In Silico Modeling of Oncogenic Drivers in Waldenstrom Macroglobulinemia to Assess Additional Therapeutic Targets within the BCR Signaling Pathway Identifies MEK1/2 As a Target: Potential Therapeutic Role of Binimetinib

Background: The observation that B-cell receptor (BCR) signaling play a critical role in the survival of malignant Waldenstrom macroglobulinemia (WM) cells is highlighted by clinical efficacy of the BTK-inhibitor, ibrutinib in WM patients. BCR signaling leads to downstream activation of several intermediary components whose activity results in increased cell proliferation. Although disruption of this axis at the proximal end (BCR) has proved successful in WM, the exact role and impact of targeting the distal intermediaries remains unknown, particularly in aggressive forms of the disease. This is important as induction of resistance to ibrutinib is clearly documented which can either be mediated through mutational changes in BTK or other members within the BCR signalosome. Using a novel simulation-based approach, we reverse-engineered the WM cell molecular architecture to uncover the role of oncogenic intermediaries distal to the BCR complex in advanced-stage WM and conducted a virtual drug-screen targeting these pathways with in vitro validation.

Methods: The human WM cell line, RPCI-WM1, was used in simulation and validation experiments. RPCI-WM1 was established from a highly drug-refractory advanced disease stage patient refractory to both rituximab and bortezomib. Publically available as well as proprietary genomic and cytogenetic data was utilized for the creation of the RPCI-WM1 patient avatar, which through simulation identified the salient and prominently dysregulated cellular pathways. Importantly, illustrating these pathways highlights common convergence points on increased proliferation and viability. These convergence points were then directly and indirectly targeted by simulated testing of a library of FDA approved drugs and those impacting these dysregulated pathways were shortlisted. A standardized library of equations models all the biological reactions such as enzymatic reactions, allosteric binding and protein modulation by phosphorylation, de-phosphorylation, ubiquitination, acetylation, prenylation and others. A library of FDA approved drug agents (n~150) and those in clinical study has been developed and was simulated individually and in combination on the RPCI-WM1 (advanced stage WM patient) avatar.

Results: MYD88_L265P mutation, absence of CXCR4 mutations and additional chromosomal aberrations (derivatives, translocations, deletions and amplifications of chromosomes 3, 6, 9, 13, 18 and 19), which are notable features of RPCI-WM1 cells were configured and modeled in silico. The RPCI-WM1 patient avatar was predicted to have increased IRAK1/4 engagement due to MYD88 mutation and high copy number (CN) of IL18. Downregulation of DUSP1 through MYD88-mediated signaling was noted to result in high ERK activity. Increase gene copy number of both FOS and ETS1, which are downstream of ERK, were noted. Notably, FOS is a key regulator of the AP1 complex, whose activity is regulated upstream by ERK.  The transcription factor, ETS1 was also predicted as over expressed and ERK-mediated phosphorylation of ETS1 regulates the activity of ETS1. The RPCI-WM1 patient avatar model also indicated high AKT due to indirect convergence of multiple aberrations. Drug screening revealed sensitivity to the MEK inhibitor, binimetinib. Although no copy number variation in MEK-ERK pathway genes were detected, per simulation, MYD88 mutation through inactivation of DUSP1 activated ERK and downstream associated survival pathways. The simulation predictions were experimentally validated. As predicted, binimetinib significantly inhibited proliferation and viability of RPCI-WM1 cells (IC₅₀ <100nM).

Conclusions: Our study demonstrates the functional role and impact of MEK1/2 – an oncogenic component distal to the BCR, and whose activity can be targeted with binimetinib to elicit a lethal effect in advanced-stage WM cells.  We also show the utility of a novel technology, which is capable of integrating genome-wide molecular data points to emulate the salient genomic drivers of a given tumor cell and test its sensitivity to numerous drugs in a high-throughput manner for truly personalized therapy.