Computer Simulation of Multi-Color Brainbow Staining and Clonal Evolution of B Cells in Germinal Centers

Abstract

Clonal evolution of B cells in germinal centers (GCs) is central to affinity maturation of antibodies in response to pathogens. Permanent or tamoxifen-induced multi-color recombination of B cells based on the brainbow allele allows monitoring the degree of color dominance in the course of the GC reaction. Here, we use computer simulations of GC reactions in order to replicate the evolution of color dominance in silico and to define rules for the interpretation of these data in terms of clonal dominance. We find that a large diversity of clonal dominance is generated in simulated GCs in agreement with experimental results. In the extremes, a GC can be dominated by a single clone or can harbor many co-existing clones. These properties can be directly derived from the measurement of color dominance when all B cells are stained before the GC onset. Upon tamoxifen-induced staining, the correlation between clonal structure and color dominance depends on the timing and duration of the staining procedure as well as on the total number of stained B cells. B cells can be stained with 4 colors if a single brainbow allele is used, using both alleles leads to 10 different colors. The advantage of staining with 10 instead of 4 colors becomes relevant only when the 10 colors are attributed with rather similar probability. Otherwise, 4 colors exhibit a comparable predictive power. These results can serve as a guideline for future experiments based on multi-color staining of evolving systems.

Calculating germinal centre reactions

“…In the future, computational models may mature to allow prediction of vaccination outcomes based on key parameters such as vaccine composition, administration schedule and the pre-vaccination B cell repertoire of individual patients. [43] Provide basis for interpretation of multi-colour stained GC reactions [38] High-resolution 3D lattice simulation comprising Tfh cells, FDCs, stromal cells, B cells and their interactions C++ and R, available on figshare link [42] Examine relation between clone abundance and affinity Combines deterministic clonal evolution with stochastic emergence of new clones R, available upon request [41] molecular mechanisms…”

“…Several GCs in parallel [24,30,35] Several consecutive exposures [24,35] Spatially resolved GC [33,34,42] Shape space sequence [33,34,50] Co-evolving epitopes [49] Binary sequence [35,49] Sequence-free [40,41,48,52,54] Seeding by memory B cells [24,35] Stochastic differential equations [49] ODE-based simulation [41,48,54] Agent-based simulation [24,33,34,35,50,40] Class-switching [54] Molecular detail of T-B interaction [33,34] Full AA alphabet sequence [24,43] Role for plasma B cells [49,54,30] Treatment of Ab CDR and FWR regions [24,52] Rugged fitness landscape [30] Several epitopes simultaneously [30,35,48,50,53] Role for memory B cells [35,24] ...…”

“…How clonal dynamics differ in settings with several, potentially differentially immunogenic epitopes present at the same time remains to be investigated experimentally. In vivo imaging tools like "brainbow GCs" [38] proved useful, but the interpretation of the data requires carebased on computer simulations several caveats regarding timing, dynamics and dosage of colour induction have been identified [42]. On a related note, GC models have been used to identify complications in the construction of B cell lineage trees with the aim of establishing mutational paths from germline Ig sequences to higher-affinity descendants.…”

Computational Model Reveals a Stochastic Mechanism behind Germinal Center Clonal Bursts

“…The method can generate up to 10 different color combinations, thus limiting the experiment to characterising the evolution of a maximum number of 10 clones. A Normalized Dominance Score (NDS), defined as the fraction of all B cells in a GC that carry the dominant color combination, was used to characterize clonal diversity [15,63]. To simulate this experiment, we cluster founders into 10 groups, and define an NDS score as the ratio between the cell count of the dominant cluster over the total number of cells.…”

São Paulo School of Advanced Sciences on Vaccines: an overview

“…Whereas the B-cell proliferation concentrates in the GC dark zones, the selection of B cell clones takes place in the GC light zones [26]. In order to explain the details of the GC cellular dynamics involved in the B cell responses, Dr. Victora introduced the "Brainbow System" that allows the visualization of affinity maturation at the single GC level, and updated the model of GC selection [27]. Apparently, only about 5% of the GC expanded B cells in a secondary response are memory cells generated in the first infection.…”