The potential for epigenetic analysis of paediatric CNS tumours to improve diagnosis, treatment and prognosis

Detection of cell-free histones in the cerebrospinal fluid of pediatric central nervous system malignancies by imaging flow cytometry

Introduction: Pediatric brain tumours (PBT) are one of the most common malignancies during childhood, with variable severity according to the location and histological type. Certain types of gliomas, such a glioblastoma and diffuse intrinsic pontine glioma (DIPG), have a much higher mortality than ependymoma and medulloblastoma. Early detection of PBT is essential for diagnosis and therapeutic interventions. Liquid biopsies have been demonstrated using cerebrospinal fluid (CSF), mostly restricted to cell free DNA, which display limitations of quantity and integrity. In this pilot study, we sought to demonstrate the detectability and robustness of cell free histones in the CSF. Methods: We collected CSF samples from a pilot cohort of 8 children with brain tumours including DIPG, medulloblastoma, glioblastoma, ependymoma and others. As controls, we collected CSF samples from nine children with unrelated blood malignancies and without brain tumours. We applied a multichannel flow imaging approach on ImageStream(X) to image indiviual histone or histone complexes on different channels. Results: Single histones (H2A, macroH2A1.1, macroH2A1.2 H2B, H3, H4 and histone H3 bearing the H3K27M mutation), and histone complexes are specifically detectable in the CSF of PBT patients. H2A and its variants macroH2A1.1/macroH2A1/2 displayed the strongest signal and abundance, together with disease associated H3K27M. In contrast, mostly H4 is detectable in the CSF of pediatric patients with blood malignancies. Discussion: In conclusion, free histones and histone complexes are detectable with a strong signal in the CSF of children affected by brain tumours, using ImageStream(X) technology and may provide additive diagnostic and predictive information.

The Neurodevelopmental and Molecular Landscape of Medulloblastoma Subgroups: Current Targets and the Potential for Combined Therapies

Medulloblastoma is the most common malignant pediatric brain tumor and is associated with significant morbidity and mortality in the pediatric population. Despite the use of multiple therapeutic approaches consisting of surgical resection, craniospinal irradiation, and multiagent chemotherapy, the prognosis of many patients with medulloblastoma remains dismal. Additionally, the high doses of radiation and the chemotherapeutic agents used are associated with significant short- and long-term complications and adverse effects, most notably neurocognitive delay. Hence, there is an urgent need for the development and clinical integration of targeted treatment regimens with greater efficacy and superior safety profiles. Since the adoption of the molecular-based classification of medulloblastoma into wingless (WNT) activated, sonic hedgehog (SHH) activated, group 3, and group 4, research efforts have been directed towards unraveling the genetic, epigenetic, transcriptomic, and proteomic profiles of each subtype. This review aims to delineate the progress that has been made in characterizing the neurodevelopmental and molecular features of each medulloblastoma subtype. It further delves into the implications that these characteristics have on the development of subgroup-specific targeted therapeutic agents. Furthermore, it highlights potential future avenues for combining multiple agents or strategies in order to obtain augmented effects and evade the development of treatment resistance in tumors.

Classifying Medulloblastoma Subgroups Based on Small, Clinically Achievable Gene Sets

As treatment protocols for medulloblastoma (MB) are becoming subgroup-specific, means for reliably distinguishing between its subgroups are a timely need. Currently available methods include immunohistochemical stains, which are subjective and often inconclusive, and molecular techniques—e.g., NanoString, microarrays, or DNA methylation assays—which are time-consuming, expensive and not widely available. Quantitative PCR (qPCR) provides a good alternative for these methods, but the current NanoString panel which includes 22 genes is impractical for qPCR. Here, we applied machine-learning–based classifiers to extract reliable, concise gene sets for distinguishing between the four MB subgroups, and we compared the accuracy of these gene sets to that of the known NanoString 22-gene set. We validated our results using an independent microarray-based dataset of 92 samples of all four subgroups. In addition, we performed a qPCR validation on a cohort of 18 patients diagnosed with SHH, Group 3 and Group 4 MB. We found that the 22-gene set can be reduced to only six genes (IMPG2, NPR3, KHDRBS2, RBM24, WIF1, and EMX2) without compromising accuracy. The identified gene set is sufficiently small to make a qPCR-based MB subgroup classification easily accessible to clinicians, even in developing, poorly equipped countries.

Pediatric low-grade gliomas: molecular characterization of patient-derived cellular models

PURPOSE

Pediatric low-grade gliomas (pLGGs), the most frequent pediatric brain tumors, include different entities harboring distinct histological and molecular features. A major limitation in the development of treatments for these tumors is the absence of reliable in vitro models that would allow a better understanding of the molecular mechanisms that support their growth. Surgical excision is the primary treatment method and the extent of resection represents one of the strongest prognostic factors. pLGGs that cannot be completely resected are prone to recur and associated with relapses and extensive morbidities, thus remaining a major clinical challenge.

METHODS

We established a protocol to successfully derive primary patient-derived pLGG cells and to fully characterize them from a molecular point of view.

RESULTS

Primary patients-derived pLGG cells were extensively analyzed in order to confirm their reliability as cellular models. Specifically, we evaluated the growth rate, senescence, and molecular features, such as BRAF mutational status, methylation, and protein expression profile.

CONCLUSION

This study extensively describes pLGG primary cellular models in terms of isolation, culture method, and molecular characterization that can be used to investigate pLGG biology.

Medulloblastoma epigenetics and the path to clinical innovation

INTRODUCTION

In the last decade, a number of genomic and pharmacological studies have demonstrated the importance of epigenetic dysregulation in medulloblastoma initiation and progression. High throughput approaches including gene expression array, next-generation sequencing (NGS), and methylation profiling have now clearly identified at least four molecular subgroups within medulloblastoma, each with distinct clinical and prognostic characteristics. These studies have clearly shown that despite the overall paucity of mutations, clinically relevant events do occur within the cellular epigenetic machinery. Thus, this review aims to provide an overview of our current understanding of the spectrum of epi-oncogenetic perturbations in medulloblastoma.

METHODS

Comprehensive review of epigenetic profiles of different subgroups of medulloblastoma in the context of molecular features. Epigenetic regulation is mediated mainly by DNA methylation, histone modifications and microRNAs (miRNA). Importantly, epigenetic mis-events are reversible and have immense therapeutic potential.

CONCLUSION

The widespread epigenetic alterations present in these tumors has generated intense interest in their use as therapeutic targets. We provide an assessment of the progress that has been made towards the development of molecular subtypes-targeted therapies and the current status of clinical trials that have leveraged these recent advances.

The Management of Childhood Intracranial Tumours and the Role of the Ophthalmologist

OBJECTIVE

This study looked at a single paediatric neuro-oncology centre's experience of childhood intracranial tumours seen in the ophthalmology clinic over an approximately five-year period. This was used to analyse the role of the ophthalmologist in their long term follow up.

METHODS

A database was compiled of all children discussed at the neuro-oncology multi-disciplinary team (MDT) meeting between January 2012 and April 2017. All children who had an intracranial tumour determined by histology or suspected on neuro-imaging, who had also been seen in the ophthalmology clinic, were included. A retrospective case review was performed to create a record for each child.

RESULTS

The database contained 129 children of which 82 (64%) were boys and 47 (36%) were girls. Of these 89 (69%) had a histological diagnosis and 40 (31%) had a tumour suspected on neuroimaging. The most common tumour locations were the posterior fossa (n = 54, 42%), diencephalon (n = 20, 16%) and the visual pathways (n = 17, 13%). Papilloedema at first presentation was only found in 39 (30%) children. The most common other neuro-ophthalmic manifestations were non-paralytic strabismus (n=33), sixth nerve palsy (n=19) and seventh nerve palsy (n=12). Non-paralytic strabismus was a presenting symptom in only one case. There were 13 ophthalmic surgical procedures required for these children, the most common being strabismus surgery.

CONCLUSION

We report the types and locations of paediatric intracranial tumours seen in the ophthalmology clinic as well as their neuro-ophthalmic manifestations. Only 30% presented with papilloedema and approximately 10% required an ophthalmic surgical procedure.

Pontine tumor in a neonate: case report and analysis of the current literature

Tumors of the central nervous system represent the largest group of solid tumors found in pediatric patients. Pilocytic astrocytoma is the most common pediatric glioma, mostly located in the posterior fossa. The majority of brainstem tumors, however, are classified as highly aggressive diffuse intrinsic pontine gliomas (DIPGs) and their prognosis is dismal.The authors report on the case of a neonate in whom MRI and neuropathological assessment were used to diagnose DIPG. Before initiation of the planned chemotherapy, the tumor regressed spontaneously, and the newborn exhibited a normal neurological development. Meanwhile, Illumina Human Methylation450 BeadChip analysis reclassified the tumor as pilocytic astrocytoma of the posterior fossa.In conclusion, the authors advocate not initiating immediate intensive therapy in newborns with brain tumors, even with classical appearance of a DIPG; rather, they would like to encourage a biopsy to define the best individual therapeutic approach and avoid ineffective chemotherapy.

MethPed: a DNA methylation classifier tool for the identification of pediatric brain tumor subtypes

Background

Classification of pediatric tumors into biologically defined subtypes is challenging, and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles.

Results

Methylation data generated by the Illumina Infinium HumanMethylation 450 BeadChip arrays were downloaded from the Gene Expression Omnibus (n = 472). Using the data, we built MethPed, which is a multiclass random forest algorithm, based on DNA methylation profiles from nine subgroups of pediatric brain tumors. DNA from 18 regional samples was used to validate MethPed. MethPed was additionally applied to a set of 28 publically available tumors with the heterogeneous diagnosis PNET. MethPed could successfully separate individual histology tumor types at a very high accuracy (κ = 0.98). Analysis of a regional cohort demonstrated the clinical benefit of MethPed, as confirmation of diagnosis of tumors with clear histology but also identified possible differential diagnoses in tumors with complicated and mixed type morphology.

Conclusions

We demonstrate the utility of methylation profiling of pediatric brain tumors and offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. This will immediately aid clinical practice and importantly increase our molecular knowledge of these tumors for further therapeutic development.

Electronic supplementary material

The online version of this article (doi:10.1186/s13148-015-0103-3) contains supplementary material, which is available to authorized users.