In a groundbreaking exploration of medulloblastoma, one of the most common malignant pediatric brain tumors, researchers have unveiled new insights into the intricate evolutionary dynamics of oncogene amplifications driving tumor progression. Traditionally, the amplification of MYC or MYCN oncogenes within medulloblastoma tumors has been viewed as mutually exclusive, a long-standing dogma supported by bulk DNA analyses. However, state-of-the-art single-cell multiomic and spatial transcriptomics technologies have shattered this paradigm by revealing the coexistence of distinct subclones harboring either MYC or MYCN amplifications within the same primary tumor.
This pivotal discovery emerged from the detailed examination of a complex primary tumor sample, designated MB272, which uniquely contained two separate tumor subclones—one amplified for MYC and the other for MYCN. Previous bulk methylation profiling had characterized this tumor as solely MYC-amplified. Yet, the application of single-nucleus ATAC-seq, RNA-seq, and spatial transcriptomic mapping unveiled a far more nuanced architecture: spatially segregated subclones with distinct oncogene amplifications and divergent biological states, reflecting discrete evolutionary trajectories within the same neoplasm.
Remarkably, the MYC-amplified subclone distinguished itself with a pronounced progenitor-like phenotype, exhibiting proliferative and stem-like activities. In contrast, the MYCN-amplified subclone presented characteristics associated with differentiation. This spatial and phenotypic segregation was not random but rather mirrored the tumor’s phylogenetic evolutionary tree constructed through single-nucleus RNA sequencing-based copy number variation (CNV) analyses. Such a degree of intratumoral heterogeneity challenges existing frameworks that rely heavily on bulk profiling methods, which often mask these subclonal complexities due to cellular admixture and low-frequency populations.
Expanding the lens beyond this exceptional case, the authors conducted a systematic survey of a larger medulloblastoma cohort to investigate the prevalence of simultaneous MYC and MYCN amplifications. They identified six additional putative cases through DNA methylation-based CNV profiling alone. Complementary immunohistochemical analyses further corroborated the presence of both MYC and MYCN expression in a single tumor specimen. Notably, during manuscript preparation, independent case reports emerged with similar findings, reinforcing the notion that co-occurrence of MYC and MYCN amplifications may be more common than previously recognized.
Despite this co-occurrence at the tumor level, single-cell resolution data clarified that individual tumor cells exclusively express either MYC or MYCN, never both simultaneously. This mutual exclusivity at the cellular level coupled with the spatial segregation of these subclones hints at competitive mechanisms and microenvironmental niches fostering discrete oncogenic programs within the tumor ecosystem.
Capitalizing on these insights, the investigators developed unique gene expression signatures for MYC- and MYCN-amplified subclones derived from single-cell transcriptomic data. This enabled a novel deconvolution approach applied to bulk transcriptomes from independent cohorts, which revealed additional tumors harboring dual oncogene-amplified subclones. Validation via fluorescence in situ hybridization (FISH) on available tumor material confirmed the presence of both subclonal populations, underscoring the utility of this approach for detecting intratumoral heterogeneity beyond the reach of traditional bulk methods.
Intriguingly, the relative abundance of MYC or MYCN subclones predicted patient outcomes, particularly within subgroup V medulloblastomas. Patients exhibiting MYC-amplified subclones identified through deconvolution analysis demonstrated significantly poorer overall survival. This aligns with clinical expectations, as MYC amplification is associated with aggressive tumor behavior. Such findings imply that the presence of subclonal MYC amplifications at diagnosis—not easily detected by standard clinical assays—may serve as a prognostic biomarker for high-risk disease and potential relapse.
Delving deeper into tumor evolution, single-nucleus molecular profiling of four relapsed MYC-amplified tumor samples revealed that relapse tumors uniformly harbored MYC amplification across all cells. Notably, in the case initially containing both MYC and MYCN subclones at diagnosis, the MYCN subclone was completely lost upon relapse. Spatial transcriptomic analyses corroborated the disappearance of MYCN-expressing cells in the relapsed tumor, reinforcing the concept that MYC-amplified subclones outcompete other oncogene-driven clones during tumor progression and recurrence.
Taken together, these findings illuminate the hierarchical and dynamic interplay among oncogene-amplified subclones driving medulloblastoma progression. The co-existence of MYC and MYCN amplifications within a single tumor, each confined to unique cellular and spatial niches, not only challenges previous dogmas but also offers profound clinical implications. Early detection of MYC-amplified subclones could refine risk stratification and therapeutic decision-making, particularly as MYC-driven subclones possess the capacity to dominate and dictate relapse.
Technologically, the success of this work underscores the transformative power of integrating single-cell multi-omic modalities with spatial transcriptomics, enabling unparalleled resolution of tumor clonal heterogeneity and spatial architecture. These methods unblock previously inaccessible layers of biological information, allowing researchers to map tumor evolution and subclone interactions in exquisite detail.
Looking ahead, translating these molecular insights into clinical practice will necessitate robust assays capable of identifying and monitoring oncogene-amplified subclones in patients. Moreover, therapeutic strategies aimed at targeting the dominant MYC-amplified subclones hold promise for improving outcomes, given their apparent role in driving tumor relapse and treatment resistance.
Ultimately, this research not only redefines our understanding of oncogene coexistence in medulloblastoma but also exemplifies the imperative role of cutting-edge single-cell and spatial technologies in decoding cancer complexity. By revealing how distinct oncogenic events spatially segregate and evolve within tumors, this study lays critical groundwork for precision oncology approaches tailored to subclonal tumor ecosystems.
Subject of Research: Medulloblastoma tumor heterogeneity and oncogene amplification dynamics
Article Title: Oncogene aberrations drive medulloblastoma progression, not initiation
Article References:
Okonechnikov, K., Joshi, P., Körber, V. et al. Oncogene aberrations drive medulloblastoma progression, not initiation. Nature (2025). https://doi.org/10.1038/s41586-025-08973-5
Image Credits: AI Generated
