Computational Model Reveals Limited Correlation between Germinal Center B-Cell Subclone Abundancy and Affinity: Implications for Repertoire Sequencing.
Immunoglobulin repertoire sequencing has successfully been applied to identify expanded antigen-activated B-cell clones that play a role in the pathogenesis of immune disorders. One challenge is the selection of the Ag-specific B cells from the measured repertoire for downstream analyses. A general feature of an immune response is the expansion of specific clones resulting in a set of subclones with common ancestry varying in abundance and in the number of acquired somatic mutations. The expanded subclones are expected to have BCR affinities for the Ag higher than the affinities of the naive B cells in the background population. For these reasons, several groups successfully proceeded or suggested selecting highly abundant subclones from the repertoire to obtain the Ag-specific B cells. Given the nature of affinity maturation one would expect that abundant subclones are of high affinity but since repertoire sequencing only provides information about abundancies, this can only be verified with additional experiments, which are very labor intensive. Moreover, this would also require knowledge of the Ag, which is often not available for clinical samples. Consequently, in general we do not know if the selected highly abundant subclone(s) are also the high(est) affinity subclones. Such knowledge would likely improve the selection of relevant subclones for further characterization and Ag screening. Therefore, to gain insight in the relation between subclone abundancy and affinity, we developed a computational model that simulates affinity maturation in a single GC while tracking individual subclones in terms of abundancy and affinity. We show that the model correctly captures the overall GC dynamics, and that the amount of expansion is qualitatively comparable to expansion observed from B cells isolated from human lymph nodes. Analysis of the fraction of high- and low-affinity subclones among the unexpanded and expanded subclones reveals a limited correlation between abundancy and affinity and shows that the low abundant subclones are of highest affinity. Thus, our model suggests that selecting highly abundant subclones from repertoire sequencing experiments would not always lead to the high(est) affinity B cells. Consequently, additional or alternative selection approaches need to be applied.
Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands; Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
Polina
P
Reshetova
Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands.
Barbera D C
BD
van Schaik
Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands.
Paul L
PL
Klarenbeek
Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands.
Marieke E
ME
Doorenspleet
Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands.
Rebecca E E
RE
Esveldt
Department of Clinical Immunology and Rheumatology, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands.
Paul-Peter
PP
Tak
Department of Pathology, Academic Medical Center, University of Amsterdam , Amsterdam , Netherlands.
Jeroen E J
JE
Guikema
Amsterdam Rheumatology and Immunology Center, Academic Medical Center , Amsterdam , Netherlands.
Niek
N
de Vries
Biosystems Data Analysis, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands; Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
Antoine H C
AH
van Kampen
BCR affinity; clonal expansion; computational modeling; germinal center; repertoire sequencing