{"entity": "researcher", "timestamp": "2026-06-07T19:56:21.169Z", "family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "affiliations": ["Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden.", "Department of Genetics, Stanford University, Stanford, CA, USA.", "Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5"}}, "publications": [{"entity": "publication", "iuid": "ba2006e120954777a021042ee6d1b63e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/ba2006e120954777a021042ee6d1b63e"}}, "title": "Cell shapes decode molecular phenotypes in image-based spatial proteomics.", "authors": [{"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Leineweber", "given": "William D", "initials": "WD", "orcid": "0000-0003-3069-398X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f6f5dd2023994301867b8bb3948a2274.json"}}, {"family": "Viana", "given": "Matheus P", "initials": "MP", "orcid": "0000-0001-9288-2108", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/57b1be92b4f549df8b09af4a7532493f.json"}}, {"family": "Cesnik", "given": "Anthony", "initials": "A", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Hansen", "given": "Jan N", "initials": "JN", "orcid": "0000-0002-0489-7535", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4047064d44674e229a3b2dd10f241607.json"}}, {"family": "Ouyang", "given": "Wei", "initials": "W", "orcid": "0000-0002-0291-926X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/56f601e1d1c6448aab0c3a1e3cffdbfc.json"}}, {"family": "Rafelski", "given": "Susanne M", "initials": "SM", "orcid": "0000-0002-1399-5970", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/33f5be9729bf4ff280b958d85df287d4.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2025-05-16", "journal": {"title": "bioRxiv", "issn": "2692-8205", "issn-l": null}, "abstract": "The diversity of cellular and tissue structures can arise from a few basic cell shapes, which undergo various transformations based on biophysical constraints on cytoskeletal organization. While cellular geometry has been linked with selected biological processes such as polarity, signaling or morphogenesis, the orchestration of the whole proteome in association to cell shape is still poorly understood. In this study, using more than 1 million images of single cells stained for 11,998 proteins across 10 cell lines in the Human Protein Atlas database, we performed an integrated analysis of organelle, pathway and single protein levels in association to a 2D cellular shapespace. We found that cell and nuclear shapes across cell lines exist in a shared continuum. We also found that the subcellular organelle topology varies across cell lines, but remains robust within each cell line's shapespace. At the single protein level, we found that cells of different shapes in the same cell cycle phase might be preparing for different fates, and that many non-cell cycle proteins expressed shape-based abundance variation. Using the same coordinate framework defined by shape, we could analyze the distribution shift of protein spatial localization under drug perturbation.", "doi": "10.1101/2025.05.13.653868", "pmid": "40463127", "labels": {"Wei Ouyang": null, "DDLS Fellow": null}, "xrefs": [{"db": "pmc", "key": "PMC12132440"}, {"db": "pii", "key": "2025.05.13.653868"}], "notes": [], "created": "2025-12-15T10:06:41.544Z", "modified": "2025-12-15T10:06:41.690Z"}, {"entity": "publication", "iuid": "df293d53882b4896bf5c0e2b9fc40e8a", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/df293d53882b4896bf5c0e2b9fc40e8a"}}, "title": "Author Correction: Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Schutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "published erratum", "published": "2022-08-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "608", "issue": "7924", "pages": "E32", "issn-l": "0028-0836"}, "abstract": null, "doi": "10.1038/s41586-022-05180-4", "pmid": "35931766", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-022-05180-4"}], "notes": [], "created": "2023-12-04T14:58:17.819Z", "modified": "2023-12-04T14:58:17.937Z"}, {"entity": "publication", "iuid": "a56bfb5717d746eea1722911e715cfe6", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/a56bfb5717d746eea1722911e715cfe6"}}, "title": "Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.", "authors": [{"family": "Mahdessian", "given": "Diana", "initials": "D"}, {"family": "Cesnik", "given": "Anthony J", "initials": "AJ", "orcid": "0000-0002-5326-7134", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/0fda549f3795457fb60ec3372b98e2d5.json"}}, {"family": "Gnann", "given": "Christian", "initials": "C"}, {"family": "Danielsson", "given": "Frida", "initials": "F"}, {"family": "Stenstr\u00f6m", "given": "Lovisa", "initials": "L"}, {"family": "Arif", "given": "Muhammad", "initials": "M", "orcid": "0000-0003-2261-0881", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/c8ffc9889ace44e3b992816601b817e2.json"}}, {"family": "Zhang", "given": "Cheng", "initials": "C", "orcid": "0000-0002-3721-8586", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/f46e4161be08458994efddb75ed75874.json"}}, {"family": "Le", "given": "Trang", "initials": "T"}, {"family": "Johansson", "given": "Fredric", "initials": "F", "orcid": "0000-0001-5160-9543", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/88e81d055b6f4c23852dfa7768e62c99.json"}}, {"family": "Shutten", "given": "Rutger", "initials": "R"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Axelsson", "given": "Ulrika", "initials": "U"}, {"family": "Thul", "given": "Peter", "initials": "P", "orcid": "0000-0002-6107-1465", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/af9dad977d4649bbbb883a9836dade94.json"}}, {"family": "Cho", "given": "Nathan H", "initials": "NH"}, {"family": "Carja", "given": "Oana", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9ea446aa574042a295d5f69437402f76.json"}}, {"family": "Mardinoglu", "given": "Adil", "initials": "A"}, {"family": "Stadler", "given": "Charlotte", "initials": "C"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/21610a810a87459c962d6da3f2ad38ad.json"}}, {"family": "Ayoglu", "given": "Burcu", "initials": "B", "orcid": "0000-0001-7843-2960", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/4d75c3ce33814d2b961aef643f0d7f0c.json"}}, {"family": "Leonetti", "given": "Manuel D", "initials": "MD"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/9f5294424542413c9ba4432c839c2b63.json"}}, {"family": "Sullivan", "given": "Devin P", "initials": "DP"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/bb07e6d0122c4528a927c1fe922e3bc8.json"}}], "type": "journal article", "published": "2021-02-00", "journal": {"title": "Nature", "issn": "1476-4687", "volume": "590", "issue": "7847", "pages": "649-654", "issn-l": "0028-0836"}, "abstract": "The cell cycle, over which cells grow and divide, is a fundamental process of life. Its dysregulation has devastating consequences, including cancer1-3. The cell cycle is driven by precise regulation of proteins in time and space, which creates variability between individual proliferating cells. To our knowledge, no systematic investigations of such cell-to-cell proteomic variability exist. Here we present a comprehensive, spatiotemporal map of human proteomic heterogeneity by integrating proteomics at subcellular resolution with single-cell transcriptomics and precise temporal measurements of individual cells in the cell cycle. We show that around one-fifth of the human proteome displays cell-to-cell variability, identify hundreds of proteins with previously unknown associations with mitosis and the cell cycle, and provide evidence that several of these proteins have oncogenic functions. Our results show that cell cycle progression explains less than half of all cell-to-cell variability, and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. These proteins are disproportionately phosphorylated by kinases that regulate cell fate, whereas non-cycling proteins that vary between cells are more likely to be modified by kinases that regulate metabolism. This spatially resolved proteomic map of the cell cycle is integrated into the Human Protein Atlas and will serve as a resource for accelerating molecular studies of the human cell cycle and cell proliferation.", "doi": "10.1038/s41586-021-03232-9", "pmid": "33627808", "labels": {"Adil Mardinoglu": null, "SciLifeLab Fellow": null}, "xrefs": [{"db": "pii", "key": "10.1038/s41586-021-03232-9"}], "notes": [], "created": "2021-10-08T14:12:30.416Z", "modified": "2022-11-04T11:32:13.601Z"}]}