Fig. 9: Dynamics of CAR⁺ Marginal Zone B cells and Germinal Center B cells during a TD-immune response.

a Time-course of counts of CAR⁺ Marginal Zone B (MZB) and CAR⁺ Germinal Center B (GCB) cells post-immunization in control/CAR (red dots, n = 53) and N2KO//CAR (blue dots, n = 18) mice. We show the mean of the predictions from the best-fitting branched model with time-dependent antigen-activation of Follicular B (FoB) and MZB cells as smooth lines. The uncertainty in estimates of the mean is shown as shaded envelopes depicting 95% credible intervals (~2 SEM). The y-axis represents total cell counts. The sequential gating strategy to retrieve the frequencies of CAR⁺ GCB and CAR⁺ MZB cells is depicted in Supplementary Fig. 11. Control/CAR mice: d4 (n = 3; 2 males (m), 1 female (f)), d7 (n = 9, 5 m, 4 f), d9 (n = 3; 2 m, 1 f), d14 (n = 15; 8 m, 7 f), d17 (n = 3; 3 f), d22 (n = 5; 1 m, 4 f), d26 (n = 4; 2 m, 2 f), d30 (n = 6; 4 m, 2 f); N2KO//CAR mice: d7 (n = 7; 2 m, 5 f), d9 (n = 5; 1 m, 4 f), (d14 n = 6; 5 m, 1 f). b Estimate of the total daily influx into the CAR-expressing MZB cell subset, as percent of total CAR⁺ MZB cell pool sizes (y-axis). We show the mean values as smooth lines and the prediction error around mean is shown as 95% credible intervals (shaded envelopes). The prediction error in the rate of influx from CAR^- MZB to CAR⁺ MZB (left panel) is calculated across all time points using mice from both the control and N2KO groups, i.e., n = 71 mice. The uncertainty in the prediction of the mean value of the rate of influx from FoB to CAR⁺ MZB (right panel) is calculated using only control/CAR data (n = 53 mice). c Clonal half-life of CAR-expressing MZB cells in control/CAR (red) and N2KO//CAR (blue) mice. Clonal half-life is defined as the \({{{{\mathrm{ln}}}}}\left(2\right)\)/net loss rate (λ for control/CAR group and λ' for N2KO//CAR group). This quantity depicts the total time taken for the size of a clonal lineage to decrease by 2-fold. The uncertainty in the estimates of clonal half-life derives from uncertainty in estimating loss rates λ across n = 53 control/CAR mice (red) and λ' across n = 18 N2KO//CAR mice (blue). Plot shows the mean (circles) estimate with ±2 SEM (error bars) of the clonal half-life of CAR⁺ MZB cells. For both (b) and (c), time point-wise mouse specifics are the same as described in (a). Source data are provided as a Source Data file (see sheets modeling data).