2024
Stochastic modeling of a gene regulatory network driving B cell development in germinal centers
Koshkin A, Herbach U, Martínez M, Gandrillon O, Crauste F. Stochastic modeling of a gene regulatory network driving B cell development in germinal centers. PLOS ONE 2024, 19: e0301022. PMID: 38547073, PMCID: PMC10977792, DOI: 10.1371/journal.pone.0301022.Peer-Reviewed Original ResearchConceptsGene regulatory network structureGene regulatory networksGene expression dataExpression dataB cell differentiationSingle-cellAssociated with cell developmentGC B cell differentiationStages of B-cell differentiationB cell developmentSelection of B cellsGene regulationRegulatory networksTranscriptome dataSystems biologyHigh-affinity antibodiesRegulatory mechanismsCell developmentGenesAdaptive immune systemMRNA distributionPlasmablast stageGerminal centersDifferentiationImmune system
2022
Multi-Scale Modeling Recapitulates the Effect of Genetic Alterations Associated With Diffuse Large B-Cell Lymphoma in the Germinal Center Dynamics
Tejero E, Mao Q, Lashgari D, García-Valiente R, Robert P, Meyer-Hermann M, Martínez M, Guikema J, Hoefsloot H, van Kampen A. Multi-Scale Modeling Recapitulates the Effect of Genetic Alterations Associated With Diffuse Large B-Cell Lymphoma in the Germinal Center Dynamics. Frontiers In Systems Biology 2022, 2: 864690. DOI: 10.3389/fsysb.2022.864690.Peer-Reviewed Original ResearchDiffuse large B-cell lymphomaLarge B-cell lymphomaB-cell lymphoma 6B-cell lymphomaB lymphocyte-induced maturation protein-1B cell lymphoma 6 expressionInterferon regulatory factor 4B cellsGC reactionPC differentiationTranscription factor dynamicsPlasma cellsSubtype of non-Hodgkin lymphomaAccumulation of B cellsGC B cell phenotypeFactor kappa-light-chain-enhancer of activated B cellsNon-Hodgkin's lymphomaNuclear factor kappa-light-chain-enhancer of activated B cellsNuclear factor kappa-light-chain-enhancerB-cell phenotypeGC B cell populationB cell populationsGC B cellsB cell differentiationRegulatory factor 4
2020
Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts
Pélissier A, Akrout Y, Jahn K, Kuipers J, Klein U, Beerenwinkel N, Martínez M. Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts. Cells 2020, 9: 1448. PMID: 32532145, PMCID: PMC7349200, DOI: 10.3390/cells9061448.Peer-Reviewed Original ResearchConceptsClonal diversityB cell receptorSequence of nucleotidesEvolutionary phylogenetic treesGC dynamicsIn silico vaccine designPhylogenetic treeClonal dominanceAffinity to antigenB cell differentiationSpecialized compartmentsAntibody genesGenetic eventsInterclonal competitionClonal burstEvolutionary processB cell maturationIntracellular componentsB-cell variantsClonal dynamicsSomatic hypermutationB cellsIncreased affinityAffinity maturationGerminal centers
2019
A Probabilistic Model of the Germinal Center Reaction
Thomas M, Klein U, Lygeros J, Martínez M. A Probabilistic Model of the Germinal Center Reaction. Frontiers In Immunology 2019, 10: 689. PMID: 31001283, PMCID: PMC6456718, DOI: 10.3389/fimmu.2019.00689.Peer-Reviewed Original ResearchConceptsB cell differentiationMemory B cell differentiationSpecialized compartmentsAntibody genesPlasma cell differentiationFate selectionB cellsIndividual cell propertiesCell differentiationB cell maturationMolecular eventsEfficient stochastic simulationExtracellular dynamicsQuantitative stochastic modelMemory B cell formationAntigen affinityB cell formationGillespie algorithmDifferentiationCell propertiesCell productionMemory B cells