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DiaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling

ABSTRACT: Protein-protein interactions (PPIs) underlie most biological functions. Devastating human conditions like cancers, neurological disorders, and infections, hijack PPI networks to initiate disease, and to drive disease progression. Understanding precisely how diseases remodel PPI networks can, therefore, help clarifying disease mechanisms and identifying therapeutic targets. Protein kinases control most cellular processes through protein phosphorylation. The 518 human kinases, known as the kinome, are frequently dysregulated in disease and highly druggable with ATP-competitive inhibitors. Kinase activity, localization, and substrate recognition are regulated by dynamic PPI networks composed of scaffolding and adapters proteins, other signaling enzymes like small GTPases and E3 ligases, and phospho-substrates. Accordingly, mapping kinase PPI networks can help determining kinome activation states, and, in turn, cellular activation states; this information can be used for studying kinase-mediated cell signaling, and for prioritizing kinases for drug discovery. Previously, we have developed a high-throughput method for kinome PPI mapping based on mass spectrometry (MS)-based chemoproteomics that we named kinobead competition and correlation analysis (kiCCA). Here, we introduce 2nd generation (gen) kiCCA which utilizes data independent acquisition (DIA) with parallel accumulation serial fragmentation (PASEF) MS and a re-designed CCA algorithm with improved selection criteria and the ability to predict multiple kinase interaction partners of the same proteins. Using neuroblastoma cell line models of the noradrenergic-mesenchymal transition (NMT), we demonstrate that 2nd gen kiCCA (1) identified 6.1-times more kinase PPIs in native cell extracts compared to our 1st gen approach, (2) determined kinase-mediated signaling pathways that underly the neuroblastoma NMT, and (3) accurately predicted pharmacological targets for manipulating NMT states. Our 2nd gen kiCCA method is broadly useful for cell signaling research and kinase drug discovery.

INSTRUMENT(S): timsTOF Pro 2

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Martin Golkowski

PROVIDER: MSV000096379 | MassIVE | Mon Nov 11 11:45:00 GMT 2024

SECONDARY ACCESSION(S): PXD057757

REPOSITORIES: MassIVE

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Project description:Triple negative breast cancer (TNBC) is heterogeneous with patients exhibiting at least two molecular subtypes, basal-like (BL) and claudin-low (CL). MEK inhibitor (MEKi) treatment of BL and CL cell lines and mouse model tumors induced subtype-specific alterations in overall kinome activity referred to as protein kinase reprogramming. BL- and CL-specific reprogramming involving increases in receptor tyrosine kinases was also seen in TNBC patients comparing tumor samples before and after a one week treatment with the MEKi, trametinib. Combination of kinase inhibitors targeted to the BL and CL reprogrammed signatures would need to be individually selected due to the heterogeneous resiliency of BL and CL kinomes. To overcome this “reprogramming dilemma” we targeted the transcriptional co-activator BRD4 with BET bromodomain inhibitors, JQI and IBET151; both strongly inhibited kinome reprogramming and onset of MEKi resistance in BL and CL cells. Targeting chromatin modifiers may therapeutically block resistance due to kinome reprogramming.BL and CL TNBC are commonly treated as a single disease despite genomic studies showing they represent distinct molecular subtypes1. Recent Cancer Genome Atlas data demonstrated that the 518 protein kinases in the human genome (the kinome) were infrequently mutated in BL breast cancer; however, EGFR, KRAS and BRAF were amplified in 22, 32 and 31% of BL tumors, respectively. These findings are consistent with frequent activation of the BRAF-MEK-ERK pathway in TNBC2,3 and inhibitors targeting kinases in this pathway are currently in clinical trials for TNBC. As single agents, targeted kinase inhibitors generally fail to sustain durable responses when used to treat a range of human cancers including TNBC4-6. Onset of kinase inhibitor resistance can be due to selection of mutations in the targeted kinase7,8, activating mutations or amplification of RAS or downstream kinases9,10 or kinome reprogramming, a process in which there are system-wide changes in kinase networks11-13. Each of these resistance mechanisms allows the cancer cell to circumvent the targeted inhibition of specific kinases14. We previously developed chemical, proteomic methods that assay the activation state of protein kinases en masse15,16. Our methods utilize ¬Multiplexed Inhibitor Beads (MIBs), mixtures of covalently immobilized, linker adapted, kinase inhibitors. The immobilized inhibitors are primarily type I kinase inhibitors that preferentially bind activated (versus inactive) kinase17. Kinase capture is highly reproducible and is a function of kinase affinity for different immobilized inhibitors as well as the kinase activation state. Activated kinases preferentially bind, inactive kinases do not. By coupling MIB capture with mass spectrometry (MIB/MS), the technique allows quantitative interrogation of hundreds of kinases in a single mass spectrometry run. This also interrogates kinases known by sequence but which have been understudied due to lack of reagents such as specific phospho-antibodies. We report here both in preclinical models and patients that BL and CL TNBC have different baseline kinome activation states and both respond differently to MEKi with subtype-specific tyrosine kinase reprogramming. To avoid treatment strategy that uses multiple kinase inhibitors in individual patients, we discovered a novel pharmacologic strategy to block the initial reprogramming response to MEKi involving inhibition of epigenetic processes.

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DiaPASEF-Powered Chemoproteomics Enables Deep Kinome Interaction Profiling

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