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 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 Original ResearchCirculating glycornas: A novel class of glycoconjugates in blood and implications for erythrocyte biology
Zheng L, Yi L, Jajosky R, Kageler L, Tulin E, Paz D, Porat J, Patel K, Cummings R, Xie Y, Flynn R, Stowell S. Circulating glycornas: A novel class of glycoconjugates in blood and implications for erythrocyte biology. Blood 2025, 146: 4668-4668. DOI: 10.1182/blood-2025-4668.Peer-Reviewed Original ResearchCell surfaceFunctional validationMass spectrometry analysisGlycan structuresErythrocyte biologyRNase AClasses of glycoconjugatesBlood group antigensMolecular identityTreated with sialidaseAnucleate natureGroup antigensOuter cell surfaceGlycophorin ARNA moleculesFree RNAMass spectrometry-based techniquesGlycoRNAPathogenesis of diseaseSignaling moleculesSurface proteinsPotential new targetsConcentrations of ribonucleaseSurface localizationRNAHigh 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 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-BB
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