Identification of Two Protein-Signaling States Delineating Transcriptionally Heterogeneous Human Medulloblastoma

Abstract

The brain cancer medulloblastoma consists of different transcriptional subgroups. To characterize medulloblastoma at the phosphoprotein-signaling level, we performed high-throughput peptide phosphorylation profiling on a large cohort of SHH (Sonic Hedgehog), group 3, and group 4 medulloblastomas. We identified two major protein-signaling profiles. One profile was associated with rapid death post-recurrence and resembled MYC-like signaling for which MYC lesions are sufficient but not necessary. The second profile showed enrichment for DNA damage, as well as apoptotic and neuronal signaling. Integrative analysis demonstrated that heterogeneous transcriptional input converges on these protein-signaling profiles: all SHH and a subset of group 3 patients exhibited the MYC-like protein-signaling profile; the majority of the other group 3 subset and group 4 patients displayed the DNA damage/apoptotic/neuronal signaling profile. Functional analysis of enriched pathways highlighted cell-cycle progression and protein synthesis as therapeutic targets for MYC-like medulloblastoma.

Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors

“…Interestingly, these tumors depend on PRKDC (Protein Kinase, DNA activated, Catalytic peptide, acting as a molecular sensor of DNA damage) activity for survival in response to DNA damage: PRKDC inhibition increases the radiation sensitivity of these tumors and may represent a potential therapeutic target [414]. Finally, a third study, through the integration of transcriptional and genetic profiling with high throughput peptide phosphorylation profiling, provided evidence that Groups 3 and 4 medulloblastomas are heterogeneous [415]. Particularly, medulloblastoma peptide phosphorylation profiling showed two phosphoprotein-signaling profiles: the first, protein-signaling profiling that was reminiscent of the signaling that could be induced by the MYC oncoprotein, in the absence of MYC aberrancies and associated with rapid death post-recurrence (most of Group 3 tumors correspond to this group and were termed 3A); the second profile displayed increased neuronal, apoptotic, and DNA-damage signaling (most of Group 4 tumors correspond to this group and were termed 4B) [415].…”

“…Finally, a third study, through the integration of transcriptional and genetic profiling with high throughput peptide phosphorylation profiling, provided evidence that Groups 3 and 4 medulloblastomas are heterogeneous [415]. Particularly, medulloblastoma peptide phosphorylation profiling showed two phosphoprotein-signaling profiles: the first, protein-signaling profiling that was reminiscent of the signaling that could be induced by the MYC oncoprotein, in the absence of MYC aberrancies and associated with rapid death post-recurrence (most of Group 3 tumors correspond to this group and were termed 3A); the second profile displayed increased neuronal, apoptotic, and DNA-damage signaling (most of Group 4 tumors correspond to this group and were termed 4B) [415]. Functional studies and analysis of activated pathways showed that cell cycle transition and protein synthesis are actionable targets in MYC-like medulloblastomas [415].…”

“…Particularly, medulloblastoma peptide phosphorylation profiling showed two phosphoprotein-signaling profiles: the first, protein-signaling profiling that was reminiscent of the signaling that could be induced by the MYC oncoprotein, in the absence of MYC aberrancies and associated with rapid death post-recurrence (most of Group 3 tumors correspond to this group and were termed 3A); the second profile displayed increased neuronal, apoptotic, and DNA-damage signaling (most of Group 4 tumors correspond to this group and were termed 4B) [415]. Functional studies and analysis of activated pathways showed that cell cycle transition and protein synthesis are actionable targets in MYC-like medulloblastomas [415]. These studies strongly support that multiomic approaches that include genomics, epigenomics, transcriptomics, and proteomics, including phosphoproteomics, are required to complete the definition of the molecular heterogeneity of medulloblastomas and to identify new potential therapeutic targets.…”

The developmental stage of the medulloblastoma cell-of-origin restricts Hedgehog pathway usage and drug sensitivity

“…The yellow cluster contained genes that were highest expressed at embryonic time points (E15.5 and E17.5, n=471 genes), the orange cluster genes that were high during embryonic and early postnatal time points (E15.5-P7, n=1541 genes), genes in the red cluster were highest expressed at early postnatal time points (P0 and P7, n=619 genes), and light and dark blue clusters contained the genes that were induced upon granule neuron maturation (P14 and P30, n=763 and 943 genes, respectively) ( Figure 1D,E). To identify enriched biological processes (Gene Ontology) within these gene clusters, we used the Database for Annotation, Visualization and Integrated Discovery (DAVID) and visualized the data using Cytoscape (Figures 2 and S1, and Table S3) [51]. At the early stages of CGNP development (yellow cluster), there is a strong enrichment of processes associated with early neural development such as axon and dendrite formation and developmental transcription factor-driven gene expression, but also glycolysis (Figures 2 and S1).…”

Molecular markers and potential therapeutic targets in non-WNT/non-SHH (group 3 and group 4) medulloblastomas

“…The first profile resembled MYC-like signaling, encompassing all of the SHH-activated and majority of group 3 samples. The other protein profile consisted of the rest of group 3 and the bulk of group 4 tumors, displaying DNA damage/apoptosis/neuronal signaling [58].…”