Unbiased profiling of clinical kinase inhibitors’ effects in activated macrophages using chromatin modifications as high-content readouts [Chromatin associated RNA-seq]

More than 500 kinases are implicated in the control of virtually every cellular process in mammals and deregulation of their activity is causally linked to diseases ranging from cancer to inflammatory and degenerative disorders. In the last three decades, massive worldwide efforts led to the approval of 62 clinical kinase inhibitors (CKI), with hundreds of additional molecules in various stages of pre-clinical or clinical development. In addition to the intended target(s), small molecule CKI commonly inhibit multiple additional kinases, resulting in both enhanced clinical effects and undesired side effects that are largely unpredictable based on in vitro selectivity profiling. To complement current CKI profiling methods, we set out a novel experimental and analytical approach grounded on the use of chromatin modifications as unbiased and information-rich readouts of the functional effects of CKI on macrophage activation, a complex biological response of biomedical relevance. This approach allowed us to characterize and dissect the distinctive behaviors of CKI with identical intended targets as well as to discover undescribed activities of CKI on macrophage activation programs.