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 Original ResearchLiquid 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 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, pwaf102. PMID: 41264770, DOI: 10.1093/procel/pwaf102.Peer-Reviewed Original ResearchHigh 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 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 typesCellsSitesProteomicsLysatesResiduesDevelopment 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 spectrometryAbstract We0072: Matrix metalloproteinases-3 promotes arteriovenous fistula failure by regulating FAK-AKT signaling
Xie Y, Zhang W, Thaxton C, Jin Y, Yatsula B, Davis S, Exsted T, Dardik A, Guzman R, Cai Y. Abstract We0072: Matrix metalloproteinases-3 promotes arteriovenous fistula failure by regulating FAK-AKT signaling. Arteriosclerosis Thrombosis And Vascular Biology 2025, 45: awe0072-awe0072. DOI: 10.1161/atv.45.suppl_1.we0072.Peer-Reviewed Original ResearchMatrix metalloproteinases-3Arteriovenous fistulaNeointimal hyperplasiaSMC proliferationMetalloproteinases-3Aggressive neointimal hyperplasiaArteriovenous fistula creationArteriovenous fistula failureCell growth in vitroSignaling pathwayVenous SMCsGrowth in vitroNeointimal SMCsMolecular signaling pathwaysFistula failureIncreased morbiditySurgical proceduresVenous SMC proliferationRodent modelsTherapeutic strategiesVascular accessImproved patencyGrowth factors PDGF-BBHyperplasiaPDGF-BBTRPM7 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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