An Atlas of Human Kinase Regulation
David Ochoa, Mindaugas Jonikas, Robert T Lawrence, Bachir El Debs, Joel Selkrig, Athanasios Typas, Judit Villén, Silvia DM Santos, Pedro Beltrao
The coordinated regulation of protein kinases is a rapid mechanism that integrates diverse cues and swiftly determines appropriate cellular responses. However, our understanding of cellular decision-making has been limited by the small number of simultaneously monitored phospho-regulatory events. Here, we have estimated changes in activity in 215 human kinases in 399 conditions derived from a large compilation of phosphopeptide quantifications. This atlas identifies commonly regulated kinases as those that are central in the signaling network and defines the logic relationships between kinase pairs. Co-regulation along the conditions predicts kinase-complex and kinase-substrate associations. Additionally, the kinase regulation profile acts as a molecular fingerprint to identify related and opposing signaling states. Using this atlas, we identified essential mediators of stem cell differentiation, modulators of Salmonella infection and new targets of AKT1. This provides a global view of human phosphorylation-based signaling and the necessary context to better understand kinase driven decision-making.
Cells need to constantly adapt to internal and external conditions in order to maintain homoeostasis. During cellular decision-making, signal-transduction networks dynamically change in response to cues, triggering cellular state-defining responses. Multiple mechanisms exist to transfer this information from sensors to the corresponding molecular responses, one of the fastest being the reversible post-translational modification of proteins (PTMs). Through these targeted modifications, such as phosphorylation, the cell can quickly alter enzymatic activities, protein interactions or sub-cellular localization in order to produce a coordinated response to a given stimulus (Pawson 2004). Protein phospho-regulation constitutes a highly conserved regulatory mechanism relevant for a broad set of biological functions and diseases (Beltrao 2012).
Over the past decades, our view of cellular signaling has advanced from an idea of isolated and linear cascades to highly complex and cooperative regulatory networks (Jordan 2000, Gibson 2009). Different perturbations in cellular conditions often activate different sets of interconnected kinases, ultimately triggering appropriate cellular responses. The complete understanding of such cell-fate decisions would require the systematic measurement of changes in kinase activities under multiple perturbations, but the small number of quantified regulatory events (i.e. tens) that were possible to date has limited our knowledge of cellular decision making and its molecular consequences (Kim 2011, Bendall 2011, Niepel 2013, Garmaroudi 2010).
Advances in mass-spectrometry and enrichment methods now allow measuring changes in thousands of phosphorylated peptides at a very high temporal resolution (Olsen 2013, Kanshin 2015, Humphrey 2015). Recent studies on human quantitative phosphorylation include responses at different cell-cycle stages (Dephoure 2008, Olsen 2010), after DNA damage (Beli 2012), EGF stimulation (Olsen 2006, Mertins 2012), prostaglandin stimulation (de Graaf 2014) and different kinase inhibitions (Weber 2012, Oppermann 2013, Kettenbach 2011, Hsu 2011) among many others. More recently, improvements in experimental and computational methods have fostered the study of differential regulation of phosphosites and kinases in different cancer types (Casado 2013), the modeling of drug resistance (Wilkes 2015) and inference of more precise pathway models (Terfve 2015). We suggest that the integrated analysis of phosphoproteomic responses after a wide panel of heterogeneous perturbations can expedite our understanding of cell decision-making processes.
In this study, we have compiled condition-dependent changes in human protein phosphorylation derived from 2,940,379 phosphopeptide quantifications in 435 heterogeneous perturbations. After quality control and normalization, we infer and benchmark the changes in 215 kinase activities in 399 conditions. We show that the similarity of kinase regulatory profiles can be used as a fingerprint to compare conditions in order to, for example, identify perturbations that modulate the kinase activity changes of a condition of interest. The large number of conditions analyzed allowed us to identify the kinases that are broad regulators (i.e. generalist kinases), found to be central kinases of the signaling network. Individual kinase profiles across conditions were also informative to recapitulate known kinase-kinase interactions and to identify novel co-regulated complexes and phosphosites acting as potential effectors.