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A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide.

Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A - Mol. Syst. Biol. (2015)

Bottom Line: B-lymphocyte population dynamics, which are predictive of immune response and vaccine effectiveness, are determined by individual cells undergoing division or death seemingly stochastically.Combining modeling and experimentation, we found that NF-κB cRel enforces the execution of a cellular decision between mutually exclusive fates by promoting survival in growing cells.We show that a multi-scale modeling approach allows for the prediction of dynamic organ-level physiology in terms of intra-cellular molecular networks.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Signaling Systems Laboratory, UCSD, La Jolla, CA, USA San Diego Center for Systems Biology, UCSD, La Jolla, CA, USA Bioinformatics and Systems Biology Graduate Program, UCSD, La Jolla, CA, USA.

No MeSH data available.


The multi-scale model predicts the effects of low stimulus, cRel knockout, and rapamycin treatmentA After parameterizing the multi-scale model using results from wild-type B cells stimulated with 250 nM CpG (red), we predicted the effects of decreasing IKK duration (green), lack of NF-κB cRel (blue), and decreased protein synthesis (purple) in silico and compared the results to those from analogous time-lapse microscopy experiments where we stimulated with only 10 nM CpG, used cRel deficient cells, or pretreated with 1 ng/ml rapamycin.B–J Side-by-side comparison of modeling and experimental results: total cell counts (B, E, H), average number of divisions (C, F, I), and fraction of growing progenitors that died (D, G, J).
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fig06: The multi-scale model predicts the effects of low stimulus, cRel knockout, and rapamycin treatmentA After parameterizing the multi-scale model using results from wild-type B cells stimulated with 250 nM CpG (red), we predicted the effects of decreasing IKK duration (green), lack of NF-κB cRel (blue), and decreased protein synthesis (purple) in silico and compared the results to those from analogous time-lapse microscopy experiments where we stimulated with only 10 nM CpG, used cRel deficient cells, or pretreated with 1 ng/ml rapamycin.B–J Side-by-side comparison of modeling and experimental results: total cell counts (B, E, H), average number of divisions (C, F, I), and fraction of growing progenitors that died (D, G, J).

Mentions: We next asked whether the model could be used for studies of genetic or pharmacological perturbations. In particular, we examined the population behavior in B cells exposed to reduced stimulus concentrations in the absence of NF-κB cRel, or when treated with the cell growth inhibitor rapamycin (Fig6A). Model predictions were compared to time-lapse microscopy experiments in which the same conditions were applied. First, we simulated the low dose stimulation condition by allowing for a faster decay of the active IKK species (see Supplementary Table S9 and Supplementary Methods). The model predicted a dramatic decrease in the total B-cell population (FigB), resulting from a decrease in the fraction of cells that divide in generations 3+ (Fig6C); however, cell size trajectories (Supplementary Fig S7B and C) and fate timing (Supplementary Fig S7D–F) were unaffected. An equivalent analysis of subsequent time-lapse experiments confirmed these predictions (FigB–D, Supplementary Fig S7), although the model predicted a later peak in total cell counts (FigB, Supplementary Table S11). Next, we simulated cRel deficiency by setting the translation rate of the cRel protein to zero. The multi-scale model recapitulated a decreased population response (FigE) previously observed, but now showed that this is caused primarily by a reduction in the number of divisions (Fig6F). Model simulations suggest that cell growth is not cRel dependent since cRel-deficient cells had highly correlated growth trajectories (Supplementary Fig S7B and C). Furthermore, the model predicted that NF-κB cRel deficiency would not affect timing of the decision, division, or death processes (Supplementary Fig S7D–F), but that a higher percentage of growing cells would die (FigG). A side-by-side comparison with the results from experimental cell tracking of cRel-deficient cells confirmed these predictions (Supplementary Table S11). Finally, treatment with rapamycin, the inhibitor of mTOR, which results in defective cell growth and ribosome biosynthesis, as well as a decrease in cells that divide more than once (FigI), was recapitulated well by simply decreasing the global protein translation rate by 30% (Fig6A, H–J). Importantly, this also resulted in longer delays prior to division (P < 0.0014, Mann–Whitney U-test) and death (P < 0.0009, Mann–Whitney U-test) in time-lapse microscopy datasets (Supplementary Fig S7E and F purple lines); although the delay in division timing and in the start of growth (Tgro) was not as dramatic as predicted (Supplementary Fig S7D purple lines), it was still statistically significant (P < 1e-6, Mann–Whitney U-test). Interestingly, while the model accurately predicted that cell growth trajectories would not be affected, it overestimated the delay in cell-cycle duration and survival timing and incorrectly predicted a delayed time to grow (Supplementary Table S11).


A multi-scale approach reveals that NF-κB cRel enforces a B-cell decision to divide.

Shokhirev MN, Almaden J, Davis-Turak J, Birnbaum HA, Russell TM, Vargas JA, Hoffmann A - Mol. Syst. Biol. (2015)

The multi-scale model predicts the effects of low stimulus, cRel knockout, and rapamycin treatmentA After parameterizing the multi-scale model using results from wild-type B cells stimulated with 250 nM CpG (red), we predicted the effects of decreasing IKK duration (green), lack of NF-κB cRel (blue), and decreased protein synthesis (purple) in silico and compared the results to those from analogous time-lapse microscopy experiments where we stimulated with only 10 nM CpG, used cRel deficient cells, or pretreated with 1 ng/ml rapamycin.B–J Side-by-side comparison of modeling and experimental results: total cell counts (B, E, H), average number of divisions (C, F, I), and fraction of growing progenitors that died (D, G, J).
© Copyright Policy - open-access
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4358656&req=5

fig06: The multi-scale model predicts the effects of low stimulus, cRel knockout, and rapamycin treatmentA After parameterizing the multi-scale model using results from wild-type B cells stimulated with 250 nM CpG (red), we predicted the effects of decreasing IKK duration (green), lack of NF-κB cRel (blue), and decreased protein synthesis (purple) in silico and compared the results to those from analogous time-lapse microscopy experiments where we stimulated with only 10 nM CpG, used cRel deficient cells, or pretreated with 1 ng/ml rapamycin.B–J Side-by-side comparison of modeling and experimental results: total cell counts (B, E, H), average number of divisions (C, F, I), and fraction of growing progenitors that died (D, G, J).
Mentions: We next asked whether the model could be used for studies of genetic or pharmacological perturbations. In particular, we examined the population behavior in B cells exposed to reduced stimulus concentrations in the absence of NF-κB cRel, or when treated with the cell growth inhibitor rapamycin (Fig6A). Model predictions were compared to time-lapse microscopy experiments in which the same conditions were applied. First, we simulated the low dose stimulation condition by allowing for a faster decay of the active IKK species (see Supplementary Table S9 and Supplementary Methods). The model predicted a dramatic decrease in the total B-cell population (FigB), resulting from a decrease in the fraction of cells that divide in generations 3+ (Fig6C); however, cell size trajectories (Supplementary Fig S7B and C) and fate timing (Supplementary Fig S7D–F) were unaffected. An equivalent analysis of subsequent time-lapse experiments confirmed these predictions (FigB–D, Supplementary Fig S7), although the model predicted a later peak in total cell counts (FigB, Supplementary Table S11). Next, we simulated cRel deficiency by setting the translation rate of the cRel protein to zero. The multi-scale model recapitulated a decreased population response (FigE) previously observed, but now showed that this is caused primarily by a reduction in the number of divisions (Fig6F). Model simulations suggest that cell growth is not cRel dependent since cRel-deficient cells had highly correlated growth trajectories (Supplementary Fig S7B and C). Furthermore, the model predicted that NF-κB cRel deficiency would not affect timing of the decision, division, or death processes (Supplementary Fig S7D–F), but that a higher percentage of growing cells would die (FigG). A side-by-side comparison with the results from experimental cell tracking of cRel-deficient cells confirmed these predictions (Supplementary Table S11). Finally, treatment with rapamycin, the inhibitor of mTOR, which results in defective cell growth and ribosome biosynthesis, as well as a decrease in cells that divide more than once (FigI), was recapitulated well by simply decreasing the global protein translation rate by 30% (Fig6A, H–J). Importantly, this also resulted in longer delays prior to division (P < 0.0014, Mann–Whitney U-test) and death (P < 0.0009, Mann–Whitney U-test) in time-lapse microscopy datasets (Supplementary Fig S7E and F purple lines); although the delay in division timing and in the start of growth (Tgro) was not as dramatic as predicted (Supplementary Fig S7D purple lines), it was still statistically significant (P < 1e-6, Mann–Whitney U-test). Interestingly, while the model accurately predicted that cell growth trajectories would not be affected, it overestimated the delay in cell-cycle duration and survival timing and incorrectly predicted a delayed time to grow (Supplementary Table S11).

Bottom Line: B-lymphocyte population dynamics, which are predictive of immune response and vaccine effectiveness, are determined by individual cells undergoing division or death seemingly stochastically.Combining modeling and experimentation, we found that NF-κB cRel enforces the execution of a cellular decision between mutually exclusive fates by promoting survival in growing cells.We show that a multi-scale modeling approach allows for the prediction of dynamic organ-level physiology in terms of intra-cellular molecular networks.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, Signaling Systems Laboratory, UCSD, La Jolla, CA, USA San Diego Center for Systems Biology, UCSD, La Jolla, CA, USA Bioinformatics and Systems Biology Graduate Program, UCSD, La Jolla, CA, USA.

No MeSH data available.