Phosphoproteome profiling uncovers a key role for CDKs in TNF signaling

Abstract

SummaryTumor necrosis factor (TNF) is one of the few cytokines successfully targeted by therapies against inflammatory diseases. However, blocking this well studied and pleiotropic ligand can cause dramatic side-effects. We reasoned that a systems-level proteomic analysis of TNF signaling could dissect its diverse functions and offer a base for developing more targeted therapies. Combining phosphoproteomics time course experiments with subcellular localization and kinase inhibitor analysis identifies functional modules of phosphorylations. The majority of regulated phosphorylations could be assigned to an upstream kinase by inhibiting master kinases and spatial proteomics revealed phosphorylation-dependent translocations of hundreds of proteins upon TNF stimulation. Phosphoproteome analysis of TNF-induced apoptosis and necroptosis uncovered a key role for transcriptional cyclin-dependent kinase (CDK) activity to promote cytokine production and prevent excessive cell death downstream of the TNF signaling receptor. Our comprehensive interrogation of TNF induced pathways and sites can be explored at http://tnfviewer.biochem.mpg.de/.Highlights-Distinct phosphorylation events mark early and late TNF signaling-Inhibition of master kinases reveals TNF stimulation dependent kinase-substrate relations-TNF induces phosphorylation-dependent spatial rearrangement of hundreds of proteins-CDK kinase activity promotes TNF-induced cytokine expression and inhibits cell death-CDK12/13 inhibitors have potential as anti-inflammatory agents