{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:18:39Z","timestamp":1792790319487,"version":"4.5.0"},"posted":{"date-parts":[[2026,10,1]]},"group-title":"Immunology","reference-count":111,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T00:00:00Z","timestamp":1790812800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"The Stavros Niarchos Foundation Institute for Global Infectious Disease Research","id":[{"id":"https:\/\/ror.org\/0210rze73","id-type":"ROR","asserted-by":"crossref"}]},{"name":"CZ Biohub New York Investigator Program","id":[{"id":"https:\/\/ror.org\/0263t7p64","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Institutes of Health","award":["T32GM136640-Tan"],"award-info":[{"award-number":["T32GM136640-Tan"]}]},{"name":"National Institutes of Health","award":["1F31CA317812"],"award-info":[{"award-number":["1F31CA317812"]}]},{"name":"National Institutes of Health","award":["R01 CA251138"],"award-info":[{"award-number":["R01 CA251138"]}]},{"name":"National Institutes of Health","award":["R01 CA242020"],"award-info":[{"award-number":["R01 CA242020"]}]},{"name":"National Institutes of Health","award":["R01 CA283364"],"award-info":[{"award-number":["R01 CA283364"]}]},{"name":"National Institutes of Health","award":["P50 CA254838"],"award-info":[{"award-number":["P50 CA254838"]}]},{"name":"The Alexandrine and Alexander L. Sinsheimer Fund"},{"name":"Herbert and Nell Singer Foundation"},{"name":"Blood Cancer United","id":[{"id":"https:\/\/ror.org\/0055acf80","id-type":"ROR","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/05t831771","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/05k7zsn51","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Neil S. Hirsch Foundation"},{"id":[{"id":"https:\/\/ror.org\/03h22gm35","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Break Through Cancer","id":[{"id":"https:\/\/ror.org\/00a8me616","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Cancer Center Support Grant","award":["P30 CA008748"],"award-info":[{"award-number":["P30 CA008748"]}]},{"id":[{"id":"https:\/\/ror.org\/04m0xav37","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Robertson Foundation","id":[{"id":"https:\/\/ror.org\/04h2x1077","id-type":"ROR","asserted-by":"crossref"}]},{"id":[{"id":"https:\/\/ror.org\/011xj1a65","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Weill Cancer Hub East"},{"name":"Searle Scholar Program"},{"name":"Pels Family Center Fellowship","id":[{"id":"https:\/\/ror.org\/031e8jz65","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Cancer Center"},{"name":"Marlene Hess Center for Research on Women\u2019s Health and Biomedicine"},{"name":"Kavli NSI Postdoctoral Fellowship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                <jats:p>Macrophages are central regulators of innate immunity, yet the post-translational mechanisms that enable rapid inflammatory responses remain incompletely understood. Here, we integrated transcriptomics, unenriched proteomics, phosphoproteomics, metabolomics, and cysteine reactivity profiling to comprehensively characterize primary human macrophages following Toll-like receptor and Stimulator of Interferon Genes (STING) activation. This approach revealed substantial discordance between transcript- and protein-level changes, as well as extensive post-translational remodeling. Differentially reactive cysteines were enriched in proteins involved in small-GTPase signaling, vesicular trafficking, and the endo-lysosomal system. Reactivity changes in two subunits of the endosomal mRNA-transport FERRY complex nominated it as a candidate target of inflammation-associated post-translational regulation. Biochemical and imaging analyses established FERRY complex assembly and early endosomal localization in primary human macrophages and identified DISC1 as a previously unrecognized FERRY-associated protein. This work provides a comprehensive resource of biochemical and post-translational remodeling during macrophage activation and implicates endosome-associated mRNA transport in innate immune regulation.<\/jats:p>","DOI":"10.64898\/2026.09.25.754469","type":"posted-content","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T23:25:16Z","timestamp":1790897116000},"source":"Crossref","is-referenced-by-count":0,"title":["Chemical proteomics reveals post-translational remodeling of endosomal pathways during macrophage activation"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4880-2195","authenticated-orcid":false,"given":"Tiffany L.","family":"Zhang","sequence":"first","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"},{"name":"Tri-Institutional PhD Program in Chemical Biology, New York, New York, 10021, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0000-2343-4280","authenticated-orcid":false,"given":"Henry","family":"Sanford","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0710-3788","authenticated-orcid":false,"given":"Railia","family":"Gabbasova","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0379-4945","authenticated-orcid":false,"given":"Anne E.","family":"van Vlimmeren","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6137-1193","authenticated-orcid":false,"given":"Yannis","family":"Kalaidzidis","sequence":"additional","affiliation":[{"name":"Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1621-9352","authenticated-orcid":false,"given":"Hiroyuki","family":"Kojima","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4622-4627","authenticated-orcid":false,"given":"Charlotte R.","family":"Wayne","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1163-539X","authenticated-orcid":false,"given":"Jeetayu","family":"Biswas","sequence":"additional","affiliation":[{"name":"Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA"},{"name":"Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9398-9345","authenticated-orcid":false,"given":"Priyam","family":"Banerjee","sequence":"additional","affiliation":[{"name":"Bio-Imaging Resource Center, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1636-600X","authenticated-orcid":false,"given":"Beatrice","family":"Zhang","sequence":"additional","affiliation":[{"name":"Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3907-6171","authenticated-orcid":false,"given":"Omar","family":"Abdel-Wahab","sequence":"additional","affiliation":[{"name":"Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA"},{"name":"Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7490-4235","authenticated-orcid":false,"given":"Marino","family":"Zerial","sequence":"additional","affiliation":[{"name":"Human Technopole, 20157 Milan, Italy"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3512-5375","authenticated-orcid":false,"given":"Ekaterina V.","family":"Vinogradova","sequence":"additional","affiliation":[{"name":"Department of Chemical Immunology and Proteomics, The Rockefeller University, New York, New York, 10065, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026100607150944000_2026.09.25.754469v1.1","doi-asserted-by":"publisher","DOI":"10.1038\/nature12034"},{"key":"2026100607150944000_2026.09.25.754469v1.2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2006.02.015"},{"key":"2026100607150944000_2026.09.25.754469v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/ni.3558"},{"key":"2026100607150944000_2026.09.25.754469v1.4","doi-asserted-by":"publisher","DOI":"10.1038\/nri1957"},{"key":"2026100607150944000_2026.09.25.754469v1.5","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-021-00524-z"},{"key":"2026100607150944000_2026.09.25.754469v1.6","doi-asserted-by":"crossref","first-page":"138","DOI":"10.3390\/biomedicines12010138","article-title":"Targeting TLR Signaling Cascades in Systemic Lupus Erythematosus and Rheumatoid Arthritis: An Update","volume":"12","year":"2024","journal-title":"Biomedicines"},{"key":"2026100607150944000_2026.09.25.754469v1.7","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.00001-11"},{"key":"2026100607150944000_2026.09.25.754469v1.8","doi-asserted-by":"crossref","first-page":"1640935","DOI":"10.3389\/fimmu.2025.1640935","article-title":"Comprehensive review of macrophage models: primary cells and immortalized lines across species","volume":"16","year":"2025","journal-title":"Frontiers in Immunology"},{"key":"2026100607150944000_2026.09.25.754469v1.9","doi-asserted-by":"crossref","first-page":"983","DOI":"10.1038\/s41423-018-0035-x","article-title":"Global transcriptional changes in response to cGAMP depend on STING in human THP-1 cells","volume":"15","year":"2018","journal-title":"Cellular & Molecular Immunology"},{"key":"2026100607150944000_2026.09.25.754469v1.10","doi-asserted-by":"crossref","unstructured":"Li, P. et al. Comparative Proteomic Analysis of Polarized Human THP-1 and Mouse RAW264.7 Macrophages. Frontiers in Immunology 12 (2021).","DOI":"10.3389\/fimmu.2021.700009"},{"key":"2026100607150944000_2026.09.25.754469v1.11","doi-asserted-by":"publisher","DOI":"10.1126\/science.1259038"},{"key":"2026100607150944000_2026.09.25.754469v1.12","doi-asserted-by":"crossref","unstructured":"Thielert, M. , et al. In the same cell, the proteome defines cellular state and the transcriptome marks transitions. bioRxiv (2026).","DOI":"10.64898\/2026.08.25.746940"},{"key":"2026100607150944000_2026.09.25.754469v1.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.03.014"},{"key":"2026100607150944000_2026.09.25.754469v1.14","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3185"},{"key":"2026100607150944000_2026.09.25.754469v1.15","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.07.001"},{"key":"2026100607150944000_2026.09.25.754469v1.16","doi-asserted-by":"publisher","DOI":"10.1038\/s41587-020-00778-3"},{"key":"2026100607150944000_2026.09.25.754469v1.17","doi-asserted-by":"crossref","first-page":"341","DOI":"10.1038\/s41592-022-01398-2","article-title":"Global profiling of phosphorylation-dependent changes in cysteine reactivity","volume":"19","year":"2022","journal-title":"Nature Methods"},{"key":"2026100607150944000_2026.09.25.754469v1.18","unstructured":"Kojima, H. , et al. A post-translational regulatory map of chronic antigen-driven human T cell dysfunction. bioRxiv (2026)."},{"key":"2026100607150944000_2026.09.25.754469v1.19","doi-asserted-by":"crossref","first-page":"781","DOI":"10.1021\/acsinfecdis.5c00984","article-title":"Cysteine Reactivity Profiling Identifies Host Regulators of Mycobacterium tuberculosis Replication in Human Macrophages","volume":"12","year":"2026","journal-title":"ACS Infectious Diseases"},{"key":"2026100607150944000_2026.09.25.754469v1.20","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.05.009"},{"key":"2026100607150944000_2026.09.25.754469v1.21","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.05.012"},{"key":"2026100607150944000_2026.09.25.754469v1.22","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2011.09.051"},{"key":"2026100607150944000_2026.09.25.754469v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/ni.1863"},{"key":"2026100607150944000_2026.09.25.754469v1.24","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/s41467-018-03106-1","article-title":"Systematic analysis of protein turnover in primary cells","volume":"9","year":"2018","journal-title":"Nature Communications"},{"key":"2026100607150944000_2026.09.25.754469v1.25","doi-asserted-by":"crossref","unstructured":"Kelly, B. & O\u2019Neill, L.A . Metabolic reprogramming in macrophages and dendritic cells in innate immunity. Cell Research 25 (2015).","DOI":"10.1038\/cr.2015.68"},{"key":"2026100607150944000_2026.09.25.754469v1.26","doi-asserted-by":"crossref","unstructured":"Ashbrook, M.J. et al. Citrate modulates lipopolysaccharide-induced monocyte inflammatory responses. Clinical and Experimental Immunology 180 (2015).","DOI":"10.1111\/cei.12591"},{"key":"2026100607150944000_2026.09.25.754469v1.27","doi-asserted-by":"crossref","unstructured":"Mills, E. et al. Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages. Cell 167 (2016).","DOI":"10.1016\/j.cell.2016.08.064"},{"key":"2026100607150944000_2026.09.25.754469v1.28","doi-asserted-by":"crossref","unstructured":"Tannahill, G.M. et al. Succinate is an inflammatory signal that induces IL-1\u03b2 through HIF-1\u03b1. Nature 496 (2013).","DOI":"10.1038\/nature11986"},{"key":"2026100607150944000_2026.09.25.754469v1.29","doi-asserted-by":"crossref","unstructured":"Hooftman, A. et al. The Immunomodulatory Metabolite Itaconate Modifies NLRP3 and Inhibits Inflammasome Activation. Cell Metabolism 32 (2020).","DOI":"10.1016\/j.cmet.2020.07.016"},{"key":"2026100607150944000_2026.09.25.754469v1.30","unstructured":"Mills, E. et al. Itaconate is an anti-inflammatory metabolite that activates Nrf2 via alkylation of KEAP1. Nature 556 (2018)."},{"key":"2026100607150944000_2026.09.25.754469v1.31","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M706271200"},{"key":"2026100607150944000_2026.09.25.754469v1.32","doi-asserted-by":"publisher","DOI":"10.1038\/s41577-021-00500-7"},{"key":"2026100607150944000_2026.09.25.754469v1.33","doi-asserted-by":"crossref","unstructured":"Stenmark, H . Rab GTPases as coordinators of vesicle traffic. Nature Reviews Molecular Cell Biology 10 (2009).","DOI":"10.1038\/nrm2728"},{"key":"2026100607150944000_2026.09.25.754469v1.34","doi-asserted-by":"publisher","DOI":"10.1091\/mbc.E03-11-0847"},{"key":"2026100607150944000_2026.09.25.754469v1.35","first-page":"538","article-title":"Cytokine Secretion in Macrophages: SNAREs, Rabs, and Membrane Trafficking","volume":"5","year":"2014","journal-title":"Frontiers in Immunology"},{"key":"2026100607150944000_2026.09.25.754469v1.36","doi-asserted-by":"crossref","unstructured":"Bandaru, P. et al. Deconstruction of the Ras switching cycle through saturation mutagenesis. eLife 6 (2017).","DOI":"10.7554\/eLife.27810"},{"key":"2026100607150944000_2026.09.25.754469v1.37","doi-asserted-by":"crossref","unstructured":"Bos, J.L. , Rehmann, H. & Wittinghofer, A . GEFs and GAPs: Critical Elements in the Control of Small G Proteins. Cell 129 (2007).","DOI":"10.1016\/j.cell.2007.05.018"},{"key":"2026100607150944000_2026.09.25.754469v1.38","unstructured":"Miura, K. et al. ARAP1: A Point of Convergence for Arf and Rho Signaling. Molecular Cell 9 (2002)."},{"key":"2026100607150944000_2026.09.25.754469v1.39","doi-asserted-by":"crossref","unstructured":"Crompton, A.M. et al. Regulation of Tiam1 Nucleotide Exchange Activity by Pleckstrin Domain Binding Ligands. Journal of Biological Chemistry 275 (2000).","DOI":"10.1074\/jbc.M002050200"},{"key":"2026100607150944000_2026.09.25.754469v1.40","doi-asserted-by":"crossref","unstructured":"Johnson, D.I . Cdc42: An Essential Rho-Type GTPase Controlling Eukaryotic Cell Polarity. Microbiology and Molecular Biology Reviews 63 (1999).","DOI":"10.1128\/MMBR.63.1.54-105.1999"},{"key":"2026100607150944000_2026.09.25.754469v1.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2411974121"},{"key":"2026100607150944000_2026.09.25.754469v1.42","doi-asserted-by":"publisher","DOI":"10.1038\/cr.2009.130"},{"key":"2026100607150944000_2026.09.25.754469v1.43","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.2411974121"},{"key":"2026100607150944000_2026.09.25.754469v1.44","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-024-07487-W"},{"key":"2026100607150944000_2026.09.25.754469v1.45","doi-asserted-by":"crossref","unstructured":"Posor, Y. et al. Phosphoinositides as membrane organizers. Nature Reviews Molecular Cell Biology 23 (2022).","DOI":"10.1038\/s41580-022-00490-x"},{"key":"2026100607150944000_2026.09.25.754469v1.46","doi-asserted-by":"crossref","first-page":"8205","DOI":"10.1038\/ncomms9205","article-title":"Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled","volume":"6","year":"2015","journal-title":"Nature Communications"},{"key":"2026100607150944000_2026.09.25.754469v1.47","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.73747"},{"key":"2026100607150944000_2026.09.25.754469v1.48","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.200909025"},{"key":"2026100607150944000_2026.09.25.754469v1.49","doi-asserted-by":"crossref","unstructured":"Warner, H. , Mahajan, S. & van den Bogaart, G. Rerouting trafficking circuits through posttranslational SNARE modifications. Journal of Cell Science 135 (2022).","DOI":"10.1242\/jcs.260112"},{"key":"2026100607150944000_2026.09.25.754469v1.50","doi-asserted-by":"crossref","unstructured":"Lei, Z. , Wang, J. , Zhang, L. & Liu, C.H . Ubiquitination-Dependent Regulation of Small GTPases in Membrane Trafficking: From Cell Biology to Human Diseases. Frontiers in Cell and Developmental Biology 9 (2021).","DOI":"10.3389\/fcell.2021.688352"},{"key":"2026100607150944000_2026.09.25.754469v1.51","doi-asserted-by":"crossref","unstructured":"Paulsen, C.E. et al. Peroxide-dependent sulfenylation of the EGFR catalytic site enhances kinase activity. Nature Chemical Biology 8 (2011).","DOI":"10.1038\/nchembio.736"},{"key":"2026100607150944000_2026.09.25.754469v1.52","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-021-03819-2"},{"key":"2026100607150944000_2026.09.25.754469v1.53","doi-asserted-by":"publisher","DOI":"10.1126\/science.adg7492"},{"key":"2026100607150944000_2026.09.25.754469v1.54","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2024.03.027"},{"key":"2026100607150944000_2026.09.25.754469v1.55","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkae1033"},{"key":"2026100607150944000_2026.09.25.754469v1.56","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac1015"},{"key":"2026100607150944000_2026.09.25.754469v1.57","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku975"},{"key":"2026100607150944000_2026.09.25.754469v1.58","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky1001"},{"key":"2026100607150944000_2026.09.25.754469v1.59","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1113"},{"key":"2026100607150944000_2026.09.25.754469v1.60","doi-asserted-by":"crossref","unstructured":"Wang, Y. et al. TBCK syndrome pathogenesis: the TBCK-PPP1R21-C12orf4 complex regulating RAB5-dependent endo-lysosomal homeostasis. Science Bulletin 71 (2026).","DOI":"10.1016\/j.scib.2025.10.034"},{"key":"2026100607150944000_2026.09.25.754469v1.61","doi-asserted-by":"crossref","unstructured":"Flores-Mendez, M. , et al. TBCK-deficiency leads to compartment-specific mRNA and lysosomal trafficking defects in patient-derived neurons. bioRxiv (2025).","DOI":"10.1101\/2025.03.02.641041"},{"key":"2026100607150944000_2026.09.25.754469v1.62","doi-asserted-by":"crossref","first-page":"123","DOI":"10.4049\/jimmunol.1302291","article-title":"Qualitatively different T cell phenotypic responses to IL-2 versus IL-15 are unified by identical dependences on receptor signal strength and duration","volume":"192","year":"2014","journal-title":"The Journal of Immunology"},{"key":"2026100607150944000_2026.09.25.754469v1.63","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-023-01353-0"},{"key":"2026100607150944000_2026.09.25.754469v1.64","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome: a contaminant repository for affinity purification-mass spectrometry data","volume":"10","year":"2013","journal-title":"Nature Methods"},{"key":"2026100607150944000_2026.09.25.754469v1.65","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4939-1221-6_1"},{"key":"2026100607150944000_2026.09.25.754469v1.66","doi-asserted-by":"publisher","DOI":"10.1038\/nature04847"},{"key":"2026100607150944000_2026.09.25.754469v1.67","doi-asserted-by":"crossref","unstructured":"Allen, W.E. , Zicha, D. , Ridley, A.J. & Jones, G.E . A Role for Cdc42 in Macrophage Chemotaxis. Journal of Cell Biology 141 (1998).","DOI":"10.1083\/jcb.141.5.1147"},{"key":"2026100607150944000_2026.09.25.754469v1.68","doi-asserted-by":"crossref","unstructured":"Hind, L.E. , Cox, D. & Hammer, D.A . Macrophage Migration and the Roles of WASP, Cdc42, and PI3K. Biophysical Journal 104 (2013).","DOI":"10.1016\/j.bpj.2012.11.1778"},{"key":"2026100607150944000_2026.09.25.754469v1.69","doi-asserted-by":"crossref","unstructured":"Lee, D.J. , Cox, D. , Li, J. & Greenberg, S . Rac1 and Cdc42 Are Required for Phagocytosis, but Not NF-\u03baB-dependent Gene Expression, in Macrophages Challenged with Pseudomonas aeruginosa. Journal of Biological Chemistry 275 (2000).","DOI":"10.1074\/jbc.275.1.141"},{"key":"2026100607150944000_2026.09.25.754469v1.70","doi-asserted-by":"crossref","unstructured":"Torres-Sanchez, A. et al. Rac and Cdc42 inhibitors reduce macrophage function in breast cancer preclinical models. Frontiers in Oncology 13 (2023).","DOI":"10.3389\/fonc.2023.1152458"},{"key":"2026100607150944000_2026.09.25.754469v1.71","doi-asserted-by":"crossref","unstructured":"Lee, J.J. et al. Toll-Like Receptor 4-Linked Janus Kinase 2 Signaling Contributes to Internalization of Brucella abortus by Macrophages. Infection and Immunity 81 (2013).","DOI":"10.1128\/IAI.00403-13"},{"key":"2026100607150944000_2026.09.25.754469v1.72","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0008045"},{"key":"2026100607150944000_2026.09.25.754469v1.73","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M504768200"},{"key":"2026100607150944000_2026.09.25.754469v1.74","doi-asserted-by":"publisher","DOI":"10.1002\/bies.202100152"},{"key":"2026100607150944000_2026.09.25.754469v1.75","doi-asserted-by":"crossref","unstructured":"Devine, M.J. , Norkett, R. & Kittler, J.T . DISC1 is a coordinator of intracellular trafficking to shape neuronal development and connectivity. The Journal of Physiology 594 (2016).","DOI":"10.1113\/JP272187"},{"key":"2026100607150944000_2026.09.25.754469v1.76","doi-asserted-by":"publisher","DOI":"10.1126\/science.1259038"},{"key":"2026100607150944000_2026.09.25.754469v1.77","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.07.001"},{"key":"2026100607150944000_2026.09.25.754469v1.78","doi-asserted-by":"publisher","DOI":"10.1126\/science.1260419"},{"key":"2026100607150944000_2026.09.25.754469v1.79","doi-asserted-by":"crossref","first-page":"8434","DOI":"10.1038\/s41467-024-52723-6","article-title":"RAB12-LRRK2 complex suppresses primary ciliogenesis and regulates centrosome homeostasis in astrocytes","volume":"15","year":"2024","journal-title":"Nature Communications"},{"key":"2026100607150944000_2026.09.25.754469v1.80","doi-asserted-by":"crossref","first-page":"8205","DOI":"10.1038\/ncomms9205","article-title":"Resolution of structure of PIP5K1A reveals molecular mechanism for its regulation by dimerization and dishevelled","volume":"6","year":"2015","journal-title":"Nature Communications"},{"key":"2026100607150944000_2026.09.25.754469v1.81","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome: a contaminant repository for affinity purification-mass spectrometry data","volume":"10","year":"2013","journal-title":"Nature Methods"},{"key":"2026100607150944000_2026.09.25.754469v1.82","doi-asserted-by":"crossref","unstructured":"Gerstberger, S. , Hafner, M. , Ascano, M. & Tuschl, T . Evolutionary Conservation and Expression of Human RNA-Binding Proteins and Their Role in Human Genetic Disease. Systems Biology of RNA Binding Proteins, 2014, pp 1\u201355.","DOI":"10.1007\/978-1-4939-1221-6_1"},{"key":"2026100607150944000_2026.09.25.754469v1.83","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.05.012"},{"key":"2026100607150944000_2026.09.25.754469v1.84","doi-asserted-by":"crossref","unstructured":"Wang, Y. et al. TBCK syndrome pathogenesis: the TBCK-PPP1R21-C12orf4 complex regulating RAB5-dependent endo-lysosomal homeostasis. Science Bulletin 71 (2026).","DOI":"10.1016\/j.scib.2025.10.034"},{"key":"2026100607150944000_2026.09.25.754469v1.85","doi-asserted-by":"crossref","first-page":"e43","DOI":"10.1002\/imt2.43","article-title":"Complex heatmap visualization","volume":"1","year":"2022","journal-title":"Imeta"},{"key":"2026100607150944000_2026.09.25.754469v1.86","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2020.07.001"},{"key":"2026100607150944000_2026.09.25.754469v1.87","unstructured":"Kojima, H. , et al. A post-translational regulatory map of chronic antigen-driven human T cell dysfunction. bioRxiv (2026)."},{"key":"2026100607150944000_2026.09.25.754469v1.88","unstructured":"Buitinck, L. , et al. API design for machine learning software: experiences from the scikit-learn project. arXiv; 2013."},{"key":"2026100607150944000_2026.09.25.754469v1.89","doi-asserted-by":"crossref","first-page":"689","DOI":"10.1038\/s41467-018-03106-1","article-title":"Systematic analysis of protein turnover in primary cells","volume":"9","year":"2018","journal-title":"Nature Communications"},{"key":"2026100607150944000_2026.09.25.754469v1.90","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.05.012"},{"key":"2026100607150944000_2026.09.25.754469v1.91","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2023.05.009"},{"key":"2026100607150944000_2026.09.25.754469v1.92","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome: a contaminant repository for affinity purification-mass spectrometry data","volume":"10","year":"2013","journal-title":"Nature Methods"},{"key":"2026100607150944000_2026.09.25.754469v1.93","doi-asserted-by":"crossref","unstructured":"Kalaidzidis, Y. , Morales-Navarrete, H. , Kalaidzidis, I. & Zerial, M . Intracellular Background Estimation for Quantitative Fluorescence Microscopy. Proceedings 33 (2019).","DOI":"10.3390\/proceedings2019033022"},{"key":"2026100607150944000_2026.09.25.754469v1.94","doi-asserted-by":"crossref","unstructured":"Lord, S.J. , Velle, K.B. , Mullins, R.D. & Fritz-Laylin, L.K . SuperPlots: Communicating reproducibility and variability in cell biology. Journal of Cell Biology 219 (2020).","DOI":"10.1083\/jcb.202001064"},{"key":"2026100607150944000_2026.09.25.754469v1.95","doi-asserted-by":"crossref","unstructured":"Kalaidzidis, Y. , Kalaidzidis, I. & Zerial, M . A probabilistic method to quantify the colocalization of markers on intracellular vesicular structures visualized by light microscopy. AIP Conference Proceedings 1641 (2015).","DOI":"10.1063\/1.4906025"},{"key":"2026100607150944000_2026.09.25.754469v1.96","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts635"},{"key":"2026100607150944000_2026.09.25.754469v1.97","doi-asserted-by":"crossref","unstructured":"Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10 (2021).","DOI":"10.1093\/gigascience\/giab008"},{"key":"2026100607150944000_2026.09.25.754469v1.98","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt656"},{"key":"2026100607150944000_2026.09.25.754469v1.99","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8"},{"key":"2026100607150944000_2026.09.25.754469v1.100","doi-asserted-by":"crossref","unstructured":"Wickham, H . ggplot2: Elegant Graphics for Data Analysis. Springer: Cham, 2016.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"2026100607150944000_2026.09.25.754469v1.101","unstructured":"Slowikowski, K. ggrepel: Automatically Position Non-Overlapping Text Labels with \u2019ggplot2\u2019. 0.9.1 ed: Comprehensive R Archive Network (CRAN); 2021."},{"key":"2026100607150944000_2026.09.25.754469v1.102","doi-asserted-by":"publisher","DOI":"10.21105\/joss.03021"},{"key":"2026100607150944000_2026.09.25.754469v1.103","doi-asserted-by":"publisher","DOI":"10.1109\/mcse.2007.55"},{"key":"2026100607150944000_2026.09.25.754469v1.104","doi-asserted-by":"publisher","DOI":"10.1016\/j.patcog.2011.04.006"},{"key":"2026100607150944000_2026.09.25.754469v1.105","doi-asserted-by":"crossref","unstructured":"McKinney, W . Data Structures for Statistical Computing in Python. Proceedings of the 9th Python in Science Conference, 56\u201361 (2010).","DOI":"10.25080\/Majora-92bf1922-00a"},{"key":"2026100607150944000_2026.09.25.754469v1.106","doi-asserted-by":"publisher","DOI":"10.1109\/MCSE.2011.37"},{"key":"2026100607150944000_2026.09.25.754469v1.107","unstructured":"Lazar, C. , Burger, T. & Wieczorek, S. imputeLCMD: A Collection of Methods for Left Censored Missing Data Imputation. 2.1 ed: Comprehensive R Archive Network (CRAN); 2022."},{"key":"2026100607150944000_2026.09.25.754469v1.108","doi-asserted-by":"crossref","unstructured":"Fang, Z. , Liu, X. & Peltz, G . GSEApy: a comprehensive package for performing gene set enrichment analysis in Python. Bioinformatics 39 (2023).","DOI":"10.1093\/bioinformatics\/btac757"},{"key":"2026100607150944000_2026.09.25.754469v1.109","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-28948-z"},{"key":"2026100607150944000_2026.09.25.754469v1.110","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1038\/nmeth.3393","article-title":"MS-DIAL: data-independent MS\/MS deconvolution for comprehensive metabolome analysis","volume":"12","year":"2015","journal-title":"Nature Methods"},{"key":"2026100607150944000_2026.09.25.754469v1.111","doi-asserted-by":"publisher","DOI":"10.1038\/S41586-024-07487-W"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.64898\/2026.09.25.754469","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T14:31:58Z","timestamp":1791297118000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.64898\/2026.09.25.754469"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,1]]},"references-count":111,"URL":"https:\/\/doi.org\/10.64898\/2026.09.25.754469","relation":{},"subject":[],"published":{"date-parts":[[2026,10,1]]},"subtype":"preprint"}}