2025
A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy
Salovska B, Li W, Bernhardt O, Germain P, Wang Q, Gandhi T, Reiter L, Liu Y. A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy. Nature Communications 2025, 16: 5034. PMID: 40447611, PMCID: PMC12125295, DOI: 10.1038/s41467-025-60319-x.Peer-Reviewed Original ResearchMeSH KeywordsAneuploidyCell Line, TumorCisplatinDrug Resistance, NeoplasmHumansIsotope LabelingMachine LearningMass SpectrometryMitochondriaProteolysisProteomeProteomicsWorkflowConceptsMS platformsMass spectrometryDrug discoveryCisplatin resistanceDegradation kineticsDegradation profileAssociated with cisplatin resistanceProtein turnoverLabeled channelsProtein complex subunitsRespiratory complex IMitochondrial metabolic adaptationRobust workflowProtein degradation profilesCancer cell modelsMeasure protein turnoverProtein turnover regulationProteome dynamicsSpectrometryHigh-throughputComplex ICellular processesComplex subunitsSILAC labelingAneuploid genomes
2024
Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis
Rosenberger G, Li W, Turunen M, He J, Subramaniam P, Pampou S, Griffin A, Karan C, Kerwin P, Murray D, Honig B, Liu Y, Califano A. Network-based elucidation of colon cancer drug resistance mechanisms by phosphoproteomic time-series analysis. Nature Communications 2024, 15: 3909. PMID: 38724493, PMCID: PMC11082183, DOI: 10.1038/s41467-024-47957-3.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAntineoplastic AgentsCell Line, TumorColonic NeoplasmsDrug Resistance, NeoplasmHumansPhosphoproteinsPhosphorylationProteomeProteomicsSignal TransductionConceptsMechanism of cell responseResistance mechanismsSignaling pathway responsesDrug resistance mechanismsEnzyme/substrate interactionsAdaptive resistance mechanismsNetwork rewiringPhosphorylation stateSignaling Pathway ActivationDrug perturbationsProteomic technologiesSignaling crosstalkPathway responsesInhibitor designPathway activationCancer drug resistance mechanismsCell adaptive responsesAdaptive responsePhosphatase activityNetwork-based methodologyRewiringTherapeutic efficacyPhosphoproteome coverageCell responsesControl medium
2021
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells
Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBreast NeoplasmsCell ProliferationCytoskeletal ProteinsDrug Resistance, NeoplasmEndocytosisFemaleHumansMembrane MicrodomainsMyelin and Lymphocyte-Associated Proteolipid ProteinsPhosphoproteinsPlasma Membrane Calcium-Transporting ATPasesReceptor, ErbB-2Sodium-Hydrogen ExchangersTrastuzumabTumor Cells, CulturedConceptsLipid raft formationBreast cancer cellsLipid raftsLipid raft resident proteinsCancer cellsRaft formationRaft-resident proteinsProximity ligation assayProtein complexesMembrane protrusionsProtein interactionsPlasma membraneLigation assayMAL2Membrane stabilityStructural organizationPotential therapeutic targetPhysical interactionMembrane retentionProteinRaftsTherapeutic targetCellsIntracellular calcium concentrationLow intracellular calcium concentration
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