2024
nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework.
Gabernet G, Marquez S, Bjornson R, Peltzer A, Meng H, Aron E, Lee N, Jensen C, Ladd D, Polster M, Hanssen F, Heumos S, , Yaari G, Kowarik M, Nahnsen S, Kleinstein S. nf-core/airrflow: An adaptive immune receptor repertoire analysis workflow employing the Immcantation framework. PLOS Computational Biology 2024, 20: e1012265. PMID: 39058741, PMCID: PMC11305553, DOI: 10.1371/journal.pcbi.1012265.Peer-Reviewed Original ResearchImmcantation frameworkAIRR-seqAIRR-seq dataAdaptive immune receptor repertoire sequencingSingle-cell sequencing datasetsClonal inferenceSequencing errorsSequencing datasetsNextflow workflowClonal relationshipReceptor sequencesRepertoire sequencingHigh-throughput processingSequenceImmune challengeAnalysis workflowT-cell receptor sequencingNextflowB cellsSARS-CoV-2Experimental toolResponse to SARS-CoV-2Infectious diseases
2023
The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties
Jiang R, Roy B, Wu Q, Mohanty S, Nowak R, Shaw A, Kleinstein S, O’Connor K. The Plasma Cell Infiltrate Populating the Muscle Tissue of Patients with Inclusion Body Myositis Features Distinct B Cell Receptor Repertoire Properties. ImmunoHorizons 2023, 7: 310-322. PMID: 37171806, PMCID: PMC10579972, DOI: 10.4049/immunohorizons.2200078.Peer-Reviewed Original ResearchConceptsInclusion body myositisMemory B cellsCell infiltrateBody myositisB cellsIBM muscle biopsiesB-cell infiltratesPlasma cell infiltrateClass-switched IgGMuscle tissueAdaptive immune receptor repertoire sequencingHumoral responseHealthy controlsIgA isotypePlasma cellsCell repertoireMuscle biopsyInfiltratesDegenerative disordersDisease pathologyRepertoire sequencingSkeletal muscleDermatomyositisPolymyositisMyositis
2021
B Cell Mobilization, Dissemination, Fine Tuning of Local Antigen Specificity and Isotype Selection in Asthma
Ohm-Laursen L, Meng H, Hoehn KB, Nouri N, Jiang Y, Clouser C, Johnstone TG, Hause R, Sandhar BS, Upton NEG, Chevretton EB, Lakhani R, Corrigan CJ, Kleinstein SH, Gould HJ. B Cell Mobilization, Dissemination, Fine Tuning of Local Antigen Specificity and Isotype Selection in Asthma. Frontiers In Immunology 2021, 12: 702074. PMID: 34721376, PMCID: PMC8552043, DOI: 10.3389/fimmu.2021.702074.Peer-Reviewed Original ResearchConceptsLower respiratory tractRespiratory tractB cellsAtopic asthmaPlasma cellsCommon respiratory tract diseaseB-cell mobilizationNon-atopic controlsRespiratory tract mucosaUpper respiratory tractRespiratory tract diseaseOrgan-specific diseasesAntibody repertoireB cell clonesAdaptive immune receptor repertoire sequencingBronchial mucosaNasal mucosaTract diseaseCell mobilizationIsotype selectionAntigen specificityAdult volunteersMucosal surfacesImmune systemAsthma
2019
Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD−CD27− Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients
Fraussen J, Marquez S, Takata K, Beckers L, Montes Diaz G, Zografou C, Van Wijmeersch B, Villar LM, O'Connor KC, Kleinstein SH, Somers V. Phenotypic and Ig Repertoire Analyses Indicate a Common Origin of IgD−CD27− Double Negative B Cells in Healthy Individuals and Multiple Sclerosis Patients. The Journal Of Immunology 2019, 203: 1650-1664. PMID: 31391234, PMCID: PMC6736705, DOI: 10.4049/jimmunol.1801236.Peer-Reviewed Original ResearchConceptsDN B cellsDouble-negative B cellsMultiple sclerosis patientsMS patientsNegative B cellsHealthy controlsClass-switched memoryB cellsAdaptive immune receptor repertoire sequencingSclerosis patientsRepertoire sequencingFrequency of CD95Naive B cellsUnique differentiation pathwayLow CD5Proinflammatory characteristicsImmune agingCD38 expressionHealthy individualsPatientsFlow cytometryLow mutation loadCD27Repertoire analysisMaturation stateInferred 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
2018
AIRR Community Standardized Representations for Annotated Immune Repertoires
Vander Heiden J, Marquez S, Marthandan N, Bukhari SAC, Busse CE, Corrie B, Hershberg U, Kleinstein SH, Matsen F, Ralph DK, Rosenfeld AM, Schramm CA, Community T, Christley S, Laserson U. AIRR Community Standardized Representations for Annotated Immune Repertoires. Frontiers In Immunology 2018, 9: 2206. PMID: 30323809, PMCID: PMC6173121, DOI: 10.3389/fimmu.2018.02206.Peer-Reviewed Original ResearchLocal Clonal Diversification and Dissemination of B Lymphocytes in the Human Bronchial Mucosa
Ohm-Laursen L, Meng H, Chen J, Zhou JQ, Corrigan CJ, Gould HJ, Kleinstein SH. Local Clonal Diversification and Dissemination of B Lymphocytes in the Human Bronchial Mucosa. Frontiers In Immunology 2018, 9: 1976. PMID: 30245687, PMCID: PMC6137163, DOI: 10.3389/fimmu.2018.01976.Peer-Reviewed Original ResearchConceptsHumoral immune responseBronchial mucosaB cell repertoireHealthy subjectsAsthmatic patientsImmune responseCell repertoireAdaptive humoral immune responseB cell antibody productionFeatures of atopyB cell clonesHuman bronchial mucosaMucosal migrationAdaptive immune receptor repertoire sequencingAtopic asthmaAsthmatic individualsBronchial biopsiesRight lungPeripheral bloodDistal biopsiesAdjacent biopsiesLarge cohortB cellsB lymphocytesAntibody production