2025
Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling
Li T, Stayrook S, Li W, Wang Y, Li H, Zhang J, Liu Y, Klein D. Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling. Nature Communications 2025, 16: 3580. PMID: 40234450, PMCID: PMC12000326, DOI: 10.1038/s41467-025-58828-w.Peer-Reviewed Original ResearchConceptsThrombospondin type I repeatsIsthmin-1Pre-adipocytesType I repeatsBacterial streptavidinSurface helicesI repeatsMolecular detailsDiverse functionsFunctional studiesAkt phosphorylationFunctional roleStructural plasticityInsulin-like propertiesCrystal structureAMOPGrowth factorDomainPhosphorylationApoptosisLiver steatosisProteinHelixAktStreptavidinAn in vivo screen identifies NAT10 as a master regulator of brain metastasis
Chen J, Xu P, Cai W, Chen H, Wingrove E, Shi X, Li W, Biancon G, Zhang M, Balabaki A, Krop E, Asare E, Zhang Y, Yin M, Tebaldi T, Meier J, Westbrook T, Halene S, Liu Y, Shen H, Nguyen D, Yan Q. An in vivo screen identifies NAT10 as a master regulator of brain metastasis. Science Advances 2025, 11: eads6021. PMID: 40138393, PMCID: PMC11939035, DOI: 10.1126/sciadv.ads6021.Peer-Reviewed Original ResearchConceptsPhosphoserine aminotransferase 1Metastasis in vivoIn vivo screeningRNA helicase domainRegulator of brain metastasisMetastatic breast cancer cellsBrain metastasis in vivoBrain metastasesRNA helicaseCell growth in vitroBreast cancer cellsCancer cell proliferationSerine biosynthesisEpigenetic regulationGrowth in vitroNAT10Migration in vitroCancer cellsTumor growthCell proliferationPrimary tumor growthDrivers of brain metastasesRNACancer metastasisCancer-related deathsTurnover 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 changesPhosphositesHuman and mouse proteomics reveals the shared pathways in Alzheimer’s disease and delayed protein turnover in the amyloidome
Yarbro J, Han X, Dasgupta A, Yang K, Liu D, Shrestha H, Zaman M, Wang Z, Yu K, Lee D, Vanderwall D, Niu M, Sun H, Xie B, Chen P, Jiao Y, Zhang X, Wu Z, Chepyala S, Fu Y, Li Y, Yuan Z, Wang X, Poudel S, Vagnerova B, He Q, Tang A, Ronaldson P, Chang R, Yu G, Liu Y, Peng J. Human and mouse proteomics reveals the shared pathways in Alzheimer’s disease and delayed protein turnover in the amyloidome. Nature Communications 2025, 16: 1533. PMID: 39934151, PMCID: PMC11814087, DOI: 10.1038/s41467-025-56853-3.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseProtein turnoverMouse model of amyloidosisMulti-omics analysisMurine model of Alzheimer's diseaseModel of Alzheimer's diseaseModel of amyloidosisProteome turnoverMouse proteomeGenetic incorporationAD pathwayAmyloid formationBrain proteomeMulti-OmicsProteomic strategyAD progressionProteomicsProtein alterationsProteinDisease mechanismsAmyloidPathwayPotential targetMouse brainTurnover
2024
PTMoreR-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 speciesPTMProteomicsKinaseMammalsProteinThe CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells
Liao X, Li W, Zhou H, Rajendran B, Li A, Ren J, Luan Y, Calderwood D, Turk B, Tang W, Liu Y, Wu D. The CUL5 E3 ligase complex negatively regulates central signaling pathways in CD8+ T cells. Nature Communications 2024, 15: 603. PMID: 38242867, PMCID: PMC10798966, DOI: 10.1038/s41467-024-44885-0.Peer-Reviewed Original ResearchConceptsCD8+ T cellsT cellsCancer immunotherapyMouse CD8+ T cellsAnti-tumor immunityTumor growth inhibition abilityAnti-tumor effectsInhibition of neddylationCD8Effector functionsTCR stimulationIL2 signalingCentral signaling pathwaysCore signaling pathwaysEffector activityNegative regulatory mechanismsTranslational implicationsImmunotherapyGrowth inhibition abilityCytokine signalingTCRProteomic alterationsSignaling pathwayCancerCRISPR-based screens
2023
The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.Peer-Reviewed Original ResearchCalponin 2 regulates ketogenesis to mitigate acute kidney injury
Gui Y, Palanza Z, Gupta P, Li H, Pan Y, Wang Y, Hargis G, Kreutzer D, Wang Y, Bastacky S, Liu Y, Liu S, Zhou D. Calponin 2 regulates ketogenesis to mitigate acute kidney injury. JCI Insight 2023, 8: e170521. PMID: 37751293, PMCID: PMC10721266, DOI: 10.1172/jci.insight.170521.Peer-Reviewed Original ResearchConceptsAcute kidney injuryEstrogen receptor 2Fatty acid oxidationKidney injuryKidney fibrosisCalponin 2Ketone body β-hydroxybutyrateTubular cell deathBody β-hydroxybutyrateSirtuin 5Endogenous ketogenesisKidney functionReceptor 2Protein posttranslational modificationsRate-limiting enzymeFAO pathwayMitochondrial sirtuin 5Animal kidneysΒ-hydroxybutyrateOrgan performanceCell proliferationSynthase 2FibrosisPosttranslational modificationsInjury
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 variability
2021
A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression
Pangou E, Bielska O, Guerber L, Schmucker S, Agote-Arán A, Ye T, Liao Y, Puig-Gamez M, Grandgirard E, Kleiss C, Liu Y, Compe E, Zhang Z, Aebersold R, Ricci R, Sumara I. A PKD-MFF signaling axis couples mitochondrial fission to mitotic progression. Cell Reports 2021, 35: 109129. PMID: 34010649, DOI: 10.1016/j.celrep.2021.109129.Peer-Reviewed Original ResearchConceptsMitochondrial fission factorProtein kinase DMitochondrial fissionMitotic progressionMFF-dependent mitochondrial fissionGenome integrityChromosome segregationDynamic organellesKinase DMitochondrial receptorDaughter cellsFission factorMammalian cellsMitotic checkpointCell divisionFusion eventsInterphasic cellsCell survivalProtein 1PhosphorylationMitochondriaCellsFissionDynaminOrganelles
2020
Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation
Gao X, Li Q, Liu Y, Zeng R. Multi-in-One: Multiple-Proteases, One-Hour-Shot Strategy for Fast and High-Coverage Phosphoproteomic Investigation. Analytical Chemistry 2020, 92: 8943-8951. PMID: 32479063, DOI: 10.1021/acs.analchem.0c00906.Peer-Reviewed Original ResearchGerm‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes
Hausmann A, Russo G, Grossmann J, Zünd M, Schwank G, Aebersold R, Liu Y, Sellin ME, Hardt W. Germ‐free and microbiota‐associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes. Cellular Microbiology 2020, 22: e13191. PMID: 32068945, PMCID: PMC7317401, DOI: 10.1111/cmi.13191.Peer-Reviewed Original Research
2019
motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs
Wang S, Cai Y, Cheng J, Li W, Liu Y, Yang H. motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. Proteomics 2019, 19: e1900245. PMID: 31622013, DOI: 10.1002/pmic.201900245.Peer-Reviewed Original ResearchConceptsUser-friendly web toolWeb softwarePublic datasetsBioinformatics backgroundLarge datasetsWeb toolMotif discoveryOptional featuresDatasetPresentation of motivesExponential growthLocation probabilitySoftwareKinase-substrate relationsModification sitesProtein post-translational modificationsPost-translational modificationsUsabilityUsersToolToolkitNetworkModification motifsPhosphoproteomic datasetsSite enrichmentIntegrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma
Gao Q, Zhu H, Dong L, Shi W, Chen R, Song Z, Huang C, Li J, Dong X, Zhou Y, Liu Q, Ma L, Wang X, Zhou J, Liu Y, Boja E, Robles A, Ma W, Wang P, Li Y, Ding L, Wen B, Zhang B, Rodriguez H, Gao D, Zhou H, Fan J. Integrated Proteogenomic Characterization of HBV-Related Hepatocellular Carcinoma. Cell 2019, 179: 561-577.e22. PMID: 31585088, DOI: 10.1016/j.cell.2019.08.052.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsbeta CateninCarcinoma, HepatocellularCell ProliferationCohort StudiesFemaleFructose-Bisphosphate AldolaseGene Expression ProfilingGene Expression Regulation, NeoplasticHep G2 CellsHepatitis B virusHepatitis B, ChronicHumansLiver NeoplasmsMaleMiceMice, Inbred BALB CMiddle AgedProteogenomicsTumor MicroenvironmentConceptsHepatitis B virus (HBV)-related hepatocellular carcinomaHBV-related HCCMetabolic reprogrammingHepatocellular carcinomaProteogenomic characterizationHBV-related hepatocellular carcinomaCell proliferationAdjacent liver tissuesIntegrative proteogenomic analysisMicroenvironment dysregulationBenefit clinical practiceTumor thrombusPatient survivalPaired tumorPrognostic biomarkerMetabolic profileActivation statusClinical practiceGenetic profileCarcinomaLiver tissueTumorSignaling pathwayPromote glycolysisPatients
2017
Protein kinase D at the Golgi controls NLRP3 inflammasome activation
Zhang Z, Meszaros G, He WT, Xu Y, de Fatima Magliarelli H, Mailly L, Mihlan M, Liu Y, Gámez M, Goginashvili A, Pasquier A, Bielska O, Neven B, Quartier P, Aebersold R, Baumert TF, Georgel P, Han J, Ricci R. Protein kinase D at the Golgi controls NLRP3 inflammasome activation. Journal Of Experimental Medicine 2017, 214: 2671-2693. PMID: 28716882, PMCID: PMC5584123, DOI: 10.1084/jem.20162040.Peer-Reviewed Original Research
2016
On the Dependency of Cellular Protein Levels on mRNA Abundance
Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016, 165: 535-550. PMID: 27104977, DOI: 10.1016/j.cell.2016.03.014.Peer-Reviewed Original ResearchConceptsProtein levelsGene expression regulationCellular protein levelsLong‐term state changeGenotype-phenotype relationshipsExpression regulationMRNA fluctuationsProtein biosynthesisGenomic informationProteomic profilingTranscript levelsGene expressionBiological processesMRNA abundanceLife science researchMRNA levelsShort-term adaptationComplete understandingProtein concentrationBiosynthesisCentral importanceLocal availabilityTranscriptsTemporal variationProtein
2015
Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications
Sajic T, Liu Y, Aebersold R. Using data‐independent, high‐resolution mass spectrometry in protein biomarker research: Perspectives and clinical applications. Proteomics Clinical Applications 2015, 9: 307-321. PMID: 25504613, DOI: 10.1002/prca.201400117.Peer-Reviewed Original Research
2010
Proteomic mining in the dysplastic liver of WHV/c‐myc mice – insights and indicators for early hepatocarcinogenesis
Liu Y, Li C, Xing Z, Yuan X, Wu Y, Xu M, Tu K, Li Q, Wu C, Zhao M, Zeng R. Proteomic mining in the dysplastic liver of WHV/c‐myc mice – insights and indicators for early hepatocarcinogenesis. The FEBS Journal 2010, 277: 4039-4053. PMID: 20807235, DOI: 10.1111/j.1742-4658.2010.07795.x.Peer-Reviewed Original ResearchConceptsHepatocellular carcinomaMouse modelFK506-binding protein 4C-myc miceTransgenic mouse modelEarly HCC diagnosisAsymptomatic processC-myc-induced hepatocarcinogenesisDysplastic liversFerritin heavy chainHCC diagnosisTissue microarrayImmunohistochemical analysisStage IIITumor onsetPutative biomarkersSerum samplesWestern blottingEarly detectionControl casesEarly hepatocarcinogenesisProtein 4Cancer initiationProtein expression profilesDysplastic stage
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