ID #125 Functional Kinase Clusters Reflect Medulloblastoma Molecular Subtypes and Highlight Potential Therapeutic Targets

Background Accurate subgrouping of medulloblastoma is critical for risk stratification and development of novel therapies. While DNA methylation profiling has advanced subgroup classification, functional kinase activity profiles may provide additional insights beyond (epi-)genetic data and reveal directly actionable therapeutic targets. Methods Serine/threonine kinase (STK) activity profiling was performed on 50 medulloblastoma samples (HIT cohort) using PamChip arrays, quantified via BioNavigator software (PamGene) and integrated with previously published STK profiling data from 50 medulloblastoma samples (Netherlands cohort)(Zomerman et al. 2018). Unsupervised clustering was conducted on datasets separately and combined to identify peptide phosphorylation profiles. Medulloblastoma subgroups were determined by DNA methylation analysis. Results In the HIT cohort, the main cluster predominantly consisted of Group 3 and Group 4 MB samples, unlike the other clusters (p = 0.033). As published, there were two clusters in the Netherlands cohort, one including SHH-activated and a subset of Group 3 MB samples, the other Group 4 and other Group 3 samples. Upon combination of the two datasets, two stable clusters were identified with excellent separation of SHH from Group 3/Group 4 samples (p < 0.001). Clinical variables (age, evidence of metastatic disease, use of radiotherapy, age of the sample) were independent from the clusters. Conclusion Functional kinase activity profiling using PamGene consistently identifies two main clusters in medulloblastoma, aligning with known molecular subgroups. This suggests that kinase activity is correlated with medulloblastoma subgroups, and that kinase pathways may have subgroup-specific roles. This data may facilitate the identification of therapeutically relevant kinase targets to support development of precision therapies in medulloblastoma. To this end, we are currently performing upstream kinase analysis aiming to identify subgroup-dependent kinases. 1. Zomerman WW, Plasschaert SLA, Conroy S, Scherpen FJ, Meeuwsen-de Boer TGJ, Lourens HJ, et al. Identification of Two Protein-Signaling States Delineating Transcriptionally Heterogeneous Human Medulloblastoma. Cell Rep. 2018;22(12):3206–16.