{"entity": "researcher", "timestamp": "2026-11-12T14:02:14.679Z", "family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "affiliations": ["J. David Gladstone Institutes, San Francisco, 94158, CA, USA.", "Quantitative Biosciences Institute (QBI), University of California San Francisco, San Francisco, 94158, CA, USA.", "Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, 94158, CA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd"}}, "publications": [{"entity": "publication", "iuid": "df9e37fcc38244128dacc5a41ba38be1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df9e37fcc38244128dacc5a41ba38be1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df9e37fcc38244128dacc5a41ba38be1"}}, "title": "Proteomic and genetic analyses of influenza A viruses identify pan-viral host targets.", "authors": [{"family": "Haas", "given": "Kelsey M", "initials": "KM", "orcid": "0000-0002-1463-6726", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b50e67ced164f2d8e825f58406b3c66.json"}}, {"family": "McGregor", "given": "Michael J", "initials": "MJ"}, {"family": "Bouhaddou", "given": "Mehdi", "initials": "M"}, {"family": "Polacco", "given": "Benjamin J", "initials": "BJ", "orcid": "0000-0003-1570-9234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b41eced550240729eae78f2d9864552.json"}}, {"family": "Kim", "given": "Eun-Young", "initials": "EY", "orcid": "0000-0002-7436-7396", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f919c62cc14542e39ee29138bbba1421.json"}}, {"family": "Nguyen", "given": "Thong T", "initials": "TT"}, {"family": "Newton", "given": "Billy W", "initials": "BW"}, {"family": "Urbanowski", "given": "Matthew", "initials": "M"}, {"family": "Kim", "given": "Heejin", "initials": "H"}, {"family": "Williams", "given": "Michael A P", "initials": "MAP"}, {"family": "Rezelj", "given": "Veronica V", "initials": "VV"}, {"family": "Hardy", "given": "Alexandra", "initials": "A"}, {"family": "Fossati", "given": "Andrea", "initials": "A"}, {"family": "Stevenson", "given": "Erica J", "initials": "EJ"}, {"family": "Sukerman", "given": "Ellie", "initials": "E"}, {"family": "Kim", "given": "Tiffany", "initials": "T", "orcid": "0000-0001-8386-7686", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b5f94b9170241e985ef81d6fbeaf601.json"}}, {"family": "Penugonda", "given": "Sudhir", "initials": "S"}, {"family": "Moreno", "given": "Elena", "initials": "E", "orcid": "0000-0002-2301-4558", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/96ac76807a374faabd225a4130e77200.json"}}, {"family": "Braberg", "given": "Hannes", "initials": "H", "orcid": "0000-0002-7070-2257", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/ba8a641dc3d843f19ceb34d75f74af5d.json"}}, {"family": "Vignuzzi", "given": "Marco", "initials": "M"}, {"family": "Zuliani-Alvarez", "given": "Lorena", "initials": "L"}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Eckhardt", "given": "Manon", "initials": "M", "orcid": "0000-0001-8143-6129", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1e3597e5c67842f2930a6e08173590e9.json"}}, {"family": "Wolinsky", "given": "Steven M", "initials": "SM"}, {"family": "White", "given": "Kris M", "initials": "KM", "orcid": "0000-0003-0889-0506", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b428159f7954cc1addd247d332ec355.json"}}, {"family": "Hultquist", "given": "Judd F", "initials": "JF", "orcid": "0000-0001-6424-4280", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/984045e2941a49bb93ffbbcd639264da.json"}}, {"family": "Kaake", "given": "Robyn M", "initials": "RM"}, {"family": "Garc\u00eda-Sastre", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-6551-1827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d9ee4b066f24fe7b2e488c00fac4938.json"}}, {"family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}}], "type": "journal article", "published": "2023-09-27", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "6030", "issn-l": "2041-1723"}, "abstract": "Influenza A Virus (IAV) is a recurring respiratory virus with limited availability of antiviral therapies. Understanding host proteins essential for IAV infection can identify targets for alternative host-directed therapies (HDTs). Using affinity purification-mass spectrometry and global phosphoproteomic and protein abundance analyses using three IAV strains (pH1N1, H3N2, H5N1) in three human cell types (A549, NHBE, THP-1), we map 332 IAV-human protein-protein interactions and identify 13 IAV-modulated kinases. Whole exome sequencing of patients who experienced severe influenza reveals several genes, including scaffold protein AHNAK, with predicted loss-of-function variants that are also identified in our proteomic analyses. Of our identified host factors, 54 significantly alter IAV infection upon siRNA knockdown, and two factors, AHNAK and coatomer subunit COPB1, are also essential for productive infection by SARS-CoV-2. Finally, 16 compounds targeting our identified host factors suppress IAV replication, with two targeting CDK2 and FLT3 showing pan-antiviral activity across influenza and coronavirus families. This study provides a comprehensive network model of IAV infection in human cells, identifying functional host targets for pan-viral HDT.", "doi": "10.1038/s41467-023-41442-z", "pmid": "37758692", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10533562"}, {"db": "pii", "key": "10.1038/s41467-023-41442-z"}], "notes": [], "created": "2026-11-06T08:03:37.050Z", "modified": "2026-11-06T08:03:38.500Z"}, {"entity": "publication", "iuid": "d24496ff298042db99f2c7999a565fe1", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/d24496ff298042db99f2c7999a565fe1"}}, "title": "Next-generation proteomics for quantitative Jumbophage-bacteria interaction mapping.", "authors": [{"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Mozumdar", "given": "Deepto", "initials": "D"}, {"family": "Kokontis", "given": "Claire", "initials": "C"}, {"family": "M\u00e8ndez-Moran", "given": "Melissa", "initials": "M", "orcid": "0000-0003-0817-7292", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/90d7c50c904f4c71be76e0ec228c04bc.json"}}, {"family": "Nieweglowska", "given": "Eliza", "initials": "E", "orcid": "0000-0002-9204-3002", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c23665a0824d4896a58e4d9115bbbca9.json"}}, {"family": "Pelin", "given": "Adrian", "initials": "A"}, {"family": "Li", "given": "Yuping", "initials": "Y", "orcid": "0000-0003-2057-3271", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b4958e5be5fb489d93350357e471d548.json"}}, {"family": "Guo", "given": "Baron", "initials": "B"}, {"family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}}, {"family": "Agard", "given": "David A", "initials": "DA", "orcid": "0000-0003-3512-695X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/acf4cd7f71944afbbe8f579e36f6dd23.json"}}, {"family": "Bondy-Denomy", "given": "Joseph", "initials": "J", "orcid": "0000-0002-4909-9481", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c4ac66d863ed429f85fefcfc5dab6666.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}], "type": "journal article", "published": "2023-08-24", "journal": {"title": "Nat Commun", "issn": "2041-1723", "volume": "14", "issue": "1", "pages": "5156", "issn-l": "2041-1723"}, "abstract": "Host-pathogen interactions are pivotal in regulating establishment, progression, and outcome of an infection. While affinity-purification mass spectrometry has become instrumental in characterizing such interactions, it suffers from limitations in scalability and biological authenticity. Here we present the use of co-fractionation mass spectrometry for high throughput analysis of host-pathogen interactions from native viral infections of two jumbophages (\u03d5KZ and \u03d5PA3) in Pseudomonas aeruginosa. This approach enabled the detection of > 6000 unique host-pathogen interactions for each phage, encompassing > 50% of their respective proteomes. This deep coverage provided evidence for interactions between KZ-like phage proteins and the host ribosome, and revealed protein complexes for previously undescribed phage ORFs, including a \u03d5PA3 complex showing strong structural and sequence similarity to \u03d5KZ non-virion RNA polymerase. Interactome-wide comparison across phages showed similar perturbed protein interactions suggesting fundamentally conserved mechanisms of phage predation within the KZ-like phage family. To enable accessibility to this data, we developed PhageMAP, an online resource for network query, visualization, and interaction prediction ( https://phagemap.ucsf.edu/ ). We anticipate this study will lay the foundation for the application of co-fractionation mass spectrometry for the scalable profiling of host-pathogen interactomes and protein complex dynamics upon infection.", "doi": "10.1038/s41467-023-40724-w", "pmid": "37620325", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC10449902"}, {"db": "pii", "key": "10.1038/s41467-023-40724-w"}], "notes": [], "created": "2026-11-06T08:03:13.304Z", "modified": "2026-11-06T08:03:13.672Z"}, {"entity": "publication", "iuid": "207c79bd8fd6481fa1d662ee7c308914", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/207c79bd8fd6481fa1d662ee7c308914.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/207c79bd8fd6481fa1d662ee7c308914"}}, "title": "Evolution of enhanced innate immune evasion by SARS-CoV-2.", "authors": [{"family": "Thorne", "given": "Lucy G", "initials": "LG", "orcid": "0000-0001-7358-6047", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/377d4c11a8174452908217e8ac3cb0ff.json"}}, {"family": "Bouhaddou", "given": "Mehdi", "initials": "M"}, {"family": "Reuschl", "given": "Ann-Kathrin", "initials": "AK"}, {"family": "Zuliani-Alvarez", "given": "Lorena", "initials": "L"}, {"family": "Polacco", "given": "Ben", "initials": "B", "orcid": "0000-0003-1570-9234", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9b41eced550240729eae78f2d9864552.json"}}, {"family": "Pelin", "given": "Adrian", "initials": "A"}, {"family": "Batra", "given": "Jyoti", "initials": "J"}, {"family": "Whelan", "given": "Matthew V X", "initials": "MVX"}, {"family": "Hosmillo", "given": "Myra", "initials": "M"}, {"family": "Fossati", "given": "Andrea", "initials": "A", "orcid": "0000-0001-5170-4903", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/658637b885384441943698722fad5944.json"}}, {"family": "Ragazzini", "given": "Roberta", "initials": "R", "orcid": "0000-0003-2186-293X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/977193338736455da68732317dc4220e.json"}}, {"family": "Jungreis", "given": "Irwin", "initials": "I", "orcid": "0000-0002-3197-5367", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f0daf23c054c59a0f58969dd5ac6db.json"}}, {"family": "Ummadi", "given": "Manisha", "initials": "M"}, {"family": "Rojc", "given": "Ajda", "initials": "A"}, {"family": "Turner", "given": "Jane", "initials": "J"}, {"family": "Bischof", "given": "Marie L", "initials": "ML"}, {"family": "Obernier", "given": "Kirsten", "initials": "K", "orcid": "0000-0002-4025-1299", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d2e68afc66484175b3d38a74979f8b4e.json"}}, {"family": "Braberg", "given": "Hannes", "initials": "H", "orcid": "0000-0002-7070-2257", "researcher": {"href": 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"https://publications-affiliated.scilifelab.se/researcher/48165c07f21245a4a21569c786a30085.json"}}, {"family": "Shokat", "given": "Kevan", "initials": "K", "orcid": "0000-0001-8590-7741", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e37dd23f9a71424d8f2c804f27fc86e7.json"}}, {"family": "Jura", "given": "Natalia", "initials": "N", "orcid": "0000-0001-5129-641X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/d6751d2c23804f56a1d117bc2734e997.json"}}, {"family": "Verba", "given": "Klim", "initials": "K", "orcid": "0000-0002-2238-8590", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fc38826304dc47ce9aee7ab94ce37561.json"}}, {"family": "Noursadeghi", "given": "Mahdad", "initials": "M", "orcid": "0000-0002-4774-0853", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/83695a663ced442aa01ad9b6f877ce8f.json"}}, {"family": "Beltrao", "given": "Pedro", "initials": "P"}, {"family": "Kellis", "given": "Manolis", "initials": "M", "orcid": "0000-0001-7113-9630", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9989fea905234f91aa4412731b93ab09.json"}}, {"family": "Swaney", "given": "Danielle L", "initials": "DL", "orcid": "0000-0001-6119-6084", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56317207941d4aaf81ab4d55de5fcba4.json"}}, {"family": "Garc\u00eda-Sastre", "given": "Adolfo", "initials": "A", "orcid": "0000-0002-6551-1827", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7d9ee4b066f24fe7b2e488c00fac4938.json"}}, {"family": "Jolly", "given": "Clare", "initials": "C", "orcid": "0000-0002-4603-2281", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fbc228b022604eb087bc0a2d2d7b21a3.json"}}, {"family": "Towers", "given": "Greg J", "initials": "GJ", "orcid": "0000-0002-7707-0264", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e979e1fe50944178a4ea51b9d146dc95.json"}}, {"family": "Krogan", "given": "Nevan J", "initials": "NJ", "orcid": "0000-0003-4902-337X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bf20e1447b9643f599f94d983b2bd9dd.json"}}], "type": "journal article", "published": "2022-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "602", "issue": "7897", "pages": "487-495", "issn-l": "0028-0836"}, "abstract": "The emergence of SARS-CoV-2 variants of concern suggests viral adaptation to enhance human-to-human transmission1,2. Although much effort has focused on the characterization of changes in the spike protein in variants of concern, mutations outside of spike are likely to contribute to adaptation. Here, using unbiased abundance proteomics, phosphoproteomics, RNA sequencing and viral replication assays, we show that isolates of the Alpha (B.1.1.7) variant3 suppress innate immune responses in airway epithelial cells more effectively than first-wave isolates. We found that the Alpha variant has markedly increased subgenomic RNA and protein levels of the nucleocapsid protein (N), Orf9b and Orf6-all known innate immune antagonists. Expression of Orf9b alone suppressed the innate immune response through interaction with TOM70, a mitochondrial protein that is required for activation of the RNA-sensing adaptor MAVS. Moreover, the activity of Orf9b and its association with TOM70 was regulated by phosphorylation. We propose that more effective innate immune suppression, through enhanced expression of specific viral antagonist proteins, increases the likelihood of successful transmission of the Alpha variant, and may increase in vivo replication and duration of infection4. The importance of mutations outside the spike coding region in the adaptation of SARS-CoV-2 to humans is underscored by the observation that similar mutations exist in the N and Orf9b regulatory regions of the Delta and Omicron variants.", "doi": "10.1038/s41586-021-04352-y", "pmid": "34942634", "labels": {"Andrea Fossati": null, "DDLS Fellow": null}, "xrefs": [{"db": "mid", "key": "NIHMS1780228"}, {"db": "pmc", "key": "PMC8850198"}, {"db": "pii", "key": "10.1038/s41586-021-04352-y"}], "notes": [], "created": "2026-11-06T08:03:44.355Z", "modified": "2026-11-06T08:03:45.294Z"}]}