2021
Single cell epigenetic visualization assay
Kint S, Van Criekinge W, Vandekerckhove L, De Vos WH, Bomsztyk K, Krause DS, Denisenko O. Single cell epigenetic visualization assay. Nucleic Acids Research 2021, 49: e43-e43. PMID: 33511400, PMCID: PMC8096246, DOI: 10.1093/nar/gkab009.Peer-Reviewed Original ResearchMeSH Keywords5-MethylcytosineAcetylationCell LineDNA MethylationEarly Growth Response Protein 1Epigenesis, GeneticEpigenomicsFemaleGene Expression RegulationGene SilencingHistonesHIV-1HumansImage Processing, Computer-AssistedIn Situ Hybridization, FluorescenceProvirusesReal-Time Polymerase Chain ReactionRNA, Long NoncodingSingle-Cell AnalysisConceptsEpigenetic marksEpigenetic statusGene allelesFemale somatic cellsCurrent sequencing approachesGene of interestGene-specific oligonucleotidesQuantitative fluorescent readoutTranscription stateRNA FISHHuman cell linesSomatic cellsTranscription statusTarget genesSequencing approachH3K9ac levelsDifferent genesGenesIndividual cellsAntibody-conjugated alkaline phosphataseDNA oligosSingle cellsCell linesSame cellsFluorescent readout
2019
Promoters to Study Vascular Smooth Muscle
Chakraborty R, Saddouk FZ, Carrao AC, Krause DS, Greif DM, Martin KA. Promoters to Study Vascular Smooth Muscle. Arteriosclerosis Thrombosis And Vascular Biology 2019, 39: 603-612. PMID: 30727757, PMCID: PMC6527360, DOI: 10.1161/atvbaha.119.312449.Peer-Reviewed Original ResearchMeSH KeywordsActinsAnimalsCell LineCell LineageCell TransdifferentiationGene Expression RegulationGene Knockout TechniquesGene TargetingHumansMiceMicrofilament ProteinsMuscle ProteinsMuscle, Smooth, VascularMyocytes, Smooth MuscleMyofibroblastsMyosin Heavy ChainsNeovascularization, PathologicNeovascularization, PhysiologicPhenotypePromoter Regions, GeneticRecombinant Fusion ProteinsConceptsSmooth muscle cellsCre driver linesDiversity of phenotypesMuscle cell typesVisceral smooth muscle cellsSMC transdifferentiationActa2 promoterRemarkable plasticityExciting new eraSMC functionCell typesCre linesEmbryonic heartExciting discoveriesPhenotypeMuscle cellsPerivascular adipocytesPromoterVascular smooth muscleNonmuscular cellsExpressionMyeloid cellsCardiovascular phenotypesCellsBlood vessel wallSingle-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation
Wang N, Zheng J, Chen Z, Liu Y, Dura B, Kwak M, Xavier-Ferrucio J, Lu YC, Zhang M, Roden C, Cheng J, Krause DS, Ding Y, Fan R, Lu J. Single-cell microRNA-mRNA co-sequencing reveals non-genetic heterogeneity and mechanisms of microRNA regulation. Nature Communications 2019, 10: 95. PMID: 30626865, PMCID: PMC6327095, DOI: 10.1038/s41467-018-07981-6.Peer-Reviewed Original ResearchConceptsSame single cellMicroRNA-mRNASingle cellsGenome-scale analysisNon-genetic cellNon-genetic heterogeneityMultiple omic profilesGenomic approachesMicroRNA regulationMolecular regulationTarget mRNAsExpression variabilityCellular pathwaysRegulatory relationshipsLevels of microRNAsIntercellular heterogeneityOmics profilesIntercellular variabilityCell heterogeneityMRNA profilesMicroRNAsMRNACellsRegulationExpression
2018
The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification
Lu YC, Sanada C, Xavier-Ferrucio J, Wang L, Zhang PX, Grimes HL, Venkatasubramanian M, Chetal K, Aronow B, Salomonis N, Krause DS. The Molecular Signature of Megakaryocyte-Erythroid Progenitors Reveals a Role for the Cell Cycle in Fate Specification. Cell Reports 2018, 25: 2083-2093.e4. PMID: 30463007, PMCID: PMC6336197, DOI: 10.1016/j.celrep.2018.10.084.Peer-Reviewed Original ResearchMeSH KeywordsBasic Helix-Loop-Helix Leucine Zipper Transcription FactorsCell CycleCell LineageGene Expression RegulationGene Regulatory NetworksHEK293 CellsHigh-Throughput Nucleotide SequencingHumansMegakaryocyte-Erythroid Progenitor CellsProto-Oncogene Proteins c-mycReproducibility of ResultsSignal TransductionTranscription, GeneticTumor Suppressor Protein p53ConceptsMegakaryocytic-erythroid progenitorsCommon myeloid progenitorsTranscription factorsCell cycleSingle-cell RNA sequencingRegulatory transcription factorsMegakaryocyte-erythroid progenitorsCell cycle regulatorsCell cycle activationFate specificationLineage specificationE lineageMalignant disease statesGenetic manipulationRNA sequencingE progenitorsErythroid maturationCycle regulatorsDifferential expressionHuman cellsHealthy human cellsCycle activationMegakaryocyte progenitorsMolecular signaturesMyeloid progenitors
2017
SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume
Zou S, Teixeira AM, Kostadima M, Astle WJ, Radhakrishnan A, Simon LM, Truman L, Fang JS, Hwa J, Zhang PX, van der Harst P, Bray PF, Ouwehand WH, Frontini M, Krause DS. SNP in human ARHGEF3 promoter is associated with DNase hypersensitivity, transcript level and platelet function, and Arhgef3 KO mice have increased mean platelet volume. PLOS ONE 2017, 12: e0178095. PMID: 28542600, PMCID: PMC5441597, DOI: 10.1371/journal.pone.0178095.Peer-Reviewed Original ResearchConceptsExpression quantitative lociMK maturationGene expressionRho guanine exchange factorsHuman megakaryocytesGenome-wide association studiesDNase I hypersensitive regionGuanine exchange factorHuman genetic studiesExchange factorReporter mouse modelDNase hypersensitivityQuantitative lociPlatelet traitsMK developmentTranscript levelsCausal SNPsHypersensitive regionARHGEF3Human phenotypesAssociation studiesGenetic studiesHematopoietic subpopulationsGenetic variantsSNPs
2016
The Wnt Antagonist Dickkopf-1 Promotes Pathological Type 2 Cell-Mediated Inflammation
Chae WJ, Ehrlich AK, Chan PY, Teixeira AM, Henegariu O, Hao L, Shin JH, Park JH, Tang WH, Kim ST, Maher SE, Goldsmith-Pestana K, Shan P, Hwa J, Lee PJ, Krause DS, Rothlin CV, McMahon-Pratt D, Bothwell AL. The Wnt Antagonist Dickkopf-1 Promotes Pathological Type 2 Cell-Mediated Inflammation. Immunity 2016, 44: 246-258. PMID: 26872695, PMCID: PMC4758884, DOI: 10.1016/j.immuni.2016.01.008.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, DermatophagoidesAntigens, ProtozoanAsthmaBlood PlateletsCell DifferentiationCells, CulturedCytokinesExtracellular Signal-Regulated MAP KinasesGene Expression RegulationHumansInflammationIntercellular Signaling Peptides and ProteinsLeishmania majorLeishmaniasis, CutaneousMiceMice, Inbred BALB CMice, Inbred C57BLMice, TransgenicModels, AnimalPyroglyphidaeSignal TransductionTh2 CellsTOR Serine-Threonine KinasesWnt ProteinsConceptsCell-mediated inflammationTh2 cell cytokine productionCell cytokine productionLeukocyte-platelet aggregatesLeukocyte infiltrationDkk-1Cytokine productionT helper 2 cellsLeishmania major infectionHouse dust miteTranscription factor c-MafAllergen challengeMajor infectionDust miteImmune responseDickkopf-1Parasitic infectionsGATA-3Pathological roleFunctional inhibitionInflammationC-MafP38 MAPKInfiltrationInfection
2012
ProxTom Lymphatic Vessel Reporter Mice Reveal Prox1 Expression in the Adrenal Medulla, Megakaryocytes, and Platelets
Truman LA, Bentley KL, Smith EC, Massaro SA, Gonzalez DG, Haberman AM, Hill M, Jones D, Min W, Krause DS, Ruddle NH. ProxTom Lymphatic Vessel Reporter Mice Reveal Prox1 Expression in the Adrenal Medulla, Megakaryocytes, and Platelets. American Journal Of Pathology 2012, 180: 1715-1725. PMID: 22310467, PMCID: PMC3349900, DOI: 10.1016/j.ajpath.2011.12.026.Peer-Reviewed Original ResearchMeSH KeywordsAdrenal MedullaAnimalsBlood PlateletsCells, CulturedCytoplasmEndothelial CellsGene Expression RegulationGenotypeGlycoproteinsHomeodomain ProteinsLuminescent ProteinsLymph NodesLymphatic VesselsMegakaryocytesMembrane Transport ProteinsMiceMice, Inbred C57BLMice, TransgenicMicroscopy, FluorescenceTumor Cells, CulturedTumor Suppressor ProteinsConceptsLymph nodesLymphatic vesselsAdrenal medullaExpression of Prox1Tumor metastasisHigh endothelial venulesProx1 expressionTwo-photon laser scanning microscopyTransplant rejectionDentate gyrusEndothelial venulesAntigen presentationC57BL/6 backgroundTransgenic miceLipid metabolismMiceNeuroendocrine cellsAdult liverNovel siteMetastasisMedullaStudy of diseasesLiving mouseUnknown rolePotential utility
2009
Role for MKL1 in megakaryocytic maturation
Cheng EC, Luo Q, Bruscia EM, Renda MJ, Troy JA, Massaro SA, Tuck D, Schulz V, Mane SM, Berliner N, Sun Y, Morris SW, Qiu C, Krause DS. Role for MKL1 in megakaryocytic maturation. Blood 2009, 113: 2826-2834. PMID: 19136660, PMCID: PMC2661865, DOI: 10.1182/blood-2008-09-180596.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBlood Cell CountBone MarrowCell DifferentiationCell Line, TumorCells, CulturedDNA-Binding ProteinsGene Expression ProfilingGene Expression RegulationHumansLeukemia, Erythroblastic, AcuteMegakaryocytesMiceMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisOncogene Proteins, FusionPloidiesRecombinant Fusion ProteinsRNA InterferenceRNA, Small InterferingSerum Response FactorThrombocytopeniaThrombopoiesisThrombopoietinTrans-ActivatorsConceptsMegakaryoblastic leukemia 1Reduced platelet countsSerum response factorMegakaryocytic differentiationPeripheral bloodPlatelet countMKL1 expressionMegakaryoblastic leukemiaBone marrow megakaryocytesMuscle cellsPresence of thrombopoietinPhysiologic maturationHuman erythroleukemia cell lineIncreased numberMarrow megakaryocytesCell linesErythroleukemia cell lineMegakaryocytesMegakaryocytic maturationDifferentiated muscle cellsOverexpressionConcurrent increaseMuscle differentiationCellsMaturation
2008
Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids
Chin JY, Kuan JY, Lonkar PS, Krause DS, Seidman MM, Peterson KR, Nielsen PE, Kole R, Glazer PM. Correction of a splice-site mutation in the beta-globin gene stimulated by triplex-forming peptide nucleic acids. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 13514-13519. PMID: 18757759, PMCID: PMC2533221, DOI: 10.1073/pnas.0711793105.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceCell LineGene Expression RegulationGenomeGlobinsHumansMolecular Sequence DataMutationPeptide Nucleic AcidsRNA Splice SitesConceptsBeta-globin geneEndogenous beta-globin locusSplice site mutationHuman cellsPrimary hematopoietic progenitor cellsBeta-globin locusAltered helical structureHuman beta-globin geneSingle base pair changeSingle base-pair modificationTriplex-forming peptide nucleic acidsDonor DNA moleculesBase pair changesCell cycle stageDisease-related genesDonor DNA fragmentsNucleic acidsProper splicingSite-specific bindingSite-specific modificationMammalian cellsHematopoietic progenitor cellsDNA repairSecond intronGene locusHepatocyte Nuclear Factor‐1 as Marker of Epithelial Phenotype Reveals Marrow‐Derived Hepatocytes, but Not Duct Cells, After Liver Injury in Mice
Swenson ES, Guest I, Ilic Z, Mazzeo‐Helgevold M, Lizardi P, Hardiman C, Sell S, Krause DS. Hepatocyte Nuclear Factor‐1 as Marker of Epithelial Phenotype Reveals Marrow‐Derived Hepatocytes, but Not Duct Cells, After Liver Injury in Mice. Stem Cells 2008, 26: 1768-1777. PMID: 18467658, PMCID: PMC2846397, DOI: 10.1634/stemcells.2008-0148.Peer-Reviewed Original ResearchConceptsMarrow-derived epithelial cellsHepatocyte nuclear factor 1Y chromosomeNuclear factor 1Ductal progenitor cellsLiver injuryInflammatory cellsFemale miceProgenitor cellsEpithelial cellsFactor 1Male bone marrowStable hematopoietic engraftmentBone marrow originColocalization of GFPNuclear markersBone marrow cellsDuctal progenitorsHematopoietic engraftmentChromosomesBone marrowMarrow originPancytokeratin stainingCholangiocyte phenotypeMarrow cells
2006
Prevention of mesangial sclerosis by bone marrow transplantation
Guo J, Ardito TA, Kashgarian M, Krause DS. Prevention of mesangial sclerosis by bone marrow transplantation. Kidney International 2006, 70: 910-913. PMID: 16850025, DOI: 10.1038/sj.ki.5001698.Peer-Reviewed Original ResearchConceptsBone marrow transplantationMesangial sclerosisMarrow transplantationUrinary albumin lossSimilar therapeutic effectsOnset of diseaseWild-type BMIntrarenal administrationRenal functionRenal histologyRenal diseaseDisease onsetRenal pathologyBM cellsTherapeutic effectEngraftment levelsRenal cellsAlbumin lossKidney samplesMiceSclerosisTransplantationUntreated controlsDiseaseAdministration
2004
Stromal Cell–Derived Factor-1α Plays a Critical Role in Stem Cell Recruitment to the Heart After Myocardial Infarction but Is Not Sufficient to Induce Homing in the Absence of Injury
Abbott JD, Huang Y, Liu D, Hickey R, Krause DS, Giordano FJ. Stromal Cell–Derived Factor-1α Plays a Critical Role in Stem Cell Recruitment to the Heart After Myocardial Infarction but Is Not Sufficient to Induce Homing in the Absence of Injury. Circulation 2004, 110: 3300-3305. PMID: 15533866, DOI: 10.1161/01.cir.0000147780.30124.cf.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBenzylaminesBone Marrow CellsBone Marrow TransplantationCell LineageCell MovementChemokine CXCL12Chemokines, CXCCyclamsFemaleGene Expression ProfilingGene Expression RegulationGenetic TherapyHeterocyclic CompoundsIntercellular Adhesion Molecule-1Matrix Metalloproteinase 9MiceMice, Inbred NODMice, SCIDMyocardial InfarctionMyocardiumReceptors, CXCR4Recombinant Fusion ProteinsStem Cell TransplantationStem CellsTransduction, GeneticVascular Cell Adhesion Molecule-1Vascular Endothelial Growth Factor AConceptsBone marrow-derived cellsStromal cell-derived factor-1alphaMyocardial infarctionBMDC recruitmentAdhesion molecule-1Molecule-1Recruitment of BMDCsInfarcted heartSerum SDF-1 levelsVascular cell adhesion molecule-1Intercellular adhesion molecule-1Stromal cell-derived factor-1αCell adhesion molecule-1Administration of AMD3100SDF-1/CXCR4 interactionMarrow-derived cellsSDF-1 levelsAbsence of MIVascular endothelial growth factorMatrix metalloproteinase-9Sham-operated controlsSDF-1 mRNAEndothelial growth factorAbsence of injuryQuantitative polymerase chain reaction
2002
Regulation of hematopoietic stem cell fate
Krause DS. Regulation of hematopoietic stem cell fate. Oncogene 2002, 21: 3262-3269. PMID: 12032767, DOI: 10.1038/sj.onc.1205316.Peer-Reviewed Original Research
2000
Regulation of CD34 transcription by Sp1 requires sites upstream and downstream of the transcription start site
Taranenko N, Krause D. Regulation of CD34 transcription by Sp1 requires sites upstream and downstream of the transcription start site. Experimental Hematology 2000, 28: 974-984. PMID: 10989198, DOI: 10.1016/s0301-472x(00)00492-6.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CD34Antigens, NuclearBinding SitesDNADNA HelicasesDNA MethylationDNA ProbesDNA-Binding ProteinsGene Expression RegulationGuanineKu AutoantigenMiceNuclear ProteinsPromoter Regions, GeneticSp1 Transcription FactorTranscription FactorsTranscription, GeneticTransfectionTumor Cells, CulturedUntranslated RegionsConceptsTranscription start sitePromoter activityCD34 promoterStart siteDrosophila S2 cellsHematopoietic cellsTranscription factor bindsDNA binding sitesElectromobility shift assaysSequence-specific mannerS2 cellsTranscriptional regulationMolecular regulationMethylation interferenceDeletion analysisEarly hematopoiesisNuclear proteinsRegulatory regionsFactor bindsShift assaysGene expressionUntranslated regionHematopoietic stemSp1CD34 transcription
1999
A nuclear factor Y (NFY) site positively regulates the human CD34 stem cell gene.
Radomska H, Satterthwaite A, Taranenko N, Narravula S, Krause D, Tenen D. A nuclear factor Y (NFY) site positively regulates the human CD34 stem cell gene. Blood 1999, 94: 3772-80. PMID: 10572091, DOI: 10.1182/blood.v94.11.3772.423k19_3772_3780.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, CD34Base SequenceBinding SitesCCAAT-Binding FactorGene Expression RegulationGenes, mybHematopoietic Stem CellsHumansMolecular Sequence DataTranscription FactorsConceptsHuman CD34 geneUntranslated regionCD34 geneC-MybPromoter activityCell-cycle regulated expressionMurine CD34 geneC-Myb binding sitesElectrophoretic mobility shift assaysNuclear factor Y (NF-Y) sitesTranscription factor NFYCCAAT box motifStem cell genesMobility shift assaysOptimal promoter activityReporter gene activityAntibody supershift experimentsEarly hematopoietic cellsTransient transfection experimentsBox motifCombinatorial actionGene activityPromoter functionOligonucleotide competitionCis elements
1997
Regulation of CD34 expression in differentiating M1 cells.
Krause DS, Kapadia SU, Raj NB, May WS. Regulation of CD34 expression in differentiating M1 cells. Experimental Hematology 1997, 25: 1051-61. PMID: 9293902.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsAntigens, CD34Base SequenceBinding SitesCell DifferentiationCells, CulturedDNA-Binding ProteinsDown-RegulationGene Expression RegulationGene Expression Regulation, DevelopmentalGene Expression Regulation, NeoplasticHematopoiesisLeukemia, MyeloidMiceMolecular Sequence DataNuclear ProteinsRNA, MessengerTranscription, GeneticConceptsTranscription initiation siteUntranslated regionPromoter activityHematopoietic stemCell type-specific expressionSecondary structureTATA-less promoterPromoter-luciferase reporter constructsFull promoter activityUpstream genomic DNAProgenitor cellsTranslation start siteMature blood cellsType-specific expressionOptimal promoter activityExtensive secondary structureP1 nuclease digestionCell-specific factorsTranscriptional initiationGene regulationTranscription factorsConsensus sitesStart siteRegulatory elementsTATA element
1996
CD34: Structure, Biology, and Clinical Utility
Krause D, Fackler M, Civin C, May W. CD34: Structure, Biology, and Clinical Utility. Blood 1996, 87: 1-13. PMID: 8547630, DOI: 10.1182/blood.v87.1.1.1.Peer-Reviewed Original ResearchAcute DiseaseAmino Acid SequenceAnimalsAntibodies, MonoclonalAntigens, CD34Antigens, NeoplasmBiomarkersCell AdhesionEndothelium, VascularFibroblastsGene Expression RegulationGenesHematopoietic Stem CellsHumansLeukemia, MyeloidMiceMolecular Sequence DataOrgan SpecificityProtein ConformationRNA Splicing