2024
Using in vivo intact structure for system-wide quantitative analysis of changes in proteins
Son A, Kim H, Diedrich J, Bamberger C, McClatchy D, Lipton S, Yates J. Using in vivo intact structure for system-wide quantitative analysis of changes in proteins. Nature Communications 2024, 15: 9310. PMID: 39468068, PMCID: PMC11519357, DOI: 10.1038/s41467-024-53582-x.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseProtein footprinting methodGlobal expression profilingIn vivo conformationStructural alterations of proteinsCo-expressed proteinsMass spectrometry-based methodsAlterations of proteinsProteostasis dysfunctionSpectrometry-based methodsProtein misfoldingConformation of proteinsStructural changesLysine residuesDynamic structural changesBiological functionsProteomics experimentsDimethyl labelingExpression profilesProtein conformationConformational changesProteinIntact proteinDesign of therapeutic interventionsMeasuring dynamic structural changesEnzymatic and non-enzymatic transnitrosylation: “SCAN”ning the SNO-proteome
Nakamura T, Lipton S. Enzymatic and non-enzymatic transnitrosylation: “SCAN”ning the SNO-proteome. Molecular Cell 2024, 84: 191-193. PMID: 38242098, DOI: 10.1016/j.molcel.2023.12.018.Peer-Reviewed Original Research
2022
Unfolded protein response IRE1/XBP1 signaling is required for healthy mammalian brain aging
Cabral‐Miranda F, Tamburini G, Martinez G, Ardiles A, Medinas D, Gerakis Y, Hung M, Vidal R, Fuentealba M, Miedema T, Duran‐Aniotz C, Diaz J, Ibaceta‐Gonzalez C, Sabusap C, Bermedo‐Garcia F, Mujica P, Adamson S, Vitangcol K, Huerta H, Zhang X, Nakamura T, Sardi S, Lipton S, Kennedy B, Henriquez J, Cárdenas J, Plate L, Palacios A, Hetz C. Unfolded protein response IRE1/XBP1 signaling is required for healthy mammalian brain aging. The EMBO Journal 2022, 41: embj2022111952. PMID: 36314651, PMCID: PMC9670206, DOI: 10.15252/embj.2022111952.Peer-Reviewed Original ResearchConceptsUnfolded protein responseER stress sensor IRE1Stress sensor IRE1IRE1/XBP1 signalingTranscription factor XBP1Mammalian brain agingNeurodegenerative diseasesProteostasis networkEndoplasmic reticulum stressProteomic profilingProtein responseCell senescenceGenetic disruptionBrain agingXBP1 expressionReticulum stressMammalian brainMajor risk factorActive formHealthy brain agingSynaptic functionXBP1Age-related cognitive declinePathwayHippocampal tissue
2009
Molecular stages of rapid and uniform neuralization of human embryonic stem cells
Bajpai R, Coppola G, Kaul M, Talantova M, Cimadamore F, Nilbratt M, Geschwind D, Lipton S, Terskikh A. Molecular stages of rapid and uniform neuralization of human embryonic stem cells. Cell Death & Differentiation 2009, 16: 807-825. PMID: 19282867, PMCID: PMC3432273, DOI: 10.1038/cdd.2009.18.Peer-Reviewed Original ResearchConceptsHuman embryonic stem cellsEmbryonic stem cellsNeural precursor cellsDynamic gene expression analysisStem cellsGene expression changesPrecursor cellsGene expression analysisEarly human developmentCoregulated genesPrimitive ectodermExpression analysisExpression changesMouse brainPotent oncogeneMolecular signalingUniform differentiationHuman biologyEfficient differentiationFuture cell-based therapiesFunctional neuronsNeuralizationPosterior markersNeonatal mouse brainNeural proliferation