Andrey Korshunov

Publications of Andrey Korshunov

• Nestin Expression Identifies Ependymoma Patients with Poor Outcome.

  Authors: Till Milde, Thomas Hielscher, Hendrik Witt, Marcel Kool, Stephen C Mack, Hedwig E Deubzer, Ina Oehme, Marco Lodrini, Axel Benner, Michael D Taylor, Andreas von Deimling, Andreas E Kulozik, Stefan M Pfister, Olaf Witt, Andrey Korshunov

  Brain pathology (Zurich, Switzerland). 05/2012;

  Ependymomas are primary brain tumors found throughout the central nervous system in children and adults. Currently, many treatment protocols stratify grade I and II ependymomas as low-risk tumors,Ependymomas are primary brain tumors found throughout the central nervous system in children and adults. Currently, many treatment protocols stratify grade I and II ependymomas as low-risk tumors, whereas grade III anaplastic ependymomas are considered high-risk tumors. The prognostic significance of WHO grade II or III however remains debated, and it is furthermore increasingly recognized that the pathologic differentiation between grade II and III is arbitrary in daily practice, thus resulting in imprecise risk stratification. Therefore, prognostic markers enabling more precise stratification to guide treatment decisions are urgently needed. Analysis of n=379 tumor samples revealed that protein expression of nestin, a marker for neural stem and progenitor cells established as a routine staining in most neuropathology centers, is associated with poor outcome in intracranial ependymomas. Most importantly, nestin positive grade II ependymomas have the same prognosis as grade III ependymomas. Multivariable analysis demonstrates that nestin positivity is an independent marker for poor progression-free survival (PFS) and overall survival (OS). Gene expression analysis for transcriptionally co-regulated genes revealed a tight association of developmental and epigenetic processes with nestin. In summary, our data implicate nestin as a useful novel marker for intracranial ependymoma risk stratification easily implementable in routine diagnostics.

• The clinical implications of medulloblastoma subgroups.

  Authors: Paul A Northcott, Andrey Korshunov, Stefan M Pfister, Michael D Taylor

  Nature reviews. Neurology. 05/2012;

  Medulloblastoma, the most common malignant paediatric brain tumour, is currently diagnosed and stratified using a combination of clinical and demographic variables. Recent transcriptomic approachesMedulloblastoma, the most common malignant paediatric brain tumour, is currently diagnosed and stratified using a combination of clinical and demographic variables. Recent transcriptomic approaches have demonstrated that the histological entity known as medulloblastoma is comprised of multiple clinically and molecularly distinct subgroups. The current consensus is that four defined subgroups of medulloblastoma exist: WNT, SHH, Group 3, and Group 4. Each subgroup probably contains at least one additional level of hierarchy, with some evidence for multiple subtypes within each subgroup. The demographic and clinical differences between the subgroups present immediate and pressing questions to be addressed in the next round of clinical trials for patients with medulloblastoma. Many of the genetically defined targets for rational medulloblastoma therapies are unique to a given subgroup, suggesting the need for subgroup-specific trials of novel therapies. The development of practical, robust and widely accepted subgroup biomarkers that are amenable to the conditions of a prospective clinical trial is, therefore, an urgent need for the paediatric neuro-oncology community. In this Review, we discuss the clinical implications of molecular subgrouping in medulloblastoma, highlighting how these subgroups are transitioning from a research topic in the laboratory to a clinically relevant topic with important implications for patient care.

• Corrigendum: Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.

  Authors: Jeremy Schwartzentruber, Andrey Korshunov, Xiao-Yang Liu, David T W Jones, Elke Pfaff, Karine Jacob, Dominik Sturm, Adam M Fontebasso, Dong-Anh Khuong Quang, Martje Tönjes [......] Olaf Witt, Cindy Zhang, Pedro Castelo-Branco, Peter Lichter, Damien Faury, Uri Tabori, Christoph Plass, Jacek Majewski, Stefan M Pfister, Nada Jabado

  Nature. 03/2012;

• Clonal selection drives genetic divergence of metastatic medulloblastoma.

  Authors: Xiaochong Wu, Paul A Northcott, Adrian Dubuc, Adam J Dupuy, David J H Shih, Hendrik Witt, Sidney Croul, Eric Bouffet, Daniel W Fults, Charles G Eberhart [......] Keiko Akagi, Tobey J MacDonald, Jan Koster, Martin G McCabe, Aaron L Sarver, V Peter Collins, William A Weiss, David A Largaespada, Lara S Collier, Michael D Taylor

  Nature. 02/2012; 482(7386):529-33.

  Medulloblastoma, the most common malignant paediatric brain tumour, arises in the cerebellum and disseminates through the cerebrospinal fluid in the leptomeningeal space to coat the brain and spinalMedulloblastoma, the most common malignant paediatric brain tumour, arises in the cerebellum and disseminates through the cerebrospinal fluid in the leptomeningeal space to coat the brain and spinal cord. Dissemination, a marker of poor prognosis, is found in up to 40% of children at diagnosis and in most children at the time of recurrence. Affected children therefore are treated with radiation to the entire developing brain and spinal cord, followed by high-dose chemotherapy, with the ensuing deleterious effects on the developing nervous system. The mechanisms of dissemination through the cerebrospinal fluid are poorly studied, and medulloblastoma metastases have been assumed to be biologically similar to the primary tumour. Here we show that in both mouse and human medulloblastoma, the metastases from an individual are extremely similar to each other but are divergent from the matched primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted subclone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize. Failure to account for the bicompartmental nature of metastatic medulloblastoma could be a major barrier to the development of effective targeted therapies.

• Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas.

  Authors: Marcel Kool, Andrey Korshunov, Marc Remke, David T W Jones, Maria Schlanstein, Paul A Northcott, Yoon-Jae Cho, Jan Koster, Antoinette Schouten-van Meeteren, Dannis van Vuurden [......] Christine Haberler, Franck Bourdeaut, Olivier Delattre, Francois Doz, David W Ellison, Richard J Gilbertson, Scott L Pomeroy, Michael D Taylor, Peter Lichter, Stefan M Pfister

  Acta neuropathologica. 02/2012; 123(4):473-84.

  Medulloblastoma is the most common malignant brain tumor in childhood. Molecular studies from several groups around the world demonstrated that medulloblastoma is not one disease but comprises aMedulloblastoma is the most common malignant brain tumor in childhood. Molecular studies from several groups around the world demonstrated that medulloblastoma is not one disease but comprises a collection of distinct molecular subgroups. However, all these studies reported on different numbers of subgroups. The current consensus is that there are only four core subgroups, which should be termed WNT, SHH, Group 3 and Group 4. Based on this, we performed a meta-analysis of all molecular and clinical data of 550 medulloblastomas brought together from seven independent studies. All cases were analyzed by gene expression profiling and for most cases SNP or array-CGH data were available. Data are presented for all medulloblastomas together and for each subgroup separately. For validation purposes, we compared the results of this meta-analysis with another large medulloblastoma cohort (n = 402) for which subgroup information was obtained by immunohistochemistry. Results from both cohorts are highly similar and show how distinct the molecular subtypes are with respect to their transcriptome, DNA copy-number aberrations, demographics, and survival. Results from these analyses will form the basis for prospective multi-center studies and will have an impact on how the different subgroups of medulloblastoma will be treated in the future.

• An animal model of MYC-driven medulloblastoma.

  Authors: Yanxin Pei, Colin E Moore, Jun Wang, Alok K Tewari, Alexey Eroshkin, Yoon-Jae Cho, Hendrik Witt, Andrey Korshunov, Tracy-Ann Read, Julia L Sun, Earlene M Schmitt, C Ryan Miller, Anne F Buckley, Roger E McLendon, Thomas F Westbrook, Paul A Northcott, Michael D Taylor, Stefan M Pfister, Phillip G Febbo, Robert J Wechsler-Reya

  Cancer cell. 02/2012; 21(2):155-67.

  Medulloblastoma (MB) is the most common malignant brain tumor in children. Patients whose tumors exhibit overexpression or amplification of the MYC oncogene (c-MYC) usually have an extremely poorMedulloblastoma (MB) is the most common malignant brain tumor in children. Patients whose tumors exhibit overexpression or amplification of the MYC oncogene (c-MYC) usually have an extremely poor prognosis, but there are no animal models of this subtype of the disease. Here, we show that cerebellar stem cells expressing Myc and mutant Trp53 (p53) generate aggressive tumors following orthotopic transplantation. These tumors consist of large, pleiomorphic cells and resemble human MYC-driven MB at a molecular level. Notably, antagonists of PI3K/mTOR signaling, but not Hedgehog signaling, inhibit growth of tumor cells. These findings suggest that cerebellar stem cells can give rise to MYC-driven MB and identify a novel model that can be used to test therapies for this devastating disease.

• Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma.

  Authors: Jeremy Schwartzentruber, Andrey Korshunov, Xiao-Yang Liu, David T W Jones, Elke Pfaff, Karine Jacob, Dominik Sturm, Adam M Fontebasso, Dong-Anh Khuong Quang, Martje Tönjes [......] Olaf Witt, Cindy Zhang, Pedro Castelo-Branco, Peter Lichter, Damien Faury, Uri Tabori, Christoph Plass, Jacek Majewski, Stefan M Pfister, Nada Jabado

  Nature. 02/2012; 482(7384):226-31.

  Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. ToGlioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.

• Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations.

  Authors: Tobias Rausch, David T W Jones, Marc Zapatka, Adrian M Stütz, Thomas Zichner, Joachim Weischenfeldt, Natalie Jäger, Marc Remke, David Shih, Paul A Northcott [......] Jan J Molenaar, Rogier Versteeg, Marcel Kool, Uri Tabori, David Malkin, Andrey Korshunov, Michael D Taylor, Peter Lichter, Stefan M Pfister, Jan O Korbel

  Cell. 01/2012; 148(1-2):59-71.

  Genomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in aGenomic rearrangements are thought to occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving massive chromosome rearrangements in a one-step catastrophic event termed chromothripsis. We report the whole-genome sequencing-based analysis of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome), uncovering massive, complex chromosome rearrangements. Integrating TP53 status with microarray and deep sequencing-based DNA rearrangement data in additional patients reveals a striking association between TP53 mutation and chromothripsis in SHH-MBs. Analysis of additional tumor entities substantiates a link between TP53 mutation and chromothripsis, and indicates a context-specific role for p53 in catastrophic DNA rearrangements. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings connect p53 status and chromothripsis in specific tumor types, providing a genetic basis for understanding particularly aggressive subtypes of cancer.

• Biological and clinical heterogeneity of MYCN-amplified medulloblastoma.

  Authors: Andrey Korshunov, Marc Remke, Marcel Kool, Thomas Hielscher, Paul A Northcott, Dan Williamson, Elke Pfaff, Hendrik Witt, David T W Jones, Marina Ryzhova [......] William A Weiss, Andreas von Deimling, Wolfram Scheurlen, Andreas E Kulozik, Steven C Clifford, V Peter Collins, Frank Westermann, Michael D Taylor, Peter Lichter, Stefan M Pfister

  Acta neuropathologica. 12/2011;

  Focal high-level amplifications of MYC (or MYCC) define a subset of high-risk medulloblastoma patients. However, the prognostic role of MYCN oncogene amplification remains unresolved. We aimed toFocal high-level amplifications of MYC (or MYCC) define a subset of high-risk medulloblastoma patients. However, the prognostic role of MYCN oncogene amplification remains unresolved. We aimed to evaluate the prognostic value of this alteration alone and in combination with biological modifiers in 67 pediatric medulloblastomas with MYCN amplification (MYCN-MB). Twenty-one MYCN-MB were examined using gene expression profiling and array-CGH, whereas for 46 tumors immunohistochemical analysis and FISH were performed. All 67 tumors were further subjected to mutational analyses. We compared molecular, clinical, and prognostic characteristics both within biological MYCN-MB groups and with non-amplified tumors. Transcriptomic analysis revealed SHH-driven tumorigenesis in a subset of MYCN-MBs indicating a biological dichotomy of MYCN-MB. Activation of SHH was accompanied by variant-specific cytogenetic aberrations including deletion of 9q in SHH tumors. Non-SHH MB were associated with gain of 7q and isochromosome 17q/17q gain. Among clinically relevant variables, SHH subtype and 10q loss for non-SHH tumors comprised the most powerful markers of favorable prognosis in MYCN-MB. In conclusion, we demonstrate considerable heterogeneity within MYCN-MB in terms of genetics, tumor biology, and clinical outcome. Thus, assessment of disease group and 10q copy-number status may improve risk stratification of this group and may delineate MYCN-MB with the same dismal prognosis as MYC amplified tumors. Furthermore, based on the enrichment of MYCN and GLI2 amplifications in SHH-driven medulloblastoma, amplification of these downstream signaling intermediates should be taken into account before a patient is enrolled into a clinical trial using a smoothened inhibitor.

• MYC family amplification and clinical risk-factors interact to predict an extremely poor prognosis in childhood medulloblastoma.

  Authors: Sarra L Ryan, Ed C Schwalbe, Michael Cole, Yuan Lu, Meryl E Lusher, Hisham Megahed, Kieran O'Toole, Sarah Leigh Nicholson, Laszlo Bognar, Miklos Garami, Peter Hauser, Andrey Korshunov, Stefan M Pfister, Daniel Williamson, Roger E Taylor, David W Ellison, Simon Bailey, Steven C Clifford

  Acta neuropathologica. 12/2011;

  The MYC oncogenes are the most commonly amplified loci in medulloblastoma, and have previously been proposed as biomarkers of adverse disease prognosis by us and others. Here, we report focussed andThe MYC oncogenes are the most commonly amplified loci in medulloblastoma, and have previously been proposed as biomarkers of adverse disease prognosis by us and others. Here, we report focussed and comprehensive investigations of MYCC, MYCN and MYCL in an extensive medulloblastoma cohort (n = 292), aimed to define more precisely their biological significance and optimal clinical application to direct improved disease risk-stratification and individualisation of therapy. MYCC and MYCN expression elevations were multifactorial, associated with high-risk (gene amplification, large-cell/anaplastic pathology (LCA)) and favourable-risk (WNT/SHH molecular subgroups) disease features. Highly variable cellular gene amplification patterns underlay overall MYC copy number elevations observed in tumour biopsies; we used these alternative measures together to define quantitative methodologies and thresholds for amplification detection in routinely collected tumour material. MYCC and MYCN amplification, but not gain, each had independent prognostic significance in non-infants (≥3.0-16.0 years), but MYCC conferred a greater hazard to survival than MYCN when considered across this treatment group. MYCN's weaker group-wide survival relationship may be explained by its pleiotropic behaviour between clinical disease-risk groups; MYCN predicted poor prognosis in clinical high-risk (metastatic (M+) or LCA), but not standard-risk, patients. Extending these findings, survival decreased in proportion to the total number of independently significant high-risk features present (LCA, M+ or MYCC/MYCN amplification). This cumulative-risk model defines a patient group characterised by ≥2 independent risk-factors and an extremely poor prognosis (<15% survival), which can be identified straightforwardly using the reported MYC amplification detection methodologies alongside clinical assessments, enabling targeting for novel/intensified therapies in future clinical studies.

• Molecular subgroups of medulloblastoma: the current consensus.

  Authors: Michael D Taylor, Paul A Northcott, Andrey Korshunov, Marc Remke, Yoon-Jae Cho, Steven C Clifford, Charles G Eberhart, D Williams Parsons, Stefan Rutkowski, Amar Gajjar, David W Ellison, Peter Lichter, Richard J Gilbertson, Scott L Pomeroy, Marcel Kool, Stefan M Pfister

  Acta neuropathologica. 12/2011;

  Medulloblastoma, a small blue cell malignancy of the cerebellum, is a major cause of morbidity and mortality in pediatric oncology. Current mechanisms for clinical prognostication and stratificationMedulloblastoma, a small blue cell malignancy of the cerebellum, is a major cause of morbidity and mortality in pediatric oncology. Current mechanisms for clinical prognostication and stratification include clinical factors (age, presence of metastases, and extent of resection) as well as histological subgrouping (classic, desmoplastic, and large cell/anaplastic histology). Transcriptional profiling studies of medulloblastoma cohorts from several research groups around the globe have suggested the existence of multiple distinct molecular subgroups that differ in their demographics, transcriptomes, somatic genetic events, and clinical outcomes. Variations in the number, composition, and nature of the subgroups between studies brought about a consensus conference in Boston in the fall of 2010. Discussants at the conference came to a consensus that the evidence supported the existence of four main subgroups of medulloblastoma (Wnt, Shh, Group 3, and Group 4). Participants outlined the demographic, transcriptional, genetic, and clinical differences between the four subgroups. While it is anticipated that the molecular classification of medulloblastoma will continue to evolve and diversify in the future as larger cohorts are studied at greater depth, herein we outline the current consensus nomenclature, and the differences between the medulloblastoma subgroups.

• MicroRNA-182 promotes leptomeningeal spread of non-sonic hedgehog-medulloblastoma.

  Authors: Alfa H C Bai, Till Milde, Marc Remke, Claudio G Rolli, Thomas Hielscher, Yoon-Jae Cho, Marcel Kool, Paul A Northcott, Manfred Jugold, Alexandr V Bazhin [......] Andreas E Kulozik, Armin Pscherer, Axel Benner, Michael D Taylor, Scott L Pomeroy, Ralf Kemkemer, Olaf Witt, Andrey Korshunov, Peter Lichter, Stefan M Pfister

  Acta neuropathologica. 12/2011;

  The contribution of microRNAs to the initiation, progression, and metastasis of medulloblastoma (MB) remains poorly understood. Metastatic dissemination at diagnosis is present in about 30% of MBThe contribution of microRNAs to the initiation, progression, and metastasis of medulloblastoma (MB) remains poorly understood. Metastatic dissemination at diagnosis is present in about 30% of MB patients, and is associated with a dismal prognosis. Using microRNA expression profiling, we demonstrate that the retinal miR-183-96-182 cluster on chromosome 7q32 is highly overexpressed in non-sonic hedgehog MBs (non-SHH-MBs). Expression of miR-182 and miR-183 is associated with cerebellar midline localization, and miR-182 is significantly overexpressed in metastatic MB as compared to non-metastatic tumors. Overexpression of miR-182 in non-SHH-MB increases and knockdown of miR-182 decreases cell migration in vitro. Xenografts overexpressing miR-182 invaded adjacent normal tissue and spread to the leptomeninges, phenotypically reminiscent of clinically highly aggressive large cell anaplastic MB. Hence, our study provides strong in vitro and in vivo evidence that miR-182 contributes to leptomeningeal metastatic dissemination in non-SHH-MB. We therefore reason that targeted inhibition of miR-182 may prevent leptomeningeal spread in patients with non-SHH-MB.

• Embryonal tumor with abundant neuropil and true rosettes (ETANTR) with loss of morphological but retained genetic key features during progression.

  Authors: Adelheid Woehrer, Irene Slavc, Andreas Peyrl, Thomas Czech, Christian Dorfer, Daniela Prayer, Susanne Stary, Berthold Streubel, Marina Ryzhova, Andrey Korshunov, Stefan M Pfister, Christine Haberler

  Acta neuropathologica. 11/2011; 122(6):787-90.

• Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples.

  Authors: Paul A Northcott, David J H Shih, Marc Remke, Yoon-Jae Cho, Marcel Kool, Cynthia Hawkins, Charles G Eberhart, Adrian Dubuc, Toumy Guettouche, Yoslayma Cardentey, Eric Bouffet, Scott L Pomeroy, Marco Marra, David Malkin, James T Rutka, Andrey Korshunov, Stefan Pfister, Michael D Taylor

  Acta neuropathologica. 11/2011;

  The diagnosis of medulloblastoma likely encompasses several distinct entities, with recent evidence for the existence of at least four unique molecular subgroups that exhibit distinct genetic,The diagnosis of medulloblastoma likely encompasses several distinct entities, with recent evidence for the existence of at least four unique molecular subgroups that exhibit distinct genetic, transcriptional, demographic, and clinical features. Assignment of molecular subgroup through routine profiling of high-quality RNA on expression microarrays is likely impractical in the clinical setting. The planning and execution of medulloblastoma clinical trials that stratify by subgroup, or which are targeted to a specific subgroup requires technologies that can be economically, rapidly, reliably, and reproducibly applied to formalin-fixed paraffin embedded (FFPE) specimens. In the current study, we have developed an assay that accurately measures the expression level of 22 medulloblastoma subgroup-specific signature genes (CodeSet) using nanoString nCounter Technology. Comparison of the nanoString assay with Affymetrix expression array data on a training series of 101 medulloblastomas of known subgroup demonstrated a high concordance (Pearson correlation r = 0.86). The assay was validated on a second set of 130 non-overlapping medulloblastomas of known subgroup, correctly assigning 98% (127/130) of tumors to the appropriate subgroup. Reproducibility was demonstrated by repeating the assay in three independent laboratories in Canada, the United States, and Switzerland. Finally, the nanoString assay could confidently predict subgroup in 88% of recent FFPE cases, of which 100% had accurate subgroup assignment. We present an assay based on nanoString technology that is capable of rapidly, reliably, and reproducibly assigning clinical FFPE medulloblastoma samples to their molecular subgroup, and which is highly suited for future medulloblastoma clinical trials.

• FSTL5 is a marker of poor prognosis in non-WNT/non-SHH medulloblastoma.

  Authors: Marc Remke, Thomas Hielscher, Andrey Korshunov, Paul A Northcott, Sebastian Bender, Marcel Kool, Frank Westermann, Axel Benner, Huriye Cin, Marina Ryzhova [......] Andrea Wittmann, Anna Schöttler, André O von Bueren, Andreas von Deimling, Stefan Rutkowski, Wolfram Scheurlen, Andreas E Kulozik, Michael D Taylor, Peter Lichter, Stefan M Pfister

  Journal of clinical oncology : official journal of the American Society of Clinical Oncology. 09/2011; 29(29):3852-61.

  Integrated genomics approaches have revealed at least four distinct biologic variants of medulloblastoma: WNT (wingless), SHH (sonic hedgehog), group C, and group D. Because of the remarkableIntegrated genomics approaches have revealed at least four distinct biologic variants of medulloblastoma: WNT (wingless), SHH (sonic hedgehog), group C, and group D. Because of the remarkable clinical heterogeneity of group D tumors and the dismal prognosis of group C patients, it is vital to identify molecular biomarkers that will allow early and effective treatment stratification in these non-WNT/non-SHH tumors. We combined transcriptome and DNA copy-number analyses for 64 primary medulloblastomas. Bioinformatic tools were used to discover marker genes of molecular variants. Differentially expressed transcripts were evaluated for prognostic value in the screening cohort. The prognostic power of follistatin-like 5 (FSTL5) immunopositivity was tested for 235 nonoverlapping medulloblastoma samples on two independent tissue microarrays. Comprehensive analyses of transcriptomic and genetic alterations delineate four distinct variants of medulloblastoma. Stable subgroup separation was achieved by using the 300 transcripts that varied the most. Distinct expression patterns of FSTL5 in each molecular subgroup were confirmed by quantitative real-time polymerase chain reaction. Immunopositivity of FSTL5 identified a large cohort of patients (84 of 235 patients; 36%) at high risk for relapse and death. Importantly, more than 50% of non-WNT/non-SHH tumors displayed FSTL5 negativity, delineating a large patient cohort with a good prognosis who would otherwise be considered intermediate or high-risk on the basis of current molecular subgrouping. FSTL5 expression denoted a dismal prognosis both within and across medulloblastoma subgroups. The addition of FSTL5 immunohistochemistry to existing molecular stratification schemes constitutes a reliable and cost-effective tool for prognostication in future clinical trials of medulloblastoma.

• A novel human high-risk ependymoma stem cell model reveals the differentiation-inducing potential of the histone deacetylase inhibitor Vorinostat.

  Authors: Till Milde, Susanne Kleber, Andrey Korshunov, Hendrik Witt, Thomas Hielscher, Philipp Koch, Hans-Georg Kopp, Manfred Jugold, Hedwig E Deubzer, Ina Oehme, Marco Lodrini, Hermann-Josef Gröne, Axel Benner, Oliver Brüstle, Richard J Gilbertson, Andreas von Deimling, Andreas E Kulozik, Stefan M Pfister, Ana Martin-Villalba, Olaf Witt

  Acta neuropathologica. 08/2011; 122(5):637-50.

  Incompletely resectable ependymomas are associated with poor prognosis despite intensive radio- and chemotherapy. Novel treatments have been difficult to develop due to the lack of appropriateIncompletely resectable ependymomas are associated with poor prognosis despite intensive radio- and chemotherapy. Novel treatments have been difficult to develop due to the lack of appropriate models. Here, we report on the generation of a high-risk cytogenetic group 3 and molecular group C ependymoma model (DKFZ-EP1NS) which is based on primary ependymoma cells obtained from a patient with metastatic disease. This model displays stem cell features such as self-renewal capacity, differentiation capacity, and specific marker expression. In vivo transplantation showed high tumorigenic potential of these cells, and xenografts phenotypically recapitulated the original tumor in a niche-dependent manner. DKFZ-EP1NS cells harbor transcriptome plasticity, enabling a shift from a neural stem cell-like program towards a profile of primary ependymoma tumor upon in vivo transplantation. Serial transplantation of DKFZ-EP1NS cells from orthotopic xenografts yielded secondary tumors in half the time compared with the initial transplantation. The cells were resistant to temozolomide, vincristine, and cisplatin, but responded to histone deacetylase inhibitor (HDACi) treatment at therapeutically achievable concentrations. In vitro treatment of DKFZ-EP1NS cells with the HDACi Vorinostat induced neuronal differentiation associated with loss of stem cell-specific properties. In summary, this is the first ependymoma model of a cytogenetic group 3 and molecular subgroup C ependymoma based on a human cell line with stem cell-like properties, which we used to demonstrate the differentiation-inducing therapeutic potential of HDACi.

• Delineation of two clinically and molecularly distinct subgroups of posterior fossa ependymoma.

  Authors: Hendrik Witt, Stephen C Mack, Marina Ryzhova, Sebastian Bender, Martin Sill, Ruth Isserlin, Axel Benner, Thomas Hielscher, Till Milde, Marc Remke [......] Olaf Witt, Gary D Bader, Cynthia E Hawkins, Uri Tabori, Abhijit Guha, James T Rutka, Peter Lichter, Andrey Korshunov, Michael D Taylor, Stefan M Pfister

  Cancer cell. 08/2011; 20(2):143-57.

  Despite the histological similarity of ependymomas from throughout the neuroaxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis.Despite the histological similarity of ependymomas from throughout the neuroaxis, the disease likely comprises multiple independent entities, each with a distinct molecular pathogenesis. Transcriptional profiling of two large independent cohorts of ependymoma reveals the existence of two demographically, transcriptionally, genetically, and clinically distinct groups of posterior fossa (PF) ependymomas. Group A patients are younger, have laterally located tumors with a balanced genome, and are much more likely to exhibit recurrence, metastasis at recurrence, and death compared with Group B patients. Identification and optimization of immunohistochemical (IHC) markers for PF ependymoma subgroups allowed validation of our findings on a third independent cohort, using a human ependymoma tissue microarray, and provides a tool for prospective prognostication and stratification of PF ependymoma patients.

• Genome-wide molecular characterization of central nervous system primitive neuroectodermal tumor and pineoblastoma.

  Authors: Suzanne Miller, Hazel A Rogers, Paul Lyon, Vikki Rand, Martyna Adamowicz-Brice, Steven C Clifford, James T Hayden, Sara Dyer, Stefan Pfister, Andrey Korshunov, Marie-Anne Brundler, James Lowe, Beth Coyle, Richard G Grundy

  Neuro-oncology. 08/2011; 13(8):866-79.

  Central nervous system primitive neuroectodermal tumor (CNS PNET) and pineoblastoma are highly malignant embryonal brain tumors with poor prognoses. Current therapies are based on the treatment ofCentral nervous system primitive neuroectodermal tumor (CNS PNET) and pineoblastoma are highly malignant embryonal brain tumors with poor prognoses. Current therapies are based on the treatment of pediatric medulloblastoma, even though these tumors are distinct at both the anatomical and molecular level. CNS PNET and pineoblastoma have a worse clinical outcome than medulloblastoma; thus, improved therapies based on an understanding of the underlying biology of CNS PNET and pineoblastoma are needed. To this end, we characterized the genomic alterations of 36 pediatric CNS PNETs and 8 pineoblastomas using Affymetrix single nucleotide polymorphism arrays. Overall, the majority of CNS PNETs contained a greater degree of genomic imbalance than pineoblastomas, with gain of 19p (8 [27.6%] of 29), 2p (7 [24.1%] of 29), and 1q (6 [20.7%] of 29) common events in primary CNS PNETs. Novel gene copy number alterations were identified and corroborated by Genomic Identification of Significant Targets In Cancer (GISTIC) analysis: gain of PCDHGA3, 5q31.3 in 62.1% of primary CNS PNETs and all primary pineoblastomas and FAM129A, 1q25 in 55.2% of primary CNS PNETs and 50% of primary pineoblastomas. Comparison of our GISTIC data with publically available data for medulloblastoma confirmed these CNS PNET-specific copy number alterations. With use of the collection of 5 primary and recurrent CNS PNET pairs, we found that gain of 2p21 was maintained at relapse in 80% of cases. Novel gene copy number losses included OR4C12, 11p11.12 in 48.2% of primary CNS PNETs and 50% of primary pineoblastomas. Loss of CDKN2A/B (9p21.3) was identified in 14% of primary CNS PNETs and was significantly associated with older age among children (P = .05). CADPS, 3p14.2 was lost in 27.6% of primary CNS PNETs and was associated with poor prognosis (P = .043). This genome-wide analysis revealed the marked molecular heterogeneity of CNS PNETs and enabled the identification of novel genes and clinical associations potentially involved in the pathogenesis of these tumors.

• Pediatric and adult sonic hedgehog medulloblastomas are clinically and molecularly distinct.

  Authors: Paul A Northcott, Thomas Hielscher, Adrian Dubuc, Stephen Mack, David Shih, Marc Remke, Hani Al-Halabi, Steffen Albrecht, Nada Jabado, Charles G Eberhart, Wieslawa Grajkowska, William A Weiss, Steven C Clifford, Eric Bouffet, James T Rutka, Andrey Korshunov, Stefan Pfister, Michael D Taylor

  Acta neuropathologica. 06/2011; 122(2):231-40.

  Recent integrative genomic approaches have defined molecular subgroups of medulloblastoma that are genetically and clinically distinct. Sonic hedgehog (Shh) medulloblastomas account for one-third ofRecent 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.

• The transcription factor evi-1 is overexpressed, promotes proliferation, and is prognostically unfavorable in infratentorial ependymomas.

  Authors: Björn Koos, Sebastian Bender, Hendrik Witt, Sonja Mertsch, Jörg Felsberg, Rudi Beschorner, Andrey Korshunov, Barbara Riesmeier, Stefan Pfister, Werner Paulus, Martin Hasselblatt

  Clinical cancer research : an official journal of the American Association for Cancer Research. 06/2011; 17(11):3631-7.

  Ependymomas are glial tumors of presumably radial glial origin that share morphologic similarities with ependymal cells. The molecular genetics of ependymomas of supratentorial, infratentorial, andEpendymomas are glial tumors of presumably radial glial origin that share morphologic similarities with ependymal cells. The molecular genetics of ependymomas of supratentorial, infratentorial, and spinal location is heterogeneous. We aimed at identifying pathways operative in the development of infratentorial ependymomas. To do so, gene expression profiles of tumor cells laser microdissected from infratentorial ependymomas (n = 15) were compared with that of nonneoplastic ependymal cells laser microdissected from autopsy tissue (n = 7). Among 31 genes significantly overexpressed (>5-fold) in ependymomas, transcription factor EVI1 (ecotropic viral integration site 1) showed the highest overexpression (35-fold). Evi-1 protein expression could be confirmed in formalin-fixed, paraffin-embedded samples of 26 of 28 infratentorial ependymomas but only in 7 of 47 nonependymal glial tumors (P < 0.001). Furthermore, MDS1/EVI1 fusion transcripts were detectable in 17 of 28 infratentorial ependymomas and significantly correlated with MGMT (O6-methylguanine-DNA-methyltransferase) promoter hypermethylation (P < 0.05). In primary infratentorial ependymoma cells, transfection with EVI1-specific siRNAs resulted in significant growth inhibition [48 hours: 87% ± 2% and 74% ± 10% as compared with control (mean ± SD; P < 0.001)]. The prognostic role of EVI1 could further be validated in an independent cohort of 39 infratentorial and 26 supratentorial ependymomas on the basis of mRNA expression profiling. Although in supratentorial ependymomas EVI1 expression status had no prognostic impact, in infratentorial ependymomas, high EVI1 expression was associated with shorter overall survival and progression-free survival. To conclude, the transcription factor Evi-1 is overexpressed in infratentorial ependymomas, promotes proliferation of ependymal tumor cells, and is prognostically unfavorable.