{"entity": "researcher", "timestamp": "2026-08-20T20:36:41.429Z", "family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "affiliations": ["Cancer Proteomics Mass Spectrometry, Department of Oncology-Pathology, Science for Life Laboratory, Karolinska Institutet, Solna, Sweden."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04"}}, "publications": [{"entity": "publication", "iuid": "03b8b76f60b94595be68f854a95c97a9", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/03b8b76f60b94595be68f854a95c97a9.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/03b8b76f60b94595be68f854a95c97a9"}}, "title": "Author Correction: Characterization of a second class Ie ribonucleotide reductase.", "authors": [{"family": "John", "given": "Juliane", "initials": "J"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}}, {"family": "Kumar", "given": "Rohit", "initials": "R", "orcid": "0000-0001-5033-2810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd150fa0a7254f878fb2ae6e564ba2e6.json"}}, {"family": "Srinivas", "given": "Vivek", "initials": "V", "orcid": "0000-0002-0265-1873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bbb4c7b9c734a87a398edc4e38cd97a.json"}}, {"family": "Lebrette", "given": "Hugo", "initials": "H", "orcid": "0000-0002-8081-181X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1df0bbc3d2f6465e8407bad4040b92b5.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b427ce46a6ea4d908d67167e51d1b7d5.json"}}], "type": "published erratum", "published": "2025-04-01", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "532", "issn-l": "2399-3642"}, "abstract": null, "doi": "10.1038/s42003-025-07982-4", "pmid": "40169876", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11961744"}, {"db": "pii", "key": "10.1038/s42003-025-07982-4"}], "notes": [], "created": "2026-08-20T09:25:26.677Z", "modified": "2026-08-20T09:25:26.759Z"}, {"entity": "publication", "iuid": "003e736990694b799b028ddf0f4379ec", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/003e736990694b799b028ddf0f4379ec.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/003e736990694b799b028ddf0f4379ec"}}, "title": "Characterization of a second class Ie ribonucleotide reductase.", "authors": [{"family": "John", "given": "Juliane", "initials": "J"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7f557cf4f7ed402c8843173ab0bbef04.json"}}, {"family": "Kumar", "given": "Rohit", "initials": "R", "orcid": "0000-0001-5033-2810", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fd150fa0a7254f878fb2ae6e564ba2e6.json"}}, {"family": "Srinivas", "given": "Vivek", "initials": "V", "orcid": "0000-0002-0265-1873", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5bbb4c7b9c734a87a398edc4e38cd97a.json"}}, {"family": "Lebrette", "given": "Hugo", "initials": "H", "orcid": "0000-0002-8081-181X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1df0bbc3d2f6465e8407bad4040b92b5.json"}}, {"family": "H\u00f6gbom", "given": "Martin", "initials": "M", "orcid": "0000-0001-5574-9383", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b427ce46a6ea4d908d67167e51d1b7d5.json"}}], "type": "journal article", "published": "2025-02-22", "journal": {"title": "Commun Biol", "issn": "2399-3642", "volume": "8", "issue": "1", "pages": "281", "issn-l": "2399-3642"}, "abstract": "Class I ribonucleotide reductases (RNRs) convert ribonucleotides into deoxyribonucleotides under oxic conditions. The R2 subunit provides a radical required for catalysis conducted by the R1 subunit. In most R2s the radical is generated on a tyrosine via oxidation by an adjacent metal site. The discovery of a metal-free R2 defined the new RNR subclass Ie. In R2e, three of the otherwise strictly conserved metal-binding glutamates in the active site are substituted. Two variants have been found, VPK and QSK. To date, the VPK version has been the focus of biochemical characterization. Here we characterize a QSK variant of R2e. We analyse the organismal distribution of the two R2e versions and find dozens of organisms relying solely on the QSK RNR for deoxyribonucleotide production. We demonstrate that the R2eQSK of the human pathogen Gardnerella vaginalis (Bifidobacterium vaginale) modifies the active site-adjacent tyrosine to DOPA. The amount of modified protein is shown to be dependent on coexpression with the other proteins encoded in the RNR operon. The DOPA containing R2eQSK can support ribonucleotide reduction in vitro while the unmodified protein cannot. Finally, we determined the first structures of R2eQSK in the unmodified and DOPA states.", "doi": "10.1038/s42003-025-07565-3", "pmid": "39987380", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC11846895"}, {"db": "pii", "key": "10.1038/s42003-025-07565-3"}], "notes": [], "created": "2026-08-20T09:25:22.863Z", "modified": "2026-08-20T09:25:23.134Z"}, {"entity": "publication", "iuid": "8dbdd622a6684fc09a07dc19fa3bf37f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/8dbdd622a6684fc09a07dc19fa3bf37f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/8dbdd622a6684fc09a07dc19fa3bf37f"}}, "title": "Harnessing T cell exhaustion and trogocytosis to isolate patient-derived tumor-specific TCR.", "authors": [{"family": "Manfredi", "given": "Francesco", "initials": "F", "orcid": "0000-0003-2409-944X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8f8173a6adb74503a2c2636bc7cd6187.json"}}, {"family": "Stasi", "given": "Lorena", "initials": "L", "orcid": "0000-0001-8044-2295", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/103e396d7f714d0eadf42ae463e23006.json"}}, {"family": "Buonanno", "given": "Silvia", "initials": "S"}, {"family": "Marzuttini", "given": "Francesca", "initials": "F"}, {"family": "Noviello", "given": "Maddalena", "initials": "M"}, {"family": "Mastaglio", "given": "Sara", "initials": "S"}, {"family": "Abbati", "given": "Danilo", "initials": "D", "orcid": "0000-0001-8517-7937", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1cf52edec41c48e7a085130d6a0f538a.json"}}, {"family": "Potenza", "given": "Alessia", "initials": "A", "orcid": "0000-0003-0298-7315", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5c2f5b34a8444def99ed10d6922b29b2.json"}}, {"family": "Balestrieri", "given": "Chiara", "initials": "C", "orcid": "0000-0001-7362-3530", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c720c467b1714e78bd49b928d1df4717.json"}}, {"family": "Cianciotti", "given": "Beatrice Claudia", "initials": "BC", "orcid": "0000-0002-1337-5915", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b80a1fa9b2d14bfe8ba9e3103fe581d6.json"}}, {"family": "Tassi", "given": "Elena", "initials": "E", "orcid": "0000-0002-2921-8666", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/650c1981b70b4dbf866d21221e0d18b7.json"}}, {"family": "Feola", "given": "Sara", "initials": "S", "orcid": "0000-0002-4012-4310", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/81e8d2f15fcf4e1aabf7b5a41a977f3f.json"}}, {"family": "Toffalori", "given": "Cristina", "initials": "C", "orcid": "0000-0002-8313-3057", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/41008f14a9b94192a9cacd2ab0710976.json"}}, {"family": "Punta", "given": "Marco", "initials": "M", "orcid": "0000-0002-0050-0676", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/083075f454224bf1a13724e85cf2bf7c.json"}}, {"family": "Magnani", "given": "Zulma", "initials": "Z", "orcid": "0000-0001-7612-6097", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8b56dd0945ff4ebf941b8c1ed107378c.json"}}, {"family": "Camisa", "given": "Barbara", "initials": "B", "orcid": "0000-0002-3867-2457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f967aca004f41e59f1e8e182851d732.json"}}, {"family": "Tiziano", "given": "Elena", "initials": "E", "orcid": "0000-0002-1794-4265", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3818be60d8a34864943b9697aa4e11bd.json"}}, {"family": "Lupo-Stanghellini", "given": "Maria Teresa", "initials": "MT"}, {"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": "Sikanen", "given": "Tiina M", "initials": "TM", "orcid": "0000-0002-0788-1301", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ee477a2ee578421c889c078b35324ce5.json"}}, {"family": "Haapala", "given": "Markus J", "initials": "MJ", "orcid": "0000-0001-7828-8663", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2241723f3734c5390b4fa4014563668.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d46c756e18bb49268b98a75a5234664a.json"}}, {"family": "Casucci", "given": "Monica", "initials": "M", "orcid": "0000-0003-4500-9060", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/a0f5a535676445f5b871cfffd7d98560.json"}}, {"family": "Vago", "given": "Luca", "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": "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"}]}