{"entity": "researcher", "timestamp": "2026-07-20T00:16:16.244Z", "family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "affiliations": ["Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94158, USA.", "Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA.", "J. David Gladstone Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, CA 94158, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944"}}, "publications": [{"entity": "publication", "iuid": "6234890ec4f9490bbc0a7d0677b47d65", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/6234890ec4f9490bbc0a7d0677b47d65"}}, "title": "Plasma proteomics for novel biomarker discovery in childhood tuberculosis", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Wambi", "given": "Peter", "initials": "P"}, {"family": "Jaganath", "given": "Devan", "initials": "D"}, {"family": "Calderon", "given": "Roger", "initials": "R"}, {"family": "Castro", "given": "Robert", "initials": "R"}, {"family": "Mohapatra", "given": "Alexander", "initials": "A"}, {"family": "McKetney", "given": "Justin", "initials": "J"}, {"family": "Luiz", "given": "Juaneta", "initials": "J"}, {"family": "Nerurkar", "given": "Rutuja", "initials": "R"}, {"family": "Nkereuwem", "given": "Esin", "initials": "E"}, {"family": "Franke", "given": "Molly F", "initials": "MF"}, {"family": "Mousavian", "given": "Zaynab", "initials": "Z"}, {"family": "Collins", "given": "Jeffrey M", "initials": "JM", "orcid": "0000-0002-2903-797X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8e55c6f4136342ad8c1874d0c0e13924.json"}}, {"family": "Sigal", "given": "George B", "initials": "GB"}, {"family": "Segal", "given": "Mark R", "initials": "MR"}, {"family": "Kampman", "given": "Beate", "initials": "B"}, {"family": "Wobudeya", "given": "Eric", "initials": "E"}, {"family": "Cattamanchi", "given": "Adithya", "initials": "A"}, {"family": "Ernst", "given": "Joel D", "initials": "JD"}, {"family": "Zar", "given": "Heather J", "initials": "HJ"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "posted-content", "published": "2024-12-08", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.12.05.24318340", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:17.973Z", "modified": "2025-03-21T13:33:21.345Z"}, {"entity": "publication", "iuid": "442cfbe882b344b6b586a3c9a349c165", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/442cfbe882b344b6b586a3c9a349c165"}}, "title": "Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.", "authors": [{"family": "Lin", "given": "Zhi", "initials": "Z", "orcid": "0000-0001-6662-7330", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/059b4f81da244058a9e7442b149daadf.json"}}, {"family": "Schaefer", "given": "Kaitlin", "initials": "K", "orcid": "0000-0003-4825-1389", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5601fa03584f40e887f7c12e005737ea.json"}}, {"family": "Lui", "given": "Irene", "initials": "I", "orcid": "0000-0002-6171-5443", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1eca2b8ec2d9461b89c962e8f225e192.json"}}, {"family": "Yao", "given": "Zi", "initials": "Z"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Palar", "given": "Ajikarunia", "initials": "A", "orcid": "0000-0001-9357-6970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/155427eafdb8474589a735c36ca9f149.json"}}, {"family": "Sali", "given": "Andrej", "initials": "A", "orcid": "0000-0003-0435-6197", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dd70ba581f7e49b886339e8883b7f053.json"}}, {"family": "Wells", "given": "James A", "initials": "JA", "orcid": "0000-0001-8267-5519", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f0c1fc2f2b584824bd489884424e333c.json"}}], "type": "journal article", "published": "2024-07-19", "journal": {"title": "Science (New York, N.Y.)", "issn": "1095-9203", "issn-l": "0036-8075", "volume": "385", "issue": "6706", "pages": "eadl5763"}, "abstract": "Proximity labeling proteomics (PLP) strategies are powerful approaches to yield snapshots of protein neighborhoods. Here, we describe a multiscale PLP method with adjustable resolution that uses a commercially available photocatalyst, Eosin Y, which upon visible light illumination activates different photo-probes with a range of labeling radii. We applied this platform to profile neighborhoods of the oncogenic epidermal growth factor receptor and orthogonally validated more than 20 neighbors using immunoassays and AlphaFold-Multimer prediction. We further profiled the protein neighborhoods of cell-cell synapses induced by bispecific T cell engagers and chimeric antigen receptor T cells. This integrated multiscale PLP platform maps local and distal protein networks on and between cell surfaces, which will aid in the systematic construction of the cell surface interactome, revealing horizontal signaling partners and reveal new immunotherapeutic opportunities.", "doi": "10.1126/science.adl5763", "pmid": "39024454", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:05.008Z", "modified": "2025-03-21T13:32:58.593Z"}, {"entity": "publication", "iuid": "0effefb552b64f16b9d47b8e0bd4482f", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0effefb552b64f16b9d47b8e0bd4482f"}}, "title": "Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.", "authors": [{"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Stevenson", "given": "Erica", "initials": "E"}, {"family": "Guan", "given": "Jingwen", "initials": "J"}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E"}, {"family": "Rao", "given": "Sanjana", "initials": "S"}, {"family": "Agard", "given": "David", "initials": "D"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J"}], "type": "journal article", "published": "2024-07-10", "journal": {"title": "Cell Host Microbe", "issn": "1934-6069", "issn-l": "1931-3128", "volume": "32", "issue": "7", "pages": "1050-1058.e7"}, "abstract": "Viral genomes are most vulnerable to cellular defenses at the start of the infection. A family of jumbo phages related to phage \u03a6KZ, which infects Pseudomonas aeruginosa, assembles a protein-based phage nucleus to protect replicating phage DNA, but how it is protected prior to phage nucleus assembly is unclear. We find that host proteins related to membrane and lipid biology interact with injected phage protein, clustering in an early phage infection (EPI) vesicle. The injected virion RNA polymerase (vRNAP) executes early gene expression until phage genome separation from the vRNAP and the EPI vesicle, moving into the nascent proteinaceous phage nucleus. Enzymes involved in DNA replication and CRISPR/restriction immune nucleases are excluded by the EPI vesicle. We propose that the EPI vesicle is rapidly constructed with injected phage proteins, phage DNA, host lipids, and host membrane proteins to enable genome protection, early transcription, localized translation, and to ensure faithful genome transfer to the proteinaceous nucleus.", "doi": "10.1016/j.chom.2024.05.016", "pmid": "38870941", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS2004244"}, {"db": "pmc", "key": "PMC11239273"}, {"db": "pii", "key": "S1931-3128(24)00188-4"}], "notes": [], "created": "2025-03-18T16:51:13.029Z", "modified": "2025-03-21T13:20:33.888Z"}, {"entity": "publication", "iuid": "65da812e265149fba8d4c311774023e2", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/65da812e265149fba8d4c311774023e2"}}, "title": "An atlas of protein-protein associations of human tissues prioritizes candidate disease genes", "authors": [{"family": "Laman Trip", "given": "Diederik S", "initials": "DS"}, {"family": "van Oostrum", "given": "Marc", "initials": "M"}, {"family": "Memon", "given": "Danish", "initials": "D"}, {"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Baptista", "given": "Delora", "initials": "D"}, {"family": "Panneerselvam", "given": "Kalpana", "initials": "K"}, {"family": "Bradley", "given": "Glyn", "initials": "G"}, {"family": "Licata", "given": "Luana", "initials": "L"}, {"family": "Hermjakob", "given": "Henning", "initials": "H", "orcid": "0000-0001-8479-0262", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7ef7fa5ba29447fba798a69b305c0228.json"}}, {"family": "Orchard", "given": "Sandra", "initials": "S"}, {"family": "Trynka", "given": "Gosia", "initials": "G"}, {"family": "McDonagh", "given": "Ellen", "initials": "E"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P", "orcid": "0000-0002-2724-7703", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/952eba119d2e4d4b89e14b294c5c6885.json"}}], "type": "posted-content", "published": "2024-05-17", "journal": {"title": null, "issn": null, "issn-l": null, "volume": null, "issue": null, "pages": null}, "abstract": null, "doi": "10.1101/2024.05.15.594301", "pmid": null, "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [], "notes": [], "created": "2025-03-18T16:51:07.686Z", "modified": "2025-03-21T13:32:48.505Z"}, {"entity": "publication", "iuid": "b44b20675f284acb911d497d1301f76c", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/b44b20675f284acb911d497d1301f76c"}}, "title": "DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.", "authors": [{"family": "Frommelt", "given": "Fabian", "initials": "F", "orcid": "0000-0003-3666-8005", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e71a93da1624a17bcbace26ba50c5a5.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Uliana", "given": "Federico", "initials": "F"}, {"family": "Wendt", "given": "Fabian", "initials": "F", "orcid": "0000-0002-2501-536X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f9f0e10e0ff84bfdba2da72790f12c32.json"}}, {"family": "Xue", "given": "Peng", "initials": "P"}, {"family": "Heusel", "given": "Moritz", "initials": "M"}, {"family": "Wollscheid", "given": "Bernd", "initials": "B", "orcid": "0000-0002-3923-1610", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fecd11050305473ca698ba6c6ee54a52.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Ciuffa", "given": "Rodolfo", "initials": "R"}, {"family": "Gstaiger", "given": "Matthias", "initials": "M", "orcid": "0000-0002-3245-3253", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8370f12358274bb2a5a4cd524ae4f465.json"}}], "type": "journal article", "published": "2024-04-00", "journal": {"title": "Nat. Methods", "issn": "1548-7105", "issn-l": "1548-7091", "volume": "21", "issue": "4", "pages": "635-647"}, "abstract": "Most proteins are organized in macromolecular assemblies, which represent key functional units regulating and catalyzing most cellular processes. Affinity purification of the protein of interest combined with liquid chromatography coupled to tandem mass spectrometry (AP-MS) represents the method of choice to identify interacting proteins. The composition of complex isoforms concurrently present in the AP sample can, however, not be resolved from a single AP-MS experiment but requires computational inference from multiple time- and resource-intensive reciprocal AP-MS experiments. Here we introduce deep interactome profiling by mass spectrometry (DIP-MS), which combines AP with blue-native-PAGE separation, data-independent acquisition with mass spectrometry and deep-learning-based signal processing to resolve complex isoforms sharing the same bait protein in a single experiment. We applied DIP-MS to probe the organization of the human prefoldin family of complexes, resolving distinct prefoldin holo- and subcomplex variants, complex-complex interactions and complex isoforms with new subunits that were experimentally validated. Our results demonstrate that DIP-MS can reveal proteome modularity at unprecedented depth and resolution.", "doi": "10.1038/s41592-024-02211-y", "pmid": "38532014", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC11009110"}, {"db": "pii", "key": "10.1038/s41592-024-02211-y"}], "notes": [], "created": "2025-03-18T16:51:10.645Z", "modified": "2025-03-21T13:32:23.292Z"}, {"entity": "publication", "iuid": "ca03446746b34f0686f25a8d0a0f5c78", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ca03446746b34f0686f25a8d0a0f5c78.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ca03446746b34f0686f25a8d0a0f5c78"}}, "title": "Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.", "authors": [{"family": "Teuscher", "given": "Alina C", "initials": "AC"}, {"family": "Statzer", "given": "Cyril", "initials": "C"}, {"family": "Goyala", "given": "Anita", "initials": "A"}, {"family": "Domenig", "given": "Seraina A", "initials": "SA"}, {"family": "Schoen", "given": "Ingmar", "initials": "I", "orcid": "0000-0002-5699-1160", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/cc84aaf9916f4ba48a9b30cf012ba69f.json"}}, {"family": "Hess", "given": "Max", "initials": "M"}, {"family": "Hofer", "given": "Alexander M", "initials": "AM", "orcid": "0009-0001-5176-1622", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d3341bfd21fc49d59395ff162ffa86dc.json"}}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Vogel", "given": "Viola", "initials": "V", "orcid": "0000-0003-2898-7671", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbcfc4590cd246f19a71e93f8e8ce6a0.json"}}, {"family": "Goksel", "given": "Orcun", "initials": "O", "orcid": "0000-0002-8639-7373", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/278c3104bb084bb2849b9f01582181b8.json"}}, {"family": "Aebersold", "given": "Ruedi", "initials": "R", "orcid": "0000-0002-9576-3267", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4aa50db862e94831b8cac04c4426daf1.json"}}, {"family": "Ewald", "given": "Collin Y", "initials": "CY", "orcid": "0000-0003-1166-4171", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33cc1fe0fbcc473da386ecd1e30b3564.json"}}], "type": "journal article", "published": "2024-01-04", "journal": {"title": "Nat Commun", "issn": "2041-1723", "issn-l": "2041-1723", "volume": "15", "issue": "1", "pages": "276"}, "abstract": "Dysfunctional extracellular matrices (ECM) contribute to aging and disease. Repairing dysfunctional ECM could potentially prevent age-related pathologies. Interventions promoting longevity also impact ECM gene expression. However, the role of ECM composition changes in healthy aging remains unclear. Here we perform proteomics and in-vivo monitoring to systematically investigate ECM composition (matreotype) during aging in C. elegans revealing three distinct collagen dynamics. Longevity interventions slow age-related collagen stiffening and prolong the expression of collagens that are turned over. These prolonged collagen dynamics are mediated by a mechanical feedback loop of hemidesmosome-containing structures that span from the exoskeletal ECM through the hypodermis, basement membrane ECM, to the muscles, coupling mechanical forces to adjust ECM gene expression and longevity via the transcriptional co-activator YAP-1 across tissues. Our results provide in-vivo evidence that coordinated ECM remodeling through mechanotransduction is required and sufficient to promote longevity, offering potential avenues for interventions targeting ECM dynamics.", "doi": "10.1038/s41467-023-44409-2", "pmid": "38177158", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10766642"}, {"db": "pii", "key": "10.1038/s41467-023-44409-2"}], "notes": [], "created": "2025-03-18T16:51:15.294Z", "modified": "2025-03-21T13:20:13.403Z"}]}