2022
Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain
Marsh SE, Walker AJ, Kamath T, Dissing-Olesen L, Hammond TR, de Soysa TY, Young AMH, Murphy S, Abdulraouf A, Nadaf N, Dufort C, Walker AC, Lucca LE, Kozareva V, Vanderburg C, Hong S, Bulstrode H, Hutchinson PJ, Gaffney DJ, Hafler DA, Franklin RJM, Macosko EZ, Stevens B. Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain. Nature Neuroscience 2022, 25: 306-316. PMID: 35260865, DOI: 10.1038/s41593-022-01022-8.Peer-Reviewed Original ResearchConceptsSingle-cell sequencing experimentsCell type diversitySingle-cell sequencingRNA-sequencing datasetsGene expression changesGene expression signaturesVivo gene expressionTranscriptional profilesGene expressionExpression changesSequencing experimentsGlial signaturesDownstream analysisExpression signaturesTissue typesSingle cell suspensionsOptimal cell yieldIntact tissueHuman tissuesCell yieldEnzymatic dissociationHuman samplesTissue digestionPostmortem human samplesTissueSingle-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19
Unterman A, Sumida TS, Nouri N, Yan X, Zhao AY, Gasque V, Schupp JC, Asashima H, Liu Y, Cosme C, Deng W, Chen M, Raredon MSB, Hoehn KB, Wang G, Wang Z, DeIuliis G, Ravindra NG, Li N, Castaldi C, Wong P, Fournier J, Bermejo S, Sharma L, Casanovas-Massana A, Vogels CBF, Wyllie AL, Grubaugh ND, Melillo A, Meng H, Stein Y, Minasyan M, Mohanty S, Ruff WE, Cohen I, Raddassi K, Niklason L, Ko A, Montgomery R, Farhadian S, Iwasaki A, Shaw A, van Dijk D, Zhao H, Kleinstein S, Hafler D, Kaminski N, Dela Cruz C. Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. Nature Communications 2022, 13: 440. PMID: 35064122, PMCID: PMC8782894, DOI: 10.1038/s41467-021-27716-4.Peer-Reviewed Original ResearchMeSH KeywordsAdaptive ImmunityAgedAntibodies, Monoclonal, HumanizedCD4-Positive T-LymphocytesCD8-Positive T-LymphocytesCells, CulturedCOVID-19COVID-19 Drug TreatmentFemaleGene Expression ProfilingGene Expression RegulationHumansImmunity, InnateMaleReceptors, Antigen, B-CellReceptors, Antigen, T-CellRNA-SeqSARS-CoV-2Single-Cell AnalysisConceptsProgressive COVID-19B cell clonesSingle-cell analysisT cellsImmune responseMulti-omics single-cell analysisCOVID-19Cell clonesAdaptive immune interactionsSevere COVID-19Dynamic immune responsesGene expressionSARS-CoV-2 virusAdaptive immune systemSomatic hypermutation frequenciesCellular effectsProtein markersEffector CD8Immune signaturesProgressive diseaseHypermutation frequencyProgressive courseClassical monocytesClonesImmune interactions
2015
Genetic basis of autoimmunity
Marson A, Housley WJ, Hafler DA. Genetic basis of autoimmunity. Journal Of Clinical Investigation 2015, 125: 2234-2241. PMID: 26030227, PMCID: PMC4497748, DOI: 10.1172/jci78086.Peer-Reviewed Original ResearchConceptsGenetic basisInterpretation of GWASMultiple genomic datasetsWide association studyCommon human autoimmune diseasesRelevant cell typesCellular conditionsCellular phenotypesGenomic datasetsGene expressionDense genotypingBiological pathwaysAssociation studiesHuman autoimmune diseasesNucleotide variantsCell typesAutoimmune diseasesPrimary immune cellsUnbiased viewMonogenic mutationsPolygenic risk factorsEssential mechanismComplex disorderEnvironmental factorsNovel diagnostics
2014
Monoallelic expression of the human FOXP2 speech gene
Adegbola AA, Cox GF, Bradshaw EM, Hafler DA, Gimelbrant A, Chess A. Monoallelic expression of the human FOXP2 speech gene. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 112: 6848-6854. PMID: 25422445, PMCID: PMC4460484, DOI: 10.1073/pnas.1411270111.Peer-Reviewed Original ResearchMeSH KeywordsApraxiasComparative Genomic HybridizationFemaleForkhead Transcription FactorsGene Expression ProfilingGene Expression Regulation, DevelopmentalGenes, X-LinkedHumansPolymorphism, Single NucleotideReverse Transcriptase Polymerase Chain ReactionSequence Analysis, DNASequence DeletionSpeechX Chromosome InactivationConceptsRandom monoallelic expressionMonoallelic expressionAllele-specific expressionNumber of genesHuman Mendelian disordersForkhead box P2 (FOXP2) geneP2 geneAutosomal genesMore genesAutosomal genomeX chromosomeGene expressionHaploinsufficiency phenotypeMendelian disordersGenesDevelopmental verbal dyspraxiaFOXP2 mutationsIntriguing possibilityFOXP2 geneExpressionRecent descriptionMutationsVerbal dyspraxiaAutosomesGenomeGenetic and epigenetic fine mapping of causal autoimmune disease variants
Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature 2014, 518: 337-343. PMID: 25363779, PMCID: PMC4336207, DOI: 10.1038/nature13835.Peer-Reviewed Original ResearchConceptsCausal variantsAutoimmune diseasesT cellsRegulatory T cellsNon-coding risk variantsT cell subsetsEnhancer-associated RNAsGenome-wide association studiesPrimary immune cellsCandidate causal variantsGene regulatory modelsImmune cellsImmune stimulationB cellsGene activationFine mappingTranscription factorsMaster regulatorHistone acetylationImmune differentiationSequence determinantsGene expressionAssociation studiesDiseaseHuman diseasesEnhanced suppressor function of TIM‐3+FoxP3+ regulatory T cells
Gautron A, Dominguez-Villar M, de Marcken M, Hafler DA. Enhanced suppressor function of TIM‐3+FoxP3+ regulatory T cells. European Journal Of Immunology 2014, 44: 2703-2711. PMID: 24838857, PMCID: PMC4165702, DOI: 10.1002/eji.201344392.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntigens, CDCell DifferentiationCTLA-4 AntigenFemaleForkhead Transcription FactorsGene Expression RegulationGranzymesHepatitis A Virus Cellular Receptor 2HumansInterleukin 1 Receptor Antagonist ProteinInterleukin-10InterleukinsLymphocyte Activation Gene 3 ProteinMaleMembrane ProteinsMiceMinor Histocompatibility AntigensReceptors, CCR6STAT3 Transcription FactorTh17 CellsT-Lymphocytes, RegulatoryConceptsTim-3 expressionRegulatory T cellsTreg cellsTim-3T cellsNatural regulatory T cellsMucin domain 3Number of TIMTh17 cell responseEffector T cellsT cell suppressionHuman Treg cellsT-cell immunoglobulinAnti-CD28 stimulationT cell differentiationSTAT-3 expressionPathogenic Th1Th17 cellsTc1 cellsImmune toleranceTh1 cellsLevel of expressionReduced gene expressionGene expressionSuppressor function
2010
Monocytes from Patients with Type 1 Diabetes Have Increased Gene Expression of Pro-inflammatory Cytokines or IL-10
Bradshaw E, Elyaman W, Raddassi K, Mousissian N, Greer A, Orban T, Gottlieb P, Kent S, Hafler D. Monocytes from Patients with Type 1 Diabetes Have Increased Gene Expression of Pro-inflammatory Cytokines or IL-10. Clinical Immunology 2010, 135: s19. DOI: 10.1016/j.clim.2010.03.061.Peer-Reviewed Original Research
2008
Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines
Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D. Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines. PLOS Genetics 2008, 4: e1000287. PMID: 19043577, PMCID: PMC2583954, DOI: 10.1371/journal.pgen.1000287.Peer-Reviewed Original ResearchConceptsLymphoblastoid cell linesBiological noiseGenome-wide significanceInternational HapMap ProjectDrug responseCell linesGenotype-phenotype relationshipsIndividual mRNAsEQTL SNPsGenetic analysisGene expressionHapMap projectHuman cellsHuman traitsNon-genetic factorsQTLMetabolic stateModel systemGenesMRNA levelsBaseline growth ratesSpurious associationsGrowth ratePharmacogenetic experimentsEQTLs
2000
Multiple differences in gene expression in regulatory Vα24JαQ T cells from identical twins discordant for type I diabetes
Wilson S, Kent S, Horton H, Hill A, Bollyky P, Hafler D, Strominger J, Byrne M. Multiple differences in gene expression in regulatory Vα24JαQ T cells from identical twins discordant for type I diabetes. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 7411-7416. PMID: 10840051, PMCID: PMC16559, DOI: 10.1073/pnas.120161297.Peer-Reviewed Original ResearchConceptsT cell receptor activationCell receptor activationT cellsTranscriptional consequencesDNA microarraysGene expressionActivation of cellsMyeloid lineageClonesMurine autoimmune diseaseInvariant T (MAIT) cellsIL-4 secretionType 1 diabetesAnti-CD3 stimulationT cell clonesIdentical twinsMRNA levelsReceptor activationCellsCell clonesAutoimmune diseasesActivationSecreting clonesQualitative defectsMultiple differences