{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T05:17:34Z","timestamp":1788239854356,"version":"build-2803163510"},"reference-count":90,"publisher":"MDPI AG","issue":"3","license":[{"start":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T00:00:00Z","timestamp":1787875200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Cancer Institute","award":["R01 CA276846"],"award-info":[{"award-number":["R01 CA276846"]}]},{"award":["R01 CA276846"],"award-info":[{"award-number":["R01 CA276846"]}],"id":[{"id":"https:\/\/ror.org\/040gcmg81","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Proteomes"],"abstract":"<jats:p>Background: Dysregulated cell migration leading to metastasis remains the primary cause of cancer-related mortality. It has been challenging to understand how cells regulate migration. We have previously created the first selective inhibitor of cell migration, KBU2046. Here, we use it as a probe to identify regulatory processes. Methods: Metastatic and primary human prostate cancer cells were treated for different times and at different concentrations with KBU2046. Immunofluorescent microscopy examined protein localization in cells. Label-free mass spectrometry (MS) was performed on total cell proteins, Tandem Mass Tag (TMT) labeling MS was used on membrane fractions, and temporal phosphoproteomic profiling was performed. Results were analyzed with a suite of bioinformatic tools. Results: KBU2046-induced migrastasis is associated with the accumulation of activated integrin \u03b21 into focal adhesions. Whole-cell proteomics demonstrated suppression of processes that mediate intracellular protein trafficking and increases in mitochondrial energy-generation signatures. Evaluation of the membrane fraction identified increases in membrane repair and maintenance processes and decreases in those that drive motility. Temporal- and concentration-dependent phosphoproteomic profiling revealed that KBU2046 initiates a dynamic, cascading sequence of transient signaling waves rather than a static block. Conclusions: KBU2046-induced migrastasis appears to operate through spatial decoupling rather than structural degradation. By restricting the intracellular trafficking machinery required for receptor recycling, KBU2046 limits focal adhesion turnover, providing, in PC3 prostate cancer cells, a correlative framework to inhibit metastatic dissemination independent of direct cytotoxicity.<\/jats:p>","DOI":"10.3390\/proteomes14030045","type":"journal-article","created":{"date-parts":[[2026,8,31]],"date-time":"2026-08-31T05:55:56Z","timestamp":1788155756000},"page":"45","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative Proteomic Analysis Implicates Inhibition of Intracellular Protein Trafficking in Therapy-Induced Migrastasis in Prostate Cancer"],"prefix":"10.3390","volume":"14","author":[{"given":"Weining","family":"Chen","sequence":"first","affiliation":[{"name":"Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794, USA"},{"name":"Eppley Institute for Research in Cancer, University of Nebraska Medical Center, Omaha, NE 68198, USA"},{"name":"Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"given":"Saadyeh","family":"Rashidi","sequence":"additional","affiliation":[{"name":"Department of Genetics, Cell Biology, and Anatomy, College of Medicine, University of Nebraska Medical Center, Omaha, NE 68198, 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Med."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"670","DOI":"10.1016\/j.cell.2016.11.037","article-title":"Emerging Biological Principles of Metastasis","volume":"168","author":"Lambert","year":"2017","journal-title":"Cell"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"563","DOI":"10.1038\/nrc865","article-title":"Dissemination and growth of cancer cells in metastatic sites","volume":"2","author":"Chambers","year":"2002","journal-title":"Nat. Rev. Cancer"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1335","DOI":"10.1007\/s00018-012-1115-1","article-title":"Tumor cell migration in complex microenvironments","volume":"70","author":"Polacheck","year":"2013","journal-title":"Cell Mol. Life Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.trecan.2017.04.008","article-title":"Migrastatics-Anti-metastatic and Anti-invasion Drugs: Promises and Challenges","volume":"3","author":"Rosel","year":"2017","journal-title":"Trends Cancer"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Solomon, J., Ra\u0161kova, M., R\u00f6sel, D., Br\u00e1bek, J., and Gil-Henn, H. (2021). Are We Ready for Migrastatics?. Cells, 10.","DOI":"10.3390\/cells10081845"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.trecan.2023.01.001","article-title":"Engine shutdown: Migrastatic strategies and prevention of metastases","volume":"9","author":"Jakubek","year":"2023","journal-title":"Trends Cancer"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"2454","DOI":"10.1038\/s41467-018-04465-5","article-title":"Precision therapeutic targeting of human cancer cell motility","volume":"9","author":"Xu","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_9","first-page":"995","article-title":"Generation and genetic characterization of immortal human prostate epithelial cell lines derived from primary cancer specimens","volume":"57","author":"Bright","year":"1997","journal-title":"Cancer Res."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1093\/jnci\/djp227","article-title":"MEK4 function, genistein treatment, and invasion of human prostate cancer cells","volume":"101","author":"Xu","year":"2009","journal-title":"J. Natl. Cancer Inst."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Pavese, J.M., Ogden, I.M., Voll, E.A., Huang, X., Xu, L., Jovanovic, B., and Bergan, R.C. (2014). Mitogen-activated protein kinase kinase 4 (MAP2K4) promotes human prostate cancer metastasis. PLoS ONE, 9.","DOI":"10.1371\/journal.pone.0102289"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1158\/1535-7163.MCT-19-0222","article-title":"A Multifunctional Therapy Approach for Cancer: Targeting Raf1-Mediated Inhibition of Cell Motility, Growth, and Interaction with the Microenvironment","volume":"19","author":"Zhang","year":"2020","journal-title":"Mol. Cancer Ther."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/j.ceb.2011.12.004","article-title":"Directed cell invasion and migration during metastasis","volume":"24","author":"Hodgson","year":"2012","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1038\/nrm2957","article-title":"Cell adhesion: Integrating cytoskeletal dynamics and cellular tension","volume":"11","author":"Parsons","year":"2010","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"dev200647","DOI":"10.1242\/dev.200647","article-title":"Focal adhesion-mediated cell anchoring and migration: From in vitro to in vivo","volume":"149","author":"Yamaguchi","year":"2022","journal-title":"Development"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"4605","DOI":"10.1242\/jcs.00792","article-title":"Early molecular events in the assembly of matrix adhesions at the leading edge of migrating cells","volume":"116","author":"Ballestrem","year":"2003","journal-title":"J. Cell Sci."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"359","DOI":"10.1016\/S0092-8674(00)81280-5","article-title":"Cell Migration: A Physically Integrated Molecular Process","volume":"84","author":"Lauffenburger","year":"1996","journal-title":"Cell"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1242\/jcs.042127","article-title":"The mechanical integrin cycle","volume":"122","author":"Sheetz","year":"2009","journal-title":"J. Cell Sci."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"a005074","DOI":"10.1101\/cshperspect.a005074","article-title":"Integrins in cell migration","volume":"3","author":"Huttenlocher","year":"2011","journal-title":"Cold Spring Harb. Perspect. Biol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1158\/1541-7786.MCR-12-0551","article-title":"Targeting constitutively activated \u03b21 integrins inhibits prostate cancer metastasis","volume":"11","author":"Lee","year":"2013","journal-title":"Mol. Cancer Res."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"1811","DOI":"10.1038\/onc.2014.116","article-title":"Talin1 phosphorylation activates \u03b21 integrins: A novel mechanism to promote prostate cancer bone metastasis","volume":"34","author":"Jin","year":"2015","journal-title":"Oncogene"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"1039","DOI":"10.2967\/jnumed.121.262743","article-title":"Enhancing (223)Ra Treatment Efficacy by Anti-beta1 Integrin Targeting","volume":"63","author":"Paindelli","year":"2022","journal-title":"J. Nucl. Med."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1016\/0014-5793(95)00301-O","article-title":"Identification of a novel anti-integrin monoclonal antibody that recognises a ligand-induced binding site epitope on the beta 1 subunit","volume":"363","author":"Mould","year":"1995","journal-title":"FEBS Lett."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"10234","DOI":"10.1074\/jbc.M411102200","article-title":"Dual functionality of the anti-beta1 integrin antibody, 12G10, exemplifies agonistic signalling from the ligand binding pocket of integrin adhesion receptors","volume":"280","author":"Humphries","year":"2005","journal-title":"J. Biol. Chem."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/ncb0807-858","article-title":"Functional atlas of the integrin adhesome","volume":"9","author":"Itzkovitz","year":"2007","journal-title":"Nat. Cell Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"bau012","DOI":"10.1093\/database\/bau012","article-title":"COMPARTMENTS: Unification and visualization of protein subcellular localization evidence","volume":"2014","author":"Binder","year":"2014","journal-title":"Database"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Chen, E.Y., Tan, C.M., Kou, Y., Duan, Q., Wang, Z., Meirelles, G.V., Clark, N.R., and Ma\u2019Ayan, A. (2013). Enrichr: Interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinform., 14.","DOI":"10.1186\/1471-2105-14-128"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"W90","DOI":"10.1093\/nar\/gkw377","article-title":"Enrichr: A comprehensive gene set enrichment analysis web server 2016 update","volume":"44","author":"Kuleshov","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"e90","DOI":"10.1002\/cpz1.90","article-title":"Gene Set Knowledge Discovery with Enrichr","volume":"1","author":"Xie","year":"2021","journal-title":"Curr. Protoc."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1083\/jcb.200904054","article-title":"Clathrin mediates integrin endocytosis for focal adhesion disassembly in migrating cells","volume":"187","author":"Ezratty","year":"2009","journal-title":"J. Cell Biol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1337","DOI":"10.1016\/j.febslet.2009.03.037","article-title":"Focal adhesion disassembly requires clathrin-dependent endocytosis of integrins","volume":"583","author":"Chao","year":"2009","journal-title":"FEBS Lett."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2905","DOI":"10.1091\/mbc.e11-12-1007","article-title":"The clathrin adaptor Dab2 recruits EH domain scaffold proteins to regulate integrin \u03b21 endocytosis","volume":"23","author":"Teckchandani","year":"2012","journal-title":"Mol. Biol. Cell"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"582","DOI":"10.1016\/j.ceb.2012.08.004","article-title":"Regulation of adhesion site dynamics by integrin traffic","volume":"24","author":"Valdembri","year":"2012","journal-title":"Curr. Opin. Cell Biol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1111\/j.1600-0854.2005.00362.x","article-title":"Integrin trafficking and the control of cell migration","volume":"7","author":"Caswell","year":"2006","journal-title":"Traffic"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"3695","DOI":"10.1242\/jcs.095810","article-title":"Integrin trafficking at a glance","volume":"125","author":"Bridgewater","year":"2012","journal-title":"J. Cell Sci."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1307","DOI":"10.1016\/j.cmet.2021.04.002","article-title":"Mechanoresponsive metabolism in cancer cell migration and metastasis","volume":"33","author":"Zanotelli","year":"2021","journal-title":"Cell Metab."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"4185","DOI":"10.1038\/s41467-019-12155-z","article-title":"Energetic costs regulated by cell mechanics and confinement are predictive of migration path during decision-making","volume":"10","author":"Zanotelli","year":"2019","journal-title":"Nat. Commun."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1016\/j.tcb.2022.09.009","article-title":"Plasticity of cancer invasion and energy metabolism","volume":"33","author":"Parlani","year":"2023","journal-title":"Trends Cell Biol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"2662","DOI":"10.1091\/mbc.e16-05-0286","article-title":"AMPK activity regulates trafficking of mitochondria to the leading edge during cell migration and matrix invasion","volume":"27","author":"Cunniff","year":"2016","journal-title":"Mol. Biol. Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"3586","DOI":"10.1021\/pr400098r","article-title":"Measuring and Managing Ratio Compression for Accurate iTRAQ\/TMT Quantification","volume":"12","author":"Savitski","year":"2013","journal-title":"J. Proteome Res."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"2341","DOI":"10.1002\/pmic.201000752","article-title":"Minimising iTRAQ ratio compression through understanding LC-MS elution dependence and high-resolution HILIC fractionation","volume":"11","author":"Ow","year":"2011","journal-title":"Proteomics"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Yang, H.C., Li, W., Sun, J., and Gross, M.L. (2023). Advances in Mass Spectrometry on Membrane Proteins. Membranes, 13.","DOI":"10.3390\/membranes13050457"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1152\/physiol.00019.2015","article-title":"Plasma Membrane Repair: A Central Process for Maintaining Cellular Homeostasis","volume":"30","author":"Blazek","year":"2015","journal-title":"Physiology"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1038\/nrc3726","article-title":"Hypoxia and the extracellular matrix: Drivers of tumour metastasis","volume":"14","author":"Gilkes","year":"2014","journal-title":"Nat. Rev. Cancer"},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1677\/ERC-09-0258","article-title":"Progesterone receptor enhances breast cancer cell motility and invasion via extranuclear activation of focal adhesion kinase","volume":"17","author":"Fu","year":"2010","journal-title":"Endocr. Relat. Cancer"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1016\/S0021-9258(17)33865-6","article-title":"Turnover of the plasma membrane proteins of hepatoma tissue culture cells","volume":"251","author":"Tweto","year":"1976","journal-title":"J. Biol. Chem."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"635","DOI":"10.1016\/j.cell.2006.09.026","article-title":"Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks","volume":"127","author":"Olsen","year":"2006","journal-title":"Cell"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1126\/science.ade3925","article-title":"Decrypting drug actions and protein modifications by dose- and time-resolved proteomics","volume":"380","author":"Zecha","year":"2023","journal-title":"Science"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1074\/mcp.M112.026575","article-title":"Phosphoproteomic analysis of protein phosphorylation networks in Tetrahymena thermophila, a model single-celled organism","volume":"13","author":"Tian","year":"2014","journal-title":"Mol. Cell Proteom."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"1510","DOI":"10.1021\/acs.jproteome.2c00131","article-title":"Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation","volume":"21","author":"Kalyuzhnyy","year":"2022","journal-title":"J. Proteome Res."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1093\/bioinformatics\/btt703","article-title":"Causal analysis approaches in Ingenuity Pathway Analysis","volume":"30","author":"Green","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"834","DOI":"10.1038\/nrm3012","article-title":"MET signalling: Principles and functions in development, organ regeneration and cancer","volume":"11","author":"Trusolino","year":"2010","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/nrc3205","article-title":"Targeting MET in cancer: Rationale and progress","volume":"12","author":"Gherardi","year":"2012","journal-title":"Nat. Rev. Cancer"},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Stanislovas, J., and Kermorgant, S. (2022). c-Met-integrin cooperation: Mechanisms, tumorigenic effects, and therapeutic relevance. Front. Cell Dev. Biol., 10.","DOI":"10.3389\/fcell.2022.994528"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1346","DOI":"10.1091\/mbc.e02-09-0578","article-title":"Endosomal dynamics of Met determine signaling output","volume":"14","author":"Hammond","year":"2003","journal-title":"Mol. Biol. Cell"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.biocel.2014.01.009","article-title":"Met endosomal signalling: In the right place, at the right time","volume":"49","author":"Kermorgant","year":"2014","journal-title":"Int. J. Biochem. Cell Biol."},{"key":"ref_58","doi-asserted-by":"crossref","unstructured":"Xiang, C., Chen, J., and Fu, P. (2017). HGF\/Met Signaling in Cancer Invasion: The Impact on Cytoskeleton Remodeling. Cancers, 9.","DOI":"10.3390\/cancers9050044"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"622","DOI":"10.1091\/mbc.E14-02-0740","article-title":"Arrestins regulate cell spreading and motility via focal adhesion dynamics","volume":"26","author":"Cleghorn","year":"2015","journal-title":"Mol. Biol. Cell"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"4841","DOI":"10.1038\/sj.onc.1206730","article-title":"p38 MAP kinase modulates Smad-dependent changes in human prostate cell adhesion","volume":"22","author":"Hayes","year":"2003","journal-title":"Oncogene"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"3470","DOI":"10.1158\/0008-5472.CAN-04-2807","article-title":"Genistein inhibits p38 map kinase activation, matrix metalloproteinase type 2, and cell invasion in human prostate epithelial cells","volume":"65","author":"Huang","year":"2005","journal-title":"Cancer Res."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/S1097-2765(01)00189-7","article-title":"The stress-induced MAP kinase p38 regulates endocytic trafficking via the GDI:Rab5 complex","volume":"7","author":"Cavalli","year":"2001","journal-title":"Mol. Cell"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3235","DOI":"10.1038\/sj.emboj.7600799","article-title":"Phosphorylation of EEA1 by p38 MAP kinase regulates mu opioid receptor endocytosis","volume":"24","author":"Mace","year":"2005","journal-title":"EMBO J."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"e202010048","DOI":"10.1083\/jcb.202010048","article-title":"Phosphorylation of SNX27 by MAPK11\/14 links cellular stress-signaling pathways with endocytic recycling","volume":"220","author":"Mao","year":"2021","journal-title":"J. Cell Biol."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"2987","DOI":"10.1038\/sj.onc.1209337","article-title":"MAPKAPK2 and HSP27 are downstream effectors of p38 MAP kinase-mediated matrix metalloproteinase type 2 activation and cell invasion in human prostate cancer","volume":"25","author":"Xu","year":"2006","journal-title":"Oncogene"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"485","DOI":"10.1158\/1541-7786.MCR-21-0266","article-title":"Mechanical Stress Signaling in Pancreatic Cancer Cells Triggers p38 MAPK- and JNK-Dependent Cytoskeleton Remodeling and Promotes Cell Migration via Rac1\/cdc42\/Myosin II","volume":"20","author":"Kalli","year":"2022","journal-title":"Mol. Cancer Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"26591","DOI":"10.1074\/jbc.M801703200","article-title":"Enzymatic activity and substrate specificity of mitogen-activated protein kinase p38alpha in different phosphorylation states","volume":"283","author":"Zhang","year":"2008","journal-title":"J. Biol. Chem."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"3489","DOI":"10.1093\/bioinformatics\/btx415","article-title":"The KSEA App: A web-based tool for kinase activity inference from quantitative phosphoproteomics","volume":"33","author":"Wiredja","year":"2017","journal-title":"Bioinformatics"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature07668","article-title":"WSTF regulates the H2A.X DNA damage response via a novel tyrosine kinase activity","volume":"457","author":"Xiao","year":"2009","journal-title":"Nature"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"14381","DOI":"10.1073\/pnas.1212366109","article-title":"Dual recognition of phosphoserine and phosphotyrosine in histone variant H2A.X by DNA damage response protein MCPH1","volume":"109","author":"Singh","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"622","DOI":"10.3892\/ijmm.2017.2861","article-title":"DNA damage response defect in Williams-Beuren syndrome","volume":"39","author":"Guenat","year":"2017","journal-title":"Int. J. Mol. Med."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1038\/nature07849","article-title":"Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions","volume":"458","author":"Cook","year":"2009","journal-title":"Nature"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1016\/j.tcb.2012.07.005","article-title":"Mechanical feedback between membrane tension and dynamics","volume":"22","author":"Gauthier","year":"2012","journal-title":"Trends Cell Biol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"jcs248385","DOI":"10.1242\/jcs.248385","article-title":"Fueling the cytoskeleton\u2014Links between cell metabolism and actin remodeling","volume":"134","author":"DeWane","year":"2021","journal-title":"J. Cell Sci."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"11942","DOI":"10.1038\/ncomms11942","article-title":"Beta 1-integrin-c-Met cooperation reveals an inside-in survival signalling on autophagy-related endomembranes","volume":"7","author":"Kishi","year":"2016","journal-title":"Nat. Commun."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Whitaker, R.H., and Cook, J.G. (2021). Stress Relief Techniques: P38 MAPK Determines the Balance of Cell Cycle and Apoptosis Pathways. Biomolecules, 11.","DOI":"10.3390\/biom11101444"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1126\/science.1196371","article-title":"Phosphorylation of ULK1 (hATG1) by AMP-activated protein kinase connects energy sensing to mitophagy","volume":"331","author":"Egan","year":"2011","journal-title":"Science"},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"1717","DOI":"10.1073\/pnas.0510664103","article-title":"Activation of the E3 ubiquitin ligase Itch through a phosphorylation-induced conformational change","volume":"103","author":"Gallagher","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"678","DOI":"10.1016\/j.molcel.2008.06.001","article-title":"JNK1-mediated phosphorylation of Bcl-2 regulates starvation-induced autophagy","volume":"30","author":"Wei","year":"2008","journal-title":"Mol. Cell"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"430","DOI":"10.1016\/j.cub.2013.01.064","article-title":"Cellular mechanotransduction relies on tension-induced and chaperone-assisted autophagy","volume":"23","author":"Ulbricht","year":"2013","journal-title":"Curr. Biol."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"186","DOI":"10.1038\/nmeth.2369","article-title":"Proteoform: A single term describing protein complexity","volume":"10","author":"Smith","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Carbonara, K., Andonovski, M., and Coorssen, J.R. (2021). Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes, 9.","DOI":"10.3390\/proteomes9030038"},{"key":"ref_83","first-page":"728","article-title":"Subnuclear domain proteins in cancer cells support the functions of RUNX2 in the DNA damage response","volume":"128","author":"Yang","year":"2015","journal-title":"J. Cell Sci."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1007\/978-1-4939-6747-6_8","article-title":"High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests","volume":"Volume 1550","author":"Comai","year":"2017","journal-title":"Proteomics: Methods in Molecular Biology"},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1021\/acschemneuro.4c00635","article-title":"Rapid Microwave Fixation of the Brain Reveals Seasonal Changes in the Phosphoproteome of Hibernating Thirteen-Lined Ground Squirrels","volume":"16","author":"Abid","year":"2025","journal-title":"ACS Chem. Neurosci."},{"key":"ref_86","unstructured":"R Core Team (2025). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. version 4.5.1."},{"key":"ref_87","doi-asserted-by":"crossref","unstructured":"Wickham, H. (2016). ggplot2: Elegant Graphics for Data Analysis, Springer.","DOI":"10.1007\/978-3-319-24277-4_9"},{"key":"ref_88","doi-asserted-by":"crossref","first-page":"284","DOI":"10.1089\/omi.2011.0118","article-title":"clusterProfiler: An R package for comparing biological themes among gene clusters","volume":"16","author":"Yu","year":"2012","journal-title":"OMICS"},{"key":"ref_89","doi-asserted-by":"crossref","first-page":"695","DOI":"10.1093\/nar\/gkm902","article-title":"NetworKIN: A resource for exploring cellular phosphorylation networks","volume":"36","author":"Linding","year":"2008","journal-title":"Nucleic Acids Res."},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"}],"container-title":["Proteomes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-7382\/14\/3\/45\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T04:35:34Z","timestamp":1788237334000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-7382\/14\/3\/45"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,28]]},"references-count":90,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["proteomes14030045"],"URL":"https:\/\/doi.org\/10.3390\/proteomes14030045","relation":{},"ISSN":["2227-7382"],"issn-type":[{"value":"2227-7382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,28]]}}}