Yi Xie
Postdoctoral Associate in NeuroscienceAbout
Research
Publications
2026
Smooth Muscle Cell-Specific Expression of Cyclic Nucleotide Phosphodiesterase 10a Promotes the Development of Medial Artery Calcification.
Jin Y, Xie Y, Davis S, Flores A, Wang X, Guzman R, Cai Y. Smooth Muscle Cell-Specific Expression of Cyclic Nucleotide Phosphodiesterase 10a Promotes the Development of Medial Artery Calcification. Journal Of The American Society Of Nephrology 2026 PMID: 42308131, DOI: 10.1681/asn.0000001164.Peer-Reviewed Original ResearchVascular smooth muscle cells in vitroSmooth muscle cells in vitroMuscle cells in vitroMedial arterial calcificationArtery calcificationCells in vitroTAK-063Calcification in vivoAssociated with high cardiovascular morbiditySmooth muscle cell calcificationPeripheral arterial disease patientsCyclic nucleotide phosphodiesterase 10AHigh cardiovascular morbidityTibial arteryInhibition of PDE10AArtery disease patientsPeripheral arterial diseaseVitamin D3 injectionIn vivo modelsAortic ring modelCyclic nucleotides cAMPArteries in vivoNephrectomy modelCardiovascular morbidityGlobal deletionBioorthogonal Heptose Phosphate Probes for Chemical Profiling of Bacterial Glycans
Cao W, Liu W, Yang M, Yu L, Li T, Zhou Y, Zheng X, Yi L, Wang H, Li L, Xu C, Hsu Y, Jin J, Hong S, Xie Y, Wang W, Wang J, Xie R. Bioorthogonal Heptose Phosphate Probes for Chemical Profiling of Bacterial Glycans. JACS Au 2026 DOI: 10.1021/jacsau.6c00391.Peer-Reviewed Original ResearchLipopolysaccharide inner coreFunctional studiesLipopolysaccharide biosynthesisLipopolysaccharide mutantsGram-negative bacterial lipopolysaccharideThreonine sitesBacterial proteinsBacterial glycansBacterial systemsHeptose sugarLPS structurePhosphate probeSubstrate diversityLive bacteriaInnate immune activationBacterial lipopolysaccharideChemical profilesLipopolysaccharideMetabolic probeMutantsBiosynthesisClick chemistryGlycansHeptoseThreonineTGM2-mediated serotonylation of GPX4 confers ferroptosis resistance to promote gastric tumorigenesis
Bai J, Geng D, Chen X, Li W, Wang X, Tian L, Han Y, Jin Z, Du M, Tang Y, Hu W, Zhu C, Zhang S, Zhao Z, Zhang R, Zhang X, Kang W, To K, Nomura S, Guo F, Jiao S, Xie Y, Zhou Z, Dong C, Li H, An L. TGM2-mediated serotonylation of GPX4 confers ferroptosis resistance to promote gastric tumorigenesis. Cell Discovery 2026, 12: 30. PMID: 42049702, PMCID: PMC13125317, DOI: 10.1038/s41421-026-00885-6.Peer-Reviewed Original ResearchGlutathione peroxidase 4Tumor growthGastric cancerLevels of serotonin (5-HTSerotonin (5-HTFerroptosis resistanceGastric tumorigenesisTransglutaminase 2Receptor-independent mechanismDose-dependent mannerResistance to ferroptosisPlasma metabolomeInhibition of transglutaminase 2Transglutaminase 2 levelsPatient specimensGPX4 expressionTherapeutic targetDiagnostic biomarkersPeroxidase 4Cell proliferationOncogenic effectsTumorProtein serotonylationFerroptosisUbiquitin-mediated degradationMass 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: aaiaf005. 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 dissociationOligosaccharidesProteinAbundance
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