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1.  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.
doi:10.1038/onc.2014.37
PMCID: PMC4722800  PMID: 24632620
medulloblastoma; WIP1; PPM1D; CXCR4; GRK5
2.  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
doi:10.1016/j.ccell.2015.04.002
PMCID: PMC4712639  PMID: 25965575
3.  Wnt/β-catenin pathway regulates MGMT gene expression in cancer and inhibition of Wnt signalling prevents chemoresistance 
Nature Communications  2015;6:8904.
The DNA repair enzyme O6-methylguanine-DNA methyltransferase (MGMT) is commonly overexpressed in cancers and is implicated in the development of chemoresistance. The use of drugs inhibiting MGMT has been hindered by their haematologic toxicity and inefficiency. As a different strategy to inhibit MGMT we investigated cellular regulators of MGMT expression in multiple cancers. Here we show a significant correlation between Wnt signalling and MGMT expression in cancers with different origin and confirm the findings by bioinformatic analysis and immunofluorescence. We demonstrate Wnt-dependent MGMT gene expression and cellular co-localization between active β-catenin and MGMT. Pharmacological or genetic inhibition of Wnt activity downregulates MGMT expression and restores chemosensitivity of DNA-alkylating drugs in mouse models. These findings have potential therapeutic implications for chemoresistant cancers, especially of brain tumours where the use of temozolomide is frequently used in treatment.
The high expression of the DNA repair enzyme O6-methylguanine DNA methyltransferase (MGMT) often confers resistance to chemotherapy in several cancers. In this study, the authors propose the inhibition of the Wnt signalling pathway as an alternative strategy to modulate MGMT expression and sensitize tumours to chemotherapy.
doi:10.1038/ncomms9904
PMCID: PMC4674781  PMID: 26603103
4.  AI-08SUBGROUP-SPECIFIC DEREGULATION OF COAGULATION AND ANGIOGENIC GENE EXPRESSION PROFILES IN MEDULLOBLASTOMA- EVIDENCE FOR CROSS-TALK BETWEEN GROWTH FACTOR AND COAGULATION PATHWAYS 
Neuro-Oncology  2014;16(Suppl 5):v2.
INTRODUCTION: Pediatric medulloblastoma (MB) is comprised of 4 distinct disease subtypes including WNT, SHH, group 3, and group 4, which co-segregate with specific clinical features and activation of distinct oncogenic pathways. Oncogenes deregulate tumour cell interactions with the vascular system including the expression, activity, and signaling properties of specific coagulation factors and their cellular receptors. The latter are often activated in aggressive cancers and involved in shaping the tumour microenvironment via coupling of coagulant, inflammatory, and angiogenic responses. Key elements of this circuitry include the tissue factor (TF), PAR-1, and PAR-2 receptors. We studied whether coagulation system effectors are expressed and activated in a manner corresponding to MB subtypes. METHODS: Using R2: microarray analysis and visualization platform, we mined MB datasets for differential expression of coagulation and angiogenesis-related factors between tumour subtypes. Focusing on TF and PAR-1 receptors, we determined whether their expression is correlated with known drivers of growth factor and pro-angiogenic pathways. We evaluated the relevance of these relationships in DAOY MB cells in vitro following SHH and HGF treatment. RESULTS: TF and PAR-1 mRNA expression is upregulated in SHH tumours and correlated with levels of MET receptor. Using DAOY as a model of SHH MB, we documented selective upregulation of PAR-1 mRNA following combined treatment with SHH + HGF. This induced hypersensitivity to a PAR-1 agonist upregulating the expression of the pro-inflammatory and pro-angiogenic factor interleukin-1β. CONCLUSION: Coagulation factors are differentially expressed between MB subtypes, and change the cellular phenotype in a manner dependent on the activation state of key oncogenic pathways. These data suggest a reciprocal interaction between classical oncogenic pathways and coagulation signaling in SHH MB and implicate the coagulation system in tumour progression.
doi:10.1093/neuonc/nou238.8
PMCID: PMC4217874
5.  CS-16THE eEF2 KINASE IS CRITICAL FOR BRAIN TUMOURS ADAPTATION TO METABOLIC STRESS 
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.
doi:10.1093/neuonc/nou242.16
PMCID: PMC4217972
6.  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.
doi:10.1038/nature13379
PMCID: PMC4201514  PMID: 25043047
7.  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.
doi:10.1007/s00401-010-0751-5
PMCID: PMC4512653  PMID: 20882288
Embryonal brain tumors; Medulloblastoma; AT/RT; ETANTR; ETMR; Molecular marker; Prognostic marker; Diagnostic marker
8.  Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma 
Cancer cell  2014;26(1):33-47.
SUMMARY
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.
doi:10.1016/j.ccr.2014.05.005
PMCID: PMC4441014  PMID: 24954133
9.  Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition 
Kool, Marcel | Jones, David T.W. | Jäger, Natalie | Northcott, Paul A. | Pugh, Trevor J. | Hovestadt, Volker | Piro, Rosario M. | Esparza, L. Adriana | Markant, Shirley L. | Remke, Marc | Milde, Till | Bourdeaut, Franck | Ryzhova, Marina | Sturm, Dominik | Pfaff, Elke | Stark, Sebastian | Hutter, Sonja | Şeker-Cin, Huriye | Johann, Pascal | Bender, Sebastian | Schmidt, Christin | Rausch, Tobias | Shih, David | Reimand, Jüri | Sieber, Laura | Wittmann, Andrea | Linke, Linda | Witt, Hendrik | Weber, Ursula D. | Zapatka, Marc | König, Rainer | Beroukhim, Rameen | Bergthold, Guillaume | van Sluis, Peter | Volckmann, Richard | Koster, Jan | Versteeg, Rogier | Schmidt, Sabine | Wolf, Stephan | Lawerenz, Chris | Bartholomae, Cynthia C. | von Kalle, Christof | Unterberg, Andreas | Herold-Mende, Christel | Hofer, Silvia | Kulozik, Andreas E. | von Deimling, Andreas | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Hasselblatt, Martin | Crawford, John R. | Grant, Gerald A. | Jabado, Nada | Perry, Arie | Cowdrey, Cynthia | Croul, Sydney | Zadeh, Gelareh | Korbel, Jan O. | Doz, Francois | Delattre, Olivier | Bader, Gary D. | McCabe, Martin G. | Collins, V. Peter | Kieran, Mark W. | Cho, Yoon-Jae | Pomeroy, Scott L. | Witt, Olaf | Brors, Benedikt | Taylor, Michael D. | Schüller, Ulrich | Korshunov, Andrey | Eils, Roland | Wechsler-Reya, Robert J. | Lichter, Peter | Pfister, Stefan M.
Cancer cell  2014;25(3):393-405.
Summary
Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.
doi:10.1016/j.ccr.2014.02.004
PMCID: PMC4493053  PMID: 24651015
10.  MOLECULAR (RE-)CLASSIFICATION OF CNS-PRIMITIVE NEUROECTODERMAL TUMORS 
Neuro-Oncology  2014;16(Suppl 3):iii23.
BACKGROUND: According to the current WHO classification of CNS tumors, childhood CNS primitive neuro-ectodermal tumors (CNS-PNETs; WHO °IV) are poorly differentiated embryonal tumors with early onset and aggressive clinical behavior. Histological diagnosis can be complicated by morphological heterogeneity and divergent differentiation. Recent studies suggest the existence of molecular subgroups of CNS-PNETs sharing biological characteristics with other childhood CNS tumors. Here, we aimed at a comprehensive molecular characterization of CNS-PNETs and compared our results to profiles of other brain tumor entities in order to define the biological nature of tumors diagnosed as CNS-PNETs. METHODS: A collection of 211 fresh-frozen or paraffin-embedded tumor samples with an institutional diagnosis “CNS-PNET” was profiled for genome-wide DNA methylation patterns and copy-number alterations, complemented by transcriptomic profiling of a subset (n = 71). (Epi-)genetic profiles of CNS-PNETs were compared to those of >3000 other childhood brain tumors including embryonal, astrocytic, and ependymal entities, and their respective molecular subgroups. We screened selected groups of tumors for recurrent mutations and expression of established molecular markers. RESULTS: DNA methylation and gene expression profiles showed a clear segregation of pediatric brain tumors by histological entities and molecular subgroups. Interestingly, CNS-PNET profiles showed a significant overlap with various well-defined entities, including AT/RT, ETMR, high-grade glioma, medulloblastoma, and ependymoma. When screening CNS-PNETs with profiles highly resembling other entities, hallmark genetic alterations of these, such as amplification of 19q13.42, mutations in IDH1 or H3F3A, or mutations/deletions of the SMARCB1 locus, were frequently detected. Also, established protein markers, such as INI-1, LIN28A, and OLIG2, confirmed the reclassification of these CNS-PNETs. Strikingly, a subset (∼25%) of CNS-PNETs which could not be reclassified segregated into 3-4 distinct molecular subgroups, each with its own characteristic pattern of copy-number aberrations, DNA-methylation and gene expression. Currently, whole genome and RNA-sequencing of these distinct subgroups of CNS-PNETs is ongoing to reveal their underlying genetics. CONCLUSIONS: The correct classification of CNS-PNETs remains challenging. Based on the detection of recurrent genetic aberrations, many cases can be reliably re-classified, indicating that a significant proportion of CNS-PNETs may comprise a variety of other tumor subtypes. These findings suggest that the use of established and novel subgroups markers is needed in order to assist the histopathological evaluation of these tumors. In addition, we have identified a number of true CNS-PNET subtypes and are currently analyzing them in more detail in order to elucidate the genetics of these distinct groups. SECONDARY CATEGORY: Tumor Biology.
doi:10.1093/neuonc/nou208.3
PMCID: PMC4144575
11.  FORETINIB IS EFFECTIVE THERAPY FOR METASTATIC SONIC HEDGEHOG MEDULLOBLASTOMA 
Neuro-Oncology  2014;16(Suppl 3):iii35.
BACKGROUND: (blind field). METHODS: Expression profiling, molecular subgrouping and analysis of somatic copy number alterations were conducted on multiple independent cohorts of patient tumour samples to examine intermediates of the MET signaling pathway in medulloblastoma. To examine the in vitro and in vivo effects of foretinib treatment; MET signalling biochemical analysis; migration and invasion assays; and foretinib pharmacokinetic studies were performed. Medulloblastoma xenografts and transgenic mouse models were used to evaluate foretinib treatment in vivo. RESULTS: We analyzed three large non-overlapping cohorts of medulloblastoma patients (discovery cohort, n = 199; validation cohort 1, n = 439; validation cohort 2, n = 285) and demonstrated that cMET, known to be involved in tumor progression and dissemination, is a marker of sonic hedgehog (SHH) medulloblastoma. Importantly, immunohistochemical analysis of activated cMET (phosphorylated cMET) in another independent patient cohort (n = 385) revealed that cMET activation correlates with increased tumor relapse and a poor survival in pediatric patients with SHH medulloblastomas, thus defining a subset of patients that may benefit from cMET targeted therapy. We show that foretinib, an FDA approved inhibitor of cMET, suppresses cMET activation, decreases proliferation and induces apoptosis, both in medulloblastoma cell lines and in SHH medulloblastoma xenografts. Furthermore foretinib penetrates the blood-brain barrier and is effective both in the primary and in the metastatic compartments. Treatment of mouse xenografts and of an aggressive transgenic model of metastatic SHH medulloblastoma with foretinib reduced primary medulloblastoma growth, decreased the incidence of metastases by 36% and increased survival by 45%. CONCLUSIONS: Our results provide strong rationale for advancing foretinib into clinical trials for SHH-driven medulloblastomas. SECONDARY CATEGORY: Tumor Biology.
doi:10.1093/neuonc/nou208.47
PMCID: PMC4144594
12.  PROGNOSTIC SIGNIFICANCE OF CLINICAL, HISTOPATHOLOGICAL, AND MOLECULAR CHARACTERISTICS OF MEDULLOBLASTOMAS IN THE PROSPECTIVE HIT2000 MULTICENTER CLINICAL TRIAL COHORT 
Neuro-Oncology  2014;16(Suppl 3):iii24-iii25.
BACKGROUND: This study aimed to prospectively evaluate clinical, histopathological and molecular variables for outcome prediction in medulloblastoma patients. METHODS: Patients from the HIT2000 cooperative clinical trial were prospectively enrolled based on the availability of sufficient tumor material and complete clinical information. This revealed a cohort of 184 patients (median age 7.6 years), which was randomly split at a 2:1 ratio into a training (n = 127), and a validation (n = 57) dataset. All samples were subjected to thorough histopathological investigation, CTNNB1 mutation analysis, quantitative PCR, MLPA and FISH analyses for cytogenetic variables, and methylome analysis. RESULTS: By univariable analysis, clinical factors (M-stage), histopathological variables (large cell component, endothelial proliferation, synaptophysin pattern), and molecular features (chromosome 6q status, MYC amplification, TOP2A copy-number, subgrouping) were found to be prognostic. Molecular consensus subgrouping (WNT, SHH, Group 3, Group 4) was validated as an independent feature to stratify patients into different risk groups. When comparing methods for the identification of WNT-driven medulloblastoma, this study identified CTNNB1 sequencing and methylation profiling to most reliably identify these patients. After removing patients with particularly favorable (CTNNB1 mutation, extensive nodularity) or unfavorable (MYC amplification) markers, a risk score for the remaining “intermediate molecular risk” population dependent on age, M-stage, pattern of synaptophysin expression, and MYCN copy-number status was identified and validated, with speckled synaptophysin expression indicating worse outcome. CONCLUSIONS: Methylation subgrouping and CTNNB1 mutation status represent robust tools for the risk-stratification of medulloblastoma. A simple clinico-pathological risk score for “intermediate molecular risk” patients was identified, which deserves further validation. SECONDARY CATEGORY: Pediatrics.
doi:10.1093/neuonc/nou208.7
PMCID: PMC4144619
13.  Serpine2/PN-1 Is Required for Proliferative Expansion of Pre-Neoplastic Lesions and Malignant Progression to Medulloblastoma 
PLoS ONE  2015;10(4):e0124870.
Background
Medulloblastomas are malignant childhood brain tumors that arise due to the aberrant activity of developmental pathways during postnatal cerebellar development and in adult humans. Transcriptome analysis has identified four major medulloblastoma subgroups. One of them, the Sonic hedgehog (SHH) subgroup, is caused by aberrant Hedgehog signal transduction due to mutations in the Patched1 (PTCH1) receptor or downstream effectors. Mice carrying a Patched-1 null allele (Ptch1∆/+) are a good model to study the alterations underlying medulloblastoma development as a consequence of aberrant Hedgehog pathway activity.
Results
Transcriptome analysis of human medulloblastomas shows that SERPINE2, also called Protease Nexin-1 (PN-1) is overexpressed in most medulloblastomas, in particular in the SHH and WNT subgroups. As siRNA-mediated lowering of SERPINE2/PN-1 in human medulloblastoma DAOY cells reduces cell proliferation, we analyzed its potential involvement in medulloblastoma development using the Ptch1∆/+ mouse model. In Ptch1∆/+ mice, medulloblastomas arise as a consequence of aberrant Hedgehog pathway activity. Genetic reduction of Serpine2/Pn-1 interferes with medulloblastoma development in Ptch1∆/+ mice, as ~60% of the pre-neoplastic lesions (PNLs) fail to develop into medulloblastomas and remain as small cerebellar nodules. In particular the transcription factor Atoh1, whose expression is essential for development of SHH subgroup medulloblastomas is lost. Comparative molecular analysis reveals the distinct nature of the PNLs in young Ptch1∆/+Pn-1Δ/+ mice. The remaining wild-type Ptch1 allele escapes transcriptional silencing in most cases and the aberrant Hedgehog pathway activity is normalized. Furthermore, cell proliferation and the expression of the cell-cycle regulators Mycn and Cdk6 are significantly reduced in PNLs of Ptch1∆/+Pn-1Δ/+ mice.
Conclusions
Our analysis provides genetic evidence that aberrant Serpine2/Pn-1 is required for proliferation of human and mouse medulloblastoma cells. In summary, our analysis shows that Serpine2/PN-1 boosts malignant progression of PNLs to medulloblastomas, in which the Hedgehog pathway is activated in a SHH ligand-independent manner.
doi:10.1371/journal.pone.0124870
PMCID: PMC4406471  PMID: 25901736
14.  Knockdown of EphB1 receptor decreases medulloblastoma cell growth and migration and increases cellular radiosensitization 
Oncotarget  2015;6(11):8929-8946.
The expression of members of the Eph family of receptor tyrosine kinases and their ephrin ligands is frequently dysregulated in medulloblastomas. We assessed the expression and functional role of EphB1 in medulloblastoma cell lines and engineered mouse models. mRNA and protein expression profiling showed expression of EphB1 receptor in the human medulloblastoma cell lines DAOY and UW228. EphB1 downregulation reduced cell growth and viability, decreased the expression of important cell cycle regulators, and increased the percentage of cells in G1 phase of the cell cycle. It also modulated the expression of proliferation, and cell survival markers. In addition, EphB1 knockdown in DAOY cells resulted in significant decrease in migration, which correlated with decreased β1-integrin expression and levels of phosphorylated Src. Furthermore, EphB1 knockdown enhanced cellular radiosensitization of medulloblastoma cells in culture and in a genetically engineered mouse medulloblastoma model. Using genetically engineered mouse models, we established that genetic loss of EphB1 resulted in a significant delay in tumor recurrence following irradiation compared to EphB1-expressing control tumors. Taken together, our findings establish that EphB1 plays a key role in medulloblastoma cell growth, viability, migration, and radiation sensitivity, making EphB1 a promising therapeutic target.
PMCID: PMC4496193  PMID: 25879388
Eph; medulloblastoma; ATM; cell cycle; radiosensitization
15.  The eEF2 Kinase Confers Resistance to Nutrient Deprivation by Blocking Translation Elongation 
Cell  2013;153(5):1064-1079.
SUMMARY
Metabolic adaptation is essential for cell survival during nutrient deprivation. We report that eukaryotic elongation factor 2 kinase (eEF2K), which is activated by AMP-kinase (AMPK), confers cell survival under acute nutrient depletion by blocking translation elongation. Tumor cells exploit this pathway to adapt to nutrient deprivation by reactivating the AMPK-eEF2K axis. Adaptation of transformed cells to nutrient withdrawal is severely compromised in cells lacking eEF2K. Moreover, eEF2K knockdown restored sensitivity to acute nutrient deprivation in highly resistant human tumor cell lines. In vivo, overexpression of eEF2K rendered murine tumors remarkably resistant to caloric restriction. Expression of eEF2K strongly correlated with overall survival in human medulloblastoma and glioblastoma multiforme. Finally, C. elegans strains deficient in efk-1, the eEF2K ortholog, were severely compromised in their response to nutrient depletion. Our data highlight a conserved role for eEF2K in protecting cells from nutrient deprivation and in conferring tumor cell adaptation to metabolic stress.
doi:10.1016/j.cell.2013.04.055
PMCID: PMC4395874  PMID: 23706743
16.  Targeting class I histone deacetylase 2 in MYC amplified group 3 medulloblastoma 
Introduction
Medulloblastoma (MB) is the most frequent malignant brain tumor in children. Four subgroups with distinct genetic, epigenetic and clinical characteristics have been identified. Survival remains particularly poor in patients with Group 3 tumors harbouring a MYC amplification. We herein explore the molecular mechanisms and translational implications of class I histone deacetylase (HDAC) inhibition in MYC driven MBs.
Material and Methods
Expression of HDACs in primary MB subgroups was compared to normal brain tissue. A panel of MB cell lines, including Group 3 MYC amplified cell lines, were used as model systems. Cells were treated with HDAC inhibitors (HDACi) selectively targeting class I or IIa HDACs. Depletion of HDAC2 was performed. Intracellular HDAC activity, cellular viability, metabolic activity, caspase activity, cell cycle progression, RNA and protein expression were analyzed.
Results
HDAC2 was found to be overexpressed in MB subgroups with poor prognosis (SHH, Group 3 and Group 4) compared to normal brain and the WNT subgroup. Inhibition of the enzymatic activity of the class I HDACs reduced metabolic activity, cell number, and viability in contrast to inhibition of class IIa HDACs. Increased sensitivity to HDACi was specifically observed in MYC amplified cells. Depletion of HDAC2 increased H4 acetylation and induced cell death. Simulation of clinical pharmacokinetics showed time-dependent on target activity that correlated with binding kinetics of HDACi compounds.
Conclusions
We conclude that HDAC2 is a valid drug target in patients with MYC amplified MB. HDACi should cover HDAC2 in their inhibitory profile and timing and dosing regimen in clinical trials should take binding kinetics of compounds into consideration.
Electronic supplementary material
The online version of this article (doi:10.1186/s40478-015-0201-7) contains supplementary material, which is available to authorized users.
doi:10.1186/s40478-015-0201-7
PMCID: PMC4382927  PMID: 25853389
Medulloblastoma; HDAC; HDAC inhibitor; HDAC2; MYC
17.  Multiple mechanisms of MYCN dysregulation in Wilms tumour 
Oncotarget  2015;6(9):7232-7243.
Genomic gain of the proto-oncogene transcription factor gene MYCN is associated with poor prognosis in several childhood cancers. Here we present a comprehensive copy number analysis of MYCN in Wilms tumour (WT), demonstrating that gain of this gene is associated with anaplasia and with poorer relapse-free and overall survival, independent of histology. Using whole exome and gene-specific sequencing, together with methylation and expression profiling, we show that MYCN is targeted by other mechanisms, including a recurrent somatic mutation, P44L, and specific DNA hypomethylation events associated with MYCN overexpression in tumours with high risk histologies. We describe parallel evolution of genomic copy number gain and point mutation of MYCN in the contralateral tumours of a remarkable bilateral case in which independent contralateral mutations of TP53 also evolve over time. We report a second bilateral case in which MYCN gain is a germline aberration. Our results suggest a significant role for MYCN dysregulation in the molecular biology of Wilms tumour. We conclude that MYCN gain is prognostically significant, and suggest that the novel P44L somatic variant is likely to be an activating mutation.
PMCID: PMC4466681  PMID: 25749049
Wilms tumour; MYCN; copy number; DNA methylation; prognostic marker
18.  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.
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.
doi:10.1200/JCO.2013.50.9539
PMCID: PMC3948094  PMID: 24493713
19.  The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma 
Nature medicine  2014;20(9):1035-1042.
Medulloblastoma, the most common malignant childhood brain tumor, exhibits distinct molecular subtypes and cellular origins. Genetic alterations driving medulloblastoma initiation and progression remain poorly understood. Herein, we identify GNAS, encoding the G-protein Gsα, as a potent tumor suppressor gene that defines a subset of aggressive Sonic Hedgehog (Shh)-driven human medulloblastomas. Ablation of the single Gnas gene in anatomically-distinct progenitors is sufficient to induce Shh-associated medulloblastomas, which recapitulate their human counterparts. Gsα is highly enriched at the primary cilium of granule neuron precursors and suppresses Shh-signaling by regulating both the cAMP-dependent pathway and ciliary trafficking of Hedgehog pathway components. Elevation of a Gsα effector, cAMP, effectively inhibits tumor cell proliferation and progression in Gnas mutants. Thus, our gain- and loss-of-function studies identify a previously unrecognized tumor suppressor function for Gsα that acts as a molecular link across Shh-group medulloblastomas of disparate cellular and anatomical origins, illuminating G-protein modulation as a potential therapeutic avenue.
doi:10.1038/nm.3666
PMCID: PMC4334261  PMID: 25150496
medulloblastoma; G-protein; cAMP; GPCR; cell lineage; sonic hedgehog signaling; cilia; cellular origins
20.  PID1 (NYGGF4), a new growth-inhibitory gene in embryonal brain tumors and gliomas 
Purpose
We present here the first report of PID1 (Phosphotyrosine Interaction Domain containing 1; NYGGF4) in cancer. PID1 was identified in 2006 as a gene that modulates insulin signaling and mitochondrial function in adipocytes and muscle cells.
Experimental Design and Results
Using four independent medulloblastoma datasets, we show that mean PID1 mRNA levels were lower in unfavorable medulloblastomas (Groups 3 and 4, and anaplastic histology) compared with favorable medulloblastomas (SHH and WNT groups, and desmoplastic/nodular histology) and with fetal cerebellum. In two large independent glioma datasets PID1 mRNA was lower in glioblastomas (GBMs), the most malignant gliomas, compared to other astrocytomas, oligodendrogliomas and non-tumor brains. Neural and proneural GBM subtypes had higher PID1 mRNA compared to classical and mesenchymal GBM. Importantly, overall survival and radiation-free progression-free survival were longer in medulloblastoma patients with higher PID1 mRNA (univariate and multivariate analyses). Higher PID1 mRNA also correlated with longer overall survival in glioma and GBM patients. In cell culture, overexpression of PID1 inhibited colony formation in medulloblastoma, atypical teratoid rhabdoid tumor (ATRT) and GBM cell lines. Increasing PID1 also increased cell death and apoptosis, inhibited proliferation, induced mitochondrial depolarization, and decreased serum-mediated phosphorylation of AKT and ERK in medulloblastoma, ATRT and/or GBM cell lines, whereas siRNA to PID1 diminished mitochondrial depolarization.
Conclusions
These data are the first to link PID1 to cancer and suggest that PID1 may have a tumor inhibitory function in these pediatric and adult brain tumors.
doi:10.1158/1078-0432.CCR-13-2053
PMCID: PMC3962776  PMID: 24300787
ATRT; apoptosis; brain cancer; glioma; glioblastoma; medulloblastoma; PID1 (NYGGF4); proliferation
21.  Brain Tumor Epidemiology – A Hub within Multidisciplinary Neuro-oncology. Report on the 15th Brain Tumor Epidemiology Consortium (BTEC) Annual Meeting, Vienna, 2014  
Clinical Neuropathology  2014;34(1):40-46.
The Brain Tumor Epidemiology Consortium (BTEC) is an open scientific forum, which fosters the development of multi-center, international and inter-disciplinary collaborations. BTEC aims to develop a better understanding of the etiology, outcomes, and prevention of brain tumors (http://epi.grants.cancer.gov/btec/). The 15th annual Brain Tumor Epidemiology Consortium Meeting, hosted by the Austrian Societies of Neuropathology and Neuro-oncology, was held on September 9 – 11, 2014 in Vienna, Austria. The meeting focused on the central role of brain tumor epidemiology within multidisciplinary neuro-oncology. Knowledge of disease incidence, outcomes, as well as risk factors is fundamental to all fields involved in research and treatment of patients with brain tumors; thus, epidemiology constitutes an important link between disciplines, indeed the very hub. This was reflected by the scientific program, which included various sessions linking brain tumor epidemiology with clinical neuro-oncology, tissue-based research, and cancer registration. Renowned experts from Europe and the United States contributed their personal perspectives stimulating further group discussions. Several concrete action plans evolved for the group to move forward until next year’s meeting, which will be held at the Mayo Clinic at Rochester, MN, USA.
doi:10.5414/NP300846
PMCID: PMC4317580  PMID: 25518914
brain tumor; epidemiology; clinical research; tissue-based research; risk factor research
22.  WNT activation by lithium abrogates TP53 mutation associated radiation resistance in medulloblastoma 
TP53 mutations confer subgroup specific poor survival for children with medulloblastoma. We hypothesized that WNT activation which is associated with improved survival for such children abrogates TP53 related radioresistance and can be used to sensitize TP53 mutant tumors for radiation. We examined the subgroup-specific role of TP53 mutations in a cohort of 314 patients treated with radiation. TP53 wild-type or mutant human medulloblastoma cell-lines and normal neural stem cells were used to test radioresistance of TP53 mutations and the radiosensitizing effect of WNT activation on tumors and the developing brain. Children with WNT/TP53 mutant medulloblastoma had higher 5-year survival than those with SHH/TP53 mutant tumours (100% and 36.6% ± 8.7%, respectively (p < 0.001)). Introduction of TP53 mutation into medulloblastoma cells induced radioresistance (survival fractions at 2Gy (SF2) of 89% ± 2% vs. 57.4% ± 1.8% (p < 0.01)). In contrast, β-catenin mutation sensitized TP53 mutant cells to radiation (p < 0.05). Lithium, an activator of the WNT pathway, sensitized TP53 mutant medulloblastoma to radiation (SF2 of 43.5% ± 1.5% in lithium treated cells vs. 56.6 ± 3% (p < 0.01)) accompanied by increased number of γH2AX foci. Normal neural stem cells were protected from lithium induced radiation damage (SF2 of 33% ± 8% for lithium treated cells vs. 27% ± 3% for untreated controls (p = 0.05). Poor survival of patients with TP53 mutant medulloblastoma may be related to radiation resistance. Since constitutive activation of the WNT pathway by lithium sensitizes TP53 mutant medulloblastoma cells and protect normal neural stem cells from radiation, this oral drug may represent an attractive novel therapy for high-risk medulloblastomas.
Electronic supplementary material
The online version of this article (doi:10.1186/s40478-014-0174-y) contains supplementary material, which is available to authorized users.
doi:10.1186/s40478-014-0174-y
PMCID: PMC4297452  PMID: 25539912
23.  Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis 
The lancet oncology  2013;14(12):1200-1207.
Background
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.
Methods
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.
Results
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.
Conclusions
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.
doi:10.1016/S1470-2045(13)70449-2
PMCID: PMC3953419  PMID: 24140199
24.  Prognostic significance of clinical, histopathological, and molecular characteristics of medulloblastomas in the prospective HIT2000 multicenter clinical trial cohort 
Acta Neuropathologica  2014;128(1):137-149.
This study aimed to prospectively evaluate clinical, histopathological and molecular variables for outcome prediction in medulloblastoma patients. Patients from the HIT2000 cooperative clinical trial were prospectively enrolled based on the availability of sufficient tumor material and complete clinical information. This revealed a cohort of 184 patients (median age 7.6 years), which was randomly split at a 2:1 ratio into a training (n = 127), and a test (n = 57) dataset in order to build and test a risk score for this population. Independent validation was performed in a non-overlapping cohort (n = 83). All samples were subjected to thorough histopathological investigation, CTNNB1 mutation analysis, quantitative PCR, MLPA and FISH analyses for cytogenetic variables, and methylome analysis. By univariable analysis, clinical factors (M-stage), histopathological variables (large cell component, endothelial proliferation, synaptophysin pattern), and molecular features (chromosome 6q status, MYC amplification, subgrouping) were found to be prognostic. Molecular consensus subgrouping (WNT, SHH, Group 3, Group 4) was validated as an independent feature to stratify patients into different risk groups. When comparing methods for the identification of WNT-driven medulloblastoma, this study identified CTNNB1 sequencing and methylation profiling to most reliably identify these patients. After removing patients with particularly favorable (CTNNB1 mutation, extensive nodularity) or unfavorable (MYC amplification) markers, a risk score for the remaining “intermediate molecular risk” population dependent on age, M-stage, pattern of synaptophysin expression, and MYCN copy-number status was identified, with speckled synaptophysin expression indicating worse outcome. Test and independent validation of the score confirmed significant discrimination of patients by risk profile. Methylation subgrouping and CTNNB1 mutation status represent robust tools for the risk stratification of medulloblastoma. A simple clinico-pathological risk score was identified, which was confirmed in a test set and by independent clinical validation.
Electronic supplementary material
The online version of this article (doi:10.1007/s00401-014-1276-0) contains supplementary material, which is available to authorized users.
doi:10.1007/s00401-014-1276-0
PMCID: PMC4059991  PMID: 24791927
Medulloblastoma; Biomarker; Risk stratification; Prospective; Clinical trial cohort; Methylation profiling
25.  Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma 
Jones, David T.W. | Hutter, Barbara | Jäger, Natalie | Korshunov, Andrey | Kool, Marcel | Warnatz, Hans-Jörg | Zichner, Thomas | Lambert, Sally R. | Ryzhova, Marina | Quang, Dong Anh Khuong | Fontebasso, Adam M. | Stütz, Adrian M. | Hutter, Sonja | Zuckermann, Marc | Sturm, Dominik | Gronych, Jan | Lasitschka, Bärbel | Schmidt, Sabine | Şeker-Cin, Huriye | Witt, Hendrik | Sultan, Marc | Ralser, Meryem | Northcott, Paul A. | Hovestadt, Volker | Bender, Sebastian | Pfaff, Elke | Stark, Sebastian | Faury, Damien | Schwartzentruber, Jeremy | Majewski, Jacek | Weber, Ursula D. | Zapatka, Marc | Raeder, Benjamin | Schlesner, Matthias | Worth, Catherine L. | Bartholomae, Cynthia C. | von Kalle, Christof | Imbusch, Charles D. | Radomski, Sylwester | Lawerenz, Chris | van Sluis, Peter | Koster, Jan | Volckmann, Richard | Versteeg, Rogier | Lehrach, Hans | Monoranu, Camelia | Winkler, Beate | Unterberg, Andreas | Herold-Mende, Christel | Milde, Till | Kulozik, Andreas E. | Ebinger, Martin | Schuhmann, Martin U. | Cho, Yoon-Jae | Pomeroy, Scott L. | von Deimling, Andreas | Witt, Olaf | Taylor, Michael D. | Wolf, Stephan | Karajannis, Matthias A. | Eberhart, Charles G. | Scheurlen, Wolfram | Hasselblatt, Martin | Ligon, Keith L. | Kieran, Mark W. | Korbel, Jan O. | Yaspo, Marie-Laure | Brors, Benedikt | Felsberg, Jörg | Reifenberger, Guido | Collins, V. Peter | Jabado, Nada | Eils, Roland | Lichter, Peter | Pfister, Stefan M.
Nature genetics  2013;45(8):927-932.
Pilocytic astrocytoma, the most common childhood brain tumor1, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations2. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression3 and often becoming a chronic disease with substantial morbidities4.
Here we describe whole-genome sequencing of 96 pilocytic astrocytomas, with matched RNA sequencing (n=73), conducted by the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. We identified recurrent activating mutations in FGFR1 and PTPN11 and novel NTRK2 fusion genes in non-cerebellar tumors. New BRAF activating changes were also observed. MAPK pathway alterations affected 100% of tumors analyzed, with no other significant mutations, indicating pilocytic astrocytoma as predominantly a single-pathway disease.
Notably, we identified the same FGFR1 mutations in a subset of H3F3A-mutated pediatric glioblastoma with additional alterations in NF15. Our findings thus identify new potential therapeutic targets in distinct subsets of pilocytic astrocytoma and childhood glioblastoma.
doi:10.1038/ng.2682
PMCID: PMC3951336  PMID: 23817572

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