{"entity": "researcher", "timestamp": "2026-09-24T14:46:57.642Z", "family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "affiliations": ["Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden.", "Theme Cancer, Karolinska University Hospital and Karolinska Comprehensive Cancer Center, Stockholm, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4ce5f98b0640778e21d53349e3a468.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4ce5f98b0640778e21d53349e3a468"}}, "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": "021d6e3671944964845d5bd3ff8a4f2b", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/021d6e3671944964845d5bd3ff8a4f2b.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/021d6e3671944964845d5bd3ff8a4f2b"}}, "title": "Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.", "authors": [{"family": "Zerdes", "given": "Ioannis", "initials": "I", "orcid": "0000-0002-8304-2462", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4f4ce5f98b0640778e21d53349e3a468.json"}}, {"family": "Simonetti", "given": "Michele", "initials": "M", "orcid": "0000-0003-3322-1697", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ac01283eacef4f2e81675653202782a5.json"}}, {"family": "Matikas", "given": "Alexios", "initials": "A", "orcid": "0000-0002-4122-9624", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/694cc730bb754271a18b029ec0c1eadf.json"}}, {"family": "Harbers", "given": "Luuk", "initials": "L", "orcid": "0000-0003-3910-6497", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b9967939c5d5494a85fac56173a49821.json"}}, {"family": "Acs", "given": "Balazs", "initials": "B"}, {"family": "Boyaci", "given": "Ceren", "initials": "C", "orcid": "0000-0001-5598-0243", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ea42415f08204e299bce41f767982d98.json"}}, {"family": "Zhang", "given": "Ning", "initials": "N", "orcid": "0000-0002-6430-4236", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f8c46858ed4641639ae4cfb6996a9ee5.json"}}, {"family": "Salgkamis", "given": "Dimitrios", "initials": "D", "orcid": "0000-0002-3020-0359", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e76cfdf1a2004e1fb8808dc3372c2d4b.json"}}, {"family": "Agartz", "given": "Susanne", "initials": "S"}, {"family": "Moreno-Ruiz", "given": "Pablo", "initials": "P"}, {"family": "Bai", "given": "Yalai", "initials": "Y"}, {"family": "Rimm", "given": "David L", "initials": "DL", "orcid": "0000-0001-5820-4397", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8391cca478a441d68e9d3b092983cb48.json"}}, {"family": "Hartman", "given": "Johan", "initials": "J", "orcid": "0000-0002-6500-8527", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d62d622200d443b7b5be34ff3c0945be.json"}}, {"family": "Mezheyeuski", "given": "Artur", "initials": "A", "orcid": "0000-0002-4394-2634", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/227a0142881848f4a1635d66cf52e673.json"}}, {"family": "Bergh", "given": "Jonas", "initials": "J", "orcid": "0000-0001-5526-1847", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a462537d526a4259b9c68da95bd4aae4.json"}}, {"family": "Crosetto", "given": "Nicola", "initials": "N", "orcid": "0000-0002-3019-6978", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0b1cef698ae749749b4017dbacb9e3db.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": "2021-11-19", "journal": {"title": "NPJ Breast Cancer", "issn": "2374-4677", "volume": "7", "issue": "1", "pages": "144", "issn-l": null}, "abstract": "Emerging data indicate that genomic alterations can shape immune cell composition in early breast cancer. However, there is a need for complementary imaging and sequencing methods for the quantitative assessment of combined somatic copy number alteration (SCNA) and immune profiling in pathological samples. Here, we tested the feasibility of three approaches-CUTseq, for high-throughput low-input SCNA profiling, multiplexed fluorescent immunohistochemistry (mfIHC) and digital-image analysis (DIA) for quantitative immuno-profiling- in archival formalin-fixed paraffin-embedded (FFPE) tissue samples from patients enrolled in the randomized SBG-2004-1 phase II trial. CUTseq was able to reproducibly identify amplification and deletion events with a resolution of 100 kb using only 6 ng of DNA extracted from FFPE tissue and pooling together 77 samples into the same sequencing library. In the same samples, mfIHC revealed that CD4 + T-cells and CD68 + macrophages were the most abundant immune cells and they mostly expressed PD-L1 and PD-1. Combined analysis showed that the SCNA burden was inversely associated with lymphocytic infiltration. Our results set the basis for further applications of CUTseq, mfIHC and DIA to larger cohorts of early breast cancer patients.", "doi": "10.1038/s41523-021-00352-3", "pmid": "34799582", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8604966"}, {"db": "pii", "key": "10.1038/s41523-021-00352-3"}], "notes": [], "created": "2026-09-23T12:07:28.425Z", "modified": "2026-09-23T12:07:28.665Z"}]}