Assessment of Kinome-Wide Activity Remodeling upon Picornavirus Infection

Picornaviridae represent a large family of single-stranded positive RNA viruses of which different members can infect both humans and animals. These include the enteroviruses (e.g., poliovirus, coxsackievirus, and rhinoviruses) as well as the cardioviruses (e.g., encephalomyocarditis virus). Picornaviruses have evolved to interact with, use, and/or evade cellular host systems to create the optimal environment for replication and spreading. It is known that viruses modify kinase activity during infection, but a proteome-wide overview of the (de)regulation of cellular kinases during picornavirus infection is lacking. To study the kinase activity landscape during picornavirus infection, we here applied dedicated targeted mass spectrometry-based assays covering ∼40% of the human kinome. Our data show that upon infection, kinases of the MAPK pathways become activated (e.g., ERK1/2, RSK1/2, JNK1/2/3, and p38), while kinases involved in regulating the cell cycle (e.g., CDK1/2, GWL, and DYRK3) become inactivated. Additionally, we observed the activation of CHK2, an important kinase involved in the DNA damage response. Using pharmacological kinase inhibitors, we demonstrate that several of these activated kinases are essential for the replication of encephalomyocarditis virus. Altogether, the data provide a quantitative understanding of the regulation of kinome activity induced by picornavirus infection, providing a resource important for developing novel antiviral therapeutic interventions. [Display omitted] •Targeted mass spectrometry quantifies kinome activity remodeling upon viral infection.•Different picornaviral infections lead to shared and distinct kinome activity alterations.•Viral security proteins are involved in kinome activity remodeling.•Picornaviruses respond to kinase inhibitors, albeit with narrow therapeutic windows. When viruses invade host cells a complex battle unfolds between the host and the pathogen: the virus seeks replication while the host cell strives to survive. Viruses purposedly alter the activity of host kinases during this interaction. Here, proteome-wide kinase activity assays capture these changes quantitatively, offering a comprehensive view of kinase regulation during picornavirus infection. The assays revealed numerous key kinases to be involved. By employing kinase inhibitors, we validated the role of activated kinases.