Methylation Profiling of Medulloblastoma in a Clinical Setting Permits Sub-classification and Reveals New Outcome Predictions

T2-FLAIR Mismatch Sign Predicts DNA Methylation Subclass and CDKN2A/B Status in IDH-Mutant Astrocytomas

PURPOSE

DNA methylation profiling stratifies isocitrate dehydrogenase (IDH)-mutant astrocytomas into methylation low- and high-grade groups. We investigated the utility of the T2-fluid-attenuated inversion recovery (T2-FLAIR) mismatch sign for predicting DNA methylation grade and cyclin-dependent kinase inhibitor 2A/B (CDKN2A/B) homozygous deletion, a molecular biomarker for grade 4 IDH-mutant astrocytomas, according to the 2021 World Health Organization classification.

EXPERIMENTAL DESIGN

Preoperative MRI scans of IDH-mutant astrocytomas subclassified by DNA methylation profiling (n = 71) were independently evaluated by two radiologists for the T2-FLAIR mismatch sign. The diagnostic utility of T2-FLAIR mismatch in predicting methylation grade, CDKN2A/B status, copy number variation, and survival was analyzed.

RESULTS

The T2-FLAIR mismatch sign was present in 21 of 45 (46.7%) methylation low-grade and 1 of 26 (3.9%) methylation high-grade cases (P < 0.001), resulting in 96.2% specificity, 95.5% positive predictive value, and 51.0% negative predictive value for predicting low methylation grade. The T2-FLAIR mismatch sign was also significantly associated with intact CDKN2A/B status (P = 0.028) with 87.5% specificity, 86.4% positive predictive value, and 42.9% negative predictive value. Overall multivariable Cox analysis showed that retained CDKN2A/B status remained significant for progression-free survival (P = 0.01). Multivariable Cox analysis of the histologic grade 3 subset, which was nearly evenly divided by CDKN2A/B status, copy number variation, and methylation grade, showed trends toward significance for DNA methylation grade with overall survival (P = 0.045) and CDKN2A/B status with progression-free survival (P = 0.052).

CONCLUSIONS

The T2-FLAIR mismatch sign is highly specific for low methylation grade and intact CDKN2A/B in IDH-mutant astrocytomas.

Long-read sequencing for brain tumors

Brain tumors and genomics have a long-standing history given that glioblastoma was the first cancer studied by the cancer genome atlas. The numerous and continuous advances through the decades in sequencing technologies have aided in the advanced molecular characterization of brain tumors for diagnosis, prognosis, and treatment. Since the implementation of molecular biomarkers by the WHO CNS in 2016, the genomics of brain tumors has been integrated into diagnostic criteria. Long-read sequencing, also known as third generation sequencing, is an emerging technique that allows for the sequencing of longer DNA segments leading to improved detection of structural variants and epigenetics. These capabilities are opening a way for better characterization of brain tumors. Here, we present a comprehensive summary of the state of the art of third-generation sequencing in the application for brain tumor diagnosis, prognosis, and treatment. We discuss the advantages and potential new implementations of long-read sequencing into clinical paradigms for neuro-oncology patients.

MBMethPred: a computational framework for the accurate classification of childhood medulloblastoma subgroups using data integration and AI-based approaches

Childhood medulloblastoma is a malignant form of brain tumor that is widely classified into four subgroups based on molecular and genetic characteristics. Accurate classification of these subgroups is crucial for appropriate treatment, monitoring plans, and targeted therapies. However, misclassification between groups 3 and 4 is common. To address this issue, an AI-based R package called MBMethPred was developed based on DNA methylation and gene expression profiles of 763 medulloblastoma samples to classify subgroups using machine learning and neural network models. The developed prediction models achieved a classification accuracy of over 96% for subgroup classification by using 399 CpGs as prediction biomarkers. We also assessed the prognostic relevance of prediction biomarkers using survival analysis. Furthermore, we identified subgroup-specific drivers of medulloblastoma using functional enrichment analysis, Shapley values, and gene network analysis. In particular, the genes involved in the nervous system development process have the potential to separate medulloblastoma subgroups with 99% accuracy. Notably, our analysis identified 16 genes that were specifically significant for subgroup classification, including EP300, CXCR4, WNT4, ZIC4, MEIS1, SLC8A1, NFASC, ASCL2, KIF5C, SYNGAP1, SEMA4F, ROR1, DPYSL4, ARTN, RTN4RL1, and TLX2. Our findings contribute to enhanced survival outcomes for patients with medulloblastoma. Continued research and validation efforts are needed to further refine and expand the utility of our approach in other cancer types, advancing personalized medicine in pediatric oncology.

11p15 Epimutations in Pediatric Embryonic Tumors: Insights from a Methylome Analysis

Embryonic tumors share few recurrent mutations, suggesting that other mechanisms, such as aberrant DNA methylation, play a prominent role in their development. The loss of imprinting (LOI) at the chromosome region 11p15 is the germline alteration behind Beckwith-Wiedemann syndrome that results in an increased risk of developing several embryonic tumors. This study analyzed the methylome, using EPIC Beadchip arrays from 99 sporadic embryonic tumors. Among these tumors, 46.5% and 14.6% presented alterations at imprinted control regions (ICRs) 1 and 2, respectively. Based on the methylation levels of ICR1 and ICR2, four clusters formed with distinct methylation patterns, mostly for medulloblastomas (ICR1 loss of methylation (LOM)), Wilms tumors, and hepatoblastomas (ICR1 gain of methylation (GOM), with or without ICR2 LOM). To validate the results, the methylation status of 29 cases was assessed with MS-MLPA, and a high level of agreement was found between both methodologies: 93% for ICR1 and 79% for ICR2. The MS-MLPA results indicate that 15 (51.7%) had ICR1 GOM and 11 (37.9%) had ICR2 LOM. To further validate our findings, the ICR1 methylation status was characterized via digital PCR (dPCR) in cell-free DNA (cfDNA) extracted from peripheral blood. At diagnosis, we detected alterations in the methylation levels of ICR1 in 62% of the cases, with an agreement of 76% between the tumor tissue (MS-MLPA) and cfDNA methods. Among the disagreements, the dPCR was able to detect ICR1 methylation level changes presented at heterogeneous levels in the tumor tissue, which were detected only in the methylome analysis. This study highlights the prevalence of 11p15 methylation status in sporadic embryonic tumors, with differences relating to methylation levels (gain or loss), location (ICR1 or ICR2), and tumor types (medulloblastomas, Wilms tumors, and hepatoblastomas).

Applications and current challenges of chimeric antigen receptor T cells in treating high-grade gliomas in adult and pediatric populations

High-grade gliomas (HGGs) continue to be some of the most devastating diseases in the USA. Despite extensive efforts, the survival of HGG patients has remained relatively stagnant. Chimeric antigen receptor (CAR) T-cell immunotherapy has recently been studied in the context of improving these tumors' clinical outcomes. HGG murine models treated with CAR T cells targeting tumor antigens have shown reduced tumor burden and longer overall survival than models without treatment. Subsequent clinical trials investigating the efficacy of CAR T cells have further shown that this therapy could be safe and might reduce tumor burden. However, there are still many challenges that need to be addressed to optimize the safety and efficacy of CAR T-cell therapy in treating HGG patients.

Clinical utility of whole-genome DNA methylation profiling as a primary molecular diagnostic assay for central nervous system tumors-A prospective study and guidelines for clinical testing

Background

Central nervous system (CNS) cancer is the 10th leading cause of cancer-associated deaths for adults, but the leading cause in pediatric patients and young adults. The variety and complexity of histologic subtypes can lead to diagnostic errors. DNA methylation is an epigenetic modification that provides a tumor type-specific signature that can be used for diagnosis.

Methods

We performed a prospective study using DNA methylation analysis as a primary diagnostic method for 1921 brain tumors. All tumors received a pathology diagnosis and profiling by whole genome DNA methylation, followed by next-generation DNA and RNA sequencing. Results were stratified by concordance between DNA methylation and histopathology, establishing diagnostic utility.

Results

Of the 1602 cases with a World Health Organization histologic diagnosis, DNA methylation identified a diagnostic mismatch in 225 cases (14%), 78 cases (5%) did not classify with any class, and in an additional 110 (7%) cases DNA methylation confirmed the diagnosis and provided prognostic information. Of 319 cases carrying 195 different descriptive histologic diagnoses, DNA methylation provided a definitive diagnosis in 273 (86%) cases, separated them into 55 methylation classes, and changed the grading in 58 (18%) cases.

Conclusions

DNA methylation analysis is a robust method to diagnose primary CNS tumors, improving diagnostic accuracy, decreasing diagnostic errors and inconclusive diagnoses, and providing prognostic subclassification. This study provides a framework for inclusion of DNA methylation profiling as a primary molecular diagnostic test into professional guidelines for CNS tumors. The benefits include increased diagnostic accuracy, improved patient management, and refinements in clinical trial design.

Primary leptomeningeal medulloblastoma: a case-based review

BACKGROUND

Medulloblastoma (MB) is the most common malignant pediatric brain tumor, accounting for 40% of childhood tumors in posterior fossa. Metastatic disease, occurring in 20-30% of all medulloblastoma cases at diagnosis, is largely exclusive to the leptomeninges. On the contrary, primary leptomeningeal medulloblastoma or so-called chameleon medulloblastoma, defined by the absence of a detectable intraparenchymal lesion with a widespread diffusion along leptomeninges, is a rare entity of difficult diagnosis with only a few cases reported in literature.

METHODS AND RESULTS

A comprehensive literature search of three databases (PubMed, Ovid Medline, and Ovid Embase) have been conducted to identify pertinent papers focusing on the diagnostic process, management, and treatment of primary leptomeningeal medulloblastoma and its peculiar features. To our knowledge, only eight cases are described in literature, including five pediatric patients and three adults, two of which with the initial involvement of the spinal cord. In addition, we report another two pediatric cases, showing widespread primary diffusion along leptomeninges of brain and spinal cord. Finally, we analyze in-depth the peculiar morphological MRI features of this tumor.

CONCLUSION

The classification and treatment of medulloblastomas are likely to change in the coming years due to new insights into the molecular biology of medulloblastoma. Primary leptomeningeal medulloblastoma could represent another potential challenge for biologists to start exploring the underlying mechanisms of this different clinical and pathological entity, with different implications for diagnosis and its management.

Spectrum of medulloblastoma subtypes and frequency of MYC amplification; Experience from a tertiary care center in Saudi Arabia

Objectives:

To clarify the spectrum of morphological and molecular subtypes of medulloblastoma (MBL), in addition to MYC and MYCN amplification statuses in a cohort of Saudi patients. The latter was correlated with patient outcome.

Methods:

We conducted a retrospective cohort study of 57 patients with MBL, diagnosed at the central laboratory of King Abdulaziz Medical City in Riyadh, Saudi Arabia, between 2006 and 2019. Molecular analysis for MYC and MYCN amplification was performed for the 19 most recently diagnosed patients.

Results:

Classic MBL was the most prevalent histologic subtype and MBL with extensive nodularity was the rarest. The non-WNT/non-SHH molecular subgroup was the most common while the WNT-activated was the least common. Among 19 patients analyzed, MYC and MYCN amplifications were discovered in 2 (10.5%) and 1 (5.3%) cases, respectively, using interphase fluorescence in-situ hybridization. The 2 MYC amplified cases belonged to the large cell/anaplastic subtype and had the worst outcomes.

Conclusion:

The MYC amplification corresponded with poor prognosis, the large cell/anaplastic variant of MBL, and the non-WNT/non-SHH molecular subtype.