NEW YORK – A German-led research team turned to single-cell genomics and spatial transcriptomics to tease out the genomic alteration types involved in tumor initiation, evolution, and progression in medulloblastoma, a form of fast-growing brain tumor typically found in children.
For a study published in Nature on Wednesday, co-senior and co-corresponding Stefan Pfister and Lena Kutscher of the Hopp Children's Cancer Center and the National Center for Tumor Diseases and colleagues in Germany and the UK used single-nucleus RNA sequencing, 10x Genomics-based single-nucleus ATAC-seq, and spatial transcriptomics to distinguish between alterations involved in medulloblastoma and those involved in tumor progression for medulloblastoma tumors in the heterogeneous and aggressive group 3 and group 4 subtypes, which encompass eight DNA methylation-based subgroups.
"A fundamental question of which genetic events initiate and drive these [group 3/4] tumors remain unanswered," Pfister, Kutscher, and colleagues explained. "Using single-cell multiomics and spatial transcriptomic approaches, we determined the interplay between large-scale copy number variants (CNVs) and single-gene somatic events driving medulloblastoma heterogeneity and evolution."
By combining the multiomic data with mutational clock, early common ancestor, most recent common ancestor, population genetics, and other mathematical models, the team was able to untangle evolutionary features in tumors and tumor subclones, along with the timing and cell type involved in tumor initiation, which appeared to stretch back as far as the first trimester of development.
Although the 16 primary medulloblastoma and four relapsed cases considered all contained alterations linked to amplification or overexpression of oncogenes such as MYC, MYCN, or PRDM6, the team's analyses argued against the notion that the single-gene mutations or expression changes had a significant role in medulloblastoma tumor initiation processes.
Instead, changes affecting individual oncogenes tended to pop up in tumor subclones during later stages of tumor evolution, contributing to tumor features such as treatment resistance or progression, or disease recurrence, while large copy number changes or chromosome-scale alterations appeared to play a more pronounced role in medulloblastoma initiation.
"We show that large-scale genomic aberrations (i.e., whole chromosome or chromosome arm gains or losses) are the likely first hit in Group 3/4 medulloblastoma, with focal oncogene aberrations (e.g. MYC amplifications) happening later in tumor evolution," Kutscher and Pfister said in an email.
Based on their findings so far, the investigators suggested that an improved understanding of the oncogene changes and larger alterations present in medulloblastoma tumor subclones could have implications for treating and managing medulloblastoma cases in a tumor evolution-informed manner.
"Because MYC clones grow out at relapse, it will become important to classify even subclonal amplifications as 'MYC-driven,' which may alter how risk is assessed and thus, how patients are treated," Kutscher and Pfister suggested.
They noted that their work also provides previously unappreciated clues to biological processes at play in normal cerebellum tissues and during the process of tumor development, where aneuploidy appears to contribute to medulloblastoma initiation.
"Because large-scale aneuploidy can be detected with much lower DNA content than point mutations, we may be able to use it for screening and very early detection, maybe as early as birth, once the assays are sensitive and specific enough," Kutscher and Pfister added, noting that there may be opportunities to leverage new knowledge on tumor trajectory to come up with better models for studying tumor behavior, as well.
"[W]e can create better models in the lab that closely mimic the disease evolution, allowing us to create a system to better test therapeutics preclinically and identify better treatment options," they explained.