Clinical and Biological Heterogeneity in MYC/MYCN-Amplified Medulloblastoma

Academic Background

Medulloblastoma (MB) is one of the most common malignant brain tumors in children. Despite recent advances in treatment, approximately 30% of patients still die from the disease, and survivors often face long-term treatment-related complications. Amplifications of the MYC and MYCN genes are the most frequent oncogenic amplification events in medulloblastoma and are typically associated with high-risk (HR) disease. However, while many MYC/MYCN-amplified tumors are refractory to treatment, some patients achieve long-term survival. This heterogeneity has prompted researchers to investigate the clinical and biological differences within MYC/MYCN-amplified medulloblastoma to provide more precise treatment strategies for patients.

Source of the Paper

This paper was co-authored by Edward C. Schwalbe, Janet C. Lindsey, Marina Danilenko, and others from institutions such as Newcastle University and Heidelberg University Hospital. It was published online ahead of print on October 8, 2024, in the journal Neuro-Oncology. The study was funded by organizations including Cancer Research UK and The Brain Tumour Charity.

Research Process

1. Study Subjects and Sample Collection

The research team screened over 1,600 diagnostic cases to identify 64 MYC-amplified medulloblastomas (MYC-MB) and 95 MYCN-amplified medulloblastomas (MYCN-MB). These samples were derived from retrospective cohorts from the UK CCLG and Heidelberg, with all samples approved by ethics committees and obtained with informed consent from patients.

2. Molecular and Clinical Feature Analysis

The team used fluorescence in situ hybridization (FISH) and DNA methylation microarray technology to detect MYC and MYCN amplifications. FISH analyzed 100-200 non-overlapping nuclei to estimate the proportion of amplified cells. Methylation microarray data were analyzed using the Conumee software for copy number variation (CNV) analysis, with amplification defined as a focal region (<10 Mb) and an amplitude >0.4.

3. Molecular Grouping and Subgroup Analysis

The study used Illumina methylation microarrays to classify tumors into molecular groups: WNT, SHH, Group 3, and Group 4. The SHH subgroup was further subdivided based on specific methylation signatures. Additionally, the study evaluated clinicopathological features such as large-cell/anaplastic (LCA) pathology, metastatic status (M+), and extent of surgical resection (STR).

4. Genomic Analysis

The team analyzed genomic instability, including chromothripsis and gene fusion events, using SNP6 microarrays and RNA sequencing (RNA-seq). Chromothripsis was inferred from SNP6 microarray CNV profiles, while gene fusions were detected via RNA-seq data and validated by RT-PCR and Sanger sequencing.

5. Survival Analysis

Progression-free survival (PFS) was used as the primary endpoint, defined as the time from diagnosis to disease progression. Kaplan-Meier curves and Cox proportional hazards models were employed to assess the impact of different clinical and molecular features on survival.

Key Findings

1. Heterogeneity in MYC-Amplified Medulloblastoma

The study found that most MYC-MB cases belonged to Group 3 (79%) and were predominantly diagnosed in children over 3 years old (69%). The MYC-MB cohort was further divided into a “canonical” high-risk group (82%) and a non-canonical group (18%). The canonical group had a dismal 5-year PFS of 11%, regardless of treatment, while the non-canonical group achieved a 5-year PFS of 61%.

2. Heterogeneity in MYCN-Amplified Medulloblastoma

MYCN-MB cases were primarily distributed between SHH and Group 4. SHH-MYCN-MB patients had a very poor prognosis, with a 5-year PFS of only 20%, while Group 4-MYCN-MB patients had a 5-year PFS of 56%. Additionally, SHH-MYCN-MB exhibited a high rate of TP53 mutations (63%), most of which were germline.

3. Genomic Instability and Gene Fusions

The study revealed significant differences in chromothripsis and gene fusion patterns between MYC-MB and MYCN-MB. Chromothripsis in MYC-MB was predominantly localized to chromosome 8 (where MYC is located), while in MYCN-MB, it involved multiple chromosomes. Furthermore, MYC-MB frequently exhibited gene fusions involving the PVT1 gene, whereas MYCN-MB fusions involved DDX1 and NBAS genes.

4. Risk Stratification and Treatment Recommendations

The study proposed a risk stratification system based on molecular groups and clinical features. Canonical MYC-MB and SHH-MYCN-MB were classified as very high-risk (VHR) groups, for which current treatments are ineffective, necessitating the development of new therapeutic strategies. Other MYC/MYCN-amplified tumors could achieve better survival rates with conventional risk-adapted therapies.

Conclusions and Significance

This study revealed significant clinical and biological heterogeneity in MYC/MYCN-amplified medulloblastoma, providing critical insights for clinical diagnosis and treatment. By integrating molecular grouping, subgroup analysis, and clinical features, the research team was able to more accurately identify high-risk patient groups and develop new treatment strategies for these patients. Additionally, the study emphasized the importance of FISH in detecting MYC/MYCN amplifications, as methylation microarrays sometimes failed to detect low-frequency amplification events.

Research Highlights

1. Heterogeneity Revealed: The study systematically uncovered the clinical and biological heterogeneity within MYC/MYCN-amplified medulloblastoma, laying the groundwork for precision medicine.
2. Risk Stratification: The proposed risk stratification system effectively identifies very high-risk patients, providing a crucial basis for clinical decision-making.
3. Genomic Instability: The study identified differences in chromothripsis and gene fusion patterns between MYC-MB and MYCN-MB, offering clues for further research into their biological mechanisms.
4. Treatment Strategies: The study highlighted the urgent need to develop new treatment strategies for very high-risk patients, guiding the design of future clinical trials.

Additional Valuable Information

The study also found that differences in genomic instability patterns between MYC-MB and MYCN-MB may explain their distinct clinical behaviors. For example, chromothripsis in MYC-MB was largely confined to chromosome 8, while in MYCN-MB, it involved multiple chromosomes, potentially accounting for their differences in treatment response and prognosis.

This research provides a significant scientific foundation for the diagnosis and treatment of MYC/MYCN-amplified medulloblastoma and points the way for future studies.