Predicting Novel Kinase-Substrate Interactions Reveals Enriched Kinases in Medulloblastoma Subtypes
Medulloblastoma (MB) is the most common pediatric brain cancer, frequently originating in the cerebellum. There are four major subtypes of medulloblastoma based on genomics profiling: wingless (WNT), sonic hedgehog (SHH), group 3, and group 4. Subtype heterogeneity and low mutation rates hinder the identification of actionable molecular targets within each group. Current treatment options following surgical resection are radiation therapy and chemotherapy, which can cause permanent neurocognitive deficits in children and increase the risk of secondary cancers, highlighting the need for more targeted therapies. Protein phosphorylation, a post-translational modification by protein kinases, regulates most cellular processes and signaling pathways. Analysis of phosphorylation levels in a cell may more accurately distinguish the molecular profiles of each MB subtype. We quantitatively profiled the globally expressed proteome and phosphoproteome of 20 medulloblastoma patient-derived xenografts. Current databases only map 7% of identified phosphosites to a known modifying kinase. Novel kinase-substrate interactions were predicted using a publicly available algorithm. With these novel predicted links, the percentage of annotated interactions in our dataset increased to 22%, providing greater insight into potential signaling pathways. Kinase activities were then scored using a kinase activity profiling tool followed by statistical calculation of differentially active kinases within each subgroup. After adding novel kinase-substrate predictions, phosphorylation patterns and kinase activities better aligned with current literature in medulloblastoma and revealed novel key signaling pathways. Cyclin-dependent kinase 4 (CDK4) had significantly higher activity in the SHH samples and was predicted to phosphorylate MYCN which is known to be amplified in SHH MB. The transcription factor JUND was also a predicted substrate of CDK4. While JUND is known to repress CDK4 transcription, we observed a positive correlation between CDK4 activity and JUND phosphorylation, suggesting a potential inhibitory mechanism between CDK4 and JUND. These findings suggest that CDK4/6 inhibitors, which are FDA-approved for use in other cancers, may be useful for treatment of medulloblastoma patients.