Patricia Rakopoulos

Genomic analysis of diffuse intrinsic pontine gliomas identifies three molecular subgroups and recurrent activating ACVR1 mutations

Diffuse intrinsic pontine glioma (DIPG) is a fatal brain cancer that arises in the brainstem of children, with no effective treatment and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and to the selection of therapies on the basis of assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic makeup of this brain cancer, with nearly 80% found to harbor a p.Lys27Met histone H3.3 or p.Lys27Met histone H3.1 alteration. However, DIPGs are still thought of as one disease, with limited understanding of the genetic drivers of these tumors. To understand what drives DIPGs, we integrated whole-genome sequencing with methylation, expression and copy number profiling, discovering that DIPGs comprise three molecularly distinct subgroups (H3-K27M, silent and MYCN) and uncovering a new recurrent activating mutation affecting the activin receptor gene ACVR1 in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of the downstream activin signaling targets ID1 and ID2. Our results highlight distinct molecular subgroups and novel therapeutic targets for this incurable pediatric cancer.

BRAF Mutation and CDKN2A Deletion Define a Clinically Distinct Subgroup of Childhood Secondary High-Grade Glioma

PURPOSE To uncover the genetic events leading to transformation of pediatric low-grade glioma (PLGG) to secondary high-grade glioma (sHGG). PATIENTS AND METHODS We retrospectively identified patients with sHGG from a population-based cohort of 886 patients with PLGG with long clinical follow-up. Exome sequencing and array CGH were performed on available samples followed by detailed genetic analysis of the entire sHGG cohort. Clinical and outcome data of genetically distinct subgroups were obtained. RESULTS sHGG was observed in 2.9% of PLGGs (26 of 886 patients). Patients with sHGG had a high frequency of nonsilent somatic mutations compared with patients with primary pediatric high-grade glioma (HGG; median, 25 mutations per exome; P = .0042). Alterations in chromatin-modifying genes and telomere-maintenance pathways were commonly observed, whereas no sHGG harbored the BRAF-KIAA1549 fusion. The most recurrent alterations were BRAF V600E and CDKN2A deletion in 39% and 57% of sHGGs, respectively. Importantly, all BRAF V600E and 80% of CDKN2A alterations could be traced back to their PLGG counterparts. BRAF V600E distinguished sHGG from primary HGG (P = .0023), whereas BRAF and CDKN2A alterations were less commonly observed in PLGG that did not transform (P < .001 and P < .001 respectively). PLGGs with BRAF mutations had longer latency to transformation than wild-type PLGG (median, 6.65 years [range, 3.5 to 20.3 years] v 1.59 years [range, 0.32 to 15.9 years], respectively; P = .0389). Furthermore, 5-year overall survival was 75% ± 15% and 29% ± 12% for children with BRAF mutant and wild-type tumors, respectively (P = .024). CONCLUSION BRAF V600E mutations and CDKN2A deletions constitute a clinically distinct subtype of sHGG. The prolonged course to transformation for BRAF V600E PLGGs provides an opportunity for surgical interventions, surveillance, and targeted therapies to mitigate the outcome of sHGG.

Study of the biodistribution of fluorescein in glioma-infiltrated mouse brain and histopathological correlation of intraoperative findings in high-grade gliomas resected under fluorescein fluorescence guidance

OBJECT Intravenous fluorescein sodium has been used during resection of high-grade gliomas to help the surgeon visualize tumor margins. Several studies have reported improved rates of gross-total resection (GTR) using high doses of fluorescein sodium under white light. The recent introduction of a fluorescein-specific camera that allows for high-quality intraoperative imaging and use of very low dose fluorescein has drawn new attention to this fluorophore. However, the ability of fluorescein to specifically stain glioma cells is not yet well understood. METHODS The authors designed an in vitro model to assess fluorescein uptake in normal human astrocytes and U251 malignant glioma cells. An in vivo experiment was also subsequently designed to study fluorescein uptake by intracranial U87 malignant glioma xenografts in male nonobese diabetic/severe combined immunodeficient mice. A genetically induced mouse glioma model was used to adjust for the possible confounding effect of an inflammatory response in the xenograft model. To assess the intraoperative application of this technology, the authors prospectively enrolled 12 patients who underwent fluorescein-guided resection of their high-grade gliomas using low-dose intravenous fluorescein and a microscope-integrated fluorescence module. Intraoperative fluorescent and nonfluorescent specimens at the tumor margins were randomly analyzed for histopathological correlation. RESULTS The in vitro and in vivo models suggest that fluorescein demarcation of glioma-invaded brain is the result of distribution of fluorescein into the extracellular space, most likely as a result of an abnormal blood-brain barrier. Glioblastoma tumor cell-specific uptake of fluorescein was not observed, and tumor cells appeared to mostly exclude fluorescein. For the 12 patients who underwent resection of their high-grade gliomas, the histopathological analysis of the resected specimens at the tumor margin confirmed the intraoperative fluorescent findings. Fluorescein fluorescence was highly specific (up to 90.9%) while its sensitivity was 82.2%. False negatives occurred due to lack of fluorescence in areas of diffuse, low-density cellular infiltration. Margins of contrast enhancement based on intraoperative MRI-guided StealthStation neuronavigation correlated well with fluorescent tumor margins. GTR of the contrast-enhancing area as guided by the fluorescent signal was achieved in 100% of cases based on postoperative MRI. CONCLUSIONS Fluorescein sodium does not appear to selectively accumulate in astrocytoma cells but in extracellular tumor cell-rich locations, suggesting that fluorescein is a marker for areas of compromised blood-brain barrier within high-grade astrocytoma. Fluorescein fluorescence appears to correlate intraoperatively with the areas of MR enhancement, thus representing a practical tool to help the surgeon achieve GTR of the enhancing tumor regions.

PINK1 is a negative regulator of growth and the warburg effect in glioblastoma

Proliferating cancer cells are characterized by high rates of glycolysis, lactate production, and altered mitochondrial metabolism. This metabolic reprogramming provides important metabolites for proliferation of tumor cells, including glioblastoma. These biological processes, however, generate oxidative stress that must be balanced through detoxification of reactive oxygen species (ROS). Using an unbiased retroviral loss-of-function screen in nontransformed human astrocytes, we demonstrate that mitochondrial PTEN-induced kinase 1 (PINK1) is a regulator of the Warburg effect and negative regulator of glioblastoma growth. We report that loss of PINK1 contributes to the Warburg effect through ROS-dependent stabilization of hypoxia-inducible factor-1A and reduced pyruvate kinase muscle isozyme 2 activity, both key regulators of aerobic glycolysis. Mechanistically, PINK1 suppresses ROS and tumor growth through FOXO3a, a master regulator of oxidative stress and superoxide dismutase 2. These findings highlight the importance of PINK1 and ROS balance in normal and tumor cells. PINK1 loss was observed in a significant number of human brain tumors including glioblastoma (n > 900) and correlated with poor patient survival. PINK1 overexpression attenuates in vivo glioblastoma growth in orthotopic mouse xenograft models and a transgenic glioblastoma model in Drosophila Cancer Res; 76(16); 4708-19. ©2016 AACR.

DETAILED MOLECULAR CHARACTERISATION OF DIFFUSE INTRINSIC PONTINE GLIOMAS IDENTIFIES THREE MOLECULAR SUBGROUPS AND A NOVEL CANCER DRIVER, ACVR1

BACKGROUND: Diffuse intrinsic pontine glioma (DIPG) is a devastating pediatric brain tumor with no effective therapy and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unraveled the unique genetic make-up of this brain cancer with nearly 80% harboring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. This data is critical for the development of better therapies for these children. METHODS: Here we describe deep-sequencing analysis of 36 tumor–normal pairs (20 whole genome sequencing (WGS; Illumina Hiseq 2000) and 16 whole exome sequencing (WES; Applied Biosystems SOLiD 5500xl)), integrated with comprehensive methylation (28 DIPGs; Illumina Infinium450K methylation array), copy number (45 DIPGs, Affymetrix SNP6.0) and expression data (35 DIPGs; Illumina HT-12 v4). RESULTS: Unsupervised subgrouping of DIPGs based on CpG island methylation resulted in three distinct subgroups; MYCN, Silent, and H3-K27M. This subgrouping was supported by multiple analyses including principal components analysis, non-negative matrix factorization and consensus clustering. Subgroup-specific differences were supported by integration of mutation, structural, expression and clinical data. The MYCN subgroup DIPGs are not associated with histone mutations and are instead characterized by hypermethylation and catastrophic shattering of chromosome 2p with high-level copy number amplifications of MYCN and ID2. The Silent subgroup has genomes with minimal instability, fewer mutations and over-expression of WNT pathway genes. The H3-K27M subgroup is highly K27M-H3 mutated but is typically associated with additional genetic alterations including activating mutations in ACVR1, frequent RB1 deletions, TP53 deletions/mutations, PVT-1/MYC or PDGFRA gains/amplifications, genomic instability and alternative lengthening of telomeres. After H3F3A and TP53, the next most frequently mutated gene in DIPG is ACVR1 (activin A receptor, type I), a novel cancer gene. Mutations of ACVR1 in four DIPGs (c.617G > A) result in a R206H substitution. One DIPG had a mutation of a neighboring codon (Q207E). Two DIPGs had a c.983G > A (G328E) mutation and five DIPGs in our cohort had a c983G > T mutation which results in a G328V substitution. In total 20% of DIPGs have ACVR1 mutations. CONCLUSIONS: Our results highlight the many pathways to tumorigenesis in DIPG. This complexity needs to be considered when designing new therapeutic approaches in order to improve outcome for these children. SECONDARY CATEGORY: n/a.

Abstract A18: Uncovering molecular subgroups and a novel cancer driver, ACVR1, in diffuse intrinsic pontine gliomas

Diffuse intrinsic pontine glioma (DIPG) is a devastating paediatric brain tumor with no effective therapy and near 100% fatality. The failure of most therapies can be attributed to the delicate location of these tumors and choosing therapies based on assumptions that DIPGs are molecularly similar to adult disease. Recent studies have unravelled the unique genetic make-up of this brain cancer with nearly 80% harbouring a K27M-H3.3 or K27M-H3.1 mutation. However, DIPGs are still thought of as one disease with limited understanding of the genetic drivers of these tumors. Here we apply methylation profiling, whole genome sequencing, expression profiling, and copy number analysis to discover that DIPGs are three molecularly distinct subgroups (H3-K27M, Silent, and MYCN) and uncover a mutations in a novel driver, ACVR1 in 20% of DIPGs. Mutations in ACVR1 were constitutively activating, leading to SMAD phosphorylation and increased expression of downstream activin signalling targets ID1 and ID2. The MYCN subgroup is not associated with histone mutations and is instead characterized by hypermethylation and chromothripsis of chromosome 2p with high-level amplifications of MYCN, ID2, and KIDINS220. The Silent subgroup affects younger children, has genomes with minimal genomic instability and fewer mutations, over-expresses WNT pathway genes, as well as genes with known cancer association such as MDM2, MSMP and ADAM33. The H3-K27M subgroup is highly K27M-H3 mutated and associated with additional hits including activating mutations in ACVR1, frequent RB1 and TP53 deletions, PVT-1/MYC or PDGFRA gains/amplifications, genomic instability and alternative lengthening of telomeres. Our results show that this seemingly homogeneous entity in fact comprises three distinct subgroups with different demographic and molecular features. This complexity needs to be considered when designing new therapeutic approaches in order to improve outcome for these children. Citation Format: Pawel Buczkowicz, Christine Hoeman, Patricia Rakopoulos, Sanja Pajovic, Andrew Morrison, Eric Bouffet, Ute Bartels, Oren Becher, Cynthia Hawkins. Uncovering molecular subgroups and a novel cancer driver, ACVR1, in diffuse intrinsic pontine gliomas. [abstract]. In: Proceedings of the AACR Special Conference on Pediatric Cancer at the Crossroads: Translating Discovery into Improved Outcomes; Nov 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;74(20 Suppl):Abstract nr A18.