{"entity": "researcher", "timestamp": "2026-08-20T20:45:12.800Z", "family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "affiliations": ["Clinical Proteomics Mass Spectrometry, Department of Oncology-Pathology, Karolinska Institutet, Science for Life Laboratory, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908"}}, "publications": [{"entity": "publication", "iuid": "2d9110b0c8b04668b2246bf7842ab3fb", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9110b0c8b04668b2246bf7842ab3fb.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9110b0c8b04668b2246bf7842ab3fb"}}, "title": "Pathway activation model for personalized prediction of drug synergy.", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Osterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Backvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas", "initials": "L"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "Soren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "journal article", "published": "2025-06-03", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "13", "issn-l": "2050-084X"}, "abstract": "Targeted monotherapies for cancer often fail due to inherent or acquired drug resistance. By aiming at multiple targets simultaneously, drug combinations can produce synergistic interactions that increase drug effectiveness and reduce resistance. Computational models based on the integration of omics data have been used to identify synergistic combinations, but predicting drug synergy remains a challenge. Here, we introduce Drug synergy Interaction Prediction (DIPx), an algorithm for personalized prediction of drug synergy based on biologically motivated tumor- and drug-specific pathway activation scores (PASs). We trained and validated DIPx in the AstraZeneca-Sanger (AZS) DREAM Challenge human cell-line dataset using two separate test sets: Test Set 1 comprised the combinations already present in the training set, while Test Set 2 contained combinations absent from the training set, thus indicating the model's ability to handle novel combinations. The Spearman's correlation coefficients between predicted and observed drug synergy were 0.50 (95% CI: 0.47-0.53) in Test Set 1 and 0.26 (95% CI: 0.22-0.30) in Test Set 2, compared to 0.38 (95% CI: 0.34-0.42) and 0.18 (95% CI: 0.16-0.20), respectively, for the best performing method in the Challenge. We show evidence that higher synergy is associated with higher functional interaction between the drug targets, and this functional interaction information is captured by PAS. We illustrate the use of PAS to provide a potential biological explanation in terms of activated pathways that mediate the synergistic effects of combined drugs. In summary, DIPx can be a useful tool for personalized prediction of drug synergy and exploration of activated pathways related to the effects of combined drugs.", "doi": "10.7554/eLife.100071", "pmid": "40459126", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC12133153"}, {"db": "pii", "key": "100071"}], "notes": [], "created": "2026-08-20T13:50:31.337Z", "modified": "2026-08-20T13:50:31.440Z"}, {"entity": "publication", "iuid": "bedbdb85145a450f91e298b33e22145c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bedbdb85145a450f91e298b33e22145c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bedbdb85145a450f91e298b33e22145c"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "Osterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Backvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas", "initials": "L"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "Soren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "journal-article", "published": "2025-06-03", "journal": {"issn": "2050-084X", "volume": "13", "title": "Elife", "issn-l": "2050-084X"}, "abstract": null, "doi": "10.7554/elife.100071.4", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:47.280Z", "modified": "2026-08-20T13:50:47.339Z"}, {"entity": "publication", "iuid": "d2d49f05d7904b3bad53fde048184fbf", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d2d49f05d7904b3bad53fde048184fbf.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d2d49f05d7904b3bad53fde048184fbf"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2025-05-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.3", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:38.643Z", "modified": "2026-08-20T13:50:38.705Z"}, {"entity": "publication", "iuid": "2d9b1475f2a74141957ffa60c7cde513", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9b1475f2a74141957ffa60c7cde513.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/2d9b1475f2a74141957ffa60c7cde513"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "posted-content", "published": "2025-03-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:34.946Z", "modified": "2026-08-20T13:50:35.029Z"}, {"entity": "publication", "iuid": "abf636b1b12940748f1d797a8dbeb225", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/abf636b1b12940748f1d797a8dbeb225.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/abf636b1b12940748f1d797a8dbeb225"}}, "title": "Author response: Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "B\u00e4ckvall", "given": "Helena", "initials": "H"}, {"family": "Kiviluoto", "given": "Santeri", "initials": "S"}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli", "initials": "O"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}, {"family": "Vu", "given": "Trung Nghia", "initials": "TN", "orcid": "0000-0001-7945-5750", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1c68ab75cfd4458aaa0cff82a637a24b.json"}}], "type": "peer-review", "published": "2025-03-20", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.100071.2.sa0", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:50:36.794Z", "modified": "2026-08-20T13:50:36.879Z"}, {"entity": "publication", "iuid": "20224117c77c4cf1825278ed9767b7d1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/20224117c77c4cf1825278ed9767b7d1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/20224117c77c4cf1825278ed9767b7d1"}}, "title": "Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets.", "authors": [{"family": "Leo", "given": "Isabelle Rose", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21801296760147b78e11b2a0ddcfd0e1.json"}}, {"family": "Kunold", "given": "Elena", "initials": "E"}, {"family": "Audrey", "given": "Anastasia", "initials": "A", "orcid": "0000-0002-8172-8575", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/436d3f91960447c384d04bf8535b35a9.json"}}, {"family": "Tampere", "given": "Marianna", "initials": "M"}, {"family": "Eirich", "given": "J\u00fcrgen", "initials": "J", "orcid": "0000-0003-0963-1872", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3070defe1f614b57ab391fa9a15c39a2.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}], "type": "journal article", "published": "2025-02-25", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "16", "issue": "1", "pages": "1948", "issn-l": "2041-1723"}, "abstract": "Proteome-wide profiling has revealed that targeted drugs can have complex protein interaction landscapes. However, it's a challenge to profile drug targets while systematically accounting for the dynamic protein variations that produce populations of multiple proteoforms. We address this problem by combining thermal proteome profiling (TPP) with functional proteoform group detection to refine the target landscape of ibrutinib. In addition to known targets, we implicate additional specific functional proteoform groups linking ibrutinib to mechanisms in immunomodulation and cellular processes like Golgi trafficking, endosomal trafficking, and glycosylation. Further, we identify variability in functional proteoform group profiles in a CLL cohort, linked to treatment status and ex vivo response and resistance. This offers deeper insights into the impacts of functional proteoform groups in a clinical treatment setting and suggests complex biological effects linked to off-target engagement. These results provide a framework for interpreting clinically observed off-target processes and adverse events, highlighting the importance of functional proteoform group-level deconvolution in understanding drug interactions and their functional impacts with potential applications in precision medicine.", "doi": "10.1038/s41467-024-54654-8", "pmid": "40000607", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11862126"}, {"db": "pii", "key": "10.1038/s41467-024-54654-8"}], "notes": [], "created": "2026-08-20T08:53:42.430Z", "modified": "2026-08-20T08:53:42.664Z"}, {"entity": "publication", "iuid": "d0e2a79c0a384ecfa7c2f9617353d66c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d0e2a79c0a384ecfa7c2f9617353d66c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d0e2a79c0a384ecfa7c2f9617353d66c"}}, "title": "Pathway activation model for personalized prediction of drug synergy", "authors": [{"family": "Trac", "given": "Quang Thinh", "initials": "QT", "orcid": "0000-0003-2429-0287", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/13e232680de04f55b195706785e79988.json"}}, {"family": "Huang", "given": "Yue", "initials": "Y"}, {"family": "Erkers", "given": "Tom", "initials": "T"}, {"family": "\u00d6stling", "given": "P\u00e4ivi", "initials": "P"}, {"family": "Bohlin", "given": "Anna", "initials": "A"}, {"family": "\u00d6sterroos", "given": "Albin", "initials": "A"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e443cdb01cc44a7fa786941b5c0b62d6.json"}}, {"family": "Jafari", "given": "Rozbeh", "initials": "R", "orcid": "0000-0002-3396-4709", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/95546f158dde40709fbfbb822a8f89c5.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": 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"initials": "L", "orcid": "0000-0003-4247-3175", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4e307dc8f3774bbfa97926dd1d1464d1.json"}}, {"family": "Ciceri", "given": "Fabio", "initials": "F", "orcid": "0000-0003-0873-0123", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9631c85f2abe41ecb26c2b96f662c19c.json"}}, {"family": "Bonini", "given": "Chiara", "initials": "C", "orcid": "0000-0002-0772-1674", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/72025c797fe74a749bb9b5945a1c4cc1.json"}}, {"family": "Ruggiero", "given": "Eliana", "initials": "E", "orcid": "0000-0002-2954-8278", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/58dd81c18e944546b46ad24074911897.json"}}], "type": "journal article", "published": "2023-12-00", "journal": {"title": "Sci Adv", "issn": "2375-2548", "volume": "9", "issue": "48", "pages": "eadg8014", "issn-l": "2375-2548"}, "abstract": "To study and then harness the tumor-specific T cell dynamics after allogeneic hematopoietic stem cell transplant, we typed the frequency, phenotype, and function of lymphocytes directed against tumor-associated antigens (TAAs) in 39 consecutive transplanted patients, for 1 year after transplant. We showed that TAA-specific T cells circulated in 90% of patients but display a limited effector function associated to an exhaustion phenotype, particularly in the subgroup of patients deemed to relapse, where exhausted stem cell memory T cells accumulated. Accordingly, cancer-specific cytolytic functions were relevant only when the TAA-specific T cell receptors (TCRs) were transferred into healthy, genome-edited T cells. We then exploited trogocytosis and ligandome-on-chip technology to unveil the specificities of tumor-specific TCRs retrieved from the exhausted T cell pool. Overall, we showed that harnessing circulating TAA-specific and exhausted T cells allow to isolate TCRs against TAAs and previously not described acute myeloid leukemia antigens, potentially relevant for T cell-based cancer immunotherapy.", "doi": "10.1126/sciadv.adg8014", "pmid": "38039364", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC10691777"}], "notes": [], "created": "2026-08-20T11:58:45.183Z", "modified": "2026-08-20T11:58:46.172Z"}, {"entity": "publication", "iuid": "6720af3b4faa4eb29c4881909e415f48", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6720af3b4faa4eb29c4881909e415f48.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6720af3b4faa4eb29c4881909e415f48"}}, "title": "Development of mesothelioma-specific oncolytic vaccine exploiting immunopeptidomic analysis of murine and human tumors", "authors": [{"family": "Chiaro", "given": "Jacopo", "initials": "J"}, {"family": "Antignani", "given": "Gabriella", "initials": "G"}, {"family": "Feola", "given": "Sara", "initials": "S", "orcid": "0000-0002-4012-4310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81e8d2f15fcf4e1aabf7b5a41a977f3f.json"}}, {"family": "Feodoroff", "given": "Michaela", "initials": "M", "orcid": "0000-0002-6094-9838", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e3052a20c64fcb977b22f9876fb32e.json"}}, {"family": "Martins", "given": "Beatriz", "initials": "B"}, {"family": "Cojoc", "given": "Hanne", "initials": "H"}, {"family": "Ferrari", "given": "Valentina", "initials": "V"}, {"family": "Ciampi", "given": "Daniele", "initials": "D"}, {"family": "Ilonen", "given": "Ilkka", "initials": "I", "orcid": "0000-0002-8149-3550", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b454bab24bc5448d83e6823d84048bc1.json"}}, {"family": "R\u00e4s\u00e4nen", "given": "Jari", "initials": "J"}, {"family": "M\u00e4yr\u00e4np\u00e4\u00e4", "given": "Mikko", "initials": "M"}, {"family": "Partanen", "given": "Jukka", "initials": "J", "orcid": "0000-0001-6681-4734", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d8e2e85ae2c41fc9a9afc0f281e68f1.json"}}, {"family": "Koskela", "given": "Satu", "initials": "S", "orcid": "0000-0001-9258-9163", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b489fc9c09b840578305871e75d6cb78.json"}}, {"family": "Kuryk", "given": "Lukasz", "initials": "L", "orcid": "0000-0003-1887-6361", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d16e4a3669242fa8d9590e6861faef5.json"}}, {"family": "Russo", "given": "Salvatore", "initials": "S"}, {"family": "Fusciello", "given": "Manlio", "initials": "M", "orcid": "0000-0002-7166-3018", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/de1fb2e094ff4d959471a9593544ca51.json"}}, {"family": "Hamdan", "given": "Firas", "initials": "F", "orcid": "0000-0003-4678-7382", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2e4b6b79da164ce0bca93cef19a0997f.json"}}, {"family": "Rescigno", "given": "Maria", "initials": "M", "orcid": "0000-0002-6464-509X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db61cb1df7ec4444881b58d32f182ecb.json"}}, {"family": "Gr\u00f6nholm", "given": "Mikaela", "initials": "M"}, {"family": "Branca", "given": "Rui Mamede", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d46c756e18bb49268b98a75a5234664a.json"}}], "type": "posted-content", "published": "2022-11-08", "journal": {"issn-l": null}, "abstract": null, "doi": "10.21203/rs.3.rs-2238403/v1", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T12:58:36.253Z", "modified": "2026-08-20T12:58:36.719Z"}, {"entity": "publication", "iuid": "3002e91d930b49d2beafc053a932899c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3002e91d930b49d2beafc053a932899c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3002e91d930b49d2beafc053a932899c"}}, "title": "Integrative multi-omics analysis reveals molecular subtypes and tumor evolution of synovial sarcoma", "authors": [{"family": "Chen", "given": "Yi", "initials": "Y", "orcid": "0000-0002-4891-8289", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2f0f26876884663bb558123face61cd.json"}}, {"family": "Su", "given": "Yanhong", "initials": "Y"}, {"family": "Leo", "given": "Isabelle Rose", "initials": "IR", "orcid": "0000-0002-7627-6690", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21801296760147b78e11b2a0ddcfd0e1.json"}}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Zeng", "given": "Jianming", "initials": "J", "orcid": "0000-0003-4835-6009", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f8905ac0fce47a0984d39c22186b103.json"}}, {"family": "Cao", "given": "Xiaofang", "initials": "X"}, {"family": "Tsagkozis", "given": "Panagiotis", "initials": "P"}, {"family": "Hesla", "given": "Asle C", "initials": "AC"}, {"family": "Papakonstantinou", "given": "Andri", "initials": "A"}, {"family": "Liu", "given": "Xiao", "initials": "X"}, {"family": "Huang", "given": "Wen Kuan", "initials": "WK"}, {"family": "Ehnman", "given": "Monika", "initials": "M"}, {"family": "Johansson", "given": "Henrik", "initials": "H", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8acb3ba52a54c7a82f2a096516a8e05.json"}}, {"family": "Lin", "given": "Yingbo", "initials": "Y"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Zhang", "given": "Yifan", "initials": "Y"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Haglund de Flon", "given": "Felix", "initials": "F", "orcid": "0000-0002-7015-3841", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/be9b0eda414549868536c4e96a3a845a.json"}}], "type": "posted-content", "published": "2022-05-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.05.09.490894", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:11:10.093Z", "modified": "2026-08-20T10:11:10.245Z"}, {"entity": "publication", "iuid": "d178ec24b2a746abaea0e2d5546a5e44", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d178ec24b2a746abaea0e2d5546a5e44.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d178ec24b2a746abaea0e2d5546a5e44"}}, "title": "A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines.", "authors": [{"family": "Feola", "given": "Sara", "initials": "S", "orcid": "0000-0002-4012-4310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81e8d2f15fcf4e1aabf7b5a41a977f3f.json"}}, {"family": "Chiaro", "given": "Jacopo", "initials": "J"}, {"family": "Martins", "given": "Beatriz", "initials": "B"}, {"family": "Russo", "given": "Salvatore", "initials": "S"}, {"family": "Fusciello", "given": "Manlio", "initials": "M"}, {"family": "Yl\u00f6sm\u00e4ki", "given": "Erkko", "initials": "E"}, {"family": "Bonini", "given": "Chiara", "initials": "C"}, {"family": "Ruggiero", "given": "Eliana", "initials": "E"}, {"family": "Hamdan", "given": "Firas", "initials": "F"}, {"family": "Feodoroff", "given": "Michaela", "initials": "M", "orcid": "0000-0002-6094-9838", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e3052a20c64fcb977b22f9876fb32e.json"}}, {"family": "Antignani", "given": "Gabriella", "initials": "G"}, {"family": "Viitala", "given": "Tapani", "initials": "T", "orcid": "0000-0001-9074-9450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccbeaba4a3ad49c7b69f606cdab227e9.json"}}, {"family": "Pesonen", "given": "Sari", "initials": "S"}, {"family": "Gr\u00f6nholm", "given": "Mikaela", "initials": "M"}, {"family": "Branca", "given": "Rui M M", "initials": "RMM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d46c756e18bb49268b98a75a5234664a.json"}}], "type": "journal article", "published": "2022-03-22", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "11", "issn-l": "2050-084X"}, "abstract": "Besides the isolation and identification of major histocompatibility complex I-restricted peptides from the surface of cancer cells, one of the challenges is eliciting an effective antitumor CD8+ T-cell-mediated response as part of therapeutic cancer vaccine. Therefore, the establishment of a solid pipeline for the downstream selection of clinically relevant peptides and the subsequent creation of therapeutic cancer vaccines are of utmost importance. Indeed, the use of peptides for eliciting specific antitumor adaptive immunity is hindered by two main limitations: the efficient selection of the most optimal candidate peptides and the use of a highly immunogenic platform to combine with the peptides to induce effective tumor-specific adaptive immune responses. Here, we describe for the first time a streamlined pipeline for the generation of personalized cancer vaccines starting from the isolation and selection of the most immunogenic peptide candidates expressed on the tumor cells and ending in the generation of efficient therapeutic oncolytic cancer vaccines. This immunopeptidomics-based pipeline was carefully validated in a murine colon tumor model CT26. Specifically, we used state-of-the-art immunoprecipitation and mass spectrometric methodologies to isolate >8000 peptide targets from the CT26 tumor cell line. The selection of the target candidates was then based on two separate approaches: RNAseq analysis and HEX software. The latter is a tool previously developed by Jacopo, 2020, able to identify tumor antigens similar to pathogen antigens in order to exploit molecular mimicry and tumor pathogen cross-reactive T cells in cancer vaccine development. The generated list of candidates (26 in total) was further tested in a functional characterization assay using interferon-\u03b3 enzyme-linked immunospot (ELISpot), reducing the number of candidates to six. These peptides were then tested in our previously described oncolytic cancer vaccine platform PeptiCRAd, a vaccine platform that combines an immunogenic oncolytic adenovirus (OAd) coated with tumor antigen peptides. In our work, PeptiCRAd was successfully used for the treatment of mice bearing CT26, controlling the primary malignant lesion and most importantly a secondary, nontreated, cancer lesion. These results confirmed the feasibility of applying the described pipeline for the selection of peptide candidates and generation of therapeutic oncolytic cancer vaccine, filling a gap in the field of cancer immunotherapy, and paving the way to translate our pipeline into human therapeutic approach.", "doi": "10.7554/eLife.71156", "pmid": "35314027", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8989416"}, {"db": "pii", "key": "71156"}, {"db": "GEO", "key": "GSE111092"}, {"db": "GEO", "key": "GSE92563"}], "notes": [], "created": "2026-08-20T13:54:00.926Z", "modified": "2026-08-20T13:54:01.055Z"}, {"entity": "publication", "iuid": "c34de836d01048a389d4cd68e74a0a08", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c34de836d01048a389d4cd68e74a0a08.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c34de836d01048a389d4cd68e74a0a08"}}, "title": "Author response: A novel immunopeptidomic-based pipeline for the generation of personalized oncolytic cancer vaccines", "authors": [{"family": "Feola", "given": "Sara", "initials": "S", "orcid": "0000-0002-4012-4310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81e8d2f15fcf4e1aabf7b5a41a977f3f.json"}}, {"family": "Chiaro", "given": "Jacopo", "initials": "J"}, {"family": "Martins", "given": "Beatriz", "initials": "B"}, {"family": "Russo", "given": "Salvatore", "initials": "S"}, {"family": "Fusciello", "given": "Manlio", "initials": "M"}, {"family": "Yl\u00f6sm\u00e4ki", "given": "Erkko", "initials": "E"}, {"family": "Bonini", "given": "Chiara", "initials": "C"}, {"family": "Ruggiero", "given": "Eliana", "initials": "E"}, {"family": "Hamdan", "given": "Firas", "initials": "F"}, {"family": "Feodoroff", "given": "Michaela", "initials": "M", "orcid": "0000-0002-6094-9838", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/26e3052a20c64fcb977b22f9876fb32e.json"}}, {"family": "Antignani", "given": "Gabriella", "initials": "G"}, {"family": "Viitala", "given": "Tapani", "initials": "T", "orcid": "0000-0001-9074-9450", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ccbeaba4a3ad49c7b69f606cdab227e9.json"}}, {"family": "Pesonen", "given": "Sari", "initials": "S"}, {"family": "Gr\u00f6nholm", "given": "Mikaela", "initials": "M"}, {"family": "Branca", "given": "Rui MM", "initials": "RM"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d46c756e18bb49268b98a75a5234664a.json"}}], "type": "peer-review", "published": "2022-02-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.71156.sa2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:54:06.276Z", "modified": "2026-08-20T13:54:06.313Z"}, {"entity": "publication", "iuid": "d3fd353ba298423eac45e5659ebf44aa", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d3fd353ba298423eac45e5659ebf44aa.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d3fd353ba298423eac45e5659ebf44aa"}}, "title": "Glioblastoma stem cells express non-canonical proteins and exclusive mesenchymal-like or non-mesenchymal-like protein signatures", "authors": [{"family": "Baba\u010di\u0107", "given": "Haris", "initials": "H", "orcid": "0000-0003-0813-0005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/69dbef8e901c4fafb00a18b6d7722acd.json"}}, {"family": "Galardi", "given": "Silvia", "initials": "S"}, {"family": "Umer", "given": "Husen M", "initials": "HM", "orcid": "0000-0003-3971-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/922625c410444833a263244d0313980e.json"}}, {"family": "Cardinali", "given": "Deborah", "initials": "D"}, {"family": "Pellegatta", "given": "Serena", "initials": "S"}, {"family": "Hellstr\u00f6m", "given": "Mats", "initials": "M"}, {"family": "Uhrbom", "given": "Lene", "initials": "L", "orcid": "0000-0001-8595-5698", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf57deb01a9340b6b5b2174195b6a549.json"}}, {"family": "Maturi", "given": "Nagaprathyusha", "initials": "N"}, {"family": "Michienzi", "given": "Alessandro", "initials": "A"}, {"family": "Trevisi", "given": "Gianluca", "initials": "G"}, {"family": "Mangiola", "given": "Annunziato", "initials": "A"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Ciafr\u00e8", "given": "Silvia Anna", "initials": "SA"}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e0806a3d142019ae8e16de8d720ef.json"}}], "type": "posted-content", "published": "2022-02-10", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.02.06.479313", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:09:24.426Z", "modified": "2026-08-20T10:09:24.500Z"}, {"entity": "publication", "iuid": "a7ce02e60546456c9e91f0cbfc6f4e73", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ce02e60546456c9e91f0cbfc6f4e73.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a7ce02e60546456c9e91f0cbfc6f4e73"}}, "title": "Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides", "authors": [{"family": "Umer", "given": "Husen M", "initials": "HM", "orcid": "0000-0003-3971-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/922625c410444833a263244d0313980e.json"}}, {"family": "Zhu", "given": "Yafeng", "initials": "Y", "orcid": "0000-0003-1947-9026", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377403d2493c4176984da3bf8802aebd.json"}}, {"family": "Pfeuffer", "given": "Julianus", "initials": "J", "orcid": "0000-0001-8948-9209", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b52fcbdb2ad745aeb6b3f06f16908e41.json"}}, {"family": "Sachsenberg", "given": "Timo", "initials": "T", "orcid": "0000-0002-2833-6070", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d5425fd7b0434642b4c6f7aef67b5f23.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Branca", "given": "Rui", "initials": "R", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}}, {"family": "Perez-Riverol", "given": "Yasset", "initials": "Y", "orcid": "0000-0001-6579-6941", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cb4449bad29741b195a7593fc39a769d.json"}}], "type": "posted-content", "published": "2021-06-09", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2021.06.08.447496", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T10:04:43.925Z", "modified": "2026-08-20T10:04:44.093Z"}, {"entity": "publication", "iuid": "6fbcc2137ebe42ef88214d68e7d66a87", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6fbcc2137ebe42ef88214d68e7d66a87.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6fbcc2137ebe42ef88214d68e7d66a87"}}, "title": "PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer.", "authors": [{"family": "Brunner", "given": "Andr\u00e4", "initials": "A", "orcid": "0000-0003-4316-5713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d4d9ca121024b599557205a00b99af0.json"}}, {"family": "Suryo Rahmanto", "given": "Aldwin", "initials": "A", "orcid": "0000-0002-4593-286X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59328511ffe441f08443f83089cc909b.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Franco", "given": "Marcela", "initials": "M", "orcid": "0000-0001-8444-1708", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46f00fdc586449a4b609c62b20587925.json"}}, {"family": "Viili\u00e4inen", "given": "Johanna", "initials": "J", "orcid": "0000-0002-5527-4266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8af24083ed2a44b3a9e10b0f6b9c97a7.json"}}, {"family": "Gazi", "given": "Mohiuddin", "initials": "M"}, {"family": "Frings", "given": "Oliver", "initials": "O"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Spruck", "given": "Charles", "initials": "C"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Rantala", "given": "Juha K", "initials": "JK"}, {"family": "Larsson", "given": "Lars-Gunnar", "initials": "LG", "orcid": "0000-0001-6914-3147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ec1f8f2738a41cb9105c142ca5374e6.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O", "orcid": "0000-0002-0316-0195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bc4930422a046f69295e2c59a569657.json"}}], "type": "journal article", "published": "2020-07-06", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "9", "issn-l": "2050-084X"}, "abstract": "Inhibition of WEE1 kinase by AZD1775 has shown promising results in clinical cancer trials, but markers predicting AZD1775 response are lacking. Here we analysed AZD1775 response in a panel of human breast cancer (BC) cell lines by global proteome/transcriptome profiling and identified two groups of basal-like BC (BLBCs): 'PTEN low' BLBCs were highly sensitive to AZD1775 and failed to recover following removal of AZD1775, while 'PTEN high' BLBCs recovered. AZD1775 induced phosphorylation of DNA-PK, protecting cells from replication-associated DNA damage and promoting cellular recovery. Deletion of DNA-PK or PTEN, or inhibition of DNA-PK sensitized recovering BLBCs to AZD1775 by abrogating replication arrest, allowing replication despite DNA damage. This was linked to reduced CHK1 activation, increased cyclin E levels and apoptosis. In conclusion, we identified PTEN and DNA-PK as essential regulators of replication checkpoint arrest in response to AZD1775 and defined PTEN as a promising biomarker for efficient WEE1 cancer therapy.", "doi": "10.7554/eLife.57894", "pmid": "32628111", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC7338058"}, {"db": "pii", "key": "57894"}, {"db": "GEO", "key": "GSE152102"}], "notes": [], "created": "2026-08-20T13:53:09.448Z", "modified": "2026-08-20T13:53:09.659Z"}, {"entity": "publication", "iuid": "a49851e70c53469e8e9b281cd226c8c1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a49851e70c53469e8e9b281cd226c8c1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a49851e70c53469e8e9b281cd226c8c1"}}, "title": "Author response: PTEN and DNA-PK determine sensitivity and recovery in response to WEE1 inhibition in human breast cancer", "authors": [{"family": "Brunner", "given": "Andr\u00e4", "initials": "A", "orcid": "0000-0003-4316-5713", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9d4d9ca121024b599557205a00b99af0.json"}}, {"family": "Suryo Rahmanto", "given": "Aldwin", "initials": "A", "orcid": "0000-0002-4593-286X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/59328511ffe441f08443f83089cc909b.json"}}, {"family": "Johansson", "given": "Henrik", "initials": "H"}, {"family": "Franco", "given": "Marcela", "initials": "M", "orcid": "0000-0001-8444-1708", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/46f00fdc586449a4b609c62b20587925.json"}}, {"family": "Viili\u00e4inen", "given": "Johanna", "initials": "J", "orcid": "0000-0002-5527-4266", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8af24083ed2a44b3a9e10b0f6b9c97a7.json"}}, {"family": "Gazi", "given": "Mohiuddin", "initials": "M"}, {"family": "Frings", "given": "Oliver", "initials": "O"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Spruck", "given": "Charles", "initials": "C"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Rantala", "given": "Juha K", "initials": "JK"}, {"family": "Larsson", "given": "Lars Gunnar", "initials": "LG", "orcid": "0000-0001-6914-3147", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5ec1f8f2738a41cb9105c142ca5374e6.json"}}, {"family": "Sangfelt", "given": "Olle", "initials": "O", "orcid": "0000-0002-0316-0195", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2bc4930422a046f69295e2c59a569657.json"}}], "type": "peer-review", "published": "2020-06-22", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.57894.sa2", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:53:11.786Z", "modified": "2026-08-20T13:53:11.829Z"}, {"entity": "publication", "iuid": "3113ee5c7c5e42c8a0831e62b2e2c8f6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/3113ee5c7c5e42c8a0831e62b2e2c8f6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/3113ee5c7c5e42c8a0831e62b2e2c8f6"}}, "title": "Early symptoms and sensations as predictors of lung cancer: a machine learning multivariate model.", "authors": [{"family": "Levitsky", "given": "Adrian", "initials": "A", "orcid": "0000-0003-4821-0691", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56d2c32efba54cfe88679bc007c67854.json"}}, {"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e0806a3d142019ae8e16de8d720ef.json"}}, {"family": "Bernhardson", "given": "Britt-Marie", "initials": "BM"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "K\u00f6lbeck", "given": "Karl", "initials": "K"}, {"family": "Olin", "given": "Maria", "initials": "M"}, {"family": "Henriksson", "given": "Roger", "initials": "R"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Tishelman", "given": "Carol", "initials": "C"}, {"family": "Eriksson", "given": "Lars E", "initials": "LE", "orcid": "0000-0001-5121-5325", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a6583e7b1b0d4dc38d27eb8ad50f1add.json"}}], "type": "journal article", "published": "2019-11-11", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "16504", "issn-l": "2045-2322"}, "abstract": "The aim of this study was to identify a combination of early predictive symptoms/sensations attributable to primary lung cancer (LC). An interactive e-questionnaire comprised of pre-diagnostic descriptors of first symptoms/sensations was administered to patients referred for suspected LC. Respondents were included in the present analysis only if they later received a primary LC diagnosis or had no cancer; and inclusion of each descriptor required \u22654 observations. Fully-completed data from 506/670 individuals later diagnosed with primary LC (n = 311) or no cancer (n = 195) were modelled with orthogonal projections to latent structures (OPLS). After analysing 145/285 descriptors, meeting inclusion criteria, through randomised seven-fold cross-validation (six-fold training set: n = 433; test set: n = 73), 63 provided best LC prediction. The most-significant LC-positive descriptors included a cough that varied over the day, back pain/aches/discomfort, early satiety, appetite loss, and having less strength. Upon combining the descriptors with the background variables current smoking, a cold/flu or pneumonia within the past two years, female sex, older age, a history of COPD (positive LC-association); antibiotics within the past two years, and a history of pneumonia (negative LC-association); the resulting 70-variable model had accurate cross-validated test set performance: area under the ROC curve = 0.767 (descriptors only: 0.736/background predictors only: 0.652), sensitivity = 84.8% (73.9/76.1%, respectively), specificity = 55.6% (66.7/51.9%, respectively). In conclusion, accurate prediction of LC was found through 63 early symptoms/sensations and seven background factors. Further research and precision in this model may lead to a tool for referral and LC diagnostic decision-making.", "doi": "10.1038/s41598-019-52915-x", "pmid": "31712735", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6848139"}, {"db": "pii", "key": "10.1038/s41598-019-52915-x"}], "notes": [], "created": "2026-08-20T09:04:42.059Z", "modified": "2026-08-20T09:04:42.195Z"}, {"entity": "publication", "iuid": "543d4340275c4c52930d4cb1f005c487", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/543d4340275c4c52930d4cb1f005c487.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/543d4340275c4c52930d4cb1f005c487"}}, "title": "Author Correction: Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin.", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8acb3ba52a54c7a82f2a096516a8e05.json"}}, {"family": "Vallhov", "given": "Helen", "initials": "H"}, {"family": "Holm", "given": "Tina", "initials": "T"}, {"family": "Gehrmann", "given": "Ulf", "initials": "U"}, {"family": "Andersson", "given": "Anna", "initials": "A"}, {"family": "Johansson", "given": "Catharina", "initials": "C"}, {"family": "Blom", "given": "Hans", "initials": "H"}, {"family": "Carroni", "given": "Marta", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Scheynius", "given": "Annika", "initials": "A"}], "type": "published erratum", "published": "2019-10-15", "journal": {"title": "Sci Rep", "issn": "2045-2322", "volume": "9", "issue": "1", "pages": "15014", "issn-l": "2045-2322"}, "abstract": "A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.", "doi": "10.1038/s41598-019-43724-3", "pmid": "31611586", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6791871"}, {"db": "pii", "key": "10.1038/s41598-019-43724-3"}], "notes": [], "created": "2026-08-20T09:04:32.772Z", "modified": "2026-08-20T09:04:32.818Z"}, {"entity": "publication", "iuid": "b86e41f154a749929f8a316ac280a772", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b86e41f154a749929f8a316ac280a772.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b86e41f154a749929f8a316ac280a772"}}, "title": "In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta.", "authors": [{"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e0806a3d142019ae8e16de8d720ef.json"}}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "\u00c5mark", "given": "Hanna", "initials": "H"}, {"family": "\u00d6stenson", "given": "Claes-G\u00f6ran", "initials": "CG"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}], "type": "journal article", "published": "2019-04-08", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "8", "issn-l": "2050-084X"}, "abstract": "Here, we present a method for in-depth human plasma proteome analysis based on high-resolution isoelectric focusing HiRIEF LC-MS/MS, demonstrating high proteome coverage, reproducibility and the potential for liquid biopsy protein profiling. By integrating genomic sequence information to the MS-based plasma proteome analysis, we enable detection of single amino acid variants and for the first time demonstrate transfer of multiple protein variants between mother and fetus across the placenta. We further show that our method has the ability to detect both low abundance tissue-annotated proteins and phosphorylated proteins in plasma, as well as quantitate differences in plasma proteomes between the mother and the newborn as well as changes related to pregnancy.", "doi": "10.7554/eLife.41608", "pmid": "30958262", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6519984"}, {"db": "pii", "key": "41608"}], "notes": [], "created": "2026-08-20T13:52:36.748Z", "modified": "2026-08-20T13:52:36.781Z"}, {"entity": "publication", "iuid": "62946e6fa6ab419a87eba4df4be913fd", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/62946e6fa6ab419a87eba4df4be913fd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/62946e6fa6ab419a87eba4df4be913fd"}}, "title": "Author response: In-depth human plasma proteome analysis captures tissue proteins and transfer of protein variants across the placenta", "authors": [{"family": "Pernemalm", "given": "Maria", "initials": "M", "orcid": "0000-0003-4624-031X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c34e0806a3d142019ae8e16de8d720ef.json"}}, {"family": "Sandberg", "given": "AnnSofi", "initials": "A"}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Tamburro", "given": "Davide", "initials": "D"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/022e140799b6466ea123319c3d70c76e.json"}}, {"family": "Bj\u00f6rk", "given": "Albin", "initials": "A"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "\u00c5mark", "given": "Hanna", "initials": "H"}, {"family": "\u00d6stenson", "given": "Claes G\u00f6ran", "initials": "CG"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}], "type": "peer-review", "published": "2019-02-13", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.41608.041", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:52:38.755Z", "modified": "2026-08-20T13:52:38.804Z"}]}