Timing of tumor initation predicts medulloblastoma heterogeneity, stem cell composition and probability of relapse [array]

Patients with medulloblastoma are typically treated with a narrow range of therapies, but may experience widely divergent outcomes; 80-90% become long-term survivors while 20% develop incurable recurrence. Transcriptomic profiling has identified four subgroups with different recurrence risks, but outcomes remain variable for individual patients within each subgroup. To gain new insight into why patients with similar-appearing tumors have variable outcomes, we examined how the timing of tumor initiation effects medulloblastomas triggered by a single, common driver mutation. We genetically-engineered mice to express an oncogenic Smo allele starting early in development in the broad lineage of neural stem cells, or later, in the more committed lineage of cerebellar granule neuron progenitors. Both groups developed medulloblastomas and no other tumors. We compared medulloblastoma progression, response to therapy, gene expression profile and cellular heterogeneity, determined by single cell transcriptomic analysis (scRNA-seq). The average transcriptomic profiles of the tumors were similar. However, stem cell-triggered medulloblastomas progressed faster, contained more OLIG2-expressing tumor stem cells, and consistently showed radioresistance. In contrast, progenitor-triggered MBs progressed slower, lost stem cell character over time and were radiosensitive. Progenitor-triggered medulloblastomas also contained more diverse stromal populations, including tumor-associated macrophages, indicating that the timing of oncogenesis affected the subsequent interactions between the tumor and microenvironment. Our findings show that developmental events in tumorigenesis may be impossible to infer from transcriptomic profile, but while remaining cryptic can nevertheless influence tumor composition and the outcome of therapy. Precise understanding of medulloblastoma pathogenesis and prognosis requires supplementing transcriptomic data with biomarkers of cellular heterogeneity. Expression microarray comparison between SHH-driven medulloblastomas that form in 2 different genotypes of mice, using Affymetrix expression arrays. We performed an expression microarray analysis of medulloblastomas that form in transgenic mice. This bulk transcriptomic analysis is complemented by a scRNA-seq analysis. We compare tumors that form in Gfap-Cre/SmoM2 (G-Smo) mice to umors that form in Math1-Cre/SmoM2 (M-Smo) mice. In both genotypes, tumors are driven by the same mutant, oncogenic allele of Smo. In G-Smo mice, SmoM2 is expressed starting from neural stem cells early brain development and continuing in most cells of the brain. In M-Smo mice, SmoM2 is expressed starting in committed neural progenitors later in development, and continuing in a subset of neurons. Both genotypes develop medulloblastoma and no othe tumor type. All mice were raised to P15 after which tumors were dissected and processed for transcriptomic anlaysis.