TCRβ Allelic Exclusion in Dynamical Models of V(D)J Recombination Based on Allele Independence This information is current as Etienne Farcot, Marie Bonnet, Sébastien Jaeger, Salvatore of October 1, 2021. Spicuglia, Bastien Fernandez and Pierre Ferrier J Immunol 2010; 185:1622-1632; Prepublished online 28 June 2010; doi: 10.4049/jimmunol.0904182 http://www.jimmunol.org/content/185/3/1622 Downloaded from Supplementary http://www.jimmunol.org/content/suppl/2010/06/28/jimmunol.090418 Material 2.DC1 http://www.jimmunol.org/ References This article cites 63 articles, 20 of which you can access for free at: http://www.jimmunol.org/content/185/3/1622.full#ref-list-1 Why The JI? Submit online. • Rapid Reviews! 30 days* from submission to initial decision • No Triage! 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The Journal of Immunology TCRb Allelic Exclusion in Dynamical Models of V(D)J Recombination Based on Allele Independence Etienne Farcot,*,1 Marie Bonnet,† Se´bastien Jaeger,† Salvatore Spicuglia,† Bastien Fernandez,* and Pierre Ferrier† Allelic exclusion represents a major aspect of TCRb gene assembly by V(D)J recombination in developing T lymphocytes. Despite recent progress, its comprehension remains problematic when confronted with experimental data. Existing models fall short in terms of incorporating into a unique distribution all the cell subsets emerging from the TCRb assembly process. To revise this issue, we propose dynamical, continuous-time Markov chain-based modeling whereby essential steps in the biological procedure (D-J and V-DJ rearrangements and feedback inhibition) evolve independently on the two TCRb alleles in every single cell while displaying random modes of initiation and duration. By selecting parameters via fitting procedures, we demonstrate the capacity of the model to offer accurate fractions of all distinct TCRb genotypes observed in studies using developing and mature T cells Downloaded from from wild-type or mutant mice. Selected parameters in turn afford relative duration for each given step, hence updating TCRb recombination distinctive timings. Overall, our dynamical modeling integrating allele independence and noise in recombination and feedback-inhibition events illustrates how the combination of these ingredients alone may enforce allelic exclusion at the TCRb locus. The Journal of Immunology, 2010, 185: 1622–1632. n developing T and B lymphocytes, allelic exclusion typically allelic exclusion continues to puzzle immunologists. For instance, restricts the assembly by V(D)J recombination of a pro- the mere fact that a small group (#5%) of allelically included http://www.jimmunol.org/ I ductively rearranged (in-frame) variable exon to only one al- abT cells carrying two productively rearranged (VDJ+/VDJ+) lele of, respectively, TCR and Ig genes. The resulting allelically TCRb alleles eventually develop alongside the overwhelming mass excluded (e.g., abT cells) commonly display a TCRb genotype ($95%) of allelically excluded cells still eludes a comprehensive made of a combination of one in-frame assembled allele (hence- explanation (2). + forth denoted VDJ ) and either one unrearranged germline (GL) Two types of modeling theories have prevailed in an attempt to 2 or partially (DJ)-rearranged allele or one out-of-frame (VDJ ) tackle this conundrum (3). The so-called stochastic models com- rearranged allele (1). Consequently, at the phenotypic level, the monly considered a low probability p for an in-frame joint to occur b TCR proteins expressed by these cells are encoded at a single due to inefficiency in either the onset or achievement of recombi- by guest on October 1, 2021 chromosome, a feature that may contribute in preserving the nation (4–6). With the probability for allelic inclusion given by the working of an adaptive immune system founded on clonal-cell square p2, the models were able to account for the rare appearance selection procedures. Despite years of efforts, the phenomenon of of allelically included cells. Soon afterward, however, these sim- plistic views appeared incoherent with a mass of experimental *Centre de Physique The´orique, Centre National de la Recherche Scientifique Unite´ findings, including those of a vast majority of T cells carrying Mixte de Recherche 6207, Universite´ de la Me´diterrane´e-Universite´ de Provence- b Universite´ Sud Toulon Var, Centre National de la Recherche Scientifique Luminy dually rearranged TCR alleles, and B cells carrying dually rear- + Case 907; and †Centre d’Immunologie de Marseille-Luminy, Centre National de la ranged Ig H chain alleles as well, to a ratio of ∼60% VDJ /DJ to Recherche Scientifique Unite´ Mixte de Recherche 6102-Institut National de la Sante´ 40% VDJ+/VDJ2 cells (not mentioning the few VDJ+/VDJ+- et de la Recherche Me´dicale U631-Universite´ de la Me´diterrane´e, Campus de Luminy Case 906, Marseille Cedex 9, France equipped cells; see Refs. 1, 2, 7). Thus, purely stochastic models 1Current address: Institut National de Recherche en Informatique et en Automatique, were found to insufficiently explain allelic exclusion. Virtual Plants Team, Cooperation Centre for Agronomic Research in Development/ Feedback inhibition is the hallmark of the current regulated Unite´ Mixte de Recherche De´veloppement et Ame´lioration des Plantes, Montpellier models of allelic exclusion. These models support the notion that Cedex 5, France. V(D)J recombination initiates at one allele at a time due to Received for publication December 29, 2009. Accepted for publication May 7, 2010. a specific yet ill-defined molecular control(s) (8–10) or as the result This work was supported by the Agence Nationale de la Recherche program BioSys number 06-135161. Work in P.F.’s laboratory is also supported by Institut National de of a stochastic, low-probability onset (11, 12). Whatever the la Sante´ et de la Recherche Me´dicale, Centre National de la Recherche Scientifique, cause, a VDJ+ outcome, one in every three (e.g., Vb-to-DJb) the Association pour la Recherche sur le Cancer, the Institut National du Cancer, the joints on average (13), eventually leads to the prohibition of Fondation Princesse Grace de Monaco, and the Commission of the European Com- munities. E.F. was supported by a fellowship from Agence Nationale de la Recherche further rearrangement via a signal conveyed from the immature BioSys, number 06-135161. M.B. was supported by fellowships from the Marseille- receptor (the so-called pre-TCR) built from the newly synthesized Nice Genopole and Association pour la Recherche sur le Cancer. TCRb polypeptide (14–17). This concept agrees with the 60:40 Address correspondence and reprint requests to Dr. Pierre Ferrier, Centre d’Immuno- logie Marseille-Luminy, Marseille, Parc Scientifique de Luminy, Case 906, Marseille ratio mentioned above. However, it remains unclear as to how Cedex 09, 13288 Paris, France (P.F.), or Bastien Fernandez, Centre de Physique The´- recombination proceeds to the opposite allele in the relatively orique, CNRS Luminy, Case 907, 13288 Marseille Cedex 09, France (B.F). E-mail frequent cases of an out-of-frame VDJ2 initial assembly. More- addresses: [email protected] (P.F.) or [email protected] (B.F.). over, these models again fall short in terms of properly depicting The online version of this article contains supplemental material. the production of VDJ+/VDJ+ cells, unless we assume that a Abbreviations used in this paper: DN, double-negative; GL, germline; WT, wild-type. loosened control sporadically tolerates a synchronization of re- Copyright Ó 2010 by The American Association of Immunologists, Inc. 0022-1767/10/$16.00 combination at the two homologous TCRb alleles. These concerns www.jimmunol.org/cgi/doi/10.4049/jimmunol.0904182 The Journal of Immunology 1623 led us to consider an alternative scenario that is not tied into possible statuses as depicted in Fig. 1), at time t in a differentiating T cell a strictly sequential mode of interallelic activation for V(D)J re- population, the recombination time window of which started at t0. The combination. Markov transition matrix Q = Q(tDJ, tVDJ, tf) (Table I), composed of the probabilities 1/tDJ, 1/3tVDJ, 2/3tVDJ, and 1/tf for transitions through the In this study, we aimed to use a dynamical approach to model corresponding cell states (for a definition of the genomic statuses, re- TCRb gene recombination in an effort to comprehend the sto- combination time window, and transition rates, see Results, Formulation of chastic and regulated premises of allelic exclusion within a de- the model: overview and Formulation of the model: basic features) is upper velopmental scheme that would integrate all the observed cell triangular due to the feed-forward structure of the transition graph. The Markov chain was exploited using the relation subsets at once. Principally, successive D-to-J and V-to-DJ rear- À Á À Á ÀÀ Á Á t0 t0 rangements at TCRb alleles of individual T cells and ensuing x t ¼ x t0 exp t2t0 Q ;t t0; ð1Þ feedback inhibition are seen throughout as independent, possibly t t0 14 t in which x 0 ðtÞ represents the vector ðxi ðtÞÞ and, likewise, x 0 ðt0Þ¼ t 14 i¼1 concurrent and mostly not stringently simultaneous biochemical ðx 0 ðt ÞÞ i 0 i¼1 denotes the initial distribution at the window origin.