Featured Publications
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
Liu Y, Yang M, Deng Y, Su G, Enninful A, Guo CC, Tebaldi T, Zhang D, Kim D, Bai Z, Norris E, Pan A, Li J, Xiao Y, Halene S, Fan R. High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue. Cell 2020, 183: 1665-1681.e18. PMID: 33188776, PMCID: PMC7736559, DOI: 10.1016/j.cell.2020.10.026.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAutomationBrainCluster AnalysisDNA Barcoding, TaxonomicDNA, ComplementaryEmbryo, MammalianEyeFemaleGene Expression Regulation, DevelopmentalGenomicsHuman Umbilical Vein Endothelial CellsHumansMice, Inbred C57BLMicrofluidicsOrgan SpecificityReproducibility of ResultsRNA, MessengerSingle-Cell AnalysisTranscriptomeConceptsDeterministic barcodingNext-generation sequencingSingle-cell transcriptomesGene expression profilesMajor tissue typesDBiT-seqDNA barcodesDevelopmental biologyExpression profilesEarly organogenesisCancer biologyCell typesBarcodingTissue typesSequencingBarcodesBiologyRapid identificationSets of barcodesTranscriptomeParallel microfluidic channelsOrganogenesisEmbryosProteinTissue pixels
2017
Pediatric non–Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes
de Rooij JD, Branstetter C, Ma J, Li Y, Walsh MP, Cheng J, Obulkasim A, Dang J, Easton J, Verboon LJ, Mulder HL, Zimmermann M, Koss C, Gupta P, Edmonson M, Rusch M, Lim JY, Reinhardt K, Pigazzi M, Song G, Yeoh AE, Shih LY, Liang DC, Halene S, Krause DS, Zhang J, Downing JR, Locatelli F, Reinhardt D, van den Heuvel-Eibrink MM, Zwaan CM, Fornerod M, Gruber TA. Pediatric non–Down syndrome acute megakaryoblastic leukemia is characterized by distinct genomic subsets with varying outcomes. Nature Genetics 2017, 49: 451-456. PMID: 28112737, PMCID: PMC5687824, DOI: 10.1038/ng.3772.Peer-Reviewed Original Research
2016
Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors
Yang J, Tanaka Y, Seay M, Li Z, Jin J, Garmire LX, Zhu X, Taylor A, Li W, Euskirchen G, Halene S, Kluger Y, Snyder MP, Park IH, Pan X, Weissman SM. Single cell transcriptomics reveals unanticipated features of early hematopoietic precursors. Nucleic Acids Research 2016, 45: 1281-1296. PMID: 28003475, PMCID: PMC5388401, DOI: 10.1093/nar/gkw1214.Peer-Reviewed Original ResearchConceptsHematopoietic stem cellsPrecursor cellsInduction of anemiaInterferon response genesG2/M phaseEarly precursor cellsHomeostatic cellsStages of differentiationTranscription factorsSurface markersCell cycle progressionLong-term hematopoietic stem cellsSpecific augmentationAnemic miceMarked increaseEarly hematopoietic precursorsHematopoietic precursorsStem cellsCycle progressionM phaseSingle-cell transcriptomicsCellsCell differentiationHematopoietic stressLineage-specific transcription factorsCooperative Activity of GABP with PU.1 or C/EBPε Regulates Lamin B Receptor Gene Expression, Implicating Their Roles in Granulocyte Nuclear Maturation
Malu K, Garhwal R, Pelletier MG, Gotur D, Halene S, Zwerger M, Yang ZF, Rosmarin AG, Gaines P. Cooperative Activity of GABP with PU.1 or C/EBPε Regulates Lamin B Receptor Gene Expression, Implicating Their Roles in Granulocyte Nuclear Maturation. The Journal Of Immunology 2016, 197: 910-922. PMID: 27342846, PMCID: PMC5022553, DOI: 10.4049/jimmunol.1402285.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCCAAT-Enhancer-Binding ProteinsCell DifferentiationCell NucleusChromatin ImmunoprecipitationElectrophoretic Mobility Shift AssayGA-Binding Protein Transcription FactorGene Expression RegulationGranulocytesHEK293 CellsHematopoietic Stem CellsHumansImmunoblottingMiceMice, Inbred C57BLMutagenesis, Site-DirectedProto-Oncogene ProteinsReal-Time Polymerase Chain ReactionReceptors, Cytoplasmic and NuclearSignal TransductionTrans-ActivatorsConceptsLamin B receptorTranscription factorsGene expressionInner nuclear membrane proteinNuclear membrane proteinsFamily transcription factorsNuclear envelope proteinsETS transcription factorsExpression of genesRole of ETSTranscriptional regulatorsTranscriptional activationCombinatorial actionMembrane proteinsLBR geneEts siteEarly myeloid progenitorsCCAAT enhancerGABPSuch cooperative interactionsNeutrophil differentiationGenesMyeloid progenitorsReceptor gene expressionPromoter
2012
MKL1 and MKL2 play redundant and crucial roles in megakaryocyte maturation and platelet formation
Smith EC, Thon JN, Devine MT, Lin S, Schulz VP, Guo Y, Massaro SA, Halene S, Gallagher P, Italiano JE, Krause DS. MKL1 and MKL2 play redundant and crucial roles in megakaryocyte maturation and platelet formation. Blood 2012, 120: 2317-2329. PMID: 22806889, PMCID: PMC3447785, DOI: 10.1182/blood-2012-04-420828.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine DiphosphateAnimalsBleeding TimeBlood PlateletsBone Marrow CellsCells, CulturedCrosses, GeneticCytoplasmCytoskeletonGene Expression ProfilingHematopoiesisMegakaryocytesMiceMice, Inbred C57BLMice, KnockoutOligonucleotide Array Sequence AnalysisPlatelet ActivationThrombocytopeniaTrans-ActivatorsTranscription FactorsConceptsMegakaryocyte maturationPlatelet formationSerum response factorSerum response factor expressionMembrane organizationGene expressionMKL1MKL2Response factorDKO miceKO backgroundMegakaryocyte compartmentMegakaryocytesCritical roleMegakaryocyte ploidyExpressionMaturationKnockout miceFactor expressionCrucial roleHomologuesGenesMiceProlonged bleeding timeRole
2010
Different Roles of G Protein Subunits β1 and β2 in Neutrophil Function Revealed by Gene Expression Silencing in Primary Mouse Neutrophils*
Zhang Y, Tang W, Jones MC, Xu W, Halene S, Wu D. Different Roles of G Protein Subunits β1 and β2 in Neutrophil Function Revealed by Gene Expression Silencing in Primary Mouse Neutrophils*. Journal Of Biological Chemistry 2010, 285: 24805-24814. PMID: 20525682, PMCID: PMC2915716, DOI: 10.1074/jbc.m110.142885.Peer-Reviewed Original ResearchConceptsGene expressionShort hairpin RNAPrimary mouse neutrophilsHairpin RNADirectional cell migrationFluorescent marker proteinsMouse neutrophilsMouse bone marrow cellsHost innate immunityDouble knockdownExcellent systemIngested bacteriaCell migrationMarker proteinsDivergent rolesKnockdownHematopoietic cellsHematopoietic systemBone marrow cellsSubunits β1Retroviral vectorsInnate immunityBacterial phagocytosisRNAExpressionSerum response factor is an essential transcription factor in megakaryocytic maturation
Halene S, Gao Y, Hahn K, Massaro S, Italiano JE, Schulz V, Lin S, Kupfer GM, Krause DS. Serum response factor is an essential transcription factor in megakaryocytic maturation. Blood 2010, 116: 1942-1950. PMID: 20525922, PMCID: PMC3173990, DOI: 10.1182/blood-2010-01-261743.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBleeding TimeBlood PlateletsBone Marrow CellsCell DifferentiationCell LineageCells, CulturedCytoskeletonFemaleFlow CytometryGene Expression ProfilingLuminescent ProteinsMaleMegakaryocytesMiceMice, Inbred C57BLMice, KnockoutMice, TransgenicMicroscopy, Electron, TransmissionPlatelet CountPlatelet Factor 4Reverse Transcriptase Polymerase Chain ReactionSerum Response FactorThrombocytopeniaTranscription FactorsConceptsSerum response factorCytoskeletal genesTranscription factorsMADS-box transcription factorsRole of SRFNormal megakaryocyte maturationAbnormal actin distributionResponse factorEssential transcription factorNormal Mendelian frequencyMegakaryocyte developmentMuscle differentiationPF4-Cre miceStress fibersMegakaryocyte maturationMegakaryocytic maturationActin distributionMegakaryocytic lineageMendelian frequencyMegakaryocyte progenitorsVivo assaysCFU-MKGenesPlatelet productionCritical role
1999
Improved Expression in Hematopoietic and Lymphoid Cells in Mice After Transplantation of Bone Marrow Transduced With a Modified Retroviral Vector
Halene S, Wang L, Cooper R, Bockstoce D, Robbins P, Kohn D. Improved Expression in Hematopoietic and Lymphoid Cells in Mice After Transplantation of Bone Marrow Transduced With a Modified Retroviral Vector. Blood 1999, 94: 3349-3357. PMID: 10552944, PMCID: PMC9071851, DOI: 10.1182/blood.v94.10.3349.422k05_3349_3357.Peer-Reviewed Original ResearchMeSH Keywords3T3 CellsAnimalsBone Marrow TransplantationFemaleGene DosageGene ExpressionGene Transfer TechniquesGenetic TherapyGenetic VectorsGreen Fluorescent ProteinsHematopoietic Stem CellsLeukemia Virus, MurineLuminescent ProteinsLymphocytesMaleMiceMice, Inbred C57BLPolymerase Chain ReactionRetroviridaeTime FactorsTransduction, GeneticConceptsEnhanced green fluorescent proteinHematopoietic cellsMoMuLV LTRMammalian hematopoietic cellsMurine embryonic stem cellsStem cellsEmbryonic stem cellsRetroviral vectorsGreen fluorescent proteinMoloney murine leukemia virusMouse bone marrow transplant modelReliable gene expressionHematopoietic stem cellsStable gene transferMurine leukemia virusGene expressionMND vectorTransduction efficiencyFluorescent proteinCopy numberGene transferIndividual cellsAmount of proteinVector copy numberBone marrow transplant modelImmune response to green fluorescent protein: implications for gene therapy
Stripecke R, del Carmen Villacres M, Skelton D, Satake N, Halene S, Kohn D. Immune response to green fluorescent protein: implications for gene therapy. Gene Therapy 1999, 6: 1305-1312. PMID: 10455440, DOI: 10.1038/sj.gt.3300951.Peer-Reviewed Original ResearchConceptsCytotoxic T lymphocytesImmune responseDevelopment of CTLImmunodeficient Nu/Nu miceT cell immune responsesNu/nu miceAnti-leukemia responseTransplantable murine modelCell immune responsesT-cell lymphomaLeukemia cell vaccinesCo-express markersMajor histocompatibility complexCell vaccineDendritic cellsLeukemia vaccineImmunocompetent miceLeukemia challengeNu miceT lymphocytesImmune stimulationCell lymphomaMurine modelGene-modified cellsFlow cytometry
1998
Consistent, persistent expression from modified retroviral vectors in murine hematopoietic stem cells
Robbins P, Skelton D, Yu X, Halene S, Leonard E, Kohn D. Consistent, persistent expression from modified retroviral vectors in murine hematopoietic stem cells. Proceedings Of The National Academy Of Sciences Of The United States Of America 1998, 95: 10182-10187. PMID: 9707621, PMCID: PMC21482, DOI: 10.1073/pnas.95.17.10182.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBase SequenceBone Marrow TransplantationColony-Forming Units AssayDNA MethylationDNA PrimersDNA, RecombinantFemaleFounder EffectGene ExpressionGene Transfer TechniquesGenetic VectorsHematopoietic Stem CellsMaleMiceMice, Inbred C57BLMoloney murine leukemia virusRepetitive Sequences, Nucleic AcidRetroviridaeTransduction, GeneticTransplantation, IsogeneicVirus Integration