2024
Multiscale 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 models
2022
Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation
Cai WL, Chen JF, Chen H, Wingrove E, Kurley SJ, Chan LH, Zhang M, Arnal-Estape A, Zhao M, Balabaki A, Li W, Yu X, Krop ED, Dou Y, Liu Y, Jin J, Westbrook TF, Nguyen DX, Yan Q. Human WDR5 promotes breast cancer growth and metastasis via KMT2-independent translation regulation. ELife 2022, 11: e78163. PMID: 36043466, PMCID: PMC9584608, DOI: 10.7554/elife.78163.Peer-Reviewed Original ResearchConceptsBreast cancer cellsMetastatic breast cancerBreast cancerRibosomal gene expressionCancer cellsKnockdown of WDR5Vivo genetic screenReversible epigenetic mechanismsGenetic screenTranslation regulationTriple-negative breast cancerEpigenetic regulatorsEpigenetic mechanismsBreast cancer growthCancer-related deathTranslation efficiencyWDR5Novel therapeutic strategiesTranslation rateGene expressionCell growthAdvanced diseaseEffective therapyMetastatic capabilityPotent suppression
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
2019
Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry
Bouchal P, Schubert OT, Faktor J, Capkova L, Imrichova H, Zoufalova K, Paralova V, Hrstka R, Liu Y, Ebhardt HA, Budinska E, Nenutil R, Aebersold R. Breast Cancer Classification Based on Proteotypes Obtained by SWATH Mass Spectrometry. Cell Reports 2019, 28: 832-843.e7. PMID: 31315058, PMCID: PMC6656695, DOI: 10.1016/j.celrep.2019.06.046.Peer-Reviewed Original Research
2017
Impact 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
Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity
Zhong Q, Rüschoff JH, Guo T, Gabrani M, Schüffler PJ, Rechsteiner M, Liu Y, Fuchs TJ, Rupp NJ, Fankhauser C, Buhmann JM, Perner S, Poyet C, Blattner M, Soldini D, Moch H, Rubin MA, Noske A, Rüschoff J, Haffner MC, Jochum W, Wild PJ. Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity. Scientific Reports 2016, 6: 24146. PMID: 27052161, PMCID: PMC4823793, DOI: 10.1038/srep24146.Peer-Reviewed Original ResearchAgedComputational BiologyDNA Copy Number VariationsEndometrial NeoplasmsFemaleGenetic HeterogeneityGenetic Predisposition to DiseaseHumansImmunohistochemistryIn Situ Hybridization, FluorescenceKaplan-Meier EstimateMaleMiddle AgedMutationNeoplasm StagingNeoplasmsOvarian NeoplasmsProstatic NeoplasmsPTEN PhosphohydrolaseReceptor, ErbB-2Stomach Neoplasms
2015
Quantitative variability of 342 plasma proteins in a human twin population
Liu Y, Buil A, Collins BC, Gillet L, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology 2015, 11: msb145728. PMID: 25652787, PMCID: PMC4358658, DOI: 10.15252/msb.20145728.Peer-Reviewed Original ResearchConceptsQuantitative variabilityUnique plasma proteinsBlood-based biomarker studiesGenetic controlBiological processesDifferent proteinsDifferent traitsPlasma proteinsProteinAbundance variabilityProtein levelsHuman populationMass spectrometry techniquesSpecific plasma proteinsHuman plasma proteinsGenesRelative contributionTraitsHeritabilitySpectrometry techniquesTwin study designDifferent patternsPopulationClinical biomarkersVariability
2013
Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS
Liu Y, Hüttenhain R, Surinova S, Gillet L, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS. Proteomics 2013, 13: 1247-1256. PMID: 23322582, DOI: 10.1002/pmic.201200417.Peer-Reviewed Original Research
2011
A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer
Luo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. Journal Of Proteomics 2011, 74: 528-538. PMID: 21262398, DOI: 10.1016/j.jprot.2011.01.011.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCellular proteomeCell lung cancerCancer secretomeLung cancerOne-dimensional gel electrophoresisA549 cellsBiomarker discoveryProteomic dataGene expressionSecretory proteinsIntracellular contaminationNovel promising biomarkerNovel serum biomarkersEnzyme-linked immunosorbent assaySecretomeProteinSerum proteomic dataClinical stagingProteomeSerum biomarkersGel electrophoresisC4BP levelsPromising biomarkerImmunosorbent assay