Integrated Molecular Meta-Analysis of 1,000 Pediatric High-Grade and Diffuse Intrinsic Pontine Glioma.

We collated data from 157 unpublished cases of pediatric high-grade glioma and diffuse intrinsic pontine glioma and 20 publicly available datasets in an integrated analysis of >1,000 cases. We identified co-segregating mutations in histone-mutant subgroups including loss of FBXW7 in H3.3G34R/V, TOP3A rearrangements in H3.3K27M, and BCOR mutations in H3.1K27M. Histone wild-type subgroups are refined by the presence of key oncogenic events or methylation profiles more closely resembling lower-grade tumors. Genomic aberrations increase with age, highlighting the infant population as biologically and clinically distinct. Uncommon pathway dysregulation is seen in small subsets of tumors, further defining the molecular diversity of the disease, opening up avenues for biological study and providing a basis for functionally defined future treatment stratification

Cytogenetic Prognostication Within Medulloblastoma Subgroups

PURPOSE: Medulloblastoma comprises four distinct molecular subgroups: WNT, SHH, Group 3, and Group 4. Current medulloblastoma protocols stratify patients based on clinical features: patient age, metastatic stage, extent of resection, and histologic variant. Stark prognostic and genetic differences among the four subgroups suggest that subgroup-specific molecular biomarkers could improve patient prognostication. PATIENTS AND METHODS: Molecular biomarkers were identified from a discovery set of 673 medulloblastomas from 43 cities around the world. Combined risk stratification models were designed based on clinical and cytogenetic biomarkers identified by multivariable Cox proportional hazards analyses. Identified biomarkers were tested using fluorescent in situ hybridization (FISH) on a nonoverlapping medulloblastoma tissue microarray (n = 453), with subsequent validation of the risk stratification models. RESULTS: Subgroup information improves the predictive accuracy of a multivariable survival model compared with clinical biomarkers alone. Most previously published cytogenetic biomarkers are only prognostic within a single medulloblastoma subgroup. Profiling six FISH biomarkers (GLI2, MYC, chromosome 11 [chr11], chr14, 17p, and 17q) on formalin-fixed paraffin-embedded tissues, we can reliably and reproducibly identify very low-risk and very high-risk patients within SHH, Group 3, and Group 4 medulloblastomas. CONCLUSION: Combining subgroup and cytogenetic biomarkers with established clinical biomarkers substantially improves patient prognostication, even in the context of heterogeneous clinical therapies. The prognostic significance of most molecular biomarkers is restricted to a specific subgroup. We have identified a small panel of cytogenetic biomarkers that reliably identifies very high-risk and very low-risk groups of patients, making it an excellent tool for selecting patients for therapy intensification and therapy de-escalation in future clinical trials

The molecular mechanisms underlying the development and progression of pediatric astrocytoma

Brain tumors are the leading cause of cancer-related mortality and morbidity in the pediatric years. Pediatric brain tumor treatment has been driven largely by findings in adult tumors, and in the case of high-grade gliomas (HGGs) including glioblastoma (GBM), universal failure of therapy across patients of all ages is continuously observed. Recent years have seen a plethora of studies emerge exploring the cancer genome of HGGs to better understand and target the molecular mechanisms that make these cancers some of the deadliest and most aggressive encountered in oncology. Recent studies have uncovered the epigenome as a critical component altered in HGGs. Mutations resulting in vital amino acid substitutions at lysine 27 (p.Lys27Met, K27M) and glycine 34 (p.Gly34Arg/Val, G34R/V) in histone variant H3.3 were shown by our lab and others to characterize about one-third of pediatric GBM tumors, a discovery that marked the first recurrent mutations identified in histone genes in human disease, which are highly conserved across species. Herein, we will discuss the major aspects of my doctoral work that was centered on better characterizing H3.3 and related mutations and alterations in pediatric HGGs as well as characterizing the genomic landscape of the low-grade astrocytoma, pilocytic astrocytoma (PA). Strikingly, we identify genetic alterations leading to changes in histone 3 lysine 36 (H3K36) methylation specifically in HGGs of the cerebral hemispheres, including mutations in the only H3K36 trimethyltransferase encoded in humans, SETD2. Conversely, when analyzing pediatric high-grade tumors of the neuroanatomical midline, we uncover a large majority with H3 K27M mutations and associated with specific growth factor receptor mutations in defined brain regions, such as recurrent ACVR1 mutations in tumors of the pontine area. In PA, we explore molecular mechanisms leading to and maintaining aneuploidy seen with increasing age in this tumor. Taken together, we describe the molecular profile of pediatric astrocytomas and lay a foundation for targeted therapeutic development in future studies.Les tumeurs cérébrales sont la première cause de mortalité et morbidité reliées au cancer chez l'enfant. Les traitements des tumeurs cérébrales pédiatriques sont dérivés des études élaborées chez les adultes, et dans le cas spécifique des gliomes de haut grade ou high-grade gliomas (HGGs), incluant le glioblastome (glioblastoma, GBM), un échec universel des thérapies chez les patients de tout âge est observé. Au cours de ces dernières années de nombreuses études sur l'aspect génomique des HGGs ont permis de mettre en exergue une meilleure compréhension des mécanismes moléculaires qui sont impliqués dans ces cancers connus pour être parmi les plus agressifs en oncologie. De récentes études ont démontré que l'altération de l'épigénome joue un rôle crucial dans les gliomes de haut grade. Des mutations, au niveau de l'histone 3 notamment au niveau du variant H3.3, ont été découverte par notre laboratoire et d'autres équipes. Celles-ci résultent de la substitution d'un acide aminé, de la lysine 27 en methionine (p.Lys27Met, K27M), de la glycine 34 en arginine ou en valine (p.Gly34Arg/Val, G34R/V). Cette découverte a été la première à identifier des mutations récurrentes au niveau des gènes des histones impliqués dans des maladies humaines et normalement hautement conservés entre les espèces. Dans cette thèse, je vais discuter des aspects majeurs de mon travail de doctorat qui ont été essentiellement centrés sur la caractérisation de l'histone H3 et des mutations qui lui sont reliées, et sur la meilleure compréhension des altérations de l'épigénome retrouvées dans les tumeurs cérébrales de haut grade. L'investigation a également été menée sur les aspects génomiques des astrocytomes pilocytaires (pilocytic astrocytoma, PA), un astrocytome de bas grade. De plus, nous avons identifiés des altérations génétiques qui peuvent affecter la méthylation de la lysine 36 de l'histone 3 (H3K36) dans plus de la moitié des tumeurs cérébrales pédiatriques de haut grade. Ces mutations ont été retrouvées dans le seul gène humain codant pour la méthyl- transférase de l'H3K36 nommée SETD2. Lors de l'analyse des tumeurs pédiatriques de haut grade au niveau de la ligne médiane (en neuro-anatomie), nous avons découvert qu'une grande majorité des mutations H3 K27M, et l'association à des mutations de récepteurs spécifiques au facteur de croissance, de prolifération et développement des différentes régions du cerveau, tel que des mutations récurrentes de ACVR1 (activin A receptor, type I) étaient localisées au niveau de la région du pons du tronc cérébral. Chez les tumeurs PA, nous avons approfondi notre étude en explorant les mécanismes moléculaires qui conduisent et entretiennent l'aneuploïdie en corrélation avec un augmentation de l'âge de diagnostique du patient portant un PA. Dans l'ensemble, nous avons décrit le profil moléculaire des astrocytomes pédiatriques et poser les bases pour développer des traitements plus efficaces chez les patients dans le futur

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy