Deciphering molecular mechanisms of synergistic growth reduction in kinase inhibitor combinations

In cancer treatment, the persistent challenge of unresponsiveness of certain patients to drugs or the development of resistance post-treatment remains a significant concern. Drug combinations that synergistically reduce tumor growth emerge as a promising avenue to address this issue. Here, we aimed to characterize the mechanism of action of two synergistic drug combinations that target PI3K together with MEK1 or with TAK1 and used time course measurements of phosphoproteomics and transcriptomics in response to single inhibitors and their combinations. Our analysis untangled those responses driven by single drugs and responses that were unique to the combinations. We observed a high overlap between single-drug responses and their combinations, suggesting that single-drug mechanisms dominate the mechanism of action of the combinations of the kinase inhibitors. Despite a high overlap, both drug combinations exhibited a synergistic modulation of several cell fate regulators found at the convergence points of the targeted pathways, including the key regulator of intrinsic apoptosis BCL2L11. Interestingly, the responses in both combinations were largely limited to the targeted pathways, namely PI3K/AKT and MAPKs, with very limited change of any other additional cell fate decision pathways. In addition, we observed a strong downregulation of nucleotide metabolism and tRNA biosynthesis uniquely in the combinations, which could be attributed to the reduced activity of mTOR and ATF4. Our approach provides insights into the molecular mechanisms affected by the PI3Ki-TAK1i and PI3Ki-MEKi combinations and can serve as a flexible framework for dissecting drug combination responses based on multi-omics measurements.