2025
Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions
Li W, Dasgupta A, Yang K, Wang S, Hemandhar-Kumar N, Chepyala S, Yarbro J, Hu Z, Salovska B, Fornasiero E, Peng J, Liu Y. Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions. Cell 2025, 188: 2267-2287.e21. PMID: 40118046, PMCID: PMC12033170, DOI: 10.1016/j.cell.2025.02.021.Peer-Reviewed Original ResearchConceptsMouse tissuesNeurodegeneration-related proteinsPost-translational modificationsImpact of phosphorylationStable isotope labelingLong-lived proteinsPeroxisomal proteinsProtein lifetimeProteomic propertiesProtein phosphorylationProtein stabilityInteractive web-based portalProtein abundanceProtein turnoverPhosphorylationMammalian tissuesComprehensive resourceProteinIsotope labelingProteomicsA-synucleinAbundanceTurnoverTurnover changesPhosphosites
2022
Proteotype coevolution and quantitative diversity across 11 mammalian species
Ba Q, Hei Y, Dighe A, Li W, Maziarz J, Pak I, Wang S, Wagner GP, Liu Y. Proteotype coevolution and quantitative diversity across 11 mammalian species. Science Advances 2022, 8: eabn0756. PMID: 36083897, PMCID: PMC9462687, DOI: 10.1126/sciadv.abn0756.Peer-Reviewed Original ResearchConceptsMammalian speciesRNA metabolic processesCommon mammalian speciesUbiquitin-proteasome systemEvolutionary profilingMammalian lineagesProteomic methodsProtein degradationProtein abundanceGene expressionProtein expression levelsHigh interspeciesMetabolic processesCovariation analysisFunctional roleNucleotide levelExpression levelsQuantitative diversityCoevolutionMammalsSpeciesRemarkable variationExpressionTranscriptomeBiological variabilityIntegrating human brain proteomic data with genome-wide association study findings identifies novel brain proteins in substance use traits
Toikumo S, Xu H, Gelernter J, Kember RL, Kranzler HR. Integrating human brain proteomic data with genome-wide association study findings identifies novel brain proteins in substance use traits. Neuropsychopharmacology 2022, 47: 2292-2299. PMID: 35941285, PMCID: PMC9630289, DOI: 10.1038/s41386-022-01406-1.Peer-Reviewed Original ResearchConceptsSubstance use traitsProteome-wide association studyUse traitsProtein abundanceAssociation studiesBrain protein abundanceWide association studyGenome-wide association study summary statisticsHuman brain proteomeFine-mapping analysisGenetic risk lociBrain transcriptomic dataEuropean ancestry individualsOpioid use disorderProteomic abundanceTranscriptomic levelTranscriptomic dataAlcohol use disorderProteomic dataBrain proteomeGenetic lociTranscript levelsRisk lociGene expressionSignificant genesIntegrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder
Wingo TS, Gerasimov ES, Liu Y, Duong DM, Vattathil SM, Lori A, Gockley J, Breen MS, Maihofer AX, Nievergelt CM, Koenen KC, Levey DF, Gelernter J, Stein MB, Ressler KJ, Bennett DA, Levey AI, Seyfried NT, Wingo AP. Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder. Molecular Psychiatry 2022, 27: 3075-3084. PMID: 35449297, PMCID: PMC9233006, DOI: 10.1038/s41380-022-01544-4.Peer-Reviewed Original ResearchConceptsProteome-wide association studyTranscriptome-wide association studyGenome-wide association studiesBrain protein abundanceHuman brain proteomeBrain proteomeAssociation studiesProtein abundanceGenome-wide association dataHuman brain transcriptomePost-traumatic stress disorderGWAS resultsNovel proteinBrain transcriptomeRisk lociProteomeGenesAssociation dataPrecursor cellsPTSD pathogenesisBrain mRNA levelsMRNA levelsOligodendrocyte precursor cellsPromising targetNew insights
2021
Sex Differences in the Ventral Tegmental Area and Nucleus Accumbens Proteome at Baseline and Following Nicotine Exposure
Lee AM, Mansuri MS, Wilson RS, Lam TT, Nairn AC, Picciotto MR. Sex Differences in the Ventral Tegmental Area and Nucleus Accumbens Proteome at Baseline and Following Nicotine Exposure. Frontiers In Molecular Neuroscience 2021, 14: 657064. PMID: 34335180, PMCID: PMC8317211, DOI: 10.3389/fnmol.2021.657064.Peer-Reviewed Original ResearchVentral tegmental areaC3H/HeJ miceGlial fibrillary acidic proteinChronic nicotine administrationNicotine administrationProtein abundanceProteomeIsobaric labelingNicotine exposureFemale miceTegmental areaHeJ miceNucleus accumbensNicotine addictionProteinSex differencesSample fractionationPathwayFibrillary acidic proteinTandem mass spectrometryNetwork analysisMouse strainsChronic nicotineMesolimbic systemNicotine rewardIntestinal TMEM16A control luminal chloride secretion in a NHERF1 dependent manner
Saha T, Aoun J, Hayashi M, Ali I, Sarkar P, Bag PK, Leblanc N, Ameen N, Woodward OM, Hoque KM. Intestinal TMEM16A control luminal chloride secretion in a NHERF1 dependent manner. Biochemistry And Biophysics Reports 2021, 25: 100912. PMID: 33537462, PMCID: PMC7838733, DOI: 10.1016/j.bbrep.2021.100912.Peer-Reviewed Original Research
2019
Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR31[OPEN]
Dong J, Chen H, Deng XW, Irish VF, Wei N. Phytochrome B Induces Intron Retention and Translational Inhibition of PHYTOCHROME-INTERACTING FACTOR31[OPEN]. Plant Physiology 2019, 182: 159-166. PMID: 31690709, PMCID: PMC6945864, DOI: 10.1104/pp.19.00835.Peer-Reviewed Original ResearchConceptsPHYTOCHROME INTERACTING FACTOR3EIN3-BINDING F-BOX PROTEINAlternative splicingProtein degradationReversible regulatory mechanismPhytochrome B photoreceptorSpecific alternative splicingF-box proteinsRapid protein degradationUpstream open reading framesLight-grown plantsShort-day light cycleOpen reading frameShort-day environmentPIF3 proteinPhytochrome BIntron retentionE3 ligasesProtein translationTranslational inhibitionLight responseReading frameProtein abundanceContinuous red lightRegulatory mechanismsMapping connections in signaling networks with ambiguous modularity
Lill D, Rukhlenko O, Mc Elwee A, Kashdan E, Timmer J, Kholodenko B. Mapping connections in signaling networks with ambiguous modularity. Npj Systems Biology And Applications 2019, 5: 19. PMID: 31149348, PMCID: PMC6533310, DOI: 10.1038/s41540-019-0096-1.Peer-Reviewed Original ResearchConceptsModular Response AnalysisProtein abundanceProtein complexesNetwork reconstructionDownstream modulesRetroactive interactionsUpstream moduleComputational restorationNetwork modulesSuite of methodsAbundanceSuch complexesExperimental approachComplexesProteinEnzymePathwaySequestration effectNetwork responseDifferent modulesDevelopment of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD)
Wilson RS, Rauniyar N, Sakaue F, Lam TT, Williams KR, Nairn AC. Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD). Proteomes 2019, 7: 12. PMID: 30986977, PMCID: PMC6630806, DOI: 10.3390/proteomes7020012.Peer-Reviewed Original ResearchParallel reaction monitoringPostsynaptic densityData-independent acquisition (DIA) approachElectron-dense regionsQuantitation of proteinsBiochemical fractionationMass spectrometry analysisMass spectrometry-based assayProtein abundanceExcitatory glutamatergic synapsesPSD compositionProtein compositionPSD proteinsInternal peptide standardsPSD fractionProteinTargeted Mass SpectrometrySpectrometry analysisGlutamatergic synapsesMass spectrometryPeptide standardsAbundanceNeuropsychiatric disordersCortical brain tissueWide variety
2018
Usp25m protease regulates ubiquitin-like processing of TUG proteins to control GLUT4 glucose transporter translocation in adipocytes
Habtemichael EN, Li DT, Alcázar-Román A, Westergaard XO, Li M, Petersen MC, Li H, DeVries SG, Li E, Julca-Zevallos O, Wolenski JS, Bogan JS. Usp25m protease regulates ubiquitin-like processing of TUG proteins to control GLUT4 glucose transporter translocation in adipocytes. Journal Of Biological Chemistry 2018, 293: 10466-10486. PMID: 29773651, PMCID: PMC6036200, DOI: 10.1074/jbc.ra118.003021.Peer-Reviewed Original ResearchMeSH KeywordsAdipocytesAnimalsCarrier ProteinsCell MembraneCells, CulturedGlucoseGlucose Transporter Type 4Hypoglycemic AgentsInsulinIntracellular Signaling Peptides and ProteinsKinesinsMaleMiceMice, Inbred C57BLMotor ActivityProtein TransportProteolysisRatsRats, Sprague-DawleySignal TransductionUbiquitinUbiquitin ThiolesteraseConceptsGLUT4 storage vesiclesTUG cleavageGolgi matrixPlasma membraneGLUT4 glucose transporter translocationMicrotubule-based movementUbiquitin-like proteinGLUT4 glucose transportersStorage vesiclesGlucose transporter translocationAttenuation of insulinKinesin motor proteinsGLUT4 vesiclesSpecialized vesiclesGLUT4 translocationTransporter translocationSplice formsMotor proteinsProtein trapProtein abundanceProteolytic pathwayDiet-induced insulin resistanceEndoproteolytic cleavageGlucose transporterProteolytic processingMultisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface
Carette X, Platig J, Young D, Helmel M, Young A, Wang Z, Potluri L, Moody C, Zeng J, Prisic S, Paulson J, Muntel J, Madduri A, Velarde J, Mayfield J, Locher C, Wang T, Quackenbush J, Rhee K, Moody D, Steen H, Husson R. Multisystem Analysis of Mycobacterium tuberculosis Reveals Kinase-Dependent Remodeling of the Pathogen-Environment Interface. MBio 2018, 9: 10.1128/mbio.02333-17. PMID: 29511081, PMCID: PMC5845002, DOI: 10.1128/mbio.02333-17.Peer-Reviewed Original ResearchConceptsMycobacterial cell envelopeCell envelopePeptidoglycan turnoverProtein abundanceResponse regulator MtrAProtein secretion systemStress responseEnvelope stress responsePhosphorylated cellular proteinsRegulate essential processesDifferentially phosphorylated proteinsSerine/threonine protein kinaseTransport of proteinsLevel of gene expressionAnalysis of phosphoproteinsEssential cell functionsLevel of phosphorylationDNA binding activityDecreased expression of genesCell wall lipidsExpression of genesLipid contentIncreasing multidrug resistanceSecretion systemVirulence determinants
2017
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells
Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications 2017, 8: 1212. PMID: 29089484, PMCID: PMC5663699, DOI: 10.1038/s41467-017-01422-6.Peer-Reviewed Original ResearchConceptsSWATH mass spectrometryPost-transcriptional effectsMitochondrial proteomeProteome remodelingProteomic resourceTranscriptomic dataProteomic dataProtein abundanceProtein turnoverEntire chromosome 21ProteomeProtein expressionPhenotypic manifestationsChromosome 21Fibroblast cellsStoichiometric complexSignificant downregulationMonozygotic twin pair discordantTwin pair discordantMass spectrometryMajor determinantChromosomesProteinPair discordantAbundanceThe RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK
Amin E, Liu Y, Deng S, Tan K, Chudgar N, Mayo M, Sanchez-Vega F, Adusumilli P, Schultz N, Jones D. The RNA-editing enzyme ADAR promotes lung adenocarcinoma migration and invasion by stabilizing FAK. Science Signaling 2017, 10 PMID: 28928239, PMCID: PMC5771642, DOI: 10.1126/scisignal.aah3941.Peer-Reviewed Original ResearchConceptsFocal adhesion kinaseRNA editing enzyme ADARPresence of ADARsAnalysis of gene expression patternsGenome-wide studiesLung adenocarcinoma cellsRNA-binding proteinsCell migration pathwaysGene expression patternsStabilized transcriptsIntron sitesADARProtein abundanceBinding proteinIncreased abundanceExpression patternsMolecular analysisStage I LUAD patientsPharmacological inhibitionProteinMesenchymal propertiesPotential therapeutic applicationsProtein levelsTranscriptionGenesImpact of Alternative Splicing on the Human Proteome
Liu Y, Gonzàlez-Porta M, Santos S, Brazma A, Marioni JC, Aebersold R, Venkitaraman AR, Wickramasinghe VO. Impact of Alternative Splicing on the Human Proteome. Cell Reports 2017, 20: 1229-1241. PMID: 28768205, PMCID: PMC5554779, DOI: 10.1016/j.celrep.2017.07.025.Peer-Reviewed Original ResearchConceptsProteomic diversityAlternative splicingAlternative splicing eventsDifferential transcript usageIntron retentionSplicing eventsHuman transcriptomeHuman proteomeTranscript usageRNA sequencingProtein abundanceTranscript levelsHuman diseasesProteomeSWATH-MSSplicingQuantitative snapshotIntegrative approachCritical determinantDiversityTranscriptomeSequencingAbundanceMRNAQuantitative manner
2016
The interdependence of transcript and protein abundance: new data–new complexities
Liu Y, Aebersold R. The interdependence of transcript and protein abundance: new data–new complexities. Molecular Systems Biology 2016, 12: msb156720. PMID: 26792872, PMCID: PMC4731012, DOI: 10.15252/msb.20156720.Peer-Reviewed Original ResearchProtein abundanceGene expression controlER stress responseExpression controlTranslational regulationEndoplasmic reticulum stressMammalian cellsTranscriptomic changesStress responseReticulum stressProtein levelsTranscriptsAbundanceCellsRelative contributionRecent reportsRegulationRecent workChallenging questions
2015
Using SRM-MS to quantify nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice
Ota A, Kovary K, Wu O, Ahrends R, Shen W, Costa M, Feldman B, Kraemer F, Teruel M. Using SRM-MS to quantify nuclear protein abundance differences between adipose tissue depots of insulin-resistant mice. Journal Of Lipid Research 2015, 56: 1068-1078. PMID: 25840986, PMCID: PMC4409283, DOI: 10.1194/jlr.d056317.Peer-Reviewed Original ResearchConceptsWhite adipose tissueStromal vascular cellsInsulin-resistant mouse modelProtein abundance differencesProtein abundance profilesPrimary adipose tissueCell culture cellsDifferentially expressed proteinsWhite adipose tissue depotsVisceral white adipose tissueInsulin-resistant miceProtein expression patternsNuclear proteinsProteomic approachProtein abundanceCell culture modelExpression patternsAdipocyte cell culturesIn vitro approachesInsulin resistanceCultured cellsAbundance profilesAdipose tissueImpaired differentiationProtein
2013
Adaptation Dynamics in Densely Clustered Chemoreceptors
Pontius W, Sneddon MW, Emonet T. Adaptation Dynamics in Densely Clustered Chemoreceptors. PLOS Computational Biology 2013, 9: e1003230. PMID: 24068908, PMCID: PMC3777915, DOI: 10.1371/journal.pcbi.1003230.Peer-Reviewed Original ResearchConceptsOrganisms senseChemotaxis pathwayTransmembrane receptorsNutrient gradientsReceptor methylationProtein abundanceReceptor substrateBacterial chemotaxisReceptor activityModification systemPathway constituentsEscherichia coliIndividual cellsEnvironmental stimuliFunctional robustnessExpression levelsMechanistic relationshipEnzymeModel systemEnzyme kineticsChemotaxis systemPrecise adaptationAdaptation dynamicsReceptor modificationModification kinetics
2010
Hypertonicity-induced Mitochondrial Membrane Permeability in Renal Medullary Interstitial Cells: Protective Role of Osmolytes
Zhang L, Chen D, Chen Z, Moeckel GW. Hypertonicity-induced Mitochondrial Membrane Permeability in Renal Medullary Interstitial Cells: Protective Role of Osmolytes. Cellular Physiology And Biochemistry 2010, 25: 753-760. PMID: 20511721, PMCID: PMC3030460, DOI: 10.1159/000315095.Peer-Reviewed Original ResearchConceptsPermeability transition poreHypertonicity-induced apoptosisOrganic osmolytesCytochrome cDelta psiFluorescence probe JC-1Cell deathMitochondrial membrane permeabilityMitochondrial membrane potentialHypertonic culture conditionsMajor organic osmolytesHypertonicity-induced changesHyperosmotic stressProtein abundanceMolecular mechanismsApoptotic pathwayTransition poreJC-1OsmolytesProapoptotic BaxCytoplasmApoptosisKidney cellsMembrane potentialImmunofluorescence labeling
2009
The ataxia3 Mutation in the N-Terminal Cytoplasmic Domain of Sodium Channel Nav1.6 Disrupts Intracellular Trafficking
Sharkey LM, Cheng X, Drews V, Buchner DA, Jones JM, Justice MJ, Waxman SG, Dib-Hajj SD, Meisler MH. The ataxia3 Mutation in the N-Terminal Cytoplasmic Domain of Sodium Channel Nav1.6 Disrupts Intracellular Trafficking. Journal Of Neuroscience 2009, 29: 2733-2741. PMID: 19261867, PMCID: PMC2679640, DOI: 10.1523/jneurosci.6026-08.2009.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlotting, WesternCell LineChromosome MappingCytoplasmData Interpretation, StatisticalDNA, ComplementaryElectrophysiologyEthylnitrosoureaImmunohistochemistryMachado-Joseph DiseaseMiceMice, Inbred C57BLMutagensMutationMutation, MissenseNAV1.6 Voltage-Gated Sodium ChannelNerve Tissue ProteinsPatch-Clamp TechniquesSciatic NerveSodium ChannelsSubcellular FractionsTransfectionConceptsMutant channelsCytoplasmic N-terminal regionN-terminal cytoplasmic domainCytoplasmic N-terminal domainMouse chromosome 15N-terminal domainN-terminal regionAmino acid substitution p.Primary cerebellar granule cellsVoltage-dependent inward sodium currentMutant proteinsCytoplasmic domainJuvenile lethalityCis-GolgiTrafficking defectsPlasma membraneSodium channelsIntracellular traffickingProtein abundanceWild typeN-terminusGolgi complexMutant transcriptsChromosome 15Whole-cell patch-clamp studiesMultistrip Western Blotting to Increase Quantitative Data Output
Kiyatkin A, Aksamitiene E. Multistrip Western Blotting to Increase Quantitative Data Output. Methods In Molecular Biology 2009, 536: 149-161. PMID: 19378054, PMCID: PMC2923389, DOI: 10.1007/978-1-59745-542-8_17.Peer-Reviewed Original ResearchConceptsCell signaling researchDiverse cellular processesWestern blottingHigh-throughput technologiesQuantitative data outputModification statesCellular processesProtein abundanceSystems biologyDifferent proteinsSingle membrane sheetMembrane sheetsPolyacrylamide gelsBlottingProteinElectrophoretic transferImmunoblotting procedureBiologyAbundance
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