{"entity": "researcher", "timestamp": "2026-08-13T17:56:54.673Z", "family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "affiliations": [], "links": {"self": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}, "display": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a"}}, "publications": [{"entity": "publication", "iuid": "8bfe93edf9d64769a9d6fef06df316a3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8bfe93edf9d64769a9d6fef06df316a3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8bfe93edf9d64769a9d6fef06df316a3"}}, "title": "Development of mesothelioma-specific oncolytic immunotherapy enabled by immunopeptidomics of murine and human mesothelioma 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.scilifelab.se/researcher/c9d2c4168aa541b5ad9a7e5155dc1069.json"}}, {"family": "Feodoroff", "given": "Michaela", "initials": "M", "orcid": "0000-0002-6094-9838", "researcher": {"href": "https://publications.scilifelab.se/researcher/b828ef2f6621496cbc6ac77cc8413c14.json"}}, {"family": "Martins", "given": "Beatriz", "initials": "B"}, {"family": "Cojoc", "given": "Hanne", "initials": "H"}, {"family": "Russo", "given": "Salvatore", "initials": "S"}, {"family": "Fusciello", "given": "Manlio", "initials": "M", "orcid": "0000-0002-7166-3018", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c74e3317cd646c1989a49b281c3e8e7.json"}}, {"family": "Hamdan", "given": "Firas", "initials": "F", "orcid": "0000-0003-4678-7382", "researcher": {"href": "https://publications.scilifelab.se/researcher/3f991da24d5c4c02945f0bfb614558a2.json"}}, {"family": "Ferrari", "given": "Valentina", "initials": "V"}, {"family": "Ciampi", "given": "Daniele", "initials": "D", "orcid": "0000-0001-6523-3049", "researcher": {"href": "https://publications.scilifelab.se/researcher/3161ddeb6095464fbd04afed3d7e56ee.json"}}, {"family": "Ilonen", "given": "Ilkka", "initials": "I", "orcid": "0000-0002-8149-3550", "researcher": {"href": "https://publications.scilifelab.se/researcher/8409282fff6b479daec8aa4e898a3aee.json"}}, {"family": "R\u00e4s\u00e4nen", "given": "Jari", "initials": "J"}, {"family": "M\u00e4yr\u00e4np\u00e4\u00e4", "given": "Mikko", "initials": "M", "orcid": "0000-0002-0877-9640", "researcher": {"href": "https://publications.scilifelab.se/researcher/63d6deb5a00141b0bb2c2f031ef8d53a.json"}}, {"family": "Partanen", "given": "Jukka", "initials": "J", "orcid": "0000-0001-6681-4734", "researcher": {"href": "https://publications.scilifelab.se/researcher/5f3b7cf9d4874b63b92556eccf060493.json"}}, {"family": "Koskela", "given": "Satu", "initials": "S", "orcid": "0000-0001-9258-9163", "researcher": {"href": "https://publications.scilifelab.se/researcher/478c0a65a147450bb5c5a7ba7d196b41.json"}}, {"family": "Honkanen", "given": "Jarno", "initials": "J"}, {"family": "Halonen", "given": "Jussi", "initials": "J"}, {"family": "Kuryk", "given": "Lukasz", "initials": "L", "orcid": "0000-0003-1887-6361", "researcher": {"href": "https://publications.scilifelab.se/researcher/cfa535fd845648f5ab10d0e1a407f8f9.json"}}, {"family": "Rescigno", "given": "Maria", "initials": "M", "orcid": "0000-0002-6464-509X", "researcher": {"href": "https://publications.scilifelab.se/researcher/ee52150f5c1c4140aaf8758fff64572c.json"}}, {"family": "Gr\u00f6nholm", "given": "Mikaela", "initials": "M"}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Cerullo", "given": "Vincenzo", "initials": "V", "orcid": "0000-0003-4901-3796", "researcher": {"href": "https://publications.scilifelab.se/researcher/6404cf54a990420fb0b63d626aa783fb.json"}}], "type": "journal article", "published": "2023-11-03", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "7056", "issn-l": "2041-1723"}, "abstract": "Malignant pleural mesothelioma (MPM) is an aggressive tumor with a poor prognosis. As the available therapeutic options show a lack of efficacy, novel therapeutic strategies are urgently needed. Given its T-cell infiltration, we hypothesized that MPM is a suitable target for therapeutic cancer vaccination. To date, research on mesothelioma has focused on the identification of molecular signatures to better classify and characterize the disease, and little is known about therapeutic targets that engage cytotoxic (CD8+) T cells. In this study we investigate the immunopeptidomic antigen-presented landscape of MPM in both murine (AB12 cell line) and human cell lines (H28, MSTO-211H, H2452, and JL1), as well as in patients' primary tumors. Applying state-of-the-art immuno-affinity purification methodologies, we identify MHC I-restricted peptides presented on the surface of malignant cells. We characterize in vitro the immunogenicity profile of the eluted peptides using T cells from human healthy donors and cancer patients. Furthermore, we use the most promising peptides to formulate an oncolytic virus-based precision immunotherapy (PeptiCRAd) and test its efficacy in a mouse model of mesothelioma in female mice. Overall, we demonstrate that the use of immunopeptidomic analysis in combination with oncolytic immunotherapy represents a feasible and effective strategy to tackle untreatable tumors.", "doi": "10.1038/s41467-023-42668-7", "pmid": "37923723", "labels": {"Global Proteomics and Proteogenomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC10624665"}, {"db": "pii", "key": "10.1038/s41467-023-42668-7"}], "notes": [], "created": "2023-11-30T10:26:49.610Z", "modified": "2023-11-30T10:26:49.935Z"}, {"entity": "publication", "iuid": "170fec648fb448e99fbe3bd024cd7e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/170fec648fb448e99fbe3bd024cd7e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/170fec648fb448e99fbe3bd024cd7e34"}}, "title": "A Mitochondrial LYR Protein Is Required for Complex I Assembly.", "authors": [{"family": "Ivanova", "given": "Aneta", "initials": "A", "orcid": "0000-0002-2465-7213", "researcher": {"href": "https://publications.scilifelab.se/researcher/3b4791ef8f5843949894df534ff8355e.json"}}, {"family": "Gill-Hille", "given": "Mabel", "initials": "M", "orcid": "0000-0001-7749-5839", "researcher": {"href": "https://publications.scilifelab.se/researcher/7eb758e47fb34b8a86f076d1574c31b1.json"}}, {"family": "Huang", "given": "Shaobai", "initials": "S", "orcid": "0000-0003-3667-611X", "researcher": {"href": "https://publications.scilifelab.se/researcher/eee12c8a03254793b1735eb4510fc90f.json"}}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Kmiec", "given": "Beata", "initials": "B", "orcid": "0000-0002-1383-0412", "researcher": {"href": "https://publications.scilifelab.se/researcher/7cacde5eab9a4ce8ada537324ed66d05.json"}}, {"family": "Teixeira", "given": "Pedro F", "initials": "PF", "orcid": "0000-0001-8638-7477", "researcher": {"href": "https://publications.scilifelab.se/researcher/9b43730fe20b424db84f091333be7244.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Whelan", "given": "James", "initials": "J", "orcid": "0000-0001-5754-025X", "researcher": {"href": "https://publications.scilifelab.se/researcher/15d6dae558a24c03b6298dc9bd5b991d.json"}}, {"family": "Murcha", "given": "Monika W", "initials": "MW", "orcid": "0000-0002-3689-6158", "researcher": {"href": "https://publications.scilifelab.se/researcher/49b1e7e1fca74be090072ad2185c9827.json"}}], "type": "journal article", "published": "2019-12-00", "journal": {"volume": "181", "issn": "1532-2548", "issue": "4", "pages": "1632-1650", "title": "Plant Physiol.", "issn-l": "0032-0889"}, "abstract": "Complex I biogenesis requires the expression of both nuclear and mitochondrial genes, the import of proteins, cofactor biosynthesis, and the assembly of at least 49 individual subunits. Assembly factors interact with subunits of Complex I but are not part of the final holocomplex. We show that in Arabidopsis (Arabidopsis thaliana), a mitochondrial matrix protein (EMB1793, At1g76060), which we term COMPLEX I ASSEMBLY FACTOR 1 (CIAF1), contains a LYR domain and is required for Complex I assembly. T-DNA insertion mutants of CIAF1 lack Complex I and the Supercomplex I+III. Biochemical characterization shows that the assembly of Complex I is stalled at 650 and 800 kD intermediates in mitochondria isolated from ciaf1 mutant lines.I. Yeast-two-hybrid interaction and complementation assays indicate that CIAF1 specifically interacts with the 23-kD TYKY-1 matrix domain subunit of Complex I and likely plays a role in Fe-S insertion into this subunit. These data show that CIAF1 plays an essential role in assembling the peripheral matrix arm Complex I subunits into the Complex I holoenzyme.", "doi": "10.1104/pp.19.00822", "pmid": "31601645", "labels": {"Global Proteomics and Proteogenomics": "Collaborative"}, "xrefs": [{"db": "pii", "key": "pp.19.00822"}, {"db": "pmc", "key": "PMC6878026"}], "notes": [], "created": "2020-01-07T12:28:27.281Z", "modified": "2021-07-08T11:16:55.122Z"}, {"entity": "publication", "iuid": "e7f90faca0e64cfe9379be8900367d06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e7f90faca0e64cfe9379be8900367d06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e7f90faca0e64cfe9379be8900367d06"}}, "title": "Breast cancer quantitative proteome and proteogenomic landscape.", "authors": [{"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Socciarelli", "given": "Fabio", "initials": "F"}, {"family": "Vacanti", "given": "Nathaniel M", "initials": "NM"}, {"family": "Haugen", "given": "Mads H", "initials": "MH"}, {"family": "Zhu", "given": "Yafeng", "initials": "Y"}, {"family": "Siavelis", "given": "Ioannis", "initials": "I"}, {"family": "Fernandez-Woodbridge", "given": "Alejandro", "initials": "A"}, {"family": "Aure", "given": "Miriam R", "initials": "MR"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Vesterlund", "given": "Mattias", "initials": "M", "orcid": "0000-0001-9471-6592", "researcher": {"href": "https://publications.scilifelab.se/researcher/0942e438993b494db2a3db914852c808.json"}}, {"family": "Branca", "given": "Rui M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "Fredlund", "given": "Erik", "initials": "E"}, {"family": "Beraki", "given": "Elsa", "initials": "E"}, {"family": "Garred", "given": "\u00d8ystein", "initials": "\u00d8"}, {"family": "Boekel", "given": "Jorrit", "initials": "J"}, {"family": "Sauer", "given": "Torill", "initials": "T"}, {"family": "Zhao", "given": "Wei", "initials": "W"}, {"family": "Nord", "given": "Silje", "initials": "S"}, {"family": "H\u00f6glander", "given": "Elen K", "initials": "EK"}, {"family": "Jans", "given": "Daniel C", "initials": "DC"}, {"family": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"family": "Haukaas", "given": "Tonje H", "initials": "TH"}, {"family": "Bathen", "given": "Tone F", "initials": "TF"}, {"family": "Schlichting", "given": "Ellen", "initials": "E"}, {"family": "Naume", "given": "Bj\u00f8rn", "initials": "B"}, {"family": "Consortia Oslo Breast Cancer Research Consortium (OSBREAC)", "given": "", "initials": ""}, {"family": "Luders", "given": "Torben", "initials": "T"}, {"family": "Borgen", "given": "Elin", "initials": "E"}, {"family": "Kristensen", "given": "Vessela N", "initials": "VN"}, {"family": "Russnes", "given": "Hege G", "initials": "HG"}, {"family": "Lingj\u00e6rde", "given": "Ole Christian", "initials": "OC", "orcid": "0000-0003-3565-4912", "researcher": {"href": "https://publications.scilifelab.se/researcher/759346ec4321470f96ca42af68ed760c.json"}}, {"family": "Mills", "given": "Gordon B", "initials": "GB"}, {"family": "Sahlberg", "given": "Kristine K", "initials": "KK"}, {"family": "B\u00f8rresen-Dale", "given": "Anne-Lise", "initials": "AL"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2019-04-08", "journal": {"volume": "10", "issn": "2041-1723", "issue": "1", "pages": "1600", "title": "Nat Commun", "issn-l": "2041-1723"}, "abstract": "In the preceding decades, molecular characterization has revolutionized breast cancer (BC) research and therapeutic approaches. Presented herein, an unbiased analysis of breast tumor proteomes, inclusive of 9995 proteins quantified across all tumors, for the first time recapitulates BC subtypes. Additionally, poor-prognosis basal-like and luminal B tumors are further subdivided by immune component infiltration, suggesting the current classification is incomplete. Proteome-based networks distinguish functional protein modules for breast tumor groups, with co-expression of EGFR and MET marking ductal carcinoma in situ regions of normal-like tumors and lending to a more accurate classification of this poorly defined subtype. Genes included within prognostic mRNA panels have significantly higher than average mRNA-protein correlations, and gene copy number alterations are dampened at the protein-level; underscoring the value of proteome quantification for prognostication and phenotypic classification. Furthermore, protein products mapping to non-coding genomic regions are identified; highlighting a potential new class of tumor-specific immunotherapeutic targets.", "doi": "10.1038/s41467-019-09018-y", "pmid": "30962452", "labels": {"Bioinformatics Support, Infrastructure and Training": "Collaborative", "Bioinformatics Long-term Support WABI": "Collaborative", "Global Proteomics and Proteogenomics": "Technology development", "Integrated Microscopy Technologies Stockholm": "Service", "Bioinformatics Support for Computational Resources": "Service", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1038/s41467-019-09018-y"}, {"db": "pmc", "key": "PMC6453966"}], "notes": [], "created": "2019-04-12T07:18:25.320Z", "modified": "2024-01-16T13:48:44.506Z"}, {"entity": "publication", "iuid": "f5ae0bcb00e84e21ab0bdf4d81044a0c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f5ae0bcb00e84e21ab0bdf4d81044a0c"}}, "title": "HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.", "authors": [{"family": "Branca", "given": "Rui M M", "initials": "RM", "orcid": "0000-0003-3890-6476", "researcher": {"href": "https://publications.scilifelab.se/researcher/87d6256540174d3da581d4572f9d182a.json"}}, {"family": "Orre", "given": "Lukas M", "initials": "LM", "orcid": "0000-0002-0384-1003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7b4e49a93b0143db88059c4d1e9fdc59.json"}}, {"family": "Johansson", "given": "Henrik J", "initials": "HJ", "orcid": "0000-0003-4729-4205", "researcher": {"href": "https://publications.scilifelab.se/researcher/18aebf211fa640f48a7c8d860c168e5a.json"}}, {"family": "Granholm", "given": "Viktor", "initials": "V"}, {"family": "Huss", "given": "Mikael", "initials": "M"}, {"family": "P\u00e9rez-Bercoff", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Forshed", "given": "Jenny", "initials": "J"}, {"family": "K\u00e4ll", "given": "Lukas", "initials": "L", "orcid": "0000-0001-5689-9797", "researcher": {"href": "https://publications.scilifelab.se/researcher/9c9f4444f83e43d79c4772a430ca3969.json"}}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}], "type": "journal article", "published": "2014-01-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "volume": "11", "issue": "1", "pages": "59-62", "issn-l": "1548-7091"}, "abstract": "We present a liquid chromatography-mass spectrometry (LC-MS)-based method permitting unbiased (gene prediction-independent) genome-wide discovery of protein-coding loci in higher eukaryotes. Using high-resolution isoelectric focusing (HiRIEF) at the peptide level in the 3.7-5.0 pH range and accurate peptide isoelectric point (pI) prediction, we probed the six-reading-frame translation of the human and mouse genomes and identified 98 and 52 previously undiscovered protein-coding loci, respectively. The method also enabled deep proteome coverage, identifying 13,078 human and 10,637 mouse proteins.", "doi": "10.1038/nmeth.2732", "pmid": "24240322", "labels": {"National Genomics Infrastructure": "Service", "Bioinformatics Support, Infrastructure and Training": "Service", "NGI Stockholm (Genomics Applications)": "Service", "NGI Stockholm (Genomics Production)": "Service", "Bioinformatics Support and Infrastructure": "Service", "Bioinformatics (NBIS)": "Service"}, "xrefs": [{"db": "pii", "key": "nmeth.2732"}], "notes": [], "created": "2023-06-16T12:47:04.864Z", "modified": "2023-06-16T12:47:27.234Z"}]}