Yi Xie
Postdoctoral Associate in NeuroscienceAbout
Research
Publications
2026
Mass spectrometry-based glycomics towards GlycoRNA
Yu L, Yi L, Lu H, Xie Y, Lu H. Mass spectrometry-based glycomics towards GlycoRNA. Glycoscience & Therapy 2026, 2: 100021. DOI: 10.1016/j.glycos.2025.100021.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsLiquid chromatography separationMS detectionGlycan releaseChromatography separationDiverse cell typesGlycosylated biomoleculesBiomarker discoveryGlycoRNABiological functionsBiological processesGlycomicsRNA extractionCell typesAnalytical strategyRNADerivatizationIntercellular communicationImmune regulationBiomedical researchBiomoleculesGlycansSeparationGlycosylationSpeciesProteinDevelopment of an immobilized system for RNA modification analysis.
Li Z, Yu L, Liu X, Deng L, Lin Z, Liu Z, Garcia B, Xie Y. Development of an immobilized system for RNA modification analysis. Molecular Omics 2026, 22 PMID: 41696908, PMCID: PMC12851623, DOI: 10.1093/momics/aaiaf005.Peer-Reviewed Original ResearchRNA modificationsRNA modification analysisShrimp alkaline phosphataseModification analysisLung cancer cellsPorous graphitic carbonRNA foldingModification dynamicsBiological processesEpithelial-mesenchymal transitionRNAHigh-throughput workflowClick reactionAgarose beadsCancer cellsGraphitic carbonNuclease P1Phosphodiesterase ITrans-cycloocteneSolution phaseMS analysisRNaseImmobilized systemSample preparationRibonucleoside
2025
GlycoRNA research: from unknown unknowns to known unknowns
Yi L, Zhou Y, Zhang C, Lu H, Xie Y. GlycoRNA research: from unknown unknowns to known unknowns. Protein & Cell 2025, 17: 1-20. PMID: 41264770, PMCID: PMC12959772, DOI: 10.1093/procel/pwaf102.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsHigh Phosphate and Low Protein Mediate Arterial and Cutaneous Vascular Calcification in CKD Mice
Jin Y, Cao F, Xie Y, Davis S, Dong G, Nigwekar S, Hansen J, Guzman R, Cai Y. High Phosphate and Low Protein Mediate Arterial and Cutaneous Vascular Calcification in CKD Mice. Journal Of The American Society Of Nephrology 2025, 37: 683-699. PMID: 40960881, PMCID: PMC12448113, DOI: 10.1681/asn.0000000875.Peer-Reviewed Original ResearchChronic kidney diseaseChronic kidney disease miceCutaneous vascular calcificationArteriolar calcificationVascular calcificationP38 MAPK signalingMedial arterial calcificationPharmacological inhibition of p38 MAPK signalingArtery calcificationLow-protein dietPharmacological inhibitionMedial arteryInhibition of p38 MAPK signalingCKD mouse modelMolecular pathwaysMAPK signalingExperimental CKD modelsPharmacological inhibitor SB203580Kidney impairmentAlizarin red stainingNephrectomy miceSignaling in vivoVascular complicationsKidney dysfunctionTreatment strategiesAn unbiased proteomic platform for ATE1-based arginylation profiling
Lin Z, Xie Y, Gongora J, Liu X, Zahn E, Palai B, Ramirez D, Searfoss R, Vitorino F, Karki R, Dann G, Zhao C, Han X, MacTaggart B, Lan X, Fu D, Greenberg L, Zhang Y, Lavine K, Greenberg M, Lv D, Kashina A, Garcia B. An unbiased proteomic platform for ATE1-based arginylation profiling. Nature Chemical Biology 2025, 21: 1970-1980. PMID: 40855110, PMCID: PMC12643917, DOI: 10.1038/s41589-025-01996-z.Peer-Reviewed Original ResearchConceptsArginyl-tRNA protein transferase 1Post-translational modificationsArginylated substratesProtein arginylationHuman proteomeModification sitesArginine residuesProtein modificationMammalian systemsBiological functionsArginylTransferase 1Functional studiesLiving cellsProteomics platformMouse samplesProteinArginyl sitesProfiling platformSample typesCellsSitesProteomicsLysatesResiduesSUV39H1 Regulates KLF4 and Chromatin Remodeling in Smooth Muscle Cell Phenotypic Plasticity
Chatterjee P, Chakraborty R, Sizer A, O’Brien B, Xu P, Hwa J, Xie Y, Yan Q, Hwa J, Martin K. SUV39H1 Regulates KLF4 and Chromatin Remodeling in Smooth Muscle Cell Phenotypic Plasticity. Arteriosclerosis Thrombosis And Vascular Biology 2025, 45: 2015-2033. PMID: 40836920, DOI: 10.1161/atvbaha.124.322179.Peer-Reviewed Original ResearchVascular Smooth Muscle Cell PlasticityHistone H3 lysine 9Transposase-accessible chromatinH3 lysine 9Vascular smooth muscle cellsSUV39H1 knockdownChromatin accessibilityPhenotypic plasticityLysine 9Smooth muscle cellsArtery smooth muscle cellsGene promoterCoronary artery smooth muscle cellsHuman coronary artery smooth muscle cellsPromoters genome-wideChromatin immunoprecipitation assaysMuscle cellsCell phenotypic plasticityCarotid ligationGenome-wideEpigenetic marksChromatin remodelingSMC gene expressionHistone methylationChromatin immunoprecipitationDevelopment and application of GlycanDIA workflow for glycomic analysis
Xie Y, Liu X, Yi L, Wang S, Lin Z, Zhao C, Chen S, Robison F, George B, Lebrilla C, Flynn R, Garcia B. Development and application of GlycanDIA workflow for glycomic analysis. Nature Communications 2025, 16: 7075. PMID: 40750788, PMCID: PMC12317082, DOI: 10.1038/s41467-025-61473-y.Peer-Reviewed Original ResearchConceptsHuman milk oligosaccharidesN-glycansGlycomic analysisLow abundanceN-glycan profilesProtein glycansProfile N-glycansTissue-specific differencesO-glycansRNA moleculesMilk oligosaccharidesRNA samplesGlycomics workflowsGlycan compositionBiological processesGlycomics methodsGlycan identificationGlycansRNAOuter coatingGlycosylationEnergy collisional dissociationOligosaccharidesProteinAbundanceMetabolic control of glycosylation forms for establishing glycan-dependent protein interaction networks
Liu X, Yi L, Lin Z, Chen S, Wang S, Sheng Y, Lebrilla C, Garcia B, Xie Y. Metabolic control of glycosylation forms for establishing glycan-dependent protein interaction networks. Proceedings Of The National Academy Of Sciences Of The United States Of America 2025, 122: e2422936122. PMID: 40531880, PMCID: PMC12207472, DOI: 10.1073/pnas.2422936122.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsInteraction networkAffinity purificationAP-MSProtein interaction networkGlycosylated formMutagenesis approachMass spectrometry analysisMembrane proteinsGlycan profilesHeterogeneity of glycosylationGlycosylation stateBiological processesSignaling pathwayMolecular mechanismsFunctional investigationsGlycosylationCultured cellsGlycosylation conditionsGlycoprotein interactionsGlycansSpectrometry analysisGlycoproteinTherapeutic developmentMass spectrometryTRPM7 channel activity promotes the pathogenesis of abdominal aortic aneurysms
Zong P, Li C, Feng J, Yue Z, Nethramangalath T, Xie Y, Qin X, Cicchetti M, Cai Y, Jellison E, Matsushita M, Runnels L, Yue L. TRPM7 channel activity promotes the pathogenesis of abdominal aortic aneurysms. Nature Cardiovascular Research 2025, 4: 197-215. PMID: 39953276, PMCID: PMC12143175, DOI: 10.1038/s44161-024-00596-9.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAorta, AbdominalAortic Aneurysm, AbdominalCalcium SignalingCells, CulturedDisease Models, AnimalHumansKruppel-Like Factor 4Kruppel-Like Transcription FactorsMaleMiceMice, Inbred C57BLMice, KnockoutMuscle, Smooth, VascularMyocytes, Smooth MuscleProtein Serine-Threonine KinasesTRPM Cation ChannelsVascular RemodelingConceptsTransient receptor potential melastatin 7Abdominal aortic aneurysmAbdominal aortic aneurysm formationAbdominal aortic aneurysm growthKruppel-like factor 4Aortic aneurysmKnockin miceAbdominal aortic aneurysm sizeTRPM7 channel activityUncontrolled lethal hemorrhagePathogenesis of abdominal aortic aneurysmEffective prophylactic medicationAbdominal aortic aneurysm progressionLethal hemorrhagePharmacological therapyChannel activityInflammatory infiltrateProphylactic medicationAAA pathogenesisChannel functionMiceTherapeutic targetPathophysiological conditionsFactor 4VSMCsQuantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks
Chen S, Xie Y, Alvarez M, Sheng Y, Bouchibti Y, Chang V, Lebrilla C. Quantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks. Analytical Chemistry 2025, 97: 1584-1593. PMID: 39805041, PMCID: PMC11780575, DOI: 10.1021/acs.analchem.4c04134.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein interaction networkCell surface glycansTerminal sialic acidAbundant membrane proteinProtein pairsCross-linking mass spectrometrySurface glycansAffinity purificationInteraction networkSialylated glycoformsMembrane proteinsLysine residuesProtein networkTarget proteinsSialic acidGlycansBiotin groupPolypeptide moietyProteinInteractomeExtensive interactionsCell membranePeptide pairsPolypeptide
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