2021
Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq
Gao Y, Chen S, Halene S, Tebaldi T. Transcriptome-wide quantification of double-stranded RNAs in live mouse tissues by dsRIP-Seq. STAR Protocols 2021, 2: 100366. PMID: 33778776, PMCID: PMC7982789, DOI: 10.1016/j.xpro.2021.100366.Peer-Reviewed Original ResearchConceptsDouble-stranded RNALive mouse tissuesDeleterious innate immune responseInnate immune responseEndogenous double-stranded RNAMouse tissuesMultiple regulatory functionsRecognition of RNADownstream computational analysisImmune responseRNA editingActivate innate immune responsesRegulatory functionsComplete detailsRNAImmunoprecipitationTissue isolationComplete protocolGao etComputational analysisSequencingTissueEditing
2019
Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression
Zhou B, Qi F, Wu F, Nie H, Song Y, Shao L, Han J, Wu Z, Saiyin H, Wei G, Wang P, Ni T, Qian F. Endogenous Retrovirus-Derived Long Noncoding RNA Enhances Innate Immune Responses via Derepressing RELA Expression. MBio 2019, 10: 10.1128/mbio.00937-19. PMID: 31363026, PMCID: PMC6667616, DOI: 10.1128/mbio.00937-19.Peer-Reviewed Original ResearchConceptsAntiviral immune responseImmune responseInnate immune responseNF-κB subunitsExpression of RelADeficient miceI interferonAntiviral responseVirus-induced cytokine productionHost genome instabilityEndogenous retrovirusesNF-κB signalingType I interferonRNA virus infectionViral RNA mimicViral loadCytokine productionViral challengeVirus infectionLong noncoding RNADeleterious roleRelA expressionViral replicationViral sensorsReduced expression
2018
Nonmuscle myosin II isoforms interact with sodium channel alpha subunits
Dash B, Han C, Waxman S, Dib-Hajj S. Nonmuscle myosin II isoforms interact with sodium channel alpha subunits. Molecular Pain 2018, 14: 1744806918788638. PMID: 29956586, PMCID: PMC6052497, DOI: 10.1177/1744806918788638.Peer-Reviewed Original ResearchMeSH KeywordsAction PotentialsAnimalsAnkyrinsBrainCell Line, TransformedElectric StimulationGanglia, SpinalGene Expression RegulationGreen Fluorescent ProteinsHumansImmunoprecipitationMiceMice, Inbred C57BLMice, TransgenicMolecular Motor ProteinsMyosin Heavy ChainsNAV1.6 Voltage-Gated Sodium ChannelNonmuscle Myosin Type IIBPatch-Clamp TechniquesRatsTransfectionConceptsSodium channel alpha subunitND7/23 cellsChannel alpha subunitDorsal root ganglion tissueAlpha subunitMyosin II motor proteinsNonmuscle myosin II isoformsRodent nervous tissueRodent brain tissueSteady-state fast inactivationVoltage-sensitive channelsFast inactivationVoltage-dependent activationSodium channel alphaGanglion tissueIsoform-dependent mannerMyosin II isoformsNervous tissueRecombinant myosinBrain tissueCommon structural motifRamp currentsMotor proteinsCellular excitabilitySodium channels
2017
Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols
Fey D, Aksamitiene E, Kiyatkin A, Kholodenko BN. Modeling of Receptor Tyrosine Kinase Signaling: Computational and Experimental Protocols. Methods In Molecular Biology 2017, 1636: 417-453. PMID: 28730495, DOI: 10.1007/978-1-4939-7154-1_27.Peer-Reviewed Original ResearchConceptsReceptor tyrosine kinasesReceptor tyrosine kinase signalingMultiple cellular processesTyrosine kinase signalingCellular processesProtein phosphorylationKinase signalingNetwork biologySystems biologyTyrosine kinaseCell survivalIntegration of experimentsPowerful approachIntegrative approachBiologyComputational protocolQuantitative datasetsKinasePhosphorylationSignalingIdentification of salientApoptosisDifferentiationGlucose metabolismRegulationInflammation-dependent cerebrospinal fluid hypersecretion by the choroid plexus epithelium in posthemorrhagic hydrocephalus
Karimy JK, Zhang J, Kurland DB, Theriault BC, Duran D, Stokum JA, Furey CG, Zhou X, Mansuri MS, Montejo J, Vera A, DiLuna ML, Delpire E, Alper SL, Gunel M, Gerzanich V, Medzhitov R, Simard JM, Kahle KT. Inflammation-dependent cerebrospinal fluid hypersecretion by the choroid plexus epithelium in posthemorrhagic hydrocephalus. Nature Medicine 2017, 23: 997-1003. PMID: 28692063, DOI: 10.1038/nm.4361.Peer-Reviewed Original ResearchMeSH KeywordsAcetazolamideAnimalsAntioxidantsBlotting, WesternBumetanideCerebral HemorrhageCerebral VentriclesCerebrospinal FluidChoroid PlexusDiureticsGene Knockdown TechniquesGene Knockout TechniquesHydrocephalusImmunoblottingImmunohistochemistryImmunoprecipitationInflammationNF-kappa BProlineProtein Serine-Threonine KinasesRatsRats, WistarSalicylanilidesSolute Carrier Family 12, Member 2SulfonamidesThiocarbamatesToll-Like Receptor 4Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense
Sasai M, Sakaguchi N, Ma JS, Nakamura S, Kawabata T, Bando H, Lee Y, Saitoh T, Akira S, Iwasaki A, Standley DM, Yoshimori T, Yamamoto M. Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense. Nature Immunology 2017, 18: 899-910. PMID: 28604719, DOI: 10.1038/ni.3767.Peer-Reviewed Original ResearchADP-Ribosylation Factor 1AnimalsApoptosis Regulatory ProteinsAutophagyAutophagy-Related Protein 8 FamilyCarrier ProteinsComputer SimulationCRISPR-Cas SystemsCytoskeletal ProteinsEnzyme-Linked Immunosorbent AssayFlow CytometryFluorescent Antibody TechniqueGene EditingGTP PhosphohydrolasesImmunoblottingImmunoprecipitationInterferon-gammaIntracellular Signaling Peptides and ProteinsMembrane ProteinsMiceMicrotubule-Associated ProteinsToxoplasmaToxoplasmosisCellular differentiation state modulates the mRNA export activity of SR proteins
Botti V, McNicoll F, Steiner MC, Richter FM, Solovyeva A, Wegener M, Schwich OD, Poser I, Zarnack K, Wittig I, Neugebauer KM, Müller-McNicoll M. Cellular differentiation state modulates the mRNA export activity of SR proteins. Journal Of Cell Biology 2017, 216: 1993-2009. PMID: 28592444, PMCID: PMC5496613, DOI: 10.1083/jcb.201610051.Peer-Reviewed Original ResearchMeSH KeywordsActive Transport, Cell NucleusAnimalsArginineCell DifferentiationCell NucleusDNA-Binding ProteinsHeLa CellsHumansImmunoprecipitationMethylationMiceNeurogenesisPhenotypePhosphorylationPluripotent Stem CellsProtein BindingProtein Processing, Post-TranslationalRepressor ProteinsRNA InterferenceRNA-Binding ProteinsRNA, MessengerSerine-Arginine Splicing FactorsTandem Mass SpectrometryTranscription FactorsTransfectionConceptsMRNA export activitySR proteinsP19 cellsMRNA exportSR protein family membersProtein-RNA interactionsMurine P19 cellsCellular differentiation stateProtein family membersLower phosphorylation levelsArginine methylationPluripotency factorsCytoplasmic mRNA levelsMRNA processingPosttranslational modificationsCellular dynamicsDifferentiated cellsNeural differentiationSRSF5Differentiation statePhosphorylation levelsHeLa cellsProteinExport activityMRNA levelsMultiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα
Hu Y, O’Boyle K, Auer J, Raju S, You F, Wang P, Fikrig E, Sutton RE. Multiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα. PLOS Pathogens 2017, 13: e1006187. PMID: 28152074, PMCID: PMC5308826, DOI: 10.1371/journal.ppat.1006187.Peer-Reviewed Original ResearchConceptsGene expressionHundreds of genesCycle assaysNFκB pathwayCo-immunoprecipitation studiesMouse embryo fibroblastsDownstream effector functionsJurkat T cellsPrimary human fibroblastsEmbryonic lethalityFamily membersUBA domainUBXN1HIV gene expressionSingle-cycle assaysProtein turnoverEmbryo fibroblastsCell adhesionGlobal regulationCanonical NFκB pathwayNFκB signalingHuman fibroblastsLike receptorsPathwayKnockdownSystematic Drug Screening Identifies Tractable Targeted Combination Therapies in Triple-Negative Breast Cancer
Wali VB, Langdon CG, Held MA, Platt JT, Patwardhan GA, Safonov A, Aktas B, Pusztai L, Stern DF, Hatzis C. Systematic Drug Screening Identifies Tractable Targeted Combination Therapies in Triple-Negative Breast Cancer. Cancer Research 2017, 77: 566-578. PMID: 27872098, PMCID: PMC5582957, DOI: 10.1158/0008-5472.can-16-1901.Peer-Reviewed Original ResearchConceptsTriple-negative breast cancerTNBC cell linesPairwise drug combinationsClinical translationAggressive diseaseCombination therapyBreast cancerPreclinical proofDrug combinationsCombination treatmentInvestigational drugsSingle agentSensitivity patternCell sensitivityCell linesTherapyApoptotic activityAnticancer activityDownregulated genesMitogenic signalingCrizotinibBlockadeClinicAgentsCancer
2016
RESA identifies mRNA-regulatory sequences at high resolution
Yartseva V, Takacs CM, Vejnar CE, Lee MT, Giraldez AJ. RESA identifies mRNA-regulatory sequences at high resolution. Nature Methods 2016, 14: 201-207. PMID: 28024160, PMCID: PMC5423094, DOI: 10.1038/nmeth.4121.Peer-Reviewed Original ResearchSH2 Domain–Containing Phosphatase-2 Is a Novel Antifibrotic Regulator in Pulmonary Fibrosis
Tzouvelekis A, Yu G, Lino Cardenas CL, Herazo-Maya JD, Wang R, Woolard T, Zhang Y, Sakamoto K, Lee H, Yi JS, DeIuliis G, Xylourgidis N, Ahangari F, Lee PJ, Aidinis V, Herzog EL, Homer R, Bennett AM, Kaminski N. SH2 Domain–Containing Phosphatase-2 Is a Novel Antifibrotic Regulator in Pulmonary Fibrosis. American Journal Of Respiratory And Critical Care Medicine 2016, 195: 500-514. PMID: 27736153, PMCID: PMC5378419, DOI: 10.1164/rccm.201602-0329oc.Peer-Reviewed Original ResearchConceptsIdiopathic pulmonary fibrosisPulmonary fibrosisProfibrotic stimuliLung fibroblastsChronic fatal lung diseaseMyofibroblast differentiationPrimary human lung fibroblastsFatal lung diseaseNovel therapeutic strategiesVivo therapeutic effectPotential therapeutic usefulnessHuman lung fibroblastsMouse lung fibroblastsDismal prognosisFibroblastic fociLung fibrosisLung diseaseBleomycin modelTherapeutic effectTherapeutic usefulnessTherapeutic strategiesTherapeutic targetTransgenic miceFibrosisSHP2 overexpressionTUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Ustianenko D, Pasulka J, Feketova Z, Bednarik L, Zigackova D, Fortova A, Zavolan M, Vanacova S. TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs. The EMBO Journal 2016, 35: 2179-2191. PMID: 27647875, PMCID: PMC5069555, DOI: 10.15252/embj.201694857.Peer-Reviewed Original ResearchMeSH KeywordsCell LineExoribonucleasesHumansImmunoprecipitationNucleotidyltransferasesRNA, UntranslatedConceptsStructured non-coding RNAsCellular RNA speciesRNA polymerase IICytoplasmic quality controlNon-coding RNAsStable secondary structureExoribonuclease DIS3L2Y-RNAsPolymerase IIStructured ncRNAsSurveillance pathwayRNA speciesWilms tumor susceptibilityRNA degradationDIS3L2Human cellsSecondary structureImmunoprecipitation methodPerlman syndromeUridylationRNAAberrant processingRNAsTumor susceptibilityUnifying featureEarly Activation of Experience-Independent Dendritic Spine Turnover in a Mouse Model of Alzheimer's Disease.
Heiss JK, Barrett J, Yu Z, Haas LT, Kostylev MA, Strittmatter SM. Early Activation of Experience-Independent Dendritic Spine Turnover in a Mouse Model of Alzheimer's Disease. Cerebral Cortex 2016, 27: 3660-3674. PMID: 27365298, PMCID: PMC6059166, DOI: 10.1093/cercor/bhw188.Peer-Reviewed Original ResearchMeSH KeywordsAge FactorsAlzheimer DiseaseAmyloid beta-Protein PrecursorAnalysis of VarianceAnimalsCerebral CortexDendritic SpinesDisease Models, AnimalGene Expression ProfilingGreen Fluorescent ProteinsHippocampusHumansImaging, Three-DimensionalImmunoprecipitationMiceMice, Inbred C57BLMice, TransgenicMutationNeuroimagingPlaque, AmyloidPresenilin-1Prion ProteinsProto-Oncogene Proteins c-fosSensory DeprivationTime FactorsVibrissaeConceptsAPP/PS1 miceDendritic spine turnoverSpine turnoverAlzheimer's diseasePS1 miceAged APP/PS1 miceYoung APP/PS1 miceAPP/PS1 mouse brainSoluble Aβ oligomersLipid-metabolizing genesAPPswe/Synaptic lossCerebral cortexSynapse densityAβ plaquesSynaptic dysregulationLack responsivenessMouse modelDendritic spinesPersistent spinesSynapse turnoverPlaque formationMouse brainYounger ageCellular prion proteinA novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection
Troupin A, Londono-Renteria B, Conway MJ, Cloherty E, Jameson S, Higgs S, Vanlandingham DL, Fikrig E, Colpitts TM. A novel mosquito ubiquitin targets viral envelope protein for degradation and reduces virion production during dengue virus infection. Biochimica Et Biophysica Acta 2016, 1860: 1898-1909. PMID: 27241849, PMCID: PMC4949077, DOI: 10.1016/j.bbagen.2016.05.033.Peer-Reviewed Original ResearchConceptsProtein degradationUbiquitin proteinGene expressionProtein expression constructsSite-directed mutagenesisViral protein degradationInnate immune signalingDengue virusProteasomal degradationProtein interactionsExpression constructsMosquito cellsSignificant human diseaseMicroarray analysisImmune signalingViral envelope proteinsVirus infectionHuman diseasesBlood feedingAmino acidsProteinMultiple functionsQRT-PCRVirion productionAntiviral functionThe Salmonella Effector Protein SopA Modulates Innate Immune Responses by Targeting TRIM E3 Ligase Family Members
Kamanova J, Sun H, Lara-Tejero M, Galán JE. The Salmonella Effector Protein SopA Modulates Innate Immune Responses by Targeting TRIM E3 Ligase Family Members. PLOS Pathogens 2016, 12: e1005552. PMID: 27058235, PMCID: PMC4825927, DOI: 10.1371/journal.ppat.1005552.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBacterial ProteinsCell LineDisease Models, AnimalGene Knockout TechniquesHost-Parasite InteractionsHumansImmunity, InnateImmunoprecipitationMass SpectrometryMiceReal-Time Polymerase Chain ReactionSalmonella InfectionsSalmonella typhimuriumSignal TransductionUbiquitin-Protein LigasesConceptsInflammatory responseImmune responseSalmonella typhimurium infectionInnate immune receptorsInnate immune responseHECT-type E3 ligaseTyphimurium infectionAnimal modelsIntestinal epitheliumIntestinal tractImmune receptorsInflammationStimulationTRIM56Type III secretion systemMDA5Pathogenicity island 1Family membersEfficient stimulationSalmonella typhimuriumIsland 1ResponseE3 ubiquitin ligasesInfectionSecretion system
2015
SENP1-mediated NEMO deSUMOylation in adipocytes limits inflammatory responses and type-1 diabetes progression
Shao L, Zhou HJ, Zhang H, Qin L, Hwa J, Yun Z, Ji W, Min W. SENP1-mediated NEMO deSUMOylation in adipocytes limits inflammatory responses and type-1 diabetes progression. Nature Communications 2015, 6: 8917. PMID: 26596471, PMCID: PMC4662081, DOI: 10.1038/ncomms9917.Peer-Reviewed Original ResearchMeSH Keywords3T3-L1 CellsAdipocytesAnimalsApoptosisChemokine CCL5Chromatin ImmunoprecipitationCysteine EndopeptidasesCytokinesDiabetes Mellitus, Type 1Diabetes Mellitus, Type 2Diet, High-FatEndopeptidasesEnzyme-Linked Immunosorbent AssayFlow CytometryGene Knockout TechniquesGlucose IntoleranceHyperglycemiaImmunoblottingImmunoprecipitationInflammationInsulin ResistanceInsulin-Secreting CellsIntracellular Signaling Peptides and ProteinsIslets of LangerhansMiceMutagenesis, Site-DirectedNF-kappa BPhenotypeReverse Transcriptase Polymerase Chain ReactionSmall Ubiquitin-Related Modifier ProteinsConceptsNF-κB activityAdipocyte dysfunctionCytokine productionType 1 diabetes progressionPancreatic isletsType 1 diabetes mellitusMild insulin resistanceDevelopment of diabetesType 2 diabetes phenotypeΒ-cell damageDirect cytotoxic effectNF-κB inhibitorAdipocyte-specific deletionProgression of T1DMDiabetes mellitusGlucose intolerancePancreatic inflammationProinflammatory cytokinesCCL5 expressionInsulin resistanceDiabetes progressionInflammatory responseNF-κBDiabetes phenotypeMice exhibitHerpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators
Guo YE, Oei T, Steitz JA. Herpesvirus saimiri MicroRNAs Preferentially Target Host Cell Cycle Regulators. Journal Of Virology 2015, 89: 10901-10911. PMID: 26292323, PMCID: PMC4621106, DOI: 10.1128/jvi.01884-15.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBinding SitesBlotting, WesternCallithrixCDC2 Protein KinaseCell Cycle ProteinsEndoplasmic Reticulum Chaperone BiPHeat-Shock ProteinsHEK293 CellsHerpesvirus 2, SaimiriineHigh-Throughput Nucleotide SequencingHumansImmunoprecipitationLuciferasesMicroRNAsPhosphorylationRNA, MessengerT-LymphocytesConceptsHost cell cycle regulatorsViral miRNAsCell cycle regulatorsHerpesvirus saimiriMRNA targetsCycle regulatorsProtein-coding genesPre-miRNA hairpinsCross-linking immunoprecipitationGene ontology analysisHigh-throughput sequencingOpen reading frameOncogenic Herpesvirus saimiriCyclin-dependent kinasesP300 transcriptional coactivatorCell cycle progressionKey negative regulatorMarmoset T cellsHITS-CLIPRepresses expressionOntology analysisTranscriptional coactivatorViral life cyclePrimary transcriptCellular transformationThe host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends
Xie M, Zhang W, Shu MD, Xu A, Lenis DA, DiMaio D, Steitz JA. The host Integrator complex acts in transcription-independent maturation of herpesvirus microRNA 3′ ends. Genes & Development 2015, 29: 1552-1564. PMID: 26220997, PMCID: PMC4526738, DOI: 10.1101/gad.266973.115.Peer-Reviewed Original ResearchConceptsEnd processing signalsSmall nuclear RNAProximity ligation assayEnd processingPre-miRNAsHerpesvirus saimiriPre-miRNA hairpinsRNA-protein interactionsSitu proximity ligation assayIntegrator complexMiRNA 3MiRNA biogenesisSnRNA 3Primary miRNAMiRNA hairpinsIntegrator activityNuclear RNASequence downstreamOncogenic γ-herpesvirusesRescue experimentsLigation assayVivo knockdownComplex actsΓ-herpesvirusesHairpinPhosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication
Avey D, Tepper S, Li W, Turpin Z, Zhu F. Phosphoproteomic Analysis of KSHV-Infected Cells Reveals Roles of ORF45-Activated RSK during Lytic Replication. PLOS Pathogens 2015, 11: e1004993. PMID: 26133373, PMCID: PMC4489790, DOI: 10.1371/journal.ppat.1004993.Peer-Reviewed Original ResearchMeSH KeywordsBlotting, WesternCell LineGene Expression Regulation, ViralGene Knockout TechniquesHerpesviridae InfectionsHerpesvirus 8, HumanHost-Parasite InteractionsHumansImmediate-Early ProteinsImmunoprecipitationMass SpectrometryPhosphorylationProteomicsReal-Time Polymerase Chain ReactionReverse Transcriptase Polymerase Chain ReactionRibosomal Protein S6 Kinases, 90-kDaTransfectionVirus ReplicationConceptsKaposi's Sarcoma-Associated HerpesvirusKSHV lytic replicationProgeny virion productionKSHV ORF45Putative substratesRSK activityExtracellular signal-regulated kinase (ERK) mitogen-activated protein kinase (MAPK) pathwayGene expressionEfficient KSHV lytic replicationLytic replicationP90 ribosomal S6 kinaseMitogen-activated protein kinase pathwayRSK-dependent phosphorylationHost cell machineryRibosomal S6 kinaseProtein kinase pathwayVirion productionActivation of RSKComplex secondary structureKSHV lytic gene expressionTranscriptional regulatorsDifferential phosphorylationLytic gene expressionCellular genesCell machineryDownregulation of the Ubiquitin Ligase RNF125 Underlies Resistance of Melanoma Cells to BRAF Inhibitors via JAK1 Deregulation
Kim H, Frederick DT, Levesque MP, Cooper ZA, Feng Y, Krepler C, Brill L, Samuels Y, Hayward NK, Perlina A, Piris A, Zhang T, Halaban R, Herlyn MM, Brown KM, Wargo JA, Dummer R, Flaherty KT, Ronai Z. Downregulation of the Ubiquitin Ligase RNF125 Underlies Resistance of Melanoma Cells to BRAF Inhibitors via JAK1 Deregulation. Cell Reports 2015, 11: 1458-1473. PMID: 26027934, PMCID: PMC4681438, DOI: 10.1016/j.celrep.2015.04.049.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCell Line, TumorChromatography, LiquidDown-RegulationDrug Resistance, NeoplasmEnzyme InhibitorsFemaleHeterograftsHumansImmunoblottingImmunohistochemistryImmunoprecipitationJanus Kinase 1Mass SpectrometryMelanomaMiceMice, NudeProto-Oncogene Proteins B-rafRNA, Small InterferingTransfectionUbiquitin-Protein LigasesConceptsBRAF inhibitorsRTK expressionReceptor tyrosine kinasesRemarkable clinical responsesBRAFi-resistant melanomasInhibition of JAK1BRAFi-resistant tumorsClinical responseCombination therapyMost tumorsBRAF mutationsTumor specimensVivo xenograftsBRAFi resistanceMelanoma cellsElevated expressionMelanomaEGFRAdaptive resistanceTumorsRNF125MITF expressionTyrosine kinaseJAK1Downregulation
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