{"entity": "researcher", "timestamp": "2026-09-25T17:31:17.604Z", "family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "affiliations": ["Department of Surgery, Institute of Clinical Sciences, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f"}}, "publications": [{"entity": "publication", "iuid": "c9cb5a5991674c759bff1395a89f2392", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c9cb5a5991674c759bff1395a89f2392.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c9cb5a5991674c759bff1395a89f2392"}}, "title": "Proteogenomics decodes the evolution of human ipsilateral breast cancer.", "authors": [{"family": "De Marchi", "given": "Tommaso", "initials": "T", "orcid": "0000-0002-4845-1084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68502c65e0754c4698a3f4d3c802acc4.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT"}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Reinsbach", "given": "Susanne Erika", "initials": "SE", "orcid": "0000-0003-0509-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35ebeb793254320982f857ec99fe02a.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S"}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f.json"}}, {"family": "Fredriksson", "given": "Irma", "initials": "I"}, {"family": "Malmstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Fern\u00f6", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-2220-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190c0c5f17f4c298855f9b13f9bb16d.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L", "orcid": "0000-0001-9885-9312", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0310c5c750a4357af859999d705cfad.json"}}, {"family": "Malmst\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c89da9268a4f47a8a99fd62de451aaa7.json"}}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E", "orcid": "0000-0003-0262-9083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c4af562bc1248ecbbb730a496675571.json"}}], "type": "journal article", "published": "2023-02-02", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "6", "issue": "1", "pages": "139", "issn-l": "2399-3642"}, "abstract": "Ipsilateral breast tumor recurrence (IBTR) is a clinically important event, where an isolated in-breast recurrence is a potentially curable event but associated with an increased risk of distant metastasis and breast cancer death. It remains unclear if IBTRs are associated with molecular changes that can be explored as a resource for precision medicine strategies. Here, we employed proteogenomics to analyze a cohort of 27 primary breast cancers and their matched IBTRs to define proteogenomic determinants of molecular tumor evolution. Our analyses revealed a relationship between hormonal receptors status and proliferation levels resulting in the gain of somatic mutations and copy number. This in turn re-programmed the transcriptome and proteome towards a highly replicating and genomically unstable IBTRs, possibly enhanced by APOBEC3B. In order to investigate the origins of IBTRs, a second analysis that included primaries with no recurrence pinpointed proliferation and immune infiltration as predictive of IBTR. In conclusion, our study shows that breast tumors evolve into different IBTRs depending on hormonal status and proliferation and that immune cell infiltration and Ki-67 are significantly elevated in primary tumors that develop IBTR. These results can serve as a starting point to explore markers to predict IBTR formation and stratify patients for adjuvant therapy.", "doi": "10.1038/s42003-023-04526-6", "pmid": "36732562", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9894938"}, {"db": "pii", "key": "10.1038/s42003-023-04526-6"}], "notes": [], "created": "2026-09-23T12:23:18.300Z", "modified": "2026-09-23T12:23:18.556Z"}, {"entity": "publication", "iuid": "bfdd351133f4418494906a622516c9f3", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/bfdd351133f4418494906a622516c9f3.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/bfdd351133f4418494906a622516c9f3"}}, "title": "Automated detection of vascular remodeling in tumor-draining lymph nodes by the deep-learning tool HEV-finder.", "authors": [{"family": "Bekkhus", "given": "Tove", "initials": "T", "orcid": "0000-0002-2868-2483", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/80f3ba137f884820bef258c8261bd051.json"}}, {"family": "Avenel", "given": "Christophe", "initials": "C", "orcid": "0000-0002-1835-921X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b65fab9c103c4551b457a801988ce728.json"}}, {"family": "Hanna", "given": "Sabella", "initials": "S"}, {"family": "Franz\u00e9n Boger", "given": "Mathias", "initials": "M"}, {"family": "Klemm", "given": "Anna", "initials": "A", "orcid": "0000-0002-3466-1320", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bda9a501396248b5a7daa41db01518dc.json"}}, {"family": "Bacovia", "given": "Daniel Vasiliu", "initials": "DV"}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f.json"}}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/833afe3444d84c24be12ea1468563bea.json"}}, {"family": "Ulvmar", "given": "Maria H", "initials": "MH", "orcid": "0000-0002-9050-0978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/081a6551b7b94c36b059410b02f25133.json"}}], "type": "journal article", "published": "2022-09-00", "journal": {"title": "J. Pathol.", "issn": "1096-9896", "volume": "258", "issue": "1", "pages": "4-11", "issn-l": "0022-3417"}, "abstract": "Vascular remodeling is common in human cancer and has potential as future biomarkers for prediction of disease progression and tumor immunity status. It can also affect metastatic sites, including the tumor-draining lymph nodes (TDLNs). Dilation of the high endothelial venules (HEVs) within TDLNs has been observed in several types of cancer. We recently demonstrated that it is a premetastatic effect that can be linked to tumor invasiveness in breast cancer. Manual visual assessment of changes in vascular morphology is a tedious and difficult task, limiting high-throughput analysis. Here we present a fully automated approach for detection and classification of HEV dilation. By using 12,524 manually classified HEVs, we trained a deep-learning model and created a graphical user interface for visualization of the results. The tool, named the HEV-finder, selectively analyses HEV dilation in specific regions of the lymph nodes. We evaluated the HEV-finder's ability to detect and classify HEV dilation in different types of breast cancer compared to manual annotations. Our results constitute a successful example of large-scale, fully automated, and user-independent, image-based quantitative assessment of vascular remodeling in human pathology and lay the ground for future exploration of HEV dilation in TDLNs as a biomarker. \u00a9 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.", "doi": "10.1002/path.5981", "pmid": "35696253", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9543492"}], "notes": [], "created": "2026-09-23T13:16:27.435Z", "modified": "2026-09-23T13:16:27.533Z"}, {"entity": "publication", "iuid": "8f3f5c2e49994d55a42fd41d2d9326b4", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8f3f5c2e49994d55a42fd41d2d9326b4.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8f3f5c2e49994d55a42fd41d2d9326b4"}}, "title": "\u201dEvolution of ipsilateral breast cancer decoded by proteogenomics\u201d", "authors": [{"family": "Marchi", "given": "Tommaso De", "initials": "TD", "orcid": "0000-0002-4845-1084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/68502c65e0754c4698a3f4d3c802acc4.json"}}, {"family": "Pyl", "given": "Paul Theodor", "initials": "PT", "orcid": "0000-0002-7651-883X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b778ed88a694ddd84a2a3358eb60b4f.json"}}, {"family": "Sj\u00f6str\u00f6m", "given": "Martin", "initials": "M", "orcid": "0000-0002-2629-9966", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b42d7aeedc844018bbe28980b73cb6c6.json"}}, {"family": "Reinsbach", "given": "Susanne Erika", "initials": "SE", "orcid": "0000-0003-0509-2488", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f35ebeb793254320982f857ec99fe02a.json"}}, {"family": "DiLorenzo", "given": "Sebastian", "initials": "S", "orcid": "0000-0002-9759-2211", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bbd59f99c568418d82c52fb9e049001a.json"}}, {"family": "Nystedt", "given": "Bj\u00f6rn", "initials": "B", "orcid": "0000-0001-7809-7664", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33ba67b99d2b477d9588d40e8cc0fed2.json"}}, {"family": "Tran", "given": "Lena", "initials": "L"}, {"family": "Pekar", "given": "Gyula", "initials": "G", "orcid": "0000-0002-0667-0270", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef9d9b551a86483d82356c914dbe826c.json"}}, {"family": "W\u00e4rnberg", "given": "Fredrik", "initials": "F", "orcid": "0000-0002-0130-7296", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/47319ea84c8d46f7999c903f6840403f.json"}}, {"family": "Fredriksson", "given": "Irma", "initials": "I", "orcid": "0000-0001-7811-9317", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/75574ec73d974ea7be24724f74f6b0cb.json"}}, {"family": "Malmstr\u00f6m", "given": "Per", "initials": "P"}, {"family": "Fern\u00f6", "given": "M\u00e5rten", "initials": "M", "orcid": "0000-0003-2220-1236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d190c0c5f17f4c298855f9b13f9bb16d.json"}}, {"family": "Malmstr\u00f6m", "given": "Lars", "initials": "L"}, {"family": "Malmst\u00f6m", "given": "Johan", "initials": "J", "orcid": "0000-0002-2889-7169", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c89da9268a4f47a8a99fd62de451aaa7.json"}}, {"family": "Nim\u00e9us", "given": "Emma", "initials": "E", "orcid": "0000-0003-0262-9083", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9c4af562bc1248ecbbb730a496675571.json"}}], "type": "posted-content", "published": "2022-07-14", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/2022.07.13.499898", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-09-23T15:19:37.685Z", "modified": "2026-09-23T15:19:37.859Z"}]}