2024
Beyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation
Holendová B, Šalovská B, Benáková Š, Plecitá-Hlavatá L. Beyond glucose: The crucial role of redox signaling in β-cell metabolic adaptation. Metabolism 2024, 161: 156027. PMID: 39260557, DOI: 10.1016/j.metabol.2024.156027.Peer-Reviewed Original ResearchPost-translational modificationsReactive oxygen speciesEndoplasmic reticulumTricarboxylic acidRedox signalingPancreatic B-cellsGlucose stimulationModification of proteinsB-cell metabolismRedox signaling pathwaysReversible cysteine oxidationIncreased ROS levelsProduction of reactive oxygen speciesB cell functionInsulin secretionB cellsProtein functionProtein processingCysteine thiol modificationsGlucose-induced increaseOxidative phosphorylationPyruvate metabolismProtein activityRegulatory mechanismsMetabolic pathwaysPTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Reports Methods 2024, 4: 100859. PMID: 39255793, PMCID: PMC11440062, DOI: 10.1016/j.crmeth.2024.100859.Peer-Reviewed Original ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProtein
2023
Oncogene-like addiction to aneuploidy in human cancers
Girish V, Lakhani A, Thompson S, Scaduto C, Brown L, Hagenson R, Sausville E, Mendelson B, Kandikuppa P, Lukow D, Yuan M, Stevens E, Lee S, Schukken K, Akalu S, Vasudevan A, Zou C, Salovska B, Li W, Smith J, Taylor A, Martienssen R, Liu Y, Sun R, Sheltzer J. Oncogene-like addiction to aneuploidy in human cancers. Science 2023, 381: eadg4521. PMID: 37410869, PMCID: PMC10753973, DOI: 10.1126/science.adg4521.Peer-Reviewed Original ResearchAn optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells
Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk B, Sessa W, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nature Communications 2023, 14: 3803. PMID: 37365174, PMCID: PMC10293293, DOI: 10.1038/s41467-023-39514-1.Peer-Reviewed Original ResearchConceptsPhosphorylation sitesSerine/threonine kinase AktMass spectrometry-based phosphoproteomicsThreonine kinase AktAkt-dependent phosphorylationAberrant Akt activationEndothelial cellsKinase substrateKinase AktCell signalingPhosphorylation profilePhenotypic outcomesDownstream signalingAkt activationAkt1 phosphorylationHuman diseasesSystem-level analysisAKT1Vascular endothelial cellsRich resourcePhosphorylationSignalingGrowth factorAktCellsPost‐translational modification and phenotype
Salovska B, Liu Y. Post‐translational modification and phenotype. Proteomics 2023, 23: e2200535. PMID: 36799530, DOI: 10.1002/pmic.202200535.Peer-Reviewed Original ResearchPhosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities
Salovska B, Gao E, Müller‐Dott S, Li W, Cordon C, Wang S, Dugourd A, Rosenberger G, Saez‐Rodriguez J, Liu Y. Phosphoproteomic analysis of metformin signaling in colorectal cancer cells elucidates mechanism of action and potential therapeutic opportunities. Clinical And Translational Medicine 2023, 13: e1179. PMID: 36781298, PMCID: PMC9925373, DOI: 10.1002/ctm2.1179.Peer-Reviewed Original ResearchConceptsColorectal cancerLong-term metformin treatmentType 2 diabetesCRC cell linesColorectal cancer cellsBiguanide drug metforminPotential therapeutic opportunitiesMechanism of actionPharmacodynamic interactionsMetformin treatmentTreatment of cancerCRC cellsCell proliferation assaysClinical trialsBcl-2/Bcl-xL inhibitorMetforminDrug metforminTherapeutic opportunitiesProliferation assaysCancer cellsPotential cancer therapeuticsPotential roleExpression levelsCell linesCancer therapeuticsA basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology
Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.Peer-Reviewed Original ResearchPost-translational modificationsData-independent acquisitionSystems biologySite-specific phosphorylation eventsImportant post-translational modificationMost human proteinsCritical protein functionsPhosphorylation eventsProtein functionPhosphoproteomic studiesPhosphoproteomic analysisBioinformatics AdvancesHuman proteinsMass spectrometry technologyBioinformatics analysisLarge-scale quantificationExperimental workflowHigh-resolution mass spectrometry technologySpectrometry technologyPhosphoproteomicsPhosphorylationBiologyProteinSystems medicineSingle experiment
2022
Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover
Li W, Salovska B, Fornasiero E, Liu Y. Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics 2022, 23: e2100387. PMID: 36422574, PMCID: PMC10964180, DOI: 10.1002/pmic.202100387.Peer-Reviewed Original ResearchConceptsPost-translational modificationsProtein turnoverDynamic stable isotope labelingCell starvationStable isotope labelingData-independent acquisition mass spectrometryAcquisition mass spectrometryProteome levelTurnover diversityPhosphoproteomic datasetsPhosphorylation stoichiometryMetabolic labelingIsotope labelingMass spectrometryPhosphorylationAmino acidsCell culturesBiological perspectiveStarvationTurnoverTurnover measurementsRecent studiesSILACProteoformsPeptidoformsSILAC-IodoTMT for Assessment of the Cellular Proteome and Its Redox Status
Vajrychova M, Salovska B, Pimkova K, Fabrik I, Hodny Z. SILAC-IodoTMT for Assessment of the Cellular Proteome and Its Redox Status. Methods In Molecular Biology 2022, 2603: 259-268. PMID: 36370286, DOI: 10.1007/978-1-0716-2863-8_21.Peer-Reviewed Original ResearchConceptsHigh-resolution mass spectrometryIodoacetyl tandem mass tagLiquid chromatography separationMass spectrometry-based approachQuantification of proteinsStable isotope labelingChromatography separationTandem mass tagsMass spectrometryCysteine modificationCellular proteomeGlobal proteomeIsotope labelingMass tagsModification levelsAmino acidsRedox statusProteomeCell culturesSpectrometrySILACSeparationProteinAcidTags
2021
Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape
Salovska B, Kondelova A, Pimkova K, Liblova Z, Pribyl M, Fabrik I, Bartek J, Vajrychova M, Hodny Z. Peroxiredoxin 6 protects irradiated cells from oxidative stress and shapes their senescence-associated cytokine landscape. Redox Biology 2021, 49: 102212. PMID: 34923300, PMCID: PMC8688892, DOI: 10.1016/j.redox.2021.102212.Peer-Reviewed Original ResearchConceptsSenescence-associated secretory phenotypePeroxiredoxin 6Senescent cellsIrreversible cell cycle arrestProtein secretory pathwayStress-induced cell deathProteome-level changesProteome-wide analysisCyclin-dependent kinasesProtein sulfhydryl oxidationOxidative stressPeroxiredoxin family membersExtracellular matrix proteinsComplex stress responseHTERT-RPE-1Cell cycle arrestSecretory pathwayRadiation-induced senescenceRedox homeostasisCellular senescenceDependent kinasesSecretome analysisStress responseSenescent phenotypeAntioxidant proteinsStudy on Radiosensitization of Human Leukemic Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis
Šalovská B, Tichý A. Study on Radiosensitization of Human Leukemic Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis. 2021, 97-115. DOI: 10.9734/bpi/nicst/v9/6869d.ChaptersBoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples
Salovska B, Li W, Di Y, Liu Y. BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. Analytical Chemistry 2021, 93: 3103-3111. PMID: 33533601, PMCID: PMC8959401, DOI: 10.1021/acs.analchem.0c04293.Peer-Reviewed Original ResearchConceptsData-independent acquisitionProtein turnoverDIA mass spectrometryStable isotope labelingValuable biological insightsRelative protein quantificationSerum starvation stressIsotopic labeling approachSILAC experimentsStarvation stressConventional DIA methodGas-phase separation strategyBiological insightsDegradation regulationIsotope labelingCultured cellsAmino acidsDIA-MSProtein quantificationLabeling approachPeptide pairsCell culturesBiological investigationsMultiplexed acquisitionComplex samplesLimited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome
Sztacho M, Šalovská B, Červenka J, Balaban C, Hoboth P, Hozák P. Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells 2021, 10: 68. PMID: 33406800, PMCID: PMC7824793, DOI: 10.3390/cells10010068.Peer-Reviewed Original ResearchConceptsGene expressionHuman nuclear proteomeLimited proteolysisLabel-free quantitative mass spectrometryNuclear pore complexGene ontology analysisCell cycle regulationQuantitative mass spectrometryNuclear proteomeProtein effectorsPore complexPol IIRNA splicingOntology analysisMRNA splicingCycle regulationPIP2 bindingProtein interactionsDNA repairBioinformatics analysisNuclear envelopeFunctional domainsMass spectrometry identifiesSpecific proteinsCell cycle
2020
Exosomes released by imatinib-resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib-sensitive cells in the presence of imatinib
Hrdinova T, Toman O, Dresler J, Klimentova J, Salovska B, Pajer P, Bartos O, Polivkova V, Linhartova J, Machova Polakova K, Kabickova H, Brodska B, Krijt M, Zivny J, Vyoral D, Petrak J, Hrdinova T, Toman O, Dresler J, Klimentova J, Salovska B, Pajer P, Bartos O, Polivkova V, Linhartova J, Machova Polakova K, Kabickova H, Brodska B, Krijt M, Zivny J, Vyoral D, Petrak J. Exosomes released by imatinib-resistant K562 cells contain specific membrane markers, IFITM3, CD146 and CD36 and increase the survival of imatinib-sensitive cells in the presence of imatinib. International Journal Of Oncology 2020, 58: 238-250. PMID: 33491750, DOI: 10.3892/ijo.2020.5163.Peer-Reviewed Original ResearchConceptsTyrosine kinase inhibitorsChronic myeloid leukemiaImatinib-resistant K562 cellsCML therapyImatinib-sensitive K562 cellsDrug resistanceK562 cellsTargeted CML therapySubset of patientsLess common mutationsSpecific tyrosine kinase inhibitorTKI drug resistanceInterferon-induced transmembrane protein 3Presence of imatinibQuality of lifeMalignant hematopoietic disordersPotential diagnostic markerFlow cytometric analysisBCR-ABL1 geneConstitutive kinase activityCell surface markersLabel-free quantification proteomics analysisMutation-independent mechanismTransmembrane protein 3Development of resistanceGlobal and Site-Specific Effect of Phosphorylation on Protein Turnover
Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Developmental Cell 2020, 56: 111-124.e6. PMID: 33238149, PMCID: PMC7855865, DOI: 10.1016/j.devcel.2020.10.025.Peer-Reviewed Original ResearchConceptsProtein turnoverProtein lifetimeCyclin-dependent kinase substrateStable isotope-labeled amino acidsSite-specific phosphorylationPulse-labeling approachIsotope-labeled amino acidsMass spectrometry-based methodCell fitnessKinase substratePhosphorylation sitesPhosphorylated sitesProteomic methodsCell signalingSpectrometry-based methodsLive cellsAmino acidsPhosphositesRich resourceDisease biologyLabeling approachPhosphorylationModification typesGlutamic acidTurnoverAberrantly elevated suprabasin in the bone marrow as a candidate biomarker of advanced disease state in myelodysplastic syndromes
Pribyl M, Hubackova S, Moudra A, Vancurova M, Polackova H, Stopka T, Jonasova A, Bokorova R, Fuchs O, Stritesky J, Salovska B, Bartek J, Hodny Z. Aberrantly elevated suprabasin in the bone marrow as a candidate biomarker of advanced disease state in myelodysplastic syndromes. Molecular Oncology 2020, 14: 2403-2419. PMID: 32696549, PMCID: PMC7530796, DOI: 10.1002/1878-0261.12768.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, DifferentiationAzacitidineBiomarkersBone MarrowCell CompartmentationCell Line, TumorChemokine CCL2Gene Expression Regulation, NeoplasticHEK293 CellsHumansInterferon-gammaLeukocytes, MononuclearLymphocyte CountMyelodysplastic SyndromesMyeloid CellsNeoplasm ProteinsPrognosisProto-Oncogene MasRNA, MessengerConceptsMyelodysplastic syndromeBone marrowMDS patientsPoor prognosisDisease progressionCandidate biomarkersHigh-risk myelodysplastic syndromeMyeloid-derived suppressor cellsAberrant cytokine levelsAdvanced disease stateMyeloid cell subpopulationsBlast percentageChemokine levelsCytokine levelsLymphocyte countSuppressor cellsPatient groupPeripheral bloodBM plasmaPreleukemic disordersImmune responseProinflammatory signalingMalignant cloneTherapy resistanceLeukemic cellsIsoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: msb199170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.Peer-Reviewed Original ResearchConceptsProtein degradationGenome-wide correlation analysisGene dosage variationProtein abundance levelsStable isotope-labeled amino acidsIndividual protein isoformsSpecific biological processesAlternative splicing isoformsData-independent acquisition mass spectrometryIsotope-labeled amino acidsAcquisition mass spectrometryProtein degradation ratesIntron retentionCellular functionsProtein isoformsSplicing isoformsCellular organellesTranscriptome variabilitySame geneTurnover controlRegulatory mechanismsBiological processesSpecific mRNAsTight associationAbundance levels
2019
Quantitative Proteome Profiling of Coxiella burnetii Reveals Major Metabolic and Stress Differences Under Axenic and Cell Culture Cultivation
Dresler J, Klimentova J, Pajer P, Salovska B, Fucikova A, Chmel M, Schmoock G, Neubauer H, Mertens-Scholz K. Quantitative Proteome Profiling of Coxiella burnetii Reveals Major Metabolic and Stress Differences Under Axenic and Cell Culture Cultivation. Frontiers In Microbiology 2019, 10: 2022. PMID: 31620097, PMCID: PMC6759588, DOI: 10.3389/fmicb.2019.02022.Peer-Reviewed Original ResearchCombining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1
Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019, 19: e1800438. PMID: 30901150, DOI: 10.1002/pmic.201800438.Peer-Reviewed Original ResearchConceptsChromosomal protein HMG-14DIA-MSDIA mass spectrometryPotential protein functionsCRISPR-Cas gene editingImmune regulation processesCancer cellsExtracellular proteomeChromatin structureHistone inactivationFunctional annotationProtein functionCellular functionsRegulation eventsImportant functional implicationsHMG 14Gene knockoutEnrichment analysisData-independent acquisitionHMGN1Protein deletionCRISPR experimentsGene editingStress pathwaysIndependent acquisitionInterferon‐regulated suprabasin is essential for stress‐induced stem‐like cell conversion and therapy resistance of human malignancies
Hubackova S, Pribyl M, Kyjacova L, Moudra A, Dzijak R, Salovska B, Strnad H, Tambor V, Imrichova T, Svec J, Vodicka P, Vaclavikova R, Rob L, Bartek J, Hodny Z. Interferon‐regulated suprabasin is essential for stress‐induced stem‐like cell conversion and therapy resistance of human malignancies. Molecular Oncology 2019, 13: 1467-1489. PMID: 30919591, PMCID: PMC6599850, DOI: 10.1002/1878-0261.12480.Peer-Reviewed Original ResearchConceptsMitogen-activated protein kinase/ERK kinaseSiRNA-mediated knockdownSBSN expressionERK pathwayProtein kinase/ERK kinaseHundreds of genesExtracellular signal-regulated kinase 1/2Signal-regulated kinase 1/2MEK/ERK pathwayCancer cellsPhenotypic plasticityTranscript profilesStress resistanceTherapy resistanceERK kinaseStem-like cellsActive NotchStem cell markersMolecular mechanismsAnoikis resistanceKinase 1/2Cancer evolutionChemical inhibitionCancer cell linesHuman clinical specimens