2024
Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser.
Jensen C, Sumner J, Kleinstein S, Hoehn K. Inferring B Cell Phylogenies from Paired H and L Chain BCR Sequences with Dowser. The Journal Of Immunology 2024, 212: 1579-1588. PMID: 38557795, PMCID: PMC11073909, DOI: 10.4049/jimmunol.2300851.Peer-Reviewed Original ResearchMeSH KeywordsB-LymphocytesHumansImmunoglobulin Heavy ChainsImmunoglobulin Light ChainsMutationPhylogenyReceptors, Antigen, B-CellSingle-Cell AnalysisConceptsPhylogenetic treeL chainsBranch lengthsBCR sequencesTree-building methodsSingle-cell sequencing dataHistory of mutationsSingle-cell sequencingPhylogenetic methodsSequence dataSequencing technologiesL chain sequencesTree accuracyEvolutionary processSingle-cellPhylogenyImmune responseSomatic hypermutationSequenceClonesMutationsB cell clonesHuman immune responseTreesBCR
2023
IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data
Peres A, Lees W, Rodriguez O, Lee N, Polak P, Hope R, Kedmi M, Collins A, Ohlin M, Kleinstein S, Watson C, Yaari G. IGHV allele similarity clustering improves genotype inference from adaptive immune receptor repertoire sequencing data. Nucleic Acids Research 2023, 51: e86-e86. PMID: 37548401, PMCID: PMC10484671, DOI: 10.1093/nar/gkad603.Peer-Reviewed Original Research
2020
Position-Dependent Differential Targeting of Somatic Hypermutation
Zhou JQ, Kleinstein SH. Position-Dependent Differential Targeting of Somatic Hypermutation. The Journal Of Immunology 2020, 205: 3468-3479. PMID: 33188076, PMCID: PMC7726104, DOI: 10.4049/jimmunol.2000496.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputer SimulationHumansImmunoglobulin Heavy ChainsModels, GeneticNucleotide MotifsSomatic Hypermutation, ImmunoglobulinConceptsSomatic hypermutationSHM targetingIg sequencesSame DNA motifTranscription start siteAllele-specific effectsInfluence of selectionGene familyVariable gene familiesDNA motifsSequence neighborhoodError-prone repairStart siteAb diversityDNA lesionsDifferential targetingUnique motifMotifSequenceTargetingHypermutationEffective humoral immunityIntrinsic biasesAffinity maturationLarge collection
2019
Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships.
Zhou JQ, Kleinstein SH. Cutting Edge: Ig H Chains Are Sufficient to Determine Most B Cell Clonal Relationships. The Journal Of Immunology 2019, 203: 1687-1692. PMID: 31484734, PMCID: PMC6865802, DOI: 10.4049/jimmunol.1900666.Peer-Reviewed Original ResearchInferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming
Ohlin M, Scheepers C, Corcoran M, Lees WD, Busse CE, Bagnara D, Thörnqvist L, Bürckert JP, Jackson KJL, Ralph D, Schramm CA, Marthandan N, Breden F, Scott J, Matsen F, Greiff V, Yaari G, Kleinstein SH, Christley S, Sherkow JS, Kossida S, Lefranc MP, van Zelm MC, Watson CT, Collins AM. Inferred Allelic Variants of Immunoglobulin Receptor Genes: A System for Their Evaluation, Documentation, and Naming. Frontiers In Immunology 2019, 10: 435. PMID: 30936866, PMCID: PMC6431624, DOI: 10.3389/fimmu.2019.00435.Peer-Reviewed Original ResearchMeSH KeywordsAllelesBase SequenceDatabases, GeneticDatasets as TopicGene LibraryGenes, ImmunoglobulinGenetic VariationGerm-Line MutationHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionPolymerase Chain ReactionSequence AlignmentSequence Homology, Nucleic AcidTerminology as TopicV(D)J RecombinationVDJ ExonsConceptsGene databaseInternational ImMunoGeneTics information systemAdaptive immune receptor repertoire sequencingLymphocyte receptor genesAllelic variantsGermline genesReceptor geneAIRR CommunityVertebrate speciesGenetic variationIg diversityAIRR-seq dataJ genesIg genesAllelic sequencesGenesIGHV genesEffector moleculesUnprecedented insightsB-cell lineageBiological interpretationT cell receptorReference databaseGene variationRepertoire studies
2016
A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data
Cui A, Di Niro R, Vander Heiden JA, Briggs AW, Adams K, Gilbert T, O'Connor KC, Vigneault F, Shlomchik MJ, Kleinstein SH. A Model of Somatic Hypermutation Targeting in Mice Based on High-Throughput Ig Sequencing Data. The Journal Of Immunology 2016, 197: 3566-3574. PMID: 27707999, PMCID: PMC5161250, DOI: 10.4049/jimmunol.1502263.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsB-LymphocytesCells, CulturedClonal Selection, Antigen-MediatedDNA RepairFemaleGerminal CenterHigh-Throughput Nucleotide SequencingHumansImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionMiceMice, Inbred BALB CMice, TransgenicModels, GeneticMutationMutation RateSomatic Hypermutation, ImmunoglobulinConceptsSpecific DNA motifsSimilar biological processesObserved mutation patternDNA repair activityIg sequencesNonfunctional sequencesDNA motifsMutation patternsHigh mutation frequencySelection pressureUnselected mutationsSequencing dataBiological processesFunctional sequencesRepair activityTransition mutationsSomatic hypermutation patternsGerminal center B cellsSomatic hypermutationNext-generation methodsHypermutation patternsMutation frequencyMutationsSequenceMotifLong-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection
Bohannon C, Powers R, Satyabhama L, Cui A, Tipton C, Michaeli M, Skountzou I, Mittler RS, Kleinstein SH, Mehr R, Lee FE, Sanz I, Jacob J. Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection. Nature Communications 2016, 7: 11826. PMID: 27270306, PMCID: PMC4899631, DOI: 10.1038/ncomms11826.Peer-Reviewed Original ResearchMeSH KeywordsAdoptive TransferAmino Acid MotifsAnimalsAntigensComplementarity Determining RegionsCytidine DeaminaseGerminal CenterImmunityImmunoglobulin Heavy ChainsImmunoglobulin MMice, Inbred C57BLMutationNeutralization TestsOrthomyxoviridaeOrthomyxoviridae InfectionsPlasma CellsSomatic Hypermutation, ImmunoglobulinSpleenConceptsIgM plasma cellsIgG plasma cellsPlasma cellsGerminal centersBone marrowLethal virus challengeProtective host immunitySomatic mutationsActivation-induced cytidine deaminaseHumoral immunityProtective antibodiesVirus challengeLong-term protectionHost immunityB cellsAffinity maturationMarrowLifelong sourceImmunityAntibodiesCellsCytidine deaminaseMutationsReplacement mutationsSpleen
2015
The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales
Yaari G, Benichou JI, Heiden J, Kleinstein SH, Louzoun Y. The mutation patterns in B-cell immunoglobulin receptors reflect the influence of selection acting at multiple time-scales. Philosophical Transactions Of The Royal Society B Biological Sciences 2015, 370: 20140242. PMID: 26194756, PMCID: PMC4528419, DOI: 10.1098/rstb.2014.0242.Peer-Reviewed Original ResearchMeSH KeywordsAntibody AffinityAntibody DiversityB-LymphocytesCell LineageClonal Selection, Antigen-MediatedComplementarity Determining RegionsGenes, ImmunoglobulinHumansImmunoglobulin Heavy ChainsImmunoglobulin Variable RegionModels, GeneticModels, ImmunologicalMutationReceptors, Antigen, B-CellSomatic Hypermutation, ImmunoglobulinTime FactorsConceptsLineage treesPositive selectionStrong selection pressureLong-term selectionInfluence of selectionGene familyVariable gene familiesComplementarity determining regionsClone membersMutation patternsSelection pressureB cell populationsImmunoglobulin genesB cellsFramework regionsSomatic hypermutationSomatic mutationsAffinity maturationMutationsClone sizeMaturation processLong trunkAffinity maturation processSignificant diversityMultiple roundsResponsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease
Di Niro R, Snir O, Kaukinen K, Yaari G, Lundin K, Gupta N, Kleinstein S, Cols M, Cerutti A, Mäki M, Shlomchik M, Sollid L. Responsive population dynamics and wide seeding into the duodenal lamina propria of transglutaminase-2-specific plasma cells in celiac disease. Mucosal Immunology 2015, 9: 254-264. PMID: 26153762, PMCID: PMC4703456, DOI: 10.1038/mi.2015.57.Peer-Reviewed Original ResearchMeSH KeywordsAutoantibodiesBiopsyCeliac DiseaseCell CountDiet, Gluten-FreeDuodenumGene Expression RegulationGlutensGTP-Binding ProteinsHumansImmunoglobulin Heavy ChainsIntestinal MucosaLaser Capture MicrodissectionPlasma CellsProtein Glutamine gamma Glutamyltransferase 2Sequence Analysis, DNATransglutaminasesConceptsTG2-specific plasma cellsPlasma cellsCeliac diseaseLamina propriaTransglutaminase 2Antibody-mediated diseasesGluten-free dietSerum antibody levelsSerum antibody titersB cell responsesAntigen-specific antibodiesDuodenal lamina propriaGluten exposureUntreated patientsAntibody levelsAntibody titersCeliac lesionAntigen stainingSubepithelial layerAntibody productionIndividual biopsiesRepertoire analysisDiseaseGut tissueAntibodies
2014
Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis
Wu YC, James LK, Vander Heiden J, Uduman M, Durham SR, Kleinstein SH, Kipling D, Gould HJ. Influence of seasonal exposure to grass pollen on local and peripheral blood IgE repertoires in patients with allergic rhinitis. Journal Of Allergy And Clinical Immunology 2014, 134: 604-612. PMID: 25171866, PMCID: PMC4151999, DOI: 10.1016/j.jaci.2014.07.010.Peer-Reviewed Original ResearchConceptsHealthy control subjectsNasal biopsy specimensAllergic rhinitisControl subjectsImmunoglobulin heavy chain geneBiopsy specimensIgE repertoireAllergic diseasesPeripheral bloodOngoing germinal center reactionsClonal relatednessNatural pollen exposureSeasonal allergic rhinitisPollen seasonRespiratory allergic diseasesIgH sequencesAntigen-driven selectionGerminal center reactionGrass pollen seasonBlood IgEAtopic statusIgG classAntibody classPatientsPollen exposure
2012
Quantifying selection in high-throughput Immunoglobulin sequencing data sets
Yaari G, Uduman M, Kleinstein SH. Quantifying selection in high-throughput Immunoglobulin sequencing data sets. Nucleic Acids Research 2012, 40: e134-e134. PMID: 22641856, PMCID: PMC3458526, DOI: 10.1093/nar/gks457.Peer-Reviewed Original ResearchConceptsQuantifying selectionDifferent selection pressuresHigh-throughput immunoglobulinSomatic hypermutationNext-generation sequencing dataDNA mutation patternsSomatic mutation patternsGroups of sequencesAntigen-driven selection processMutation patternsSequence dataSelection pressureSequencing dataB cell affinity maturationB-cell cancersNegative selection