{"entity": "researcher", "timestamp": "2026-09-24T16:24:51.687Z", "family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "affiliations": ["Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/3521ffb7f954427b97d4da9c497f9556.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/3521ffb7f954427b97d4da9c497f9556"}}, "publications": [{"entity": "publication", "iuid": "e16092e5bb23404fa289bb3dcb7891c5", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/e16092e5bb23404fa289bb3dcb7891c5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/e16092e5bb23404fa289bb3dcb7891c5"}}, "title": "Longitudinal molecular profiling elucidates immunometabolism dynamics in breast cancer.", "authors": [{"family": "Wang", "given": "Kang", "initials": "K", "orcid": "0000-0001-5401-1803", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c8221243ba04aa4b306b22cee6c713a.json"}}, {"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4ce5f98b0640778e21d53349e3a468.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e8acb3ba52a54c7a82f2a096516a8e05.json"}}, {"family": "Sarhan", "given": "Dhifaf", "initials": "D", "orcid": "0000-0003-0196-4496", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21138e97f7094430a43dfb5d24f3d5f8.json"}}, {"family": "Sun", "given": "Yizhe", "initials": "Y"}, {"family": "Kanellis", "given": "Dimitris C", "initials": "DC", "orcid": "0000-0001-8690-2010", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/14307e4299ce40a49d2e45265398676c.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3521ffb7f954427b97d4da9c497f9556.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A"}, {"family": "Liu", "given": "Xingrong", "initials": "X"}, {"family": "Loman", "given": "Niklas", "initials": "N"}, {"family": "Hedenfalk", "given": "Ingrid", "initials": "I", "orcid": "0000-0002-6840-3397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3e10ee54fe3241cd9c848babbdcc95ac.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a462537d526a4259b9c68da95bd4aae4.json"}}, {"family": "Bartek", "given": "Jiri", "initials": "J", "orcid": "0000-0003-2013-7525", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/288939950c0c4c6393d35c84e5128b5f.json"}}, {"family": "Hatschek", "given": "Thomas", "initials": "T"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/561efcf32e2648c8a10fee692fc4e908.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/694cc730bb754271a18b029ec0c1eadf.json"}}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8d949ec9ece444da6676f68f062c787.json"}}], "type": "journal article", "published": "2024-05-07", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "15", "issue": "1", "pages": "3837", "issn-l": "2041-1723"}, "abstract": "Although metabolic reprogramming within tumor cells and tumor microenvironment (TME) is well described in breast cancer, little is known about how the interplay of immune state and cancer metabolism evolves during treatment. Here, we characterize the immunometabolic profiles of tumor tissue samples longitudinally collected from individuals with breast cancer before, during and after neoadjuvant chemotherapy (NAC) using proteomics, genomics and histopathology. We show that the pre-, on-treatment and dynamic changes of the immune state, tumor metabolic proteins and tumor cell gene expression profiling-based metabolic phenotype are associated with treatment response. Single-cell/nucleus RNA sequencing revealed distinct tumor and immune cell states in metabolism between cold and hot tumors. Potential drivers of NAC based on above analyses were validated in vitro. In summary, the study shows that the interaction of tumor-intrinsic metabolic states and TME is associated with treatment outcome, supporting the concept of targeting tumor metabolism for immunoregulation.", "doi": "10.1038/s41467-024-47932-y", "pmid": "38714665", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11076527"}, {"db": "pii", "key": "10.1038/s41467-024-47932-y"}], "notes": [], "created": "2026-09-23T09:07:15.621Z", "modified": "2026-09-23T09:07:16.101Z"}, {"entity": "publication", "iuid": "05534a90eb244ae2bba1c7bbf0b4f78d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/05534a90eb244ae2bba1c7bbf0b4f78d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/05534a90eb244ae2bba1c7bbf0b4f78d"}}, "title": "Breast cancer patient-derived whole-tumor cell culture model for efficient drug profiling and treatment response prediction.", "authors": [{"family": "Chen", "given": "Xinsong", "initials": "X", "orcid": "0000-0002-3214-9075", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4a7d95a9799a4c23bb01bf05fa6351cc.json"}}, {"family": "Sifakis", "given": "Emmanouil G", "initials": "EG", "orcid": "0000-0001-9919-4471", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3521ffb7f954427b97d4da9c497f9556.json"}}, {"family": "Robertson", "given": "Stephanie", "initials": "S"}, {"family": "Neo", "given": "Shi Yong", "initials": "SY"}, {"family": "Jun", "given": "Seong-Hwan", "initials": "SH"}, {"family": "Tong", "given": "Le", "initials": "L"}, {"family": "Hui Min", "given": "Apple Tay", "initials": "AT", "orcid": "0000-0002-0600-6599", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8218e0b1f6454bdd89a6861649520c5a.json"}}, {"family": "L\u00f6vrot", "given": "John", "initials": "J", "orcid": "0000-0002-9339-8059", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a98f337b65db4bf485313e1d819d933e.json"}}, {"family": "Hellgren", "given": "Roxanna", "initials": "R", "orcid": "0000-0003-4234-8323", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af7f301a5eae4394a70931a1c56b7ea4.json"}}, {"family": "Margolin", "given": "Sara", "initials": "S"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Foukakis", "given": "Theodoros", "initials": "T", "orcid": "0000-0001-8952-9987", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8d949ec9ece444da6676f68f062c787.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J", "orcid": "0000-0002-4552-0240", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4024d2a29dc14b5289616d90a4265863.json"}}, {"family": "Lundqvist", "given": "Andreas", "initials": "A"}, {"family": "Ma", "given": "Ran", "initials": "R"}, {"family": "Hartman", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2023-01-03", "journal": {"title": "Proc. Natl. Acad. Sci. U.S.A.", "issn": "1091-6490", "volume": "120", "issue": "1", "pages": "e2209856120", "issn-l": "0027-8424"}, "abstract": "Breast cancer (BC) is a complex disease comprising multiple distinct subtypes with different genetic features and pathological characteristics. Although a large number of antineoplastic compounds have been approved for clinical use, patient-to-patient variability in drug response is frequently observed, highlighting the need for efficient treatment prediction for individualized therapy. Several patient-derived models have been established lately for the prediction of drug response. However, each of these models has its limitations that impede their clinical application. Here, we report that the whole-tumor cell culture (WTC) ex vivo model could be stably established from all breast tumors with a high success rate (98 out of 116), and it could reassemble the parental tumors with the endogenous microenvironment. We observed strong clinical associations and predictive values from the investigation of a broad range of BC therapies with WTCs derived from a patient cohort. The accuracy was further supported by the correlation between WTC-based test results and patients' clinical responses in a separate validation study, where the neoadjuvant treatment regimens of 15 BC patients were mimicked. Collectively, the WTC model allows us to accomplish personalized drug testing within 10 d, even for small-sized tumors, highlighting its potential for individualized BC therapy. Furthermore, coupled with genomic and transcriptomic analyses, WTC-based testing can also help to stratify specific patient groups for assignment into appropriate clinical trials, as well as validate potential biomarkers during drug development.", "doi": "10.1073/pnas.2209856120", "pmid": "36574653", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC9910599"}], "notes": [], "created": "2026-09-23T10:10:10.672Z", "modified": "2026-09-23T10:48:29.854Z"}]}