Quantitative modeling of signaling in aggressive B cell lymphoma unveils conserved core network

Abstract

B cell receptor (BCR) signaling is required for the survival and maturation of B cells and is deregulated in B cell lymphomas. While proximal BCR signaling is well studied, little is known about the crosstalk of downstream effector pathways, and a comprehensive quantitative network analysis of BCR signaling is missing. Here, we semi-quantitatively modelled BCR signaling in Burkitt lymphoma (BL) cells using systematically perturbed phosphorylation data of BL-2 and BL-41 cells. The models unveiled feedback and crosstalk structures in the BCR signaling network, including a negative crosstalk from p38 to MEK/ERK. The relevance of the crosstalk was verified for BCR and CD40 signaling in different BL cells and confirmed by global phosphoproteomics on ERK itself and known ERK target sites. Compared to the starting network, the trained network for BL-2 cells was better transferable to BL-41 cells. Moreover, the BL-2 network was also suited to model BCR signaling in Diffuse large B cell lymphoma cells lines with aberrant BCR signaling (HBL-1, OCI-LY3), indicating that BCR aberration does not cause a major downstream rewiring.

B cell receptors bind specific antigens, and upon binding, they activate a signal transduction network which ultimately primes the cells for proliferation and affinity maturation. B-cell receptor signaling is often altered in B-cell lymphoma, leading to altered or chronic activation of the network. In this study we compared the signal transduction network downstream of acute and aberrant B cell receptor activity in cell lines originating from Burkitt and diffuse large B-cell lymphoma, respectively. By applying kinase inhibitors, we measured phosphorylation state changes in the network nodes. Mathematical modeling revealed a 16-node core network conserved in cells with acute and abberant B cell receptor signaling. In the network we detected hitherto undescribed crosstalks and feedbacks, structures known to confer treatment robustness. We elucidated and verified a negative crosstalk between the mitogen-activated protein kinases (MAPK) p38 and ERK. We further discovered that the negative feedback from ERK to its upstream kinase RAF, which in solid tumors neutralizes treatments targeting ERK or MEK, is also present in B cells. Altogether these findings may inform future treatment strategies targeting overactive B cell receptor or help to explain treatment resistance.