigo", "initials": "R"}, {"family": "Rachid", "given": "Maan Haj", "initials": "MH"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Lopez-Fernandez", "given": "Adria", "initials": "A", "orcid": "0000-0002-2844-5998", "researcher": {"href": "https://publications.scilifelab.se/researcher/959015b1815647edaee690c9d59b1913.json"}}, {"family": "Jonsson", "given": "Markus", "initials": "M"}, {"family": "Razzak", "given": "Ali", "initials": "A"}, {"family": "Bra\u00f1a", "given": "Irene", "initials": "I"}, {"family": "De Petris", "given": "Luigi", "initials": "L"}, {"family": "Yachnin", "given": "Jeffrey", "initials": "J"}, {"family": "Baird", "given": "Richard D", "initials": "RD", "orcid": "0000-0001-7071-6483", "researcher": {"href": "https://publications.scilifelab.se/researcher/11aa354bf2f74c4d8c31f3e0faf650db.json"}}, {"family": "Loriot", "given": "Yohann", "initials": "Y"}, {"family": "Massard", "given": "Christophe", "initials": "C"}, {"family": "Martin-Romano", "given": "Patricia", "initials": "P"}, {"family": "Opdam", "given": "Frans", "initials": "F"}, {"family": "Schlenk", "given": "Richard F", "initials": "RF"}, {"family": "Vernieri", "given": "Claudio", "initials": "C"}, {"family": "Masucci", "given": "Michele", "initials": "M"}, {"family": "Villalobos", "given": "Xenia", "initials": "X"}, {"family": "Chavarria", "given": "Elena", "initials": "E"}, {"family": "Cancer Core Europe consortium", "given": "", "initials": ""}, {"family": "Balma\u00f1a", "given": "Judith", "initials": "J", "orcid": "0000-0002-0762-6415", "researcher": {"href": "https://publications.scilifelab.se/researcher/3bd06da8f9fa4d56bdc176d31695f78f.json"}}, {"family": "Apolone", "given": "Giovanni", "initials": "G"}, {"family": "Caldas", "given": "Carlos", "initials": "C", "orcid": "0000-0003-3547-1489", "researcher": {"href": "https://publications.scilifelab.se/researcher/0cc09ee06f6c4391ba062ac65e85cb55.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd38f4f7704144ed9e3f869e197175e6.json"}}, {"family": "Ernberg", "given": "Ingemar", "initials": "I", "orcid": "0000-0001-6518-1648", "researcher": {"href": "https://publications.scilifelab.se/researcher/1da842a1d09c4268840407774e351809.json"}}, {"family": "Fr\u00f6hling", "given": "Stefan", "initials": "S", "orcid": "0000-0001-7907-4595", "researcher": {"href": "https://publications.scilifelab.se/researcher/cd46d3f4c2084ce7922ceb0220b09277.json"}}, {"family": "Garralda", "given": "Elena", "initials": "E"}, {"family": "Karlsson", "given": "Claes", "initials": "C"}, {"family": "Tabernero", "given": "Josep", "initials": "J", "orcid": "0000-0002-2495-8139", "researcher": {"href": "https://publications.scilifelab.se/researcher/c9be0e16fc3f415e92754a6135bfc164.json"}}, {"family": "Voest", "given": "Emile", "initials": "E", "orcid": "0000-0001-8249-9586", "researcher": {"href": "https://publications.scilifelab.se/researcher/e5a8340e3b0445bea291f971e1c2c75e.json"}}, {"family": "Rodon", "given": "Jordi", "initials": "J"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "3", "issue": "2", "pages": "251-261", "issn-l": null}, "abstract": "There is a growing need for systems that efficiently support the work of medical teams at the precision-oncology point of care. Here, we present the implementation of the Molecular Tumor Board Portal (MTBP), an academic clinical decision support system developed under the umbrella of Cancer Core Europe that creates a unified legal, scientific and technological platform to share and harness next-generation sequencing data. Automating the interpretation and reporting of sequencing results decrease the need for time-consuming manual procedures that are prone to errors. The adoption of an expert-agreed process to systematically link tumor molecular profiles with clinical actions promotes consistent decision-making and structured data capture across the connected centers. The use of information-rich patient reports with interactive content facilitates collaborative discussion of complex cases during virtual molecular tumor board meetings. Overall, streamlined digital systems like the MTBP are crucial to better address the challenges brought by precision oncology and accelerate the use of emerging biomarkers.", "doi": "10.1038/s43018-022-00332-x", "pmid": "35221333", "labels": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC8882467"}, {"db": "pii", "key": "10.1038/s43018-022-00332-x"}], "notes": [], "created": "2022-11-25T19:59:26.171Z", "modified": "2022-11-25T19:59:26.239Z"}, {"entity": "publication", "iuid": "483fd25be0c940a88ec33ee37fd176c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/483fd25be0c940a88ec33ee37fd176c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/483fd25be0c940a88ec33ee37fd176c8"}}, "title": "Pharmacological targeting of MTHFD2 suppresses acute myeloid leukemia by inducing thymidine depletion and replication stress.", "authors": [{"family": "Bonagas", "given": "Nadilly", "initials": "N", "orcid": "0000-0001-7336-4065", "researcher": {"href": "https://publications.scilifelab.se/researcher/1e38f3b0752740969c5c13fb77885b27.json"}}, {"family": "Gustafsson", "given": "Nina M S", "initials": "NMS"}, {"family": "Henriksson", "given": "Martin", "initials": "M"}, {"family": "Marttila", "given": "Petra", "initials": "P", "orcid": "0000-0002-0115-8067", "researcher": {"href": "https://publications.scilifelab.se/researcher/2e3e92bdf843456784f98d3b521d2ccd.json"}}, {"family": "Gustafsson", "given": "Robert", "initials": "R", "orcid": "0000-0002-4854-5531", "researcher": {"href": "https://publications.scilifelab.se/researcher/16dd7e73adad4f85972d1d546bfa6d2a.json"}}, {"family": "Wiita", "given": "Elis\u00e9e", "initials": "E"}, {"family": "Borhade", "given": "Sanjay", "initials": "S"}, {"family": "Green", "given": "Alanna C", "initials": "AC"}, {"family": "Vallin", "given": "Karl S A", "initials": "KSA"}, {"family": "Sarno", "given": "Antonio", "initials": "A"}, {"family": "Svensson", "given": "Richard", "initials": "R"}, {"family": "G\u00f6kt\u00fcrk", "given": "Camilla", "initials": "C"}, {"family": "Pham", "given": "Therese", "initials": "T"}, {"family": "Jemth", "given": "Ann-Sofie", "initials": "AS", "orcid": "0000-0002-7550-1833", "researcher": {"href": "https://publications.scilifelab.se/researcher/fd07c6c543544af1a904e039f73ba857.json"}}, {"family": "Loseva", "given": "Olga", "initials": "O"}, {"family": "Cookson", "given": "Victoria", "initials": "V", "orcid": "0000-0003-3089-4837", "researcher": {"href": "https://publications.scilifelab.se/researcher/3cd81b473de74c26bad811b3c2f25b7f.json"}}, {"family": "Kiweler", "given": "Nicole", "initials": "N", "orcid": "0000-0001-7493-703X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f8b0eaee2d574b4daba1ee735c512797.json"}}, {"family": "Sandberg", "given": "Lars", "initials": "L"}, {"family": "Rasti", "given": "Azita", "initials": "A"}, {"family": "Unterlass", "given": "Judith E", "initials": "JE"}, {"family": "Haraldsson", "given": "Martin", "initials": "M"}, {"family": "Andersson", "given": "Yasmin", "initials": "Y"}, {"family": "Scaletti", "given": "Emma R", "initials": "ER"}, {"family": "Bengtsson", "given": "Christoffer", "initials": "C"}, {"family": "Paulin", "given": "Cynthia B J", "initials": "CBJ"}, {"family": "Sanjiv", "given": "Kumar", "initials": "K"}, {"family": "Abdurakhmanov", "given": "Eldar", "initials": "E"}, {"family": "Pudelko", "given": "Linda", "initials": "L"}, {"family": "Kunz", "given": "Ben", "initials": "B"}, {"family": "Desroses", "given": "Matthieu", "initials": "M"}, {"family": "Iliev", "given": "Petar", "initials": "P"}, {"family": "F\u00e4rneg\u00e5rdh", "given": "Katarina", "initials": "K"}, {"family": "Kr\u00e4mer", "given": "Andreas", "initials": "A", "orcid": "0000-0003-3294-2660", "researcher": {"href": "https://publications.scilifelab.se/researcher/37f158e9b24d43b69753ccbf029cb793.json"}}, {"family": "Garg", "given": "Neeraj", "initials": "N"}, {"family": "Michel", "given": "Maurice", "initials": "M"}, {"family": "H\u00e4ggblad", "given": "Sara", "initials": "S"}, {"family": "Jarvius", "given": "Malin", "initials": "M"}, {"family": "Kalder\u00e9n", "given": "Christina", "initials": "C"}, {"family": "Jensen", "given": "Amanda B\u00f6gedahl", "initials": "AB"}, {"family": "Alml\u00f6f", "given": "Ingrid", "initials": "I"}, {"family": "Karsten", "given": "Stella", "initials": "S", "orcid": "0000-0001-6191-4314", "researcher": {"href": "https://publications.scilifelab.se/researcher/4cbde9247c7145ff8ea0bbc0b0c5c477.json"}}, {"family": "Zhang", "given": "Si Min", "initials": "SM"}, {"family": "H\u00e4ggblad", "given": "Maria", "initials": "M"}, {"family": "Eriksson", "given": "Anders", "initials": "A"}, {"family": "Liu", "given": "Jianping", "initials": "J", "orcid": "0000-0002-7336-3895", "researcher": {"href": "https://publications.scilifelab.se/researcher/e77624d9d5b841608e142afbe2ead1d7.json"}}, {"family": "Glinghammar", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nekhotiaeva", "given": "Natalia", "initials": "N"}, {"family": "Klingeg\u00e5rd", "given": "Fredrik", "initials": "F"}, {"family": "Koolmeister", "given": "Tobias", "initials": "T"}, {"family": "Martens", "given": "Ulf", "initials": "U"}, {"family": "Llona-Minguez", "given": "Sabin", "initials": "S"}, {"family": "Moulson", "given": "Ruth", "initials": "R"}, {"family": "Nordstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Parrow", "given": "Vendela", "initials": "V"}, {"family": "Dahllund", "given": "Leif", "initials": "L"}, {"family": "Sj\u00f6berg", "given": "Birger", "initials": "B"}, {"family": "Vargas", "given": "Irene L", "initials": "IL"}, {"family": "Vo", "given": "Duy Duc", "initials": "DD"}, {"family": "Wannberg", "given": "Johan", "initials": "J", "orcid": "0000-0001-5494-0848", "researcher": {"href": "https://publications.scilifelab.se/researcher/d093f5fb52f644ce8994f3a6308272a8.json"}}, {"family": "Knapp", "given": "Stefan", "initials": "S", "orcid": "0000-0001-5995-6494", "researcher": {"href": "https://publications.scilifelab.se/researcher/c4d84c40612d48f280d4ead25558d835.json"}}, {"family": "Krokan", "given": "Hans E", "initials": "HE"}, {"family": "Arvidsson", "given": "Per I", "initials": "PI", "orcid": "0000-0002-9453-6812", "researcher": {"href": "https://publications.scilifelab.se/researcher/ae064b90b750457e80e974947f2dfc7a.json"}}, {"family": "Scobie", "given": "Martin", "initials": "M"}, {"family": "Meiser", "given": "Johannes", "initials": "J"}, {"family": "Stenmark", "given": "P\u00e5l", "initials": "P", "orcid": "0000-0003-4777-3417", "researcher": {"href": "https://publications.scilifelab.se/researcher/d97eba9f5edf4d76a5259c4baa8366c5.json"}}, {"family": "Berglund", "given": "Ulrika Warpman", "initials": "UW"}, {"family": "Homan", "given": "Evert J", "initials": "EJ"}, {"family": "Helleday", "given": "Thomas", "initials": "T", "orcid": "0000-0002-7384-092X", "researcher": {"href": "https://publications.scilifelab.se/researcher/3d7256c271ea4adea404d4ff355f804e.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "volume": "3", "issue": "2", "pages": "156-172", "issn-l": null}, "abstract": "The folate metabolism enzyme MTHFD2 (methylenetetrahydrofolate dehydrogenase/cyclohydrolase) is consistently overexpressed in cancer but its roles are not fully characterized, and current candidate inhibitors have limited potency for clinical development. In the present study, we demonstrate a role for MTHFD2 in DNA replication and genomic stability in cancer cells, and perform a drug screen to identify potent and selective nanomolar MTHFD2 inhibitors; protein cocrystal structures demonstrated binding to the active site of MTHFD2 and target engagement. MTHFD2 inhibitors reduced replication fork speed and induced replication stress followed by S-phase arrest and apoptosis of acute myeloid leukemia cells in vitro and in vivo, with a therapeutic window spanning four orders of magnitude compared with nontumorigenic cells. Mechanistically, MTHFD2 inhibitors prevented thymidine production leading to misincorporation of uracil into DNA and replication stress. Overall, these results demonstrate a functional link between MTHFD2-dependent cancer metabolism and replication stress that can be exploited therapeutically with this new class of inhibitors.", "doi": "10.1038/s43018-022-00331-y", "pmid": "35228749", "labels": {"Drug Discovery and Development": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s43018-022-00331-y"}, {"db": "pmc", "key": "PMC8885417"}], "notes": [], "created": "2022-05-07T05:35:33.240Z", "modified": "2025-10-17T13:05:07.816Z"}, {"entity": "publication", "iuid": "1d2095351dae4fda9d7971cb7e5860cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1d2095351dae4fda9d7971cb7e5860cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1d2095351dae4fda9d7971cb7e5860cd"}}, "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"}, {"family": "Arslan", "given": "Taner", "initials": "T"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Pan", "given": "Yanbo", "initials": "Y"}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Berkovska", "given": "Olena", "initials": "O"}, {"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"}, {"family": "Brustugun", "given": "Odd Terje", "initials": "OT"}, {"family": "Purohit", "given": "Krishna Pinganksha", "initials": "KP"}, {"family": "Cunningham", "given": "Richard", "initials": "R"}, {"family": "Asl", "given": "Hassan Foroughi", "initials": "HF"}, {"family": "Isaksson", "given": "Sofi", "initials": "S"}, {"family": "Arbajian", "given": "Elsa", "initials": "E"}, {"family": "Aine", "given": "Mattias", "initials": "M"}, {"family": "Karlsson", "given": "Anna", "initials": "A"}, {"family": "Kotevska", "given": "Marija", "initials": "M"}, {"family": "Hansen", "given": "Carsten Gram", "initials": "CG"}, {"family": "Haakensen", "given": "Vilde Drageset", "initials": "VD"}, {"family": "Helland", "given": "\u00c5slaug", "initials": "\u00c5"}, {"family": "Tamborero", "given": "David", "initials": "D"}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ"}, {"family": "Branca", "given": "Rui M", "initials": "RM"}, {"family": "Planck", "given": "Maria", "initials": "M"}, {"family": "Staaf", "given": "Johan", "initials": "J"}, {"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": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC7612062"}, {"db": "mid", "key": "EMS133264"}], "notes": [], "created": "2021-12-10T07:03:36.789Z", "modified": "2021-12-10T07:03:36.824Z"}, {"entity": "publication", "iuid": "f4c47f02826749cbafe16bedd0a59d3b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4c47f02826749cbafe16bedd0a59d3b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4c47f02826749cbafe16bedd0a59d3b"}}, "title": "The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome.", "authors": [{"family": "Duran-Ferrer", "given": "Mart\u00ed", "initials": "M", "orcid": "0000-0003-1666-5819", "researcher": {"href": "https://publications.scilifelab.se/researcher/00de5a3a802143d184c21e397fc9b3e3.json"}}, {"family": "Clot", "given": "Guillem", "initials": "G"}, {"family": "Nadeu", "given": "Ferran", "initials": "F", "orcid": "0000-0003-2910-9440", "researcher": {"href": "https://publications.scilifelab.se/researcher/d4654f6b3cd74ddfb4d859edff5fbc95.json"}}, {"family": "Beekman", "given": "Ren\u00e9e", "initials": "R"}, {"family": "Baumann", "given": "Tycho", "initials": "T"}, {"family": "Nordlund", "given": "Jessica", "initials": "J"}, {"family": "Marincevic-Zuniga", "given": "Yanara", "initials": "Y"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"family": "Rivas-Delgado", "given": "Alfredo", "initials": "A", "orcid": "0000-0003-0385-3415", "researcher": {"href": "https://publications.scilifelab.se/researcher/7fad7e4db089481582fbc48fe312b7c2.json"}}, {"family": "Mart\u00edn", "given": "Silvia", "initials": "S"}, {"family": "Ordo\u00f1ez", "given": "Raquel", "initials": "R"}, {"family": "Castellano", "given": "Giancarlo", "initials": "G"}, {"family": "Kulis", "given": "Marta", "initials": "M"}, {"family": "Queir\u00f3s", "given": "Ana C", "initials": "AC"}, {"family": "Lee", "given": "Seung-Tae", "initials": "S"}, {"family": "Wiemels", "given": "Joseph", "initials": "J"}, {"family": "Royo", "given": "Romina", "initials": "R"}, {"family": "Puiggr\u00f3s", "given": "Montserrat", "initials": "M", "orcid": "0000-0001-5034-7924", "researcher": {"href": "https://publications.scilifelab.se/researcher/c92c686a51b44dae85d15e867dc8a9b3.json"}}, {"family": "Lu", "given": "Junyan", "initials": "J"}, {"family": "Gin\u00e9", "given": "Eva", "initials": "E"}, {"family": "Be\u00e0", "given": "S\u00edlvia", "initials": "S"}, {"family": "Jares", "given": "Pedro", "initials": "P", "orcid": "0000-0002-8401-579X", "researcher": {"href": "https://publications.scilifelab.se/researcher/763b4efd77664b8aa47a70bb9a577b0f.json"}}, {"family": "Agirre", "given": "Xabier", "initials": "X", "orcid": "0000-0002-6558-9560", "researcher": {"href": "https://publications.scilifelab.se/researcher/4226533ab5484c698a0aa6471dabf848.json"}}, {"family": "Prosper", "given": "Felipe", "initials": "F"}, {"family": "L\u00f3pez-Ot\u00edn", "given": "Carlos", "initials": "C", "orcid": "0000-0001-6964-1904", "researcher": {"href": "https://publications.scilifelab.se/researcher/accdad365e904fd9a8b3c64dcaabbaf5.json"}}, {"family": "Puente", "given": "Xos\u00e9 S", "initials": "XS", "orcid": "0000-0001-9525-1483", "researcher": {"href": "https://publications.scilifelab.se/researcher/3c757bd329184ea2a2aa9183802fefb1.json"}}, {"family": "Oakes", "given": "Christopher C", "initials": "CC"}, {"family": "Zenz", "given": "Thorsten", "initials": "T", "orcid": "0000-0001-7890-9845", "researcher": {"href": "https://publications.scilifelab.se/researcher/8f6b107b1ec94de7bbc260f92f2dcc9f.json"}}, {"family": "Delgado", "given": "Julio", "initials": "J"}, {"family": "L\u00f3pez-Guillermo", "given": "Armando", "initials": "A"}, {"family": "Campo", "given": "El\u00edas", "initials": "E", "orcid": "0000-0001-9850-9793", "researcher": {"href": "https://publications.scilifelab.se/researcher/5642afaa4ed648dfabe66194e42bc01b.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"}}], "type": "journal article", "published": "2020-11-00", "journal": {"title": "Nat Cancer", "issn": "2662-1347", "issn-l": null, "volume": "1", "issue": "11", "pages": "1066-1081"}, "abstract": "We report a systematic analysis of the DNA methylation variability in 1,595 samples of normal cell subpopulations and 14 tumor subtypes spanning the entire human B-cell lineage. Differential methylation among tumor entities relates to differences in cellular origin and to de novo epigenetic alterations, which allowed us to build an accurate machine learning-based diagnostic algorithm. We identify extensive patient-specific methylation variability in silenced chromatin associated with the proliferative history of normal and neoplastic B cells. Mitotic activity generally leaves both hyper- and hypomethylation imprints, but some B-cell neoplasms preferentially gain or lose DNA methylation. Subsequently, we construct a DNA methylation-based mitotic clock called epiCMIT, whose lapse magnitude represents a strong independent prognostic variable in B-cell tumors and is associated with particular driver genetic alterations. Our findings reveal DNA methylation as a holistic tracer of B-cell tumor developmental history, with implications in the differential diagnosis and prediction of clinical outcome.", "doi": "10.1038/s43018-020-00131-2", "pmid": "34079956", "labels": {"NGI SNP genotyping": "Collaborative", "National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "mid", "key": "NIHMS1700108"}, {"db": "pmc", "key": "PMC8168619"}, {"db": "pii", "key": "10.1038/s43018-020-00131-2"}], "notes": [], "created": "2023-01-03T14:47:04.559Z", "modified": "2023-01-03T14:53:28.577Z"}], "created": "2021-12-10T07:03:36.813Z", "modified": "2021-12-10T07:03:36.813Z"}