Featured Publications
Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions.
Li W, Dasgupta A, Yang K, Wang S, Hemandhar-Kumar N, Chepyala SR, Yarbro JM, Hu Z, Salovska B, Fornasiero EF, Peng J, Liu Y. Turnover atlas of proteome and phosphoproteome across mouse tissues and brain regions. Cell 2025 PMID: 40118046, DOI: 10.1016/j.cell.2025.02.021.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 factorAktCellsProteotype 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 variabilityGlobal 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 acidTurnoverOncogene-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 ResearchMulti-omic measurements of heterogeneity in HeLa cells across laboratories
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology 2019, 37: 314-322. PMID: 30778230, DOI: 10.1038/s41587-019-0037-y.Peer-Reviewed Original ResearchConceptsCell linesGenome-wide copy numberMulti-omic measurementsHuman cultured cellsProtein turnover ratesPhenotypic responsesGenomic variabilityDifferent cell linesHeLa variantsSpecific cell linesCopy numberHeLa cellsCultured cellsHeLa cell linePhenotypic variabilityProgressive divergenceTurnover rateCellsBiological variationTechnical variationUniform conditionsTranscriptomeProteomeSuccessive passagesLines
2025
An in vivo screen identifies NAT10 as a master regulator of brain metastasis.
Chen JF, Xu P, Cai WL, Chen H, Wingrove E, Shi X, Li W, Biancon G, Zhang M, Balabaki A, Krop ED, Asare E, Zhang Y, Yin M, Tebaldi T, Meier JL, Westbrook TF, Halene S, Liu Y, Shen H, Nguyen DX, Yan Q. An in vivo screen identifies NAT10 as a master regulator of brain metastasis. Sci Adv 2025, 11: eads6021. PMID: 40138393, DOI: 10.1126/sciadv.ads6021.Peer-Reviewed Original ResearchMass spectrometry-based mapping of plasma protein QTLs in children and adolescents.
Liu Y. Mass spectrometry-based mapping of plasma protein QTLs in children and adolescents. Nat Genet 2025 PMID: 39972213, DOI: 10.1038/s41588-025-02088-3.Commentaries, Editorials and LettersHuman and mouse proteomics reveals the shared pathways in Alzheimer's disease and delayed protein turnover in the amyloidome.
Yarbro JM, Han X, Dasgupta A, Yang K, Liu D, Shrestha HK, Zaman M, Wang Z, Yu K, Lee DG, Vanderwall D, Niu M, Sun H, Xie B, Chen PC, Jiao Y, Zhang X, Wu Z, Chepyala SR, Fu Y, Li Y, Yuan ZF, Wang X, Poudel S, Vagnerova B, He Q, Tang A, Ronaldson PT, 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. Nat Commun 2025, 16: 1533. PMID: 39934151, DOI: 10.1038/s41467-025-56853-3.Peer-Reviewed Original ResearchAdvancing Scientific Communication in Proteomics.
Searle BC, Chazarin B, Collins BC, Kundu DJ, Huang S, Lin Q, Liu Y, Low TY, Saba J, Guo T, Palmisano G, Fert-Bober J. Advancing Scientific Communication in Proteomics. J Proteome Res 2025, 24: 381-382. PMID: 39916559, DOI: 10.1021/acs.jproteome.4c01098.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus Statements
2024
Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation.
Black EM, RamÃrez Parrado CA, Trier I, Li W, Joo YK, Pichurin J, Liu Y, Kabeche L. Chk2 sustains PLK1 activity in mitosis to ensure proper chromosome segregation. Nat Commun 2024, 15: 10782. PMID: 39737931, DOI: 10.1038/s41467-024-54922-7.Peer-Reviewed Original ResearchÏ€-HuB: the proteomic navigator of the human body.
He F, Aebersold R, Baker MS, Bian X, Bo X, Chan DW, Chang C, Chen L, Chen X, Chen YJ, Cheng H, Collins BC, Corrales F, Cox J, E W, Van Eyk JE, Fan J, Faridi P, Figeys D, Gao GF, Gao W, Gao ZH, Goda K, Goh WWB, Gu D, Guo C, Guo T, He Y, Heck AJR, Hermjakob H, Hunter T, Iyer NG, Jiang Y, Jimenez CR, Joshi L, Kelleher NL, Li M, Li Y, Lin Q, Liu CH, Liu F, Liu GH, Liu Y, Liu Z, Low TY, Lu B, Mann M, Meng A, Moritz RL, Nice E, Ning G, Omenn GS, Overall CM, Palmisano G, Peng Y, Pineau C, Poon TCW, Purcell AW, Qiao J, Reddel RR, Robinson PJ, Roncada P, Sander C, Sha J, Song E, Srivastava S, Sun A, Sze SK, Tang C, Tang L, Tian R, VizcaÃno JA, Wang C, Wang C, Wang X, Wang X, Wang Y, Weiss T, Wilhelm M, Winkler R, Wollscheid B, Wong L, Xie L, Xie W, Xu T, Xu T, Yan L, Yang J, Yang X, Yates J, Yun T, Zhai Q, Zhang B, Zhang H, Zhang L, Zhang L, Zhang P, Zhang Y, Zheng YZ, Zhong Q, Zhu Y, Ï€-HuB Consortium. Ï€-HuB: the proteomic navigator of the human body. Nature 2024, 636: 322-331. PMID: 39663494, DOI: 10.1038/s41586-024-08280-5.Peer-Reviewed Original ResearchA proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman J, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. Nature Methods 2024, 1-10. PMID: 39609567, DOI: 10.1038/s41592-024-02517-x.Peer-Reviewed Original ResearchTarget membrane proteinsMembrane proteinsMembrane contextSynaptic vesicle membrane proteinVesicle membrane proteinsMammalian membrane proteinsMembrane-active polymersExtraction of membrane proteinsNative nanodiscsOrganellar membranesNative membrane environmentMultiprotein complexesMolecular contextCellular membranesMembrane environmentQuantitative platformBioanalytical approachesExtraction efficiencyOpen-access databasesProteinMembraneExtraction conditionsNanodiscsTarget MPGABAA receptor π forms channels that stimulate ERK through a G-protein-dependent pathway
Wang Y, Zhang Y, Li W, Salovska B, Zhang J, Li T, Li H, Liu Y, Kaczmarek L, Pusztai L, Klein D. GABAA receptor π forms channels that stimulate ERK through a G-protein-dependent pathway. Molecular Cell 2024 PMID: 39642883, DOI: 10.1016/j.molcel.2024.11.016.Peer-Reviewed Original ResearchExtracellular regulated kinaseStimulated extracellular regulated kinaseExtracellular-regulated kinase signalingG-protein-dependent pathwayG protein-coupled pathwayUncharacterized pathwayGrowth signalsSignaling functionsCryoelectron microscopyCryo-EMSignaling mechanismsGABRPFunctional assaysNative nanodiscsPathwayStimulate growthPhysiological concentrationsAbsence of GABATargeted inhibitionType A receptorConcentrations of GABAMetabotropic receptorsIonotropic activitySignalGABA bindingA proteogenomic analysis of cervical cancer reveals therapeutic and biological insights.
Yu J, Gui X, Zou Y, Liu Q, Yang Z, An J, Guo X, Wang K, Guo J, Huang M, Zhou S, Zuo J, Chen Y, Deng L, Yuan G, Li N, Song Y, Jia J, Zeng J, Zhao Y, Liu X, Du X, Liu Y, Wang P, Zhang B, Ding L, Robles AI, Rodriguez H, Zhou H, Shao Z, Wu L, Gao D. A proteogenomic analysis of cervical cancer reveals therapeutic and biological insights. Nat Commun 2024, 15: 10114. PMID: 39578447, DOI: 10.1038/s41467-024-53830-0.Peer-Reviewed Original ResearchPTMoreR-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 speciesPTMProteomicsKinaseMammalsProteinMultiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability
Mihailovich M, Germain P, Shyti R, Pozzi D, Noberini R, Liu Y, Aprile D, Tenderini E, Troglio F, Trattaro S, Fabris S, Ciptasari U, Rigoli M, Caporale N, D’Agostino G, Mirabella F, Vitriolo A, Capocefalo D, Skaros A, Franchini A, Ricciardi S, Biunno I, Neri A, Kasri N, Bonaldi T, Aebersold R, Matteoli M, Testa G. Multiscale modeling uncovers 7q11.23 copy number variation–dependent changes in ribosomal biogenesis and neuronal maturation and excitability. Journal Of Clinical Investigation 2024, 134: e168982. PMID: 39007270, PMCID: PMC11245157, DOI: 10.1172/jci168982.Peer-Reviewed Original ResearchConceptsCopy number variationsWilliams-Beuren syndromeRibosome biogenesisP-RPS6Neurodevelopmental disordersRibosomal genesP-4EBPNumber variationsTranslation factorsMicroduplication syndromeMolecular mechanismsGenesNeuronal differentiationPatient-derivedIntrinsic excitabilityMTOR pathwayBiogenesisNeuronal maturationPhosphorylated rpS6Neuronal transmissionWilliams-BeurenPathophysiological relevanceNeurocognitive featuresIntellectual disabilityDisease modelsNetwork-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 ResearchConceptsMechanism 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 mediumFibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury
Gui Y, Fu H, Palanza Z, Tao J, Lin Y, Min W, Qiao Y, Bonin C, Hargis G, Wang Y, Yang P, Kreutzer D, Wang Y, Liu Y, Yu Y, Liu Y, Zhou D. Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury. Journal Of Clinical Investigation 2024, 134: e165836. PMID: 38713523, PMCID: PMC11213467, DOI: 10.1172/jci165836.Peer-Reviewed Original ResearchNidogen-1Expression of transmembrane proteinsCell-matrix interactionsAcute kidney injuryExtracellular matrix proteinsWnt signaling pathwayGlobal proteomeHedgehog signalingTransmembrane proteinsTubular cell apoptosisSignaling pathwayCell apoptosisMatrix proteinsIntegrin B1Kidney fibroblastsMesenchymal cell activationKidney injuryHedgehogProteinMitigate acute kidney injurySMOPreserved kidney functionAcute kidney injury pathogenesisFibroblastsPhosphoproteomeReciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry.
Ke S, Dang F, Wang L, Chen JY, Naik MT, Li W, Thavamani A, Kim N, Naik NM, Sui H, Tang W, Qiu C, Koikawa K, Batalini F, Stern Gatof E, Isaza DA, Patel JM, Wang X, Clohessy JG, Heng YJ, Lahav G, Liu Y, Gray NS, Zhou XZ, Wei W, Wulf GM, Lu KP. Reciprocal antagonism of PIN1-APC/C(CDH1) governs mitotic protein stability and cell cycle entry. Nat Commun 2024, 15: 3220. PMID: 38622115, DOI: 10.1038/s41467-024-47427-w.Peer-Reviewed Original Research