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1.  Medulloblastoma subgroups remain stable across primary and metastatic compartments 
Acta neuropathologica  2015;129(3):449-457.
Medulloblastoma comprises four distinct molecular variants with distinct genetics, transcriptomes, and outcomes. Subgroup affiliation has been previously shown to remain stable at the time of recurrence, which likely reflects their distinct cells of origin. However, a therapeutically relevant question that remains unanswered is subgroup stability in the metastatic compartment. We assembled a cohort of 12-paired primary-metastatic tumors collected in the MAGIC consortium, and established their molecular subgroup affiliation by performing integrative gene expression and DNA methylation analysis. Frozen tissues were collected and profiled using Affymetrix gene expression arrays and Illumina methylation arrays. Class prediction and hierarchical clustering were performed using existing published datasets. Our molecular analysis, using consensus integrative genomic data, establishes the unequivocal maintenance of molecular subgroup affiliation in metastatic medulloblastoma. We further validated these findings by interrogating a non-overlapping cohort of 19-pairs of primary-metastatic tumors from the Burdenko Neurosurgical Institute using an orthogonal technique of immunohistochemical staining. This investigation represents the largest reported primary-metastatic paired cohort profiled to date and provides a unique opportunity to evaluate subgroup-specific molecular aberrations within the metastatic compartment. Our findings further support the hypothesis that medulloblastoma subgroups arise from distinct cells of origin, which are carried forward from ontogeny to oncology.
PMCID: PMC4333718  PMID: 25689980
Medulloblastoma; Metastasis; Molecular Subgroups; Integrative Genomics; Gene Expression; DNA Methylation
2.  Cytogenetic Prognostication Within Medulloblastoma Subgroups 
Shih, David J.H. | Northcott, Paul A. | Remke, Marc | Korshunov, Andrey | Ramaswamy, Vijay | Kool, Marcel | Luu, Betty | Yao, Yuan | Wang, Xin | Dubuc, Adrian M. | Garzia, Livia | Peacock, John | Mack, Stephen C. | Wu, Xiaochong | Rolider, Adi | Morrissy, A. Sorana | Cavalli, Florence M.G. | Jones, David T.W. | Zitterbart, Karel | Faria, Claudia C. | Schüller, Ulrich | Kren, Leos | Kumabe, Toshihiro | Tominaga, Teiji | Shin Ra, Young | Garami, Miklós | Hauser, Peter | Chan, Jennifer A. | Robinson, Shenandoah | Bognár, László | Klekner, Almos | Saad, Ali G. | Liau, Linda M. | Albrecht, Steffen | Fontebasso, Adam | Cinalli, Giuseppe | De Antonellis, Pasqualino | Zollo, Massimo | Cooper, Michael K. | Thompson, Reid C. | Bailey, Simon | Lindsey, Janet C. | Di Rocco, Concezio | Massimi, Luca | Michiels, Erna M.C. | Scherer, Stephen W. | Phillips, Joanna J. | Gupta, Nalin | Fan, Xing | Muraszko, Karin M. | Vibhakar, Rajeev | Eberhart, Charles G. | Fouladi, Maryam | Lach, Boleslaw | Jung, Shin | Wechsler-Reya, Robert J. | Fèvre-Montange, Michelle | Jouvet, Anne | Jabado, Nada | Pollack, Ian F. | Weiss, William A. | Lee, Ji-Yeoun | Cho, Byung-Kyu | Kim, Seung-Ki | Wang, Kyu-Chang | Leonard, Jeffrey R. | Rubin, Joshua B. | de Torres, Carmen | Lavarino, Cinzia | Mora, Jaume | Cho, Yoon-Jae | Tabori, Uri | Olson, James M. | Gajjar, Amar | Packer, Roger J. | Rutkowski, Stefan | Pomeroy, Scott L. | French, Pim J. | Kloosterhof, Nanne K. | Kros, Johan M. | Van Meir, Erwin G. | Clifford, Steven C. | Bourdeaut, Franck | Delattre, Olivier | Doz, François F. | Hawkins, Cynthia E. | Malkin, David | Grajkowska, Wieslawa A. | Perek-Polnik, Marta | Bouffet, Eric | Rutka, James T. | Pfister, Stefan M. | Taylor, Michael D.
Journal of Clinical Oncology  2014;32(9):886-896.
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.
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.
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.
PMCID: PMC3948094  PMID: 24493713
3.  EAG2 potassium channel with evolutionarily conserved function as a brain tumor target 
Nature neuroscience  2015;18(9):1236-1246.
Over 20% of the drugs for treating human diseases target ion channels, however, no cancer drug approved by the U.S. Food and Drug Administration (FDA) is intended to target an ion channel. Here, we demonstrate the evolutionarily conserved function of EAG2 potassium channel in promoting brain tumor growth and metastasis, delineate downstream pathways and uncover a mechanism for different potassium channels to functionally corporate and regulate mitotic cell volume and tumor progression. We show that EAG2 potassium channel is enriched at the trailing edge of migrating MB cells to regulate local cell volume dynamics, thereby facilitating cell motility. We identify the FDA-approved antipsychotic drug thioridazine as an EAG2 channel blocker that reduces xenografted MB growth and metastasis, and present a case report of repurposing thioridazine for treating a human patient. Our findings thus illustrate the potential of targeting ion channels in cancer treatment.
PMCID: PMC4639927  PMID: 26258683
EAG potassium channel; medulloblastoma; brain tumor; metastasis; Drosophila
4.  MB3W1 is an orthotopic xenograft model for anaplastic medulloblastoma displaying cancer stem cell- and Group 3-properties 
BMC Cancer  2016;16:115.
Medulloblastoma is the most common malignant brain tumor in children and can be divided in different molecular subgroups. Patients whose tumor is classified as a Group 3 tumor have a dismal prognosis. However only very few tumor models are available for this subgroup.
We established a robust orthotopic xenograft model with a cell line derived from the malignant pleural effusions of a child suffering from a Group 3 medulloblastoma.
Besides classical characteristics of this tumor subgroup, the cells display cancer stem cell characteristics including neurosphere formation, multilineage differentiation, CD133/CD15 expression, high ALDH-activity and high tumorigenicity in immunocompromised mice with xenografts exactly recapitulating the original tumor architecture.
This model using unmanipulated, human medulloblastoma cells will enable translational research, specifically focused on Group 3 medulloblastoma.
Electronic supplementary material
The online version of this article (doi:10.1186/s12885-016-2170-z) contains supplementary material, which is available to authorized users.
PMCID: PMC4756501  PMID: 26883117
Anaplastic medulloblastoma; Group 3; Orthotopic xenograft; Cancer stem cells; Animal model; Brain tumor; Children
5.  The WIP1 Oncogene Promotes Progression and Invasion of Aggressive Medulloblastoma Variants 
Oncogene  2014;34(9):1126-1140.
Recent studies suggest that medulloblastoma, the most common malignant brain tumor of childhood, is comprised of four disease variants. The WIP1 oncogene is overexpressed in Group 3 and 4 tumors, which contain medulloblastomas with the most aggressive clinical behavior. Our data demonstrate increased WIP1 expression in metastatic medulloblastomas, and inferior progression-free and overall survival of patients with WIP1 high-expressing medulloblastoma. Microarray analysis identified up-regulation of genes involved in tumor metastasis, including the G protein-coupled receptor CXCR4, in medulloblastoma cells with high WIP1 expression. Stimulation with the CXCR4 ligand SDF1ααactivated PI-3 kinase signaling, and promoted growth and invasion of WIP1 high-expressing medulloblastoma cells in a p53-dependent manner. When xenografted into the cerebellum of immunodeficient mice, medulloblastoma cells with stable or endogenous high WIP1 expression exhibited strong expression of CXCR4 and activated AKT in primary and invasive tumor cells. WIP1 or CXCR4 knock-down inhibited medulloblastoma growth and invasion. WIP1 knock-down also improved the survival of mice xenografted with WIP1 high-expressing medulloblastoma cells. WIP1 knock-down inhibited cell surface localization of CXCR4 by suppressing expression of the G protein receptor kinase 5, GRK5. Restoration of wild-type GRK5 promoted Ser339 phosphorylation of CXCR4 and inhibited the growth of WIP1-stable medulloblastoma cells. Conversely, GRK5 knock-down inhibited Ser339 phosphorylation of CXCR4, increased cell surface localization of CXCR4, and promoted the growth of medulloblastoma cells with low WIP1 expression. These results demonstrate cross-talk among WIP1, CXCR4, and GRK5, which may be important for the aggressive phenotype of a subclass of medulloblastomas in children.
PMCID: PMC4722800  PMID: 24632620
medulloblastoma; WIP1; PPM1D; CXCR4; GRK5
6.  Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups 
Cancer cell  2015;27(5):728-743.
Ependymal tumors across age groups are currently classified and graded solely by histopathology. It is, however, commonly accepted that this classification scheme has limited clinical utility based on its lack of reproducibility in predicting patients’ outcome. We aimed at establishing a uniform molecular classification using DNA methylation profiling. Nine molecular subgroups were identified in a large cohort of 500 tumors, 3 in each anatomical compartment of the CNS, spine, posterior fossa, supratentorial. Two supratentorial subgroups are characterized by prototypic fusion genes involving RELA and YAP1, respectively. Regarding clinical associations, the molecular classification proposed herein outperforms the current histopathological classification and thus might serve as a basis for the next World Health Organization classification of CNS tumors.
Graphical Abstract
PMCID: PMC4712639  PMID: 25965575
7.  Characterization of novel biomarkers in selecting for subtype specific medulloblastoma phenotypes 
Oncotarget  2015;6(36):38881-38900.
Major research efforts have focused on defining cell surface marker profiles for characterization and selection of brain tumor stem/progenitor cells. Medulloblastoma is the most common primary malignant pediatric brain cancer and consists of 4 molecular subgroups: WNT, SHH, Group 3 and Group 4. Given the heterogeneity within and between medulloblastoma variants, surface marker profiles may be subtype-specific. Here, we employed a high throughput flow cytometry screen to identify differentially expressed cell surface markers in self-renewing vs. non-self-renewing SHH medulloblastoma cells. The top 25 markers were reduced to 4, CD271/p75NTR/NGFR, CD106/VCAM1, EGFR and CD171/NCAM-L1, by evaluating transcript levels in SHH tumors relative to samples representing the other variants. However, only CD271/p75NTR/NGFR and CD171/NCAM-L1 maintain differential expression between variants at the protein level. Functional characterization of CD271, a low affinity neurotrophin receptor, in cell lines and primary cultures suggested that CD271 selects for lower self-renewing progenitors or stem cells. Moreover, CD271 levels were negatively correlated with expression of SHH pathway genes. Our study reveals a novel role for CD271 in SHH medulloblastoma and suggests that targeting CD271 pathways could lead to the design of more selective therapies that lessen the broad impact of current treatments on developing nervous systems.
PMCID: PMC4770744  PMID: 26497209
medulloblastoma; biomarkers; progenitors; self-renewal; high-throughput flow cytometry
8.  Molecular Insights into Pediatric Brain Tumors Have the Potential to Transform Therapy 
High-throughput genomic technologies have shed light on the biologic heterogeneity of several pediatric brain tumors. The biology of the four common pediatric brain tumors—namely medulloblastoma, ependymoma, high-grade glioma including diffuse intrinsic pontine glioma and low-grade glioma are highlighted in this CCR Focus article. The discovery that medulloblastoma consists of 4 different subgroups namely WNT, SHH, Group 3 and Group 4, each with distinct clinical and molecular features, has impacted the treatment of children with medulloblastoma. Prospective studies have documented the efficacy of SMO inhibitors in a subgroup of patients with SHH medulloblastoma. Efforts are ongoing to develop specific therapies for each of the subgroups of medulloblastoma. Similar efforts are being pursued for ependymoma, high grade glioma and diffuse intrinsic pontine glioma where the disease outcome for the latter two tumors has not changed over the past 3 decades despite several prospective clinical trials. Developing and testing targeted therapies based on this new understanding remains a major challenge to the pediatric neuro-oncology community. The focus of this review is to summarize the rapidly evolving understanding of the common pediatric brain tumors based on genome wide analysis. These novel insights will add impetus to translating these laboratory based discoveries to newer therapies for children diagnosed with these tumors.
PMCID: PMC4234174  PMID: 25398846
9.  Myocardial Fibrosis Burden Predicts Left Ventricular Ejection Fraction and Is Associated With Age and Steroid Treatment Duration in Duchenne Muscular Dystrophy 
Patients with Duchenne muscular dystrophy exhibit progressive cardiac and skeletal muscle dysfunction. Based on prior data, cardiac dysfunction in Duchenne muscular dystrophy patients may be influenced by myocardial fibrosis and steroid therapy. We examined the longitudinal relationship of myocardial fibrosis and ventricular dysfunction using cardiac magnetic resonance in a large Duchenne muscular dystrophy cohort.
Methods and Results
We reviewed 465 serial cardiac magnetic resonance studies (98 Duchenne muscular dystrophy patients with ≥4 cardiac magnetic resonance studies) for left ventricular ejection fraction (LVEF) and presence of late gadolinium enhancement (LGE), a marker for myocardial fibrosis. LVEF was modeled by examining LGE status, myocardial fibrosis burden (as assessed by the number of LGE‐positive left ventricular segments), patient age, and steroid treatment duration. An age‐only model demonstrated that LVEF declined 0.58±0.10% per year. In patients with both LGE‐negative and LGE‐positive studies (n=51), LVEF did not decline significantly over time if LGE was absent but declined 2.2±0.31% per year when LGE was present. Univariate modeling showed significant associations between LVEF and steroid treatment duration, presence of LGE, and number of LGE‐positive left ventricular segments; multivariate modeling showed that LVEF declined by 0.93±0.09% for each LGE‐positive left ventricular segment, whereas age and steroid treatment duration were not significant. The number of LGE‐positive left ventricular segments increased with age, and longer steroid treatment duration was associated with lower age‐related increases.
Progressive myocardial fibrosis, as detected by LGE, was strongly correlated with the LVEF decline in Duchenne muscular dystrophy patients. Longer steroid treatment duration was associated with a lower age‐related increase in myocardial fibrosis burden.
PMCID: PMC4579941  PMID: 25814625
cardiomyopathy; magnetic resonance imaging; morbidity
Neuro-Oncology  2014;16(Suppl 5):v51.
Medulloblastoma is the most common malignant pediatric brain tumor and is divided in four subgroups by gene profiling. The well-known subgroup harboring an activation of the Sonic Hedgehog (SHH)/Patched (PTCH) pathway shows an upregulation of the pro-neural basic helix-loop-helix transcription factor Atoh1. Atoh1 is essential for cerebellum development and more specifically for the formation of the granule neuron progenitors (GNPs), which are the cells of origin of SHH induced medulloblastoma. In tumoral context, Atoh1 acts as a pro-tumor factor in cooperation with SHH/PTCH pathway and its inhibition prevents medulloblastoma proliferation in vitro and in vivo. However, to date, mechanisms underlying Atoh1 regulation remained to be elucidated. We recently found that the mitogen SHH, by regulating Atoh1 phosphorylation, can protect Atoh1 against Huwe1-mediated degradation. We also showed that Atoh1 degradation by the E3 ubiquitin ligase Huwe1 was required for proper cerebellum development. Moreover, low expression of HUWE1 in human Sonic Hedgehog medulloblastoma subgroup was associated with a poor survival rate of patients. Together, we uncovered a signaling pathway that controls the balance between neuronal proliferation and differentiation in GNPs and that could be further targeted in order to elaborate new therapeutic strategies.
PMCID: PMC4217965
Neuro-Oncology  2014;16(Suppl 5):v54.
During tumour progression, brain tumour cells are exposed to metabolic stress, such as nutrient deprivation, due to abnormal tumour vasculature. The ability of tumour cells to respond and manage reduced nutrient availability has a strong impact on tumour outcome. The molecular pathways supporting metabolic adaptation of brain tumour cells to nutrient stress represent potential therapeutic targets which are still not well defined. We report that the translation elongation factor 2 (eEF2) kinase mediates a protective response under nutrient starvation by restraining mRNA translation at the step of elongation. In aggressive human tumour cells, such as medulloblastoma (MB) cells, ablation of eEF2K expression increases sensitivity to nutrient removal. In addition, gene expression analysis in patient samples show that eEF2K expression is upregulated in the most aggressive subgroup of MB, namely group 3, and that high eEF2K expression is strongly associated with poor survival in both MB and glioblastoma (GBM). In vivo, eEF2K overexpression confers resistance of tumour xenografts to calorie restriction. Finally, our data reveal that eEF2K is an evolutionarily conserved mediator of the physiological response to nutrient starvation, as genetic removal of eEF2K compromises survival of C. elegans in absence of nutrients. Overall, our works highlight a novel pro-survival factor which is hijacked by brain tumour cells to support their adaptation to nutrient stress. The potential for therapeutic targeting of eEF2 kinase in brain tumors will be discussed.
PMCID: PMC4217972
Neuro-Oncology  2014;16(Suppl 5):v52.
Cerebellar development requires a balance between several biological processes including proliferation, differentiation and migration. The pro-neural basic helix-loop-helix transcription factor Atoh1 was shown to be a key player controlling the formation of granule neuron progenitors (GNPs). Its uncontrolled levels in collaboration with Sonic Hedgehog (SHH) activation are critical for medulloblastoma (MB) formation, a devastating pediatric tumor that originates from the cerebellum. Because Atoh1 acts as a lineage dependency transcription factor in MB, mechanisms controlling Atoh1 expression are keen interest in the field. However, how this master transcription factor is regulated has remained poorly understood. In our study, we dissected the machinery that regulates Atoh1 in GNPs and in MB. We first identified two phosphorylation sites that regulate Atoh1 stability and function in GNPs. Second, combining tandem affinity purification with an Atoh1 phospho-deficient mutant and multidimensional protein identification technology analysis, we identified the E3 ubiquitin ligase Huwe1 as Atoh1 binding partner. We showed that Atoh1 physically interacted with Huwe1 in a phospho-dependent manner in GNPs, mediating its ubiquitylation whereas Cre-mediated deletion of Huwe1 from postnatal GNPs increased Atoh1 protein levels. Next, we uncovered that SHH regulates Atoh1 stability by preventing its phospho-dependent degradation by Huwe1. In the tumoral context, consistent with Atoh1 upregulation in MBs driven by SHH activation, Huwe1 was found downregulated in primary mouse tumors. In human SHH MB, low HUWE1 expression was found specifically associated with poor prognosis. Overall, our results reveal that SHH and Atoh1 contribute to a positive autoregulatory loop promoting neuronal precursor expansion. Consequently, Huwe1 alterations in SHH MB illustrate the disruption of this developmental mechanism in cancer. This crosstalk between SHH signaling and Atoh1 during cerebellar development highlights a new collaborative network that could be further targeted in MB.
PMCID: PMC4218001
Neuro-Oncology  2014;16(Suppl 5):v78.
The Myst family of acetyltransferase proteins has been shown to play important role in development and self-renewal, primarily through lysine acetylation on Histones H3 and H4. In neural development, Myst4 (Morf/KAT6B) has been found to be critical for self-renewal and for neuron generation in the developing nervous system and during adult neurogenesis. This chromatin modifier exists in a complex with Myst3 (Moz/KAT6A), the bromodomain factor Brpf1, which acts as a protein scaffold, targeting histone acetyltransferases to chromatin, as well as Inhibitor of Growth 5 (ING5) and Esa1-associated factor 6 (EAF6). Our laboratories have found alteration of these elements in pediatric brain cancers, suggesting a pathological role in abnormal neural progenitor growth. Exon-specific microarrays, DNA methylation studies and functional perturbation were performed to study the impact on tumor behavior. RNA interference in tumors and neural progenitors led to loss of H3K4acetylation in target genes and altered expression, including Spondin-1. Conversely, exogenous over-expression of targeting factors, such as Brpf1, enhanced expression of target genes, assessed by quantitative PCR analysis. Furthermore, expression of Myst3/4 and Brpf1 positively correlated with tumor malignancy markers in large patient cohorts, including Ki67, PCNA, and MELK, and with decreased overall survival. Assessment of direct functional relationships with tumor markers using ChIP-Seq approaches is currently being pursued to investigate direct Myst3/4/Brpf1-mediated promoter activity at known and novel target genes. These studies aim to elucidate the role of an important epigenetic mechanism in neurogenesis, the alteration of which may underlie global chromatin changes that contribute to tumor growth or initiation. Sustained progenitor growth may be suppressed by targeted therapies that disrupt these factors.
PMCID: PMC4218094
Neuro-Oncology  2014;16(Suppl 5):v99-v100.
Recent intensive molecular biological analyses revealed that pediatric brain tumors can be subclassified into multiple distinct molecular subgroups. The current consensus is that medulloblastomas consist of four core subgroups, and the sub-grouping of ependymomas is being proposed. This molecular sub-grouping system will not only improve our understanding of the biology of these tumors, but may also contribute for the development of novel therapeutic targets and strategies in the future. We have formed the Japanese Pediatric Molecular Neuro-oncology Group (JPMNG) and initiated a new clinical research project to establish a nationwide network of a molecular diagnosis system for pediatric brain tumors in Japan with the aim to provide a standardized molecular diagnosis according to the international consensus. We initially focus on medulloblastomas and ependymomas. Fresh, fresh-frozen and/or formalin-fixed paraffin-embedded archived tissue specimens are collected. Optimal diagnostic methods are being set up to reliably and reproducibly classify them into molecular subgroups according to the consensus criteria. These include gene expression analysis using the NanoString nCounter system, immunohistochemistry, RT-PCR, DNA sequencing, fluorescence in situ hybridization, and DNA methylation analysis. We have so far collected a total of 85 tissue samples including 30 medulloblastomas and 55 ependymomas. Preliminary study using 17 meduloblastomas indicated that proportions of four core subgroups were WNT (12%), SHH (35%), Group 3 (0%) and Group 4 (53%), respectively. Driver gene analysis showed that two WNT medulloblastomas had CTNNB1 mutations and TP53 mutations were found in one WNT and one SHH tumors. Mutation of TERT promoter was also found in one adult SHH tumors. We expect that this research will provide a highly accurate molecular diagnosis of medulloblastoma and ependymoma comparable to the international standard, leading to form a basis for better clinical management and outcomes and to develop new therapeutic strategies of the pediatric brain tumors in Japan.
PMCID: PMC4218180
Neuro-Oncology  2014;16(Suppl 5):v102.
INTRODUCTION: Comprehensive, genome-wide profiling and next-generation sequencing based studies have dramatically improved our understanding of pediatric brain tumor biology in recent years. However, the vast majority of these studies rely on the assumption that single biopsies are representative of all areas within a tumor. Intratumor heterogeneity comprises a common phenomenon previously described in glioblastoma multiforme and other tumors. Highly disparate genetic profiles of spatially separated areas within the same tumor may preclude development of personalized, molecularly targeted therapies based on single tumor biopsies. MATERIAL AND METHODS: To assess the degree of intratumor heterogeneity, we conducted multiregion whole exome sequencing, high-resolution DNA copy number analysis (Cytoscan HD) and DNA methylation profiling (Infinium HumanMethylation450 BeadChip) on over 25 distinct pediatric and adult brain tumors with a median of six biopsies per tumor (range 4-9). Histological entities comprised ATRT (n = 2), DIPG (n = 2), ependymoma (n = 1), glioblastoma (n = 10), medulloblastoma (n = 10), and medulloepithelioma (n = 1). We elucidated the degree of intratumor heterogeneity and subgroup affiliation using integrated genomics and unsupervised hierarchical clustering algorithms. RESULTS: Epigenetic signatures were highly similar in multiregion biopsies from a single tumor. However, we identified up to 250,000 CpG dinucleotides that were differentially methylated when determining the intertumor heterogeneity of DNA methylation patterns even within disease subgroups. In addition, pediatric brain tumors displayed highly similar focal and broad DNA copy number alterations compared to their adult counterparts. Multiregion sequencing further reinforced the relatively higher degree of intratumor homogeneity in pediatric brain tumors. Lastly, we showed that subgroup affiliation was stable in all multiregion biopsies in medulloblastomas and glioblastomas. CONCLUSIONS: Our results reveal that single biopsies are representative of the tumor genomics landscape in pediatric brain tumors and that DNA methylation based subgrouping is geographically stable.
PMCID: PMC4218192
17.  A microRNA-1280/JAG2 network comprises a novel biological target in high-risk medulloblastoma 
Oncotarget  2014;6(5):2709-2724.
Over-expression of PDGF receptors (PDGFRs) has been previously implicated in high-risk medulloblastoma (MB) pathogenesis. However, the exact biological functions of PDGFRα and PDGFRβ signaling in MB biology remain poorly understood. Here, we report the subgroup specific expression of PDGFRα and PDGFRβ and their associated biological pathways in MB tumors. c-MYC, a downstream target of PDGFRβ but not PDGFRα, is involved in PDGFRβ signaling associated with cell proliferation, cell death, and invasion. Concurrent inhibition of PDGFRβ and c-MYC blocks MB cell proliferation and migration synergistically. Integrated analysis of miRNA and miRNA targets regulated by both PDGFRβ and c-MYC reveals that increased expression of JAG2, a target of miR-1280, is associated with high metastatic dissemination at diagnosis and a poor outcome in MB patients. Our study may resolve the controversy on the role of PDGFRs in MB and unveils JAG2 as a key downstream effector of a PDGFRβ-driven signaling cascade and a potential therapeutic target.
PMCID: PMC4413612  PMID: 25576913
PDGFR; c-MYC; JAG2; miR-1280; medulloblastoma
18.  Epigenetic states of cells of origin and tumor evolution drive tumor initiating cell phenotype and tumor heterogeneity 
Cancer research  2014;74(17):4864-4874.
A central confounding factor in the development of targeted therapies is tumor cell heterogeneity, including as it occurs in tumor-initiating cells (TIC) within clinically identical tumors. Here we show how activation of the Sonic Hedgehog (SHH) pathway in neural stem and progenitor cells creates a foundation for tumor cell evolution to heterogeneous states that are histologically indistinguishable but molecularly distinct. In spontaneous medulloblastomas that arise in Patched (Ptch)+/− mice, we identified three distinct tumor subtypes. Through cell type-specific activation of the SHH pathway in vivo, we determined that different cells of origin evolved in unique ways to generate these subtypes. Moreover, TICs in each subtype had distinct molecular and cellular phenotypes. At the bulk tumor level, the three tumor subtypes could be distinguished by a 465-gene signature and by differential activation levels of the ERK and AKT pathways. Notably, TICs from different subtypes were differentially sensitive to SHH or AKT pathway inhibitors, highlighting new mechanisms of resistance to targeted therapies. In summary, our results show how evolutionary processes act on distinct cells of origin to contribute to tumoral heterogeneity, at both bulk tumor and TIC levels.
PMCID: PMC4154983  PMID: 25136069
tumor initiating cells; medulloblastoma; tumor heterogeneity; TIC evolution; drug resistance
19.  New Mechanistic and Therapeutic Targets for Pediatric Heart Failure 
Circulation  2014;130(1):79-86.
PMCID: PMC4554711  PMID: 24982119
heart defects; congenital; heart failure; pediatrics
20.  Identification of alsterpaullone as a novel small molecule inhibitor to target group 3 medulloblastoma 
Oncotarget  2015;6(25):21718-21729.
Advances in the molecular biology of medulloblastoma revealed four genetically and clinically distinct subgroups. Group 3 medulloblastomas are characterized by frequent amplifications of the oncogene MYC, a high incidence of metastasis, and poor prognosis despite aggressive therapy. We investigated several potential small molecule inhibitors to target Group 3 medulloblastomas based on gene expression data using an in silico drug screen. The Connectivity Map (C-MAP) analysis identified piperlongumine as the top candidate drug for non-WNT medulloblastomas and the cyclin-dependent kinase (CDK) inhibitor alsterpaullone as the compound predicted to have specific antitumor activity against Group 3 medulloblastomas. To validate our findings we used these inhibitors against established Group 3 medulloblastoma cell lines. The C-MAP predicted drugs reduced cell proliferation in vitro and increased survival in Group 3 medulloblastoma xenografts. Alsterpaullone had the highest efficacy in Group 3 medulloblastoma cells. Genomic profiling of Group 3 medulloblastoma cells treated with alsterpaullone confirmed inhibition of cell cycle-related genes, and down-regulation of MYC. Our results demonstrate the preclinical efficacy of using a targeted therapy approach for Group 3 medulloblastomas. Specifically, we provide rationale for advancing alsterpaullone as a targeted therapy in Group 3 medulloblastoma.
PMCID: PMC4673298  PMID: 26061748
group 3 medulloblastoma; alsterpaullone; piperlongumine; connectivity map
21.  Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct 
Acta neuropathologica  2011;122(2):231-240.
Recent integrative genomic approaches have defined molecular subgroups of medulloblastoma that are genetically and clinically distinct. Sonic hedgehog (Shh) medulloblastomas account for one-third of all cases and comprise the majority of infant and adult medulloblastomas. To discern molecular heterogeneity among Shh-medulloblastomas, we analyzed transcriptional profiles from four independent Shh-medulloblastoma expression datasets (n = 66). Unsupervised clustering analyses demonstrated a clear distinction between infant and adult Shh-medulloblastomas, which was reliably replicated across datasets. Comparison of transcriptomes from infant and adult Shh-medulloblastomas revealed deregulation of multiple gene families, including genes implicated in cellular development, synaptogenesis, and extracellular matrix maintenance. Furthermore, metastatic dissemination is a marker of poor prognosis in adult, but not in pediatric Shh-medulloblastomas. Children with desmoplastic Shh-medulloblastomas have a better prognosis than those with Shh-medulloblastomas and classic histology. Desmoplasia is not prognostic for adult Shh-medulloblastoma. Cytogenetic analysis of a large, non-overlapping cohort of Shh-medulloblastomas (n = 151) revealed significant over-representation of chromosome 10q deletion (P < 0.001) and MYCN amplification (P < 0.05) in pediatric Shh cases compared with adults. Adult Shh-medulloblastomas harboring chromosome 10q deletion, 2 gain, 17p deletion, 17q gain, and/or GLI2 amplification have a much worse prognosis as compared to pediatric cases exhibiting the same aberrations. Collectively, our data demonstrate that pediatric and adult Shh-medulloblastomas are clinically, transcriptionally, genetically, and prognostically distinct.
PMCID: PMC4538327  PMID: 21681522
Medulloblastoma; Sonic hedgehog; Molecular classification; Genomics
22.  Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis 
The lancet oncology  2013;14(12):1200-1207.
Recurrent medulloblastoma is a daunting therapeutic challenge as it is almost universally fatal. Recent studies confirmed that medulloblastoma comprises four distinct subgroups. We sought to delineate subgroup specific differences in medulloblastoma recurrence patterns.
We retrospectively identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children between 1994-2012, and performed molecular subgrouping on FFPE tissues using a nanoString-based assay. The anatomical site of recurrence (local tumour bed or leptomeningeal metastasis), time to recurrence and survival post-recurrence were determined in a subgroup specific fashion. Subgroup specific recurrence patterns were confirmed in two independent, non-overlapping FFPE validation cohorts. Where possible molecular subgrouping was performed on tissue obtained from both the initial surgery and at recurrence.
A screening cohort of 30 recurrent medulloblastomas was assembled; nine with local recurrences, and 21 metastatic. When re-analysed in a subgroup specific manner, local recurrences were more frequent in SHH tumours (8/9, 88%) and metastatic recurrences were more common in Group 3 and 4 (17/20 [85%] with one WNT, p=0.0014, local vs metastatic recurrence, SHH vs Group 3 vs Group 4). The subgroup specific location of recurrence was confirmed in a multicenter validation cohort (p=0·0013 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=77), and a second independent validation cohort comprising 96 recurrences (p<0·0001 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=96). Treatment with craniospinal irradiation at diagnosis was not significantly associated with the anatomical pattern of recurrence. Survival post recurrence was significantly longer in Group 4 patients (p=0·013) as confirmed in a multicenter validation cohort (p=0·0075). Strikingly, subgroup affiliation remained stable at recurrence in all 34 cases with available matched primary and recurrent pairs.
Medulloblastoma does not switch subgroup at the time of recurrence further highlighting the stability of the four principle medulloblastoma subgroups. Significant differences in the location and timing of recurrence across medulloblastoma subgroups were observed which have potential treatment ramifications. Specifically, intensified local (posterior fossa) therapy should be tested in the initial treatment of SHH patients. Refinement of therapy for Groups 3 and 4 should focus on the metastatic compartment, as it is the near universal cause of patient deaths.
PMCID: PMC3953419  PMID: 24140199
23.  Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma 
Northcott, Paul A | Lee, Catherine | Zichner, Thomas | Stütz, Adrian M | Erkek, Serap | Kawauchi, Daisuke | Shih, David JH | Hovestadt, Volker | Zapatka, Marc | Sturm, Dominik | Jones, David TW | Kool, Marcel | Remke, Marc | Cavalli, Florence | Zuyderduyn, Scott | Bader, Gary | VandenBerg, Scott | Esparza, Lourdes Adriana | Ryzhova, Marina | Wang, Wei | Wittmann, Andrea | Stark, Sebastian | Sieber, Laura | Seker-Cin, Huriye | Linke, Linda | Kratochwil, Fabian | Jäger, Natalie | Buchhalter, Ivo | Imbusch, Charles D | Zipprich, Gideon | Raeder, Benjamin | Schmidt, Sabine | Diessl, Nicolle | Wolf, Stephan | Wiemann, Stefan | Brors, Benedikt | Lawerenz, Chris | Eils, Jürgen | Warnatz, Hans-Jörg | Risch, Thomas | Yaspo, Marie-Laure | Weber, Ursula D | Bartholomae, Cynthia C | von Kalle, Christof | Turányi, Eszter | Hauser, Peter | Sanden, Emma | Darabi, Anna | Siesjö, Peter | Sterba, Jaroslav | Zitterbart, Karel | Sumerauer, David | van Sluis, Peter | Versteeg, Rogier | Volckmann, Richard | Koster, Jan | Schuhmann, Martin U | Ebinger, Martin | Grimes, H. Leighton | Robinson, Giles W | Gajjar, Amar | Mynarek, Martin | von Hoff, Katja | Rutkowski, Stefan | Pietsch, Torsten | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Kulozik, Andreas E | von Deimlmg, Andreas | Witt, Olaf | Eils, Roland | Gilbertson, Richard J | Korshunov, Andrey | Taylor, Michael D | Lichter, Peter | Korbel, Jan O | Wechsler-Reya, Robert J | Pfister, Stefan M
Nature  2014;511(7510):428-434.
Summary Paragraph
Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation, and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoural heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and Group 4 subgroup medulloblastomas account for the majority of paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to Groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family protooncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1/GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate ‘enhancer hijacking’ as an efficient mechanism driving oncogene activation in a childhood cancer.
PMCID: PMC4201514  PMID: 25043047
24.  Molecular diagnostics of CNS embryonal tumors 
Acta neuropathologica  2010;120(5):553-566.
Tremendous progress has recently been made in both molecular subgrouping, and the establishment of prognostic biomarkers for embryonal brain tumors, particularly medulloblastoma. Several prognostic biomarkers that were initially identified in retrospective cohorts of medulloblastoma, including MYC and MYCN amplification, nuclear β-catenin accumulation, and chromosome 17 aberrations have now been validated in clinical trials. Moreover, molecular subgroups based on distinct transcriptome profiles have been consistently reported from various groups on different platforms demonstrating that the concept of distinct medulloblastoma subgroups is very robust. Well-described subgroups of medulloblastomas include tumors showing wingless signaling pathway (Wnt) activation, and another characterized by sonic hedgehog pathway activity. Two or more additional subgroups were consistently reported to contain the vast majority of high-risk tumors, including most tumors with metastatic disease at diagnosis and/or large cell/anaplastic histology. Several years ago, atypical teratoid rhabdoid tumor (AT/RT) was recognized as a separate entity based on its distinct biology and particularly aggressive clinical behavior. These tumors may occur supra or infratentorially and are usually found to have genetic alterations of SMARCB1 (INI1/hSNF5), a tumor suppressor gene located on chromosome 22q. Subsequent loss of SMARCB1 protein expression comprises a relatively specific and sensitive diagnostic marker for AT/RT. For CNS primitive neuroectodermal tumors (CNS PNETs), a consistent finding has been that they are molecularly distinct from medulloblastoma. Furthermore, a distinct fraction of CNS PNETs with particularly poor prognosis only occurring in young children was delineated, which was previously labeled ependymoblastoma or embryonal tumor with abundant neuropil and true rosettes (ETANTR) and which is morphologically characterized by the presence of multilayered “ependymoblastic” rosettes. This group of tumors shows a unique cytogenetic abnormality not seen in other brain tumors: focal amplification of a micro-RNA cluster at chromosome 19q13.42, which has never been found to be amplified in other CNS PNETs, medulloblastoma or AT/RT. In summary, these consistent findings have significantly contributed to our ability to sub-classify embryonal brain tumors into clinically and biologically meaningful strata and, for some of the subgroups, have led to the identification of specific targets for future development of molecularly targeted therapies.
PMCID: PMC4512653  PMID: 20882288
Embryonal brain tumors; Medulloblastoma; AT/RT; ETANTR; ETMR; Molecular marker; Prognostic marker; Diagnostic marker
25.  Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma 
Cancer cell  2014;26(1):33-47.
Functional heterogeneity within tumors presents a significant therapeutic challenge. Here we show that quiescent, therapy-resistant Sox2+ cells propagate sonic hedgehog subgroup medulloblastoma by a mechanism that mirrors a neurogenic program. Rare Sox2+ cells produce rapidly cycling doublecortin+ progenitors that, together with their postmitotic progeny expressing NeuN, comprise tumor bulk. Sox2+ cells are enriched following anti-mitotic chemotherapy and Smoothened inhibition, creating a reservoir for tumor regrowth. Lineage traces from Sox2+ cells increase following treatment, suggesting that this population is responsible for relapse. Targeting Sox2+ cells with the antineoplastic mithramycin abrogated tumor growth. Addressing functional heterogeneity and eliminating Sox2+ cells presents a promising therapeutic paradigm for treatment of sonic hedgehog subgroup medulloblastoma.
PMCID: PMC4441014  PMID: 24954133

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