Integrated Single-Dose Kinome Profiling Data is Predictive of Cancer Cell Line Sensitivity to Kinase Inhibitors

Abstract

Protein kinase activity forms the backbone of cellular information transfer, acting both individually and as part of a broader network, the kinome. Correspondingly, their central role in signaling implicates kinome dysfunction as a common driver of cancer, where numerous kinases have been identified as having a causal or modulating role in cancer development and progression. Driven by their importance, the development of therapies targeting kinases has rapidly grown, with over 70 kinase inhibitors approved for use in the clinic and over double this number currently in clinical trials. Given the growing importance of kinase-targeted therapies, linking the relationship between kinase inhibitor treatment and their effects on downstream cellular phenotype is of clear importance for understanding treatment mechanisms and streamlining compound screening in therapy development. In this work, we combine two large-scale kinome profiling data sets and use them to link inhibitor-kinome interactions with cell line treatment responses (AUC/IC50). We then built computational models on this data set that achieve a high degree of prediction accuracy (R2 of 0.7 and RMSE of 0.9), and were able to identify a set of well-characterized and understudied kinases that significantly affect cell responses. Further, we validated these models experimentally by testing predicted effects in breast cancer cell lines, and extended the model scope by performing additional validation in patient-derived pancreatic cancer cell lines. Overall, these results demonstrate that broad quantification of kinome inhibition state is highly predictive of downstream cellular phenotypes.