Bio

Clinical Focus


  • Neurology - Child Neurology
  • Neuro-oncology

Academic Appointments


Honors & Awards


  • co-Chair, Biology Committee, Pediatric Brain Tumor Consortium (2012-)
  • Philip R. Dodge Young Investigator Award, Child Neurology Society (2012)
  • Beirne Faculty Scholar in Pediatirc Neuro-oncology, Stanford University (2011-)
  • Scholar, St. Baldrick's Foundation (2011-)
  • Faculty Development Award, Shore Fellowship Program for Scholars in Medicine, Harvard Medical School (2009-2011)
  • Young Investigator Award, Pediatric Brain Tumor Foundation (2007)
  • Laurel MD-PhD Scholar, Oregon Medical Research Foundation (1994-2002)

Professional Education


  • Fellowship:Children's Hospital Boston (2008) MA
  • Board Certification: Neurology - Child Neurology, American Board of Psychiatry and Neurology (2009)
  • Residency:Children's Hospital Boston (2007) MA
  • Residency:Children's Hospital Oakland (2004) CA
  • Internship:Children's Hospital of Pittsburgh (2003) PA
  • Medical Education:Oregon Health Science University (2002) OR
  • B.A., Rice University, Chemistry, Anthropology (1993)

Research & Scholarship

Current Research and Scholarly Interests


Overview
My laboratory studies childhood brain tumors with a particular focus on medulloblastoma and pediatric high grade glioma. We utilize computational/genomic and cell biological approaches to 1) understand the molecular and cellular basis of these diseases, 2) identify and target the genetic, epigenetic and metabolic vulnerabilities in these tumors and 3) inform the current and next generation of clinical trials focused on bringing the most promising and novel therapies to patients with these diseases.

Projects:
Functional annotation of the medulloblastoma genome
We are currently combining genome-wide RNAi with chemical biology and chemical genomic screens to systematically define the functional consequence of targeting genes and biological pathways enriched in medulloblastoma. Using this approach, we have uncovered genetic, epigenetic and metabolic vulnerabilities the clinically aggressive MYC-amplified/Group3 tumors, which we are developing into novel therapies.

Genome-wide mapping of cell-identity genes in medulloblastoma
We are characterizing the epigenetic states of various childhood brain tumors and how modulation of these epigenetic states alters their behavior. We have identified bromodomain and extra-terminal containing proteins (BET) as critical effectors of gene expression in two of the most lethal forms of medulloblastoma (MYC-amplified/'Group3' tumors and p53-mutated SHH tumors) and have established BET inhibitors as promising therapies for treating patients with these tumors. BET proteins, such as BRD4, facilitate gene expression through their recognition of acetylated lysines, such as at the K27 residue on the histone tail, and subsequent positive interactions with the pTEFb and Pol II transcriptional machinery. BET proteins have also been identified as critical components of large transcriptional co-activator complexes referred to as "super-enhancers" that activate key cell identity genes in development and oncogenesis. We hypothesize the genes regulated by super-enhancers represent high-value therapeutic target and are now mapping and functionally annotating super-enhancer regions in various subtypes of medulloblastoma with a focus on MYC-amplified/Group3 and SHH subforms of this disease.

Epigenomic dysregulation in pediatric glioblastoma and DIPG
We have a keen interest in understanding how mutations in Histone H3 proteins, that commonly occur in pediatric high grade gliomas, influence oncogenesis. The mutations in these histones substitute a methionine at the lysine-27 residues of either H3.1 or H3.3 proteins ("K27M" mutant histone) and we and others have shown these K27M mutant histones are potent inhibitors of the PRC2 complex, resulting in a striking global hypomethylation of Histone K27 residues across the genome and in turn, global changes in DNA methylation and gene expression patterns in glioblastoma and DIPG. One of our major goals is to identify vulnerabilities that arise on account of K27M mutation in these cancers through "synthetic lethal" screens and then to exploit these vulnerabilities for therapeutic gain.

Contribution of DDX3 and RNA helicases in cancer
Using whole-exome and genome sequencing, we have identified a number of previously unreported mutations in medulloblastoma. We are functionally characterizing several of these using in vitro and in vivo assays and determining whether such events carry clinical significance in terms of prognosis, treatment response or potential for targeted therapy. Through this effort, we have identified an RNA helicase, DDX3X, as one of the most commonly mutated genes in medulloblastoma, occurring predominantly in either WNT pathway or SHH pathway activated tumors. We are now characterizing how mutations in DDX3 alter its global interactions with proteins and RNAs using IP-MS and CLIPseq, respectively, and identifying how these shifts facilitate cance

Clinical Trials


  • Vismodegib in Treating Younger Patients With Recurrent or Refractory Medulloblastoma Not Recruiting

    This phase II trial studies how well vismodegib works in treating younger patients with recurrent or refractory medulloblastoma. Vismodegib may slow the growth of tumor cells.

    Stanford is currently not accepting patients for this trial. For more information, please contact Christina Huang, 650-723-0574.

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  • DNA Analysis of Tumor Tissue Samples From Patients With Diffuse Brain Stem Glioma Not Recruiting

    This multi-institutional study will prospectively collect tumor and constitutional tissue samples from patients with diffuse brainstem glioma and other types of brainstem gliomas either during therapy or at autopsy to perform an extensive analysis of genetic and molecular abnormalities in these tumors.

    Stanford is currently not accepting patients for this trial. For more information, please contact Carissa Bailey , 650-725-4708.

    View full details

  • Selumetinib in Treating Young Patients With Recurrent or Refractory Low Grade Glioma Recruiting

    This phase I/II trial studies the side effects and the best dose of selumetinib and how well it works in treating young patients with recurrent or refractory low grade glioma. Selumetinib may stop the growth of tumor cells by blocking some of the enzymes needed for cell growth.

    View full details

Teaching

2013-14 Courses


Postdoctoral Advisees


Publications

Journal Articles


  • Reduced H3K27me3 and DNA Hypomethylation Are Major Drivers of Gene Expression in K27M Mutant Pediatric High-Grade Gliomas. Cancer cell Bender, S., Tang, Y., Lindroth, A. M., Hovestadt, V., Jones, D. T., Kool, M., Zapatka, M., Northcott, P. A., Sturm, D., Wang, W., Radlwimmer, B., Højfeldt, J. W., Truffaux, N., Castel, D., Schubert, S., Ryzhova, M., Seker-Cin, H., Gronych, J., Johann, P. D., Stark, S., Meyer, J., Milde, T., Schuhmann, M., Ebinger, M., Monoranu, C., Ponnuswami, A., Chen, S., Jones, C., Witt, O., Collins, V. P., von Deimling, A., Jabado, N., Puget, S., Grill, J., Helin, K., Korshunov, A., Lichter, P., Monje, M., Plass, C., Cho, Y., Pfister, S. M. 2013; 24 (5): 660-672

    Abstract

    Two recurrent mutations, K27M and G34R/V, within histone variant H3.3 were recently identified in ?50% of pHGGs. Both mutations define clinically and biologically distinct subgroups of pHGGs. Here, we provide further insight about the dominant-negative effect of K27M mutant H3.3, leading to a global reduction of the repressive histone mark H3K27me3. We demonstrate that this is caused by aberrant recruitment of the PRC2 complex to K27M mutant H3.3 and enzymatic inhibition of the H3K27me3-establishing methyltransferase EZH2. By performing chromatin immunoprecipitation followed by next-generation sequencing and whole-genome bisulfite sequencing in primary pHGGs, we show that reduced H3K27me3 levels and DNA hypomethylation act in concert to activate gene expression in K27M mutant pHGGs.

    View details for DOI 10.1016/j.ccr.2013.10.006

    View details for PubMedID 24183680

  • Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations NATURE Pugh, T. J., Weeraratne, S. D., Archer, T. C., Krummel, D. A., Auclair, D., Bochicchio, J., Carneiro, M. O., Carter, S. L., Cibulskis, K., Erlich, R. L., Greulich, H., Lawrence, M. S., Lennon, N. J., McKenna, A., Meldrim, J., Ramos, A. H., Ross, M. G., Russ, C., Shefler, E., Sivachenko, A., Sogoloff, B., Stojanov, P., Tamayo, P., Mesirov, J. P., Amani, V., Teider, N., Sengupta, S., Francois, J. P., Northcott, P. A., Taylor, M. D., Yu, F., Crabtree, G. R., Kautzman, A. G., Gabriel, S. B., Getz, G., Jaeger, N., Jones, D. T., Lichter, P., Pfister, S. M., Roberts, T. M., Meyerson, M., Pomeroy, S. L., Cho, Y. 2012; 488 (7409): 106-110

    Abstract

    Medulloblastomas are the most common malignant brain tumours in children. Identifying and understanding the genetic events that drive these tumours is critical for the development of more effective diagnostic, prognostic and therapeutic strategies. Recently, our group and others described distinct molecular subtypes of medulloblastoma on the basis of transcriptional and copy number profiles. Here we use whole-exome hybrid capture and deep sequencing to identify somatic mutations across the coding regions of 92 primary medulloblastoma/normal pairs. Overall, medulloblastomas have low mutation rates consistent with other paediatric tumours, with a median of 0.35 non-silent mutations per megabase. We identified twelve genes mutated at statistically significant frequencies, including previously known mutated genes in medulloblastoma such as CTNNB1, PTCH1, MLL2, SMARCA4 and TP53. Recurrent somatic mutations were newly identified in an RNA helicase gene, DDX3X, often concurrent with CTNNB1 mutations, and in the nuclear co-repressor (N-CoR) complex genes GPS2, BCOR and LDB1. We show that mutant DDX3X potentiates transactivation of a TCF promoter and enhances cell viability in combination with mutant, but not wild-type, ?-catenin. Together, our study reveals the alteration of WNT, hedgehog, histone methyltransferase and now N-CoR pathways across medulloblastomas and within specific subtypes of this disease, and nominates the RNA helicase DDX3X as a component of pathogenic ?-catenin signalling in medulloblastoma.

    View details for DOI 10.1038/nature11329

    View details for Web of Science ID 000307010700042

    View details for PubMedID 22820256

  • Dissecting the genomic complexity underlying medulloblastoma NATURE Jones, D. T., Jaeger, N., Kool, M., Zichner, T., Hutter, B., Sultan, M., Cho, Y., Pugh, T. J., Hovestadt, V., Stuetz, A. M., Rausch, T., Warnatz, H., Ryzhova, M., Bender, S., Sturm, D., Pleier, S., Cin, H., Pfaff, E., Sieber, L., Wittmann, A., Remke, M., Witt, H., Hutter, S., Tzaridis, T., Weischenfeldt, J., Raeder, B., Avci, M., Amstislavskiy, V., Zapatka, M., Weber, U. D., Wang, Q., Lasitschka, B., Bartholomae, C. C., Schmidt, M., von Kalle, C., Ast, V., Lawerenz, C., Eils, J., Kabbe, R., Benes, V., Van Sluis, P., Koster, J., Volckmann, R., Shih, D., Betts, M. J., Russell, R. B., Coco, S., Tonini, G. P., Schueller, U., Hans, V., Graf, N., Kim, Y., Monoranu, C., Roggendorf, W., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A. E., von Deimling, A., Witt, O., Maass, E., Roessler, J., Ebinger, M., Schuhmann, M. U., Fruehwald, M. C., Hasselblatt, M., Jabado, N., Rutkowski, S., von Bueren, A. O., Williamson, D., Clifford, S. C., McCabe, M. G., Collins, V. P., Wolf, S., Wiemann, S., Lehrach, H., Brors, B., Scheurlen, W., Felsberg, J., Reifenberger, G., Northcott, P. A., Taylor, M. D., Meyerson, M., Pomeroy, S. L., Yaspo, M., Korbel, J. O., Korshunov, A., Eils, R., Pfister, S. M., Lichter, P. 2012; 488 (7409): 100-105

    Abstract

    Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.

    View details for DOI 10.1038/nature11284

    View details for Web of Science ID 000307010700041

    View details for PubMedID 22832583

  • Subgroup-specific structural variation across 1,000 medulloblastoma genomes NATURE Northcott, P. A., Shih, D. J., Peacock, J., Garzia, L., Morrissy, A. S., Zichner, T., Stuetz, A. M., Korshunov, A., Reimand, J., Schumacher, S. E., Beroukhim, R., Ellison, D. W., Marshall, C. R., Lionel, A. C., Mack, S., Dubuc, A., Yao, Y., Ramaswamy, V., Luu, B., Rolider, A., Cavalli, F. M., Wang, X., Remke, M., Wu, X., Chiu, R. Y., Chu, A., Chuah, E., Corbett, R. D., Hoad, G. R., Jackman, S. D., Li, Y., Lo, A., Mungall, K. L., Nip, K. M., Qian, J. Q., Raymond, A. G., Thiessen, N., Varhol, R. J., Birol, I., Moore, R. A., Mungall, A. J., Holt, R., Kawauchi, D., Roussel, M. F., Kool, M., Jones, D. T., Witt, H., Fernandez-L, A., Kenney, A. M., Wechsler-Reya, R. J., Dirks, P., Aviv, T., Grajkowska, W. A., Perek-Polnik, M., Haberler, C. C., Delattre, O., Reynaud, S. S., Doz, F. F., Pernet-Fattet, S. S., Cho, B., Kim, S., Wang, K., Scheurlen, W., Eberhart, C. G., Fevre-Montange, M., Jouvet, A., Pollack, I. F., Fan, X., Muraszko, K. M., Gillespie, G. Y., Di Rocco, C., Massimi, L., Michiels, E. M., Kloosterhof, N. K., French, P. J., Kros, J. M., Olson, J. M., Ellenbogen, R. G., Zitterbart, K., Kren, L., Thompson, R. C., Cooper, M. K., Lach, B., McLendon, R. E., Bigner, D. D., Fontebasso, A., Albrecht, S., Jabado, N., Lindsey, J. C., Bailey, S., Gupta, N., Weiss, W. A., Bognar, L., Klekner, A., Van Meter, T. E., Kumabe, T., Tominaga, T., Elbabaa, S. K., Leonard, J. R., Rubin, J. B., Liau, L. M., Van Meir, E. G., Fouladi, M., Nakamura, H., Cinalli, G., Garami, M., Hauser, P., Saad, A. G., Iolascon, A., Jung, S., Carlotti, C. G., Vibhakar, R., Ra, Y. S., Robinson, S., Zollo, M., Faria, C. C., Chan, J. A., Levy, M. L., Sorensen, P. H., Meyerson, M., Pomeroy, S. L., Cho, Y., Bader, G. D., Tabori, U., Hawkins, C. E., Bouffet, E., Scherer, S. W., Rutka, J. T., Malkin, D., Clifford, S. C., Jones, S. J., Korbel, J. O., Pfister, S. M., Marra, M. A., Taylor, M. D. 2012; 488 (7409): 49-56

    Abstract

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

    View details for DOI 10.1038/nature11327

    View details for Web of Science ID 000307010700030

    View details for PubMedID 22832581

  • Integrative Genomic Analysis of Medulloblastoma Identifies a Molecular Subgroup That Drives Poor Clinical Outcome JOURNAL OF CLINICAL ONCOLOGY Cho, Y., Tsherniak, A., Tamayo, P., Santagata, S., Ligon, A., Greulich, H., Berhoukim, R., Amani, V., Goumnerova, L., Eberhart, C. G., Lau, C. C., Olson, J. M., Gilbertson, R. J., Gajjar, A., Delattre, O., Kool, M., Ligon, K., Meyerson, M., Mesirov, J. P., Pomeroy, S. L. 2011; 29 (11): 1424-1430

    Abstract

    Medulloblastomas are heterogeneous tumors that collectively represent the most common malignant brain tumor in children. To understand the molecular characteristics underlying their heterogeneity and to identify whether such characteristics represent risk factors for patients with this disease, we performed an integrated genomic analysis of a large series of primary tumors.We profiled the mRNA transcriptome of 194 medulloblastomas and performed high-density single nucleotide polymorphism array and miRNA analysis on 115 and 98 of these, respectively. Non-negative matrix factorization-based clustering of mRNA expression data was used to identify molecular subgroups of medulloblastoma; DNA copy number, miRNA profiles, and clinical outcomes were analyzed for each. We additionally validated our findings in three previously published independent medulloblastoma data sets.Identified are six molecular subgroups of medulloblastoma, each with a unique combination of numerical and structural chromosomal aberrations that globally influence mRNA and miRNA expression. We reveal the relative contribution of each subgroup to clinical outcome as a whole and show that a previously unidentified molecular subgroup, characterized genetically by c-MYC copy number gains and transcriptionally by enrichment of photoreceptor pathways and increased miR-183?96?182 expression, is associated with significantly lower rates of event-free and overall survivals.Our results detail the complex genomic heterogeneity of medulloblastomas and identify a previously unrecognized molecular subgroup with poor clinical outcome for which more effective therapeutic strategies should be developed.

    View details for DOI 10.1200/JCO.2010.28.5148

    View details for Web of Science ID 000289276900022

    View details for PubMedID 21098324

  • BET Bromodomain Inhibition of MYC-Amplified Medulloblastoma. Clinical cancer research Bandopadhayay, P., Bergthold, G., Nguyen, B., Schubert, S., Gholamin, S., Tang, Y., Bolin, S., Schumacher, S. E., Zeid, R., Masoud, S., Yu, F., Vue, N., Gibson, W. J., Paolella, B. R., Mitra, S. S., Cheshier, S. H., Qi, J., Liu, K., Wechsler-Reya, R., Weiss, W. A., Swartling, F. J., Kieran, M. W., Bradner, J. E., Beroukhim, R., Cho, Y. 2014; 20 (4): 912-925

    Abstract

    MYC-amplified medulloblastomas are highly lethal tumors. BET bromodomain inhibition has recently been shown to suppress MYC-associated transcriptional activity in other cancers. The compound JQ1 inhibits BET bromodomain-containing proteins, including BRD4. Here we investigate BET bromodomain targeting for the treatment of MYC-amplified medulloblastoma.We evaluated the effects of genetic and pharmacological inhibition of BET bromodomains on proliferation, cell cycle, and apoptosis in established and newly generated patient- and GEMM-derived medulloblastoma cell lines and xenografts that harbored amplifications of MYC or MYCN. We also assessed the effect of JQ1 on MYC expression and global MYC-associated transcriptional activity. We assessed in vivo efficacy of JQ1 in orthotopic xenografts established in immunocompromised mice.Treatment of MYC-amplified medulloblastoma cells with JQ1 decreased cell viability associated with arrest at G1 and apoptosis. We observed down-regulation of MYC expression and confirmed inhibition of MYC-associated transcriptional targets. Exogenous expression of MYC from a retroviral promoter reduced the effect of JQ1 on cell viability, suggesting that attenuated levels of MYC contribute to the functional effects of JQ1. JQ1 significantly prolonged survival of orthotopic xenograft models of MYC-amplified medulloblastoma (p<0.001). Xenografts harvested from mice after five doses of JQ1 had reduced expression of MYC mRNA and a reduced proliferative index.JQ1 suppresses MYC expression and MYC-associated transcriptional activity in medulloblastomas, resulting in an overall decrease in medulloblastoma cell viability. These preclinical findings highlight the promise of BET bromodomain inhibitors as novel agents for MYC-amplified medulloblastoma.

    View details for DOI 10.1158/1078-0432.CCR-13-2281

    View details for PubMedID 24297863

  • Medulloblastoma Down Under 2013: a report from the third annual meeting of the International Medulloblastoma Working Group ACTA NEUROPATHOLOGICA Gottardo, N. G., Hansford, J. R., McGlade, J. P., Alvaro, F., Ashley, D. M., Bailey, S., Baker, D. L., Bourdeaut, F., Cho, Y., Clay, M., Clifford, S. C., Cohn, R. J., Cole, C. H., Dallas, P. B., Downie, P., Doz, F., Ellison, D. W., Endersby, R., Fisher, P. G., Hassall, T., Heath, J. A., Hii, H. L., Jones, D. T., Junckerstorff, R., Kellie, S., Kool, M., Kotecha, R. S., Lichter, P., Laughton, S. J., Lee, S., McCowage, G., Northcott, P. A., Olson, J. M., Packer, R. J., Pfister, S. M., Pietsch, T., Pizer, B., Pomeroy, S. L., Remke, M., Robinson, G. W., Rutkowski, S., Schoep, T., Shelat, A. A., Stewart, C. F., Sullivan, M., Taylor, M. D., Wainwright, B., Walwyn, T., Weiss, W. A., Williamson, D., Gajjar, A. 2014; 127 (2): 189-201

    Abstract

    Medulloblastoma is curable in approximately 70 % of patients. Over the past decade, progress in improving survival using conventional therapies has stalled, resulting in reduced quality of life due to treatment-related side effects, which are a major concern in survivors. The vast amount of genomic and molecular data generated over the last 5-10 years encourages optimism that improved risk stratification and new molecular targets will improve outcomes. It is now clear that medulloblastoma is not a single-disease entity, but instead consists of at least four distinct molecular subgroups: WNT/Wingless, Sonic Hedgehog, Group 3, and Group 4. The Medulloblastoma Down Under 2013 meeting, which convened at Bunker Bay, Australia, brought together 50 leading clinicians and scientists. The 2-day agenda included focused sessions on pathology and molecular stratification, genomics and mouse models, high-throughput drug screening, and clinical trial design. The meeting established a global action plan to translate novel biologic insights and drug targeting into treatment regimens to improve outcomes. A consensus was reached in several key areas, with the most important being that a novel classification scheme for medulloblastoma based on the four molecular subgroups, as well as histopathologic features, should be presented for consideration in the upcoming fifth edition of the World Health Organization's classification of tumours of the central nervous system. Three other notable areas of agreement were as follows: (1) to establish a central repository of annotated mouse models that are readily accessible and freely available to the international research community; (2) to institute common eligibility criteria between the Children's Oncology Group and the International Society of Paediatric Oncology Europe and initiate joint or parallel clinical trials; (3) to share preliminary high-throughput screening data across discovery labs to hasten the development of novel therapeutics. Medulloblastoma Down Under 2013 was an effective forum for meaningful discussion, which resulted in enhancing international collaborative clinical and translational research of this rare disease. This template could be applied to other fields to devise global action plans addressing all aspects of a disease, from improved disease classification, treatment stratification, and drug targeting to superior treatment regimens to be assessed in cooperative international clinical trials.

    View details for DOI 10.1007/s00401-013-1213-7

    View details for Web of Science ID 000329993100003

    View details for PubMedID 24264598

  • TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma. Acta neuropathologica Remke, M., Ramaswamy, V., Peacock, J., Shih, D. J., Koelsche, C., Northcott, P. A., Hill, N., Cavalli, F. M., Kool, M., Wang, X., Mack, S. C., Barszczyk, M., Morrissy, A. S., Wu, X., Agnihotri, S., Luu, B., Jones, D. T., Garzia, L., Dubuc, A. M., Zhukova, N., Vanner, R., Kros, J. M., French, P. J., Van Meir, E. G., Vibhakar, R., Zitterbart, K., Chan, J. A., Bognár, L., Klekner, A., Lach, B., Jung, S., Saad, A. G., Liau, L. M., Albrecht, S., Zollo, M., Cooper, M. K., Thompson, R. C., Delattre, O. O., Bourdeaut, F., Doz, F. F., Garami, M., Hauser, P., Carlotti, C. G., Van Meter, T. E., Massimi, L., Fults, D., Pomeroy, S. L., Kumabe, T., Ra, Y. S., Leonard, J. R., Elbabaa, S. K., Mora, J., Rubin, J. B., Cho, Y., McLendon, R. E., Bigner, D. D., Eberhart, C. G., Fouladi, M., Wechsler-Reya, R. J., Faria, C. C., Croul, S. E., Huang, A., Bouffet, E., Hawkins, C. E., Dirks, P. B., Weiss, W. A., Schüller, U., Pollack, I. F., Rutkowski, S., Meyronet, D., Jouvet, A., Fèvre-Montange, M., Jabado, N., Perek-Polnik, M., Grajkowska, W. A., Kim, S., Rutka, J. T., Malkin, D., Tabori, U., Pfister, S. M., Korshunov, A., von Deimling, A., Taylor, M. D. 2013; 126 (6): 917-929

    Abstract

    Telomerase reverse transcriptase (TERT) promoter mutations were recently shown to drive telomerase activity in various cancer types, including medulloblastoma. However, the clinical and biological implications of TERT mutations in medulloblastoma have not been described. Hence, we sought to describe these mutations and their impact in a subgroup-specific manner. We analyzed the TERT promoter by direct sequencing and genotyping in 466 medulloblastomas. The mutational distributions were determined according to subgroup affiliation, demographics, and clinical, prognostic, and molecular features. Integrated genomics approaches were used to identify specific somatic copy number alterations in TERT promoter-mutated and wild-type tumors. Overall, TERT promoter mutations were identified in 21 % of medulloblastomas. Strikingly, the highest frequencies of TERT mutations were observed in SHH (83 %; 55/66) and WNT (31 %; 4/13) medulloblastomas derived from adult patients. Group 3 and Group 4 harbored this alteration in <5 % of cases and showed no association with increased patient age. The prognostic implications of these mutations were highly subgroup-specific. TERT mutations identified a subset with good and poor prognosis in SHH and Group 4 tumors, respectively. Monosomy 6 was mostly restricted to WNT tumors without TERT mutations. Hallmark SHH focal copy number aberrations and chromosome 10q deletion were mutually exclusive with TERT mutations within SHH tumors. TERT promoter mutations are the most common recurrent somatic point mutation in medulloblastoma, and are very highly enriched in adult SHH and WNT tumors. TERT mutations define a subset of SHH medulloblastoma with distinct demographics, cytogenetics, and outcomes.

    View details for DOI 10.1007/s00401-013-1198-2

    View details for PubMedID 24174164

  • Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis. lancet oncology Ramaswamy, V., Remke, M., Bouffet, E., Faria, C. C., Perreault, S., Cho, Y., Shih, D. J., Luu, B., Dubuc, A. M., Northcott, P. A., Schüller, U., Gururangan, S., McLendon, R., Bigner, D., Fouladi, M., Ligon, K. L., Pomeroy, S. L., Dunn, S., Triscott, J., Jabado, N., Fontebasso, A., Jones, D. T., Kool, M., Karajannis, M. A., Gardner, S. L., Zagzag, D., Nunes, S., Pimentel, J., Mora, J., Lipp, E., Walter, A. W., Ryzhova, M., Zheludkova, O., Kumirova, E., Alshami, J., Croul, S. E., Rutka, J. T., Hawkins, C., Tabori, U., Codispoti, K. T., Packer, R. J., Pfister, S. M., Korshunov, A., Taylor, M. D. 2013; 14 (12): 1200-1207

    Abstract

    Recurrent medulloblastoma is a therapeutic challenge because it is almost always fatal. Studies have confirmed that medulloblastoma consists of at least four distinct subgroups. We sought to delineate subgroup-specific differences in medulloblastoma recurrence patterns.We retrospectively identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children (Toronto, ON, Canada) from 1994 to 2012 (cohort 1), and established molecular subgroups using a nanoString-based assay on formalin-fixed paraffin-embedded tissues or frozen tissue. The anatomical site of recurrence (local tumour bed or leptomeningeal metastasis), time to recurrence, and survival after recurrence were assessed in a subgroup-specific manner. Two independent, non-overlapping cohorts (cohort 2: samples from patients with recurrent medulloblastomas from 13 centres worldwide, obtained between 1991 and 2012; cohort 3: samples from patients with recurrent medulloblastoma obtained at the NN Burdenko Neurosurgical Institute [Moscow, Russia] between 1994 and 2011) were analysed to confirm and validate observations. When possible, molecular subgrouping was done on tissue obtained from both the initial surgery and at recurrence.Cohort 1 consisted of 30 patients with recurrent medulloblastomas; nine with local recurrences, and 21 with metastatic recurrences. Cohort 2 consisted of 77 patients and cohort 3 of 96 patients with recurrent medulloblastoma. Subgroup affiliation remained stable at recurrence in all 34 cases with available matched primary and recurrent pairs (five pairs from cohort 1 and 29 pairs from cohort 2 [15 SHH, five group 3, 14 group 4]). This finding was validated in 17 pairs from cohort 3. When analysed in a subgroup-specific manner, local recurrences in cohort 1 were more frequent in SHH tumours (eight of nine [89%]) and metastatic recurrences were more common in group 3 and group 4 tumours (17 of 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 cohort 2 (p=0·0013 for local vs metastatic recurrence, SHH vs group 3 vs group 4,), and cohort 3 (p<0·0001). Treatment with craniospinal irradiation at diagnosis was not significantly associated with the anatomical pattern of recurrence. Survival after recurrence was significantly longer in patients with group 4 tumours in cohort 1 (p=0·013) than with other subgroups, which was confirmed in cohort 2 (p=0·0075), but not cohort 3 (p=0·70).Medulloblastoma does not change subgroup at the time of recurrence, reinforcing the stability of the four main medulloblastoma subgroups. Significant differences in the location and timing of recurrence across medulloblastoma subgroups have potential treatment ramifications. Specifically, intensified local (posterior fossa) therapy should be tested in the initial treatment of patients with SHH tumours. Refinement of therapy for patients with group 3 or group 4 tumours should focus on metastases.Canadian Institutes of Health Research, National Institutes of Health, Pediatric Brain Tumor Foundation, Garron Family Chair in Childhood Cancer Research at The Hospital for Sick Children and The University of Toronto.

    View details for DOI 10.1016/S1470-2045(13)70449-2

    View details for PubMedID 24140199

  • Subgroup-Specific Prognostic Implications of TP53 Mutation in Medulloblastoma. Journal of clinical oncology Zhukova, N., Ramaswamy, V., Remke, M., Pfaff, E., Shih, D. J., Martin, D. C., Castelo-Branco, P., Baskin, B., Ray, P. N., Bouffet, E., von Bueren, A. O., Jones, D. T., Northcott, P. A., Kool, M., Sturm, D., Pugh, T. J., Pomeroy, S. L., Cho, Y., Pietsch, T., Gessi, M., Rutkowski, S., Bognar, L., Klekner, A., Cho, B., Kim, S., Wang, K., Eberhart, C. G., Fevre-Montange, M., Fouladi, M., French, P. J., Kros, M., Grajkowska, W. A., Gupta, N., Weiss, W. A., Hauser, P., Jabado, N., Jouvet, A., Jung, S., Kumabe, T., Lach, B., Leonard, J. R., Rubin, J. B., Liau, L. M., Massimi, L., Pollack, I. F., Shin Ra, Y., Van Meir, E. G., Zitterbart, K., Schüller, U., Hill, R. M., Lindsey, J. C., Schwalbe, E. C., Bailey, S., Ellison, D. W., Hawkins, C., Malkin, D., Clifford, S. C., Korshunov, A., Pfister, S., Taylor, M. D., Tabori, U. 2013; 31 (23): 2927-2935

    Abstract

    PURPOSEReports detailing the prognostic impact of TP53 mutations in medulloblastoma offer conflicting conclusions. We resolve this issue through the inclusion of molecular subgroup profiles.Patients And methodsWe determined subgroup affiliation, TP53 mutation status, and clinical outcome in a discovery cohort of 397 medulloblastomas. We subsequently validated our results on an independent cohort of 156 medulloblastomas.ResultsTP53 mutations are enriched in wingless (WNT; 16%) and sonic hedgehog (SHH; 21%) medulloblastomas and are virtually absent in subgroups 3 and 4 tumors (P < .001). Patients with SHH/TP53 mutant tumors are almost exclusively between ages 5 and 18 years, dramatically different from the general SHH distribution (P < .001). Children with SHH/TP53 mutant tumors harbor 56% germline TP53 mutations, which are not observed in children with WNT/TP53 mutant tumors. Five-year overall survival (OS; ± SE) was 41% ± 9% and 81% ± 5% for patients with SHH medulloblastomas with and without TP53 mutations, respectively (P < .001). Furthermore, TP53 mutations accounted for 72% of deaths in children older than 5 years with SHH medulloblastomas. In contrast, 5-year OS rates were 90% ± 9% and 97% ± 3% for patients with WNT tumors with and without TP53 mutations (P = .21). Multivariate analysis revealed that TP53 status was the most important risk factor for SHH medulloblastoma. Survival rates in the validation cohort mimicked the discovery results, revealing that poor survival of TP53 mutations is restricted to patients with SHH medulloblastomas (P = .012) and not WNT tumors. CONCLUSIONSubgroup-specific analysis reconciles prior conflicting publications and confirms that TP53 mutations are enriched among SHH medulloblastomas, in which they portend poor outcome and account for a large proportion of treatment failures in these patients.

    View details for DOI 10.1200/JCO.2012.48.5052

    View details for PubMedID 23835706

  • Recurrent somatic alterations of FGFR1 and NTRK2 in pilocytic astrocytoma. Nature genetics Jones, D. T., Hutter, B., Jäger, N., Korshunov, A., Kool, M., Warnatz, H., Zichner, T., Lambert, S. R., Ryzhova, M., Quang, D. A., Fontebasso, A. M., Stütz, A. M., Hutter, S., Zuckermann, M., Sturm, D., Gronych, J., Lasitschka, B., Schmidt, S., Seker-Cin, H., Witt, H., Sultan, M., Ralser, M., Northcott, P. A., Hovestadt, V., Bender, S., Pfaff, E., Stark, S., Faury, D., Schwartzentruber, J., Majewski, J., Weber, U. D., Zapatka, M., Raeder, B., Schlesner, M., Worth, C. L., Bartholomae, C. C., von Kalle, C., Imbusch, C. D., Radomski, S., Lawerenz, C., Van Sluis, P., Koster, J., Volckmann, R., Versteeg, R., Lehrach, H., Monoranu, C., Winkler, B., Unterberg, A., Herold-Mende, C., Milde, T., Kulozik, A. E., Ebinger, M., Schuhmann, M. U., Cho, Y., Pomeroy, S. L., von Deimling, A., Witt, O., Taylor, M. D., Wolf, S., Karajannis, M. A., Eberhart, C. G., Scheurlen, W., Hasselblatt, M., Ligon, K. L., Kieran, M. W., Korbel, J. O., Yaspo, M., Brors, B., Felsberg, J., Reifenberger, G., Collins, V. P., Jabado, N., Eils, R., Lichter, P., Pfister, S. M. 2013; 45 (8): 927-932

    Abstract

    Pilocytic astrocytoma, the most common childhood brain tumor, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations. Surgically inaccessible midline tumors are therapeutically challenging, showing sustained tendency for progression and often becoming a chronic disease with substantial morbidities. 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 new NTRK2 fusion genes in non-cerebellar tumors. New BRAF-activating changes were also observed. MAPK pathway alterations affected all tumors analyzed, with no other significant mutations identified, indicating that pilocytic astrocytoma is predominantly a single-pathway disease. Notably, we identified the same FGFR1 mutations in a subset of H3F3A-mutated pediatric glioblastoma with additional alterations in the NF1 gene. Our findings thus identify new potential therapeutic targets in distinct subsets of pilocytic astrocytoma and childhood glioblastoma.

    View details for DOI 10.1038/ng.2682

    View details for PubMedID 23817572

  • BAF complexes facilitate decatenation of DNA by topoisomerase IIa. Nature Dykhuizen, E. C., Hargreaves, D. C., Miller, E. L., Cui, K., Korshunov, A., Kool, M., Pfister, S., Cho, Y., Zhao, K., Crabtree, G. R. 2013; 497 (7451): 624-627

    Abstract

    Recent exon-sequencing studies of human tumours have revealed that subunits of BAF (mammalian SWI/SNF) complexes are mutated in more than 20% of all human malignancies, but the mechanisms involved in tumour suppression are unclear. BAF chromatin-remodelling complexes are polymorphic assemblies that use energy provided by ATP hydrolysis to regulate transcription through the control of chromatin structure and the placement of Polycomb repressive complex 2 (PRC2) across the genome. Several proteins dedicated to this multisubunit complex, including BRG1 (also known as SMARCA4) and BAF250a (also known as ARID1A), are mutated at frequencies similar to those of recognized tumour suppressors. In particular, the core ATPase BRG1 is mutated in 5-10% of childhood medulloblastomas and more than 15% of Burkitt's lymphomas. Here we show a previously unknown function of BAF complexes in decatenating newly replicated sister chromatids, a requirement for proper chromosome segregation during mitosis. We find that deletion of Brg1 in mouse cells, as well as the expression of BRG1 point mutants identified in human tumours, leads to anaphase bridge formation (in which sister chromatids are linked by catenated strands of DNA) and a G2/M-phase block characteristic of the decatenation checkpoint. Endogenous BAF complexes interact directly with endogenous topoisomerase II? (TOP2A) through BAF250a and are required for the binding of TOP2A to approximately 12,000 sites across the genome. Our results demonstrate that TOP2A chromatin binding is dependent on the ATPase activity of BRG1, which is compromised in oncogenic BRG1 mutants. These studies indicate that the ability of TOP2A to prevent DNA entanglement at mitosis requires BAF complexes and suggest that this activity contributes to the role of BAF subunits as tumour suppressors.

    View details for DOI 10.1038/nature12146

    View details for PubMedID 23698369

  • Genomic analysis of diffuse pediatric low-grade gliomas identifies recurrent oncogenic truncating rearrangements in the transcription factor MYBL1. Proceedings of the National Academy of Sciences of the United States of America Ramkissoon, L. A., Horowitz, P. M., Craig, J. M., Ramkissoon, S. H., Rich, B. E., Schumacher, S. E., McKenna, A., Lawrence, M. S., Bergthold, G., Brastianos, P. K., Tabak, B., Ducar, M. D., Van Hummelen, P., MacConaill, L. E., Pouissant-Young, T., Cho, Y., Taha, H., Mahmoud, M., Bowers, D. C., Margraf, L., Tabori, U., Hawkins, C., Packer, R. J., Hill, D. A., Pomeroy, S. L., Eberhart, C. G., Dunn, I. F., Goumnerova, L., Getz, G., Chan, J. A., Santagata, S., Hahn, W. C., Stiles, C. D., Ligon, A. H., Kieran, M. W., Beroukhim, R., Ligon, K. L. 2013; 110 (20): 8188-8193

    Abstract

    Pediatric low-grade gliomas (PLGGs) are among the most common solid tumors in children but, apart from BRAF kinase mutations or duplications in specific subclasses, few genetic driver events are known. Diffuse PLGGs comprise a set of uncommon subtypes that exhibit invasive growth and are therefore especially challenging clinically. We performed high-resolution copy-number analysis on 44 formalin-fixed, paraffin-embedded diffuse PLGGs to identify recurrent alterations. Diffuse PLGGs exhibited fewer such alterations than adult low-grade gliomas, but we identified several significantly recurrent events. The most significant event, 8q13.1 gain, was observed in 28% of diffuse astrocytoma grade IIs and resulted in partial duplication of the transcription factor MYBL1 with truncation of its C-terminal negative-regulatory domain. A similar recurrent deletion-truncation breakpoint was identified in two angiocentric gliomas in the related gene v-myb avian myeloblastosis viral oncogene homolog (MYB) on 6q23.3. Whole-genome sequencing of a MYBL1-rearranged diffuse astrocytoma grade II demonstrated MYBL1 tandem duplication and few other events. Truncated MYBL1 transcripts identified in this tumor induced anchorage-independent growth in 3T3 cells and tumor formation in nude mice. Truncated transcripts were also expressed in two additional tumors with MYBL1 partial duplication. Our results define clinically relevant molecular subclasses of diffuse PLGGs and highlight a potential role for the MYB family in the biology of low-grade gliomas.

    View details for DOI 10.1073/pnas.1300252110

    View details for PubMedID 23633565

  • Inhibition of TWIST1 Leads to Activation of Oncogene-Induced Senescence in Oncogene-Driven Non-Small Cell Lung Cancer MOLECULAR CANCER RESEARCH Burns, T. F., Dobromilskaya, I., Murphy, S. C., Gajula, R. P., Thiyagarajan, S., Chatley, S. N., Aziz, K., Cho, Y., Tran, P. T., Rudin, C. M. 2013; 11 (4): 329-338

    Abstract

    A large fraction of non-small cell lung cancers (NSCLC) are dependent on defined oncogenic driver mutations. Although targeted agents exist for EGFR- and EML4-ALK-driven NSCLCs, no therapies target the most frequently found driver mutation, KRAS. Furthermore, acquired resistance to the currently targetable driver mutations is nearly universally observed. Clearly a novel therapeutic approach is needed to target oncogene-driven NSCLCs. We recently showed that the basic helix-loop-helix transcription factor Twist1 cooperates with mutant Kras to induce lung adenocarcinoma in transgenic mouse models and that inhibition of Twist1 in these models led to Kras-induced senescence. In the current study, we examine the role of TWIST1 in oncogene-driven human NSCLCs. Silencing of TWIST1 in KRAS-mutant human NSCLC cell lines resulted in dramatic growth inhibition and either activation of a latent oncogene-induced senescence program or, in some cases, apoptosis. Similar effects were observed in EGFR mutation-driven and c-Met-amplified NSCLC cell lines. Growth inhibition by silencing of TWIST1 was independent of p53 or p16 mutational status and did not require previously defined mediators of senescence, p21 and p27, nor could this phenotype be rescued by overexpression of SKP2. In xenograft models, silencing of TWIST1 resulted in significant growth inhibition of KRAS-mutant, EGFR-mutant, and c-Met-amplified NSCLCs. Remarkably, inducible silencing of TWIST1 resulted in significant growth inhibition of established KRAS-mutant tumors. Together these findings suggest that silencing of TWIST1 in oncogene driver-dependent NSCLCs represents a novel and promising therapeutic strategy.

    View details for DOI 10.1158/1541-7786.MCR-12-0456

    View details for Web of Science ID 000317646200002

    View details for PubMedID 23364532

  • Growth factor receptor-Src-mediated suppression of GRK6 dysregulates CXCR4 signaling and promotes medulloblastoma migration MOLECULAR CANCER Yuan, L., Zhang, H., Liu, J., Rubin, J. B., Cho, Y., Shu, H. K., Schniederjan, M., MacDonald, T. J. 2013; 12

    Abstract

    Metastasis in medulloblastoma (MB) is associated with poor survival. Recent genetic studies revealed MB to comprise distinct molecular subgroups, including the sonic hedgehog (SHH) subgroup that exhibits a relatively high rate of progression. To identify targeted therapeutics against metastasis, a better understanding of the regulation of MB cell migration is needed. G protein-coupled receptor kinases (GRKs) have been implicated in cancer metastasis through their regulation of G-protein coupled receptors (GPCRs) involved in growth factor (GF)-mediated cell migration. However, the specific roles and regulation of GRKs in MB have not been investigated.Microarray mRNA analysis was performed for GRKs, GPCRs, and GFs in 29 human MB, and real time RT-PCR was used to detect GRK6 expression in MB cells. Lenti- or retro-virus infection, and siRNA or shRNA transfection, of MB cells was used to overexpress and knockdown target genes, respectively. Western blot was used to confirm altered expression of proteins. The effect of altered target protein on cell migration was determined by Boyden chamber assay and xCELLigence migration assays.We observed co-overexpression of PDGFRA, CXCR4, and CXCL12 in the SHH MB subtype compared to non-SHH MB (5, 7, and 5-fold higher, respectively). GRK6, which typically acts as a negative regulator of CXCR4 signaling, is downregulated in MB, relative to other GRKs, while the percentage of GRK6 expression is lower in MB tumors with metastasis (22%), compared to those without metastasis (43%). In SHH-responsive MB cells, functional blockade of PDGFR abolished CXCR4-mediated signaling. shPDGFR transfected MB cells demonstrated increased GRK6 expression, while PDGF or 10% FBS treatment of native MB cells reduced the stability of GRK6 by inducing its proteosomal degradation. Overexpression or downregulation of Src, a key mediator of GF receptor/PDGFR signaling, similarly inhibited or induced GRK6 expression, respectively. siRNA downregulation of GRK6 enhanced CXCR4 signaling and promoted MB migration, while lentiviral-GRK6 overexpression suppressed CXCR4 signaling, potentiated the effect of AMD3100, a CXCR4 antagonist, and impaired migration.Our findings demonstrate a novel mechanism of GF receptor/PDGFR-Src-mediated dysregulation of CXCR4 signaling that promotes MB cell migration, which could potentially be exploited for therapeutic targeting in SHH MB.

    View details for DOI 10.1186/1476-4598-12-18

    View details for Web of Science ID 000317043600001

    View details for PubMedID 23497290

  • ?5-GABAA receptors negatively regulate MYC-amplified medulloblastoma growth. Acta neuropathologica Sengupta, S., Weeraratne, S. D., Sun, H., Phallen, J., Rallapalli, S. K., Teider, N., Kosaras, B., Amani, V., Pierre-Francois, J., Tang, Y., Nguyen, B., Yu, F., Schubert, S., Balansay, B., Mathios, D., Lechpammer, M., Archer, T. C., Tran, P., Reimer, R. J., Cook, J. M., Lim, M., Jensen, F. E., Pomeroy, S. L., Cho, Y. J. 2013

    Abstract

    Neural tumors often express neurotransmitter receptors as markers of their developmental lineage. Although these receptors have been well characterized in electrophysiological, developmental and pharmacological settings, their importance in the maintenance and progression of brain tumors and, importantly, the effect of their targeting in brain cancers remains obscure. Here, we demonstrate high levels of GABRA5, which encodes the ?5-subunit of the GABAA receptor complex, in aggressive MYC-driven, "Group 3" medulloblastomas. We hypothesized that modulation of ?5-GABAA receptors alters medulloblastoma cell survival and monitored biological and electrophysiological responses of GABRA5-expressing medulloblastoma cells upon pharmacological targeting of the GABAA receptor. While antagonists, inverse agonists and non-specific positive allosteric modulators had limited effects on medulloblastoma cells, a highly specific and potent ?5-GABAA receptor agonist, QHii066, resulted in marked membrane depolarization and a significant decrease in cell survival. This effect was GABRA5 dependent and mediated through the induction of apoptosis as well as accumulation of cells in S and G2 phases of the cell cycle. Chemical genomic profiling of QHii066-treated medulloblastoma cells confirmed inhibition of MYC-related transcriptional activity and revealed an enrichment of HOXA5 target gene expression. siRNA-mediated knockdown of HOXA5 markedly blunted the response of medulloblastoma cells to QHii066. Furthermore, QHii066 sensitized GABRA5 positive medulloblastoma cells to radiation and chemotherapy consistent with the role of HOXA5 in directly regulating p53 expression and inducing apoptosis. Thus, our results provide novel insights into the synthetic lethal nature of ?5-GABAA receptor activation in MYC-driven/Group 3 medulloblastomas and propose its targeting as a novel strategy for the management of this highly aggressive tumor.

    View details for DOI 10.1007/s00401-013-1205-7

    View details for PubMedID 24196163

  • Activation of ?-catenin/TCF targets following loss of the tumor suppressor SNF5. Oncogene Mora-Blanco, E. L., Mishina, Y., Tillman, E. J., Cho, Y. J., Thom, C. S., Pomeroy, S. L., Shao, W., Roberts, C. W. 2013

    Abstract

    The SWI/SNF chromatin remodeling complex is a master regulator of developmental cell-fate decisions, although the key target pathways are poorly characterized. Here, we interrogated the contribution of the SWI/SNF subunit and tumor suppressor SNF5 to the regulation of developmental pathways using conditional mouse and cell culture models. We find that loss of SNF5 phenocopies ?-catenin hyperactivation and that SNF5 is essential for regulating Wnt/?-catenin pathway target expression. These data provide insight into chromatin-based mechanisms that underlie developmental regulation and elucidate the emerging theme that mutation of this tumor suppressor complex can activate developmental pathways by uncoupling them from upstream control.Oncogene advance online publication, 25 February 2013; doi:10.1038/onc.2013.37.

    View details for PubMedID 23435428

  • The VEGF Pathway in Cancer and Disease: Responses, Resistance, and the Path Forward COLD SPRING HARBOR PERSPECTIVES IN MEDICINE Kieran, M. W., Kalluri, R., Cho, Y. 2012; 2 (12)

    Abstract

    Antiangiogenesis was proposed as a novel target for the treatment of cancer 40 years ago. Since the original hypothesis put forward by Judah Folkman in 1971, factors that mediate angiogenesis, their cellular targets, many of the pathways they signal, and inhibitors of the cytokines and receptors have been identified. Vascular endothelial growth factor (VEGF) is the most prominent among the angiogenic cytokines and is believed to play a central role in the process of neovascularization, both in cancer as well as other inflammatory diseases. This article reviews the biology of VEGF and its receptors, the use of anti-VEGF approaches in clinical disease, the toxicity of these therapies, and the resistance mechanisms that have limited the activity of these agents when used as monotherapy.

    View details for DOI 10.1101/cshperspect.a006593

    View details for Web of Science ID 000314282700007

    View details for PubMedID 23209176

  • Medulloblastomics: the end of the beginning NATURE REVIEWS CANCER Northcott, P. A., Jones, D. T., Kool, M., Robinson, G. W., Gilbertson, R. J., Cho, Y., Pomeroy, S. L., Korshunov, A., Lichter, P., Taylor, M. D., Pfister, S. M. 2012; 12 (12): 818-834

    Abstract

    The division of medulloblastoma into different subgroups by microarray expression profiling has dramatically changed our perspective of this malignant childhood brain tumour. Now, the availability of next-generation sequencing and complementary high-density genomic technologies has unmasked novel driver mutations in each medulloblastoma subgroup. The implications of these findings for the management of patients are readily apparent, pinpointing previously unappreciated diagnostic and therapeutic targets. In this Review, we summarize the 'explosion' of data emerging from the application of modern genomics to medulloblastoma, and in particular the recurrent targets of mutation in medulloblastoma subgroups. These data are currently making their way into clinical trials as we seek to integrate conventional and molecularly targeted therapies.

    View details for DOI 10.1038/nrc3410

    View details for Web of Science ID 000311714200012

    View details for PubMedID 23175120

  • Epigenetic inactivation of the tumor suppressor BIN1 drives proliferation of SNF5-deficient tumors CELL CYCLE McKenna, E. S., Tamayo, P., Cho, Y., Tillman, E. J., Mora-Blanco, E. L., Sansam, C. G., Koellhoffer, E. C., Pomeroy, S. L., Roberts, C. W. 2012; 11 (10): 1956-1965

    Abstract

    Emerging evidence demonstrates that subunits of the SWI/SNF chromatin remodeling complex are specifically mutated at high frequency in a variety of human cancer types. SNF5 (SMARCB1/INI1/BAF47), a core subunit of the SWI/SNF complex, is inactivated in the vast majority of rhabdoid tumors (RT), an aggressive type of pediatric cancer. SNF5-deficient cancers are diploid and genomically stable, suggesting that epigenetically based changes in transcription are key drivers of tumor formation caused by SNF5 loss. However, there is limited understanding of the target genes that drive cancer formation following SNF5 loss. Here we performed comparative expression analyses upon three independent SNF5-deficient cancer data sets from both human and mouse and identify downregulation of the BIN1 tumor suppressor as a conserved event in primary SNF5-deficient cancers. We show that SNF5 recruits the SWI/SNF complex to the BIN1 promoter, and that the marked reduction of BIN1 expression in RT correlates with decreased SWI/SNF occupancy. Functionally, we demonstrate that re-expression of BIN1 specifically compromises the proliferation of SNF5-deficient RT cell lines. Identification of BIN1 as a SNF5 target gene reveals a novel tumor suppressive regulatory mechanism whose disruption can drive cancer formation.

    View details for DOI 10.4161/cc.20280

    View details for Web of Science ID 000304039900021

    View details for PubMedID 22544318

  • Twist1 Suppresses Senescence Programs and Thereby Accelerates and Maintains Mutant Kras-Induced Lung Tumorigenesis PLOS GENETICS Tran, P. T., Shroff, E. H., Burns, T. F., Thiyagarajan, S., Das, S. T., Zabuawala, T., Chen, J., Cho, Y., Luong, R., Tamayo, P., Salih, T., Aziz, K., Adam, S. J., Vicent, S., Nielsen, C. H., Withofs, N., Sweet-Cordero, A., Gambhir, S. S., Rudin, C. M., Felsher, D. W. 2012; 8 (5)

    Abstract

    KRAS mutant lung cancers are generally refractory to chemotherapy as well targeted agents. To date, the identification of drugs to therapeutically inhibit K-RAS have been unsuccessful, suggesting that other approaches are required. We demonstrate in both a novel transgenic mutant Kras lung cancer mouse model and in human lung tumors that the inhibition of Twist1 restores a senescence program inducing the loss of a neoplastic phenotype. The Twist1 gene encodes for a transcription factor that is essential during embryogenesis. Twist1 has been suggested to play an important role during tumor progression. However, there is no in vivo evidence that Twist1 plays a role in autochthonous tumorigenesis. Through two novel transgenic mouse models, we show that Twist1 cooperates with Kras(G12D) to markedly accelerate lung tumorigenesis by abrogating cellular senescence programs and promoting the progression from benign adenomas to adenocarcinomas. Moreover, the suppression of Twist1 to physiological levels is sufficient to cause Kras mutant lung tumors to undergo senescence and lose their neoplastic features. Finally, we analyzed more than 500 human tumors to demonstrate that TWIST1 is frequently overexpressed in primary human lung tumors. The suppression of TWIST1 in human lung cancer cells also induced cellular senescence. Hence, TWIST1 is a critical regulator of cellular senescence programs, and the suppression of TWIST1 in human tumors may be an effective example of pro-senescence therapy.

    View details for DOI 10.1371/journal.pgen.1002650

    View details for Web of Science ID 000304864000004

    View details for PubMedID 22654667

  • Rapid, reliable, and reproducible molecular sub-grouping of clinical medulloblastoma samples ACTA NEUROPATHOLOGICA Northcott, P. A., Shih, D. J., Remke, M., Cho, Y., Kool, M., Hawkins, C., Eberhart, C. G., Dubuc, A., Guettouche, T., Cardentey, Y., Bouffet, E., Pomeroy, S. L., Marra, M., Malkin, D., Rutka, J. T., Korshunov, A., Pfister, S., Taylor, M. D. 2012; 123 (4): 615-626

    Abstract

    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.

    View details for DOI 10.1007/s00401-011-0899-7

    View details for Web of Science ID 000301849000013

    View details for PubMedID 22057785

  • Molecular subgroups of medulloblastoma: an international meta-analysis of transcriptome, genetic aberrations, and clinical data of WNT, SHH, Group 3, and Group 4 medulloblastomas ACTA NEUROPATHOLOGICA Kool, M., Korshunov, A., Remke, M., Jones, D. T., Schlanstein, M., Northcott, P. A., Cho, Y., Koster, J., Schouten-van Meeteren, A., Van Vuurden, D., Clifford, S. C., Pietsch, T., von Bueren, A. O., Rutkowski, S., McCabe, M., Collins, V. P., Backlund, M. L., Haberler, C., Bourdeaut, F., Delattre, O., Doz, F., Ellison, D. W., Gilbertson, R. J., Pomeroy, S. L., Taylor, M. D., Lichter, P., Pfister, S. M. 2012; 123 (4): 473-484

    Abstract

    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 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.

    View details for DOI 10.1007/s00401-012-0958-8

    View details for Web of Science ID 000301849000003

    View details for PubMedID 22358457

  • MicroRNA-182 promotes leptomeningeal spread of non-sonic hedgehog-medulloblastoma ACTA NEUROPATHOLOGICA Bai, A. H., Milde, T., Remke, M., Rolli, C. G., Hielscher, T., Cho, Y., Kool, M., Northcott, P. A., Jugold, M., Bazhin, A. V., Eichmueller, S. B., Kulozik, A. E., Pscherer, A., Benner, A., Taylor, M. D., Pomeroy, S. L., Kemkemer, R., Witt, O., Korshunov, A., Lichter, P., Pfister, S. M. 2012; 123 (4): 529-538

    Abstract

    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 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.

    View details for DOI 10.1007/s00401-011-0924-x

    View details for Web of Science ID 000301849000007

    View details for PubMedID 22134538

  • Pleiotropic effects of miR-183 similar to 96 similar to 182 converge to regulate cell survival, proliferation and migration in medulloblastoma ACTA NEUROPATHOLOGICA Weeraratne, S. D., Amani, V., Teider, N., Pierre-Francois, J., Winter, D., Kye, M. J., Sengupta, S., Archer, T., Remke, M., Bai, A. H., Warren, P., Pfister, S. M., Steen, J. A., Pomeroy, S. L., Cho, Y. 2012; 123 (4): 539-552

    Abstract

    Medulloblastomas are the most common malignant brain tumors in children. Several large-scale genomic studies have detailed their heterogeneity, defining multiple subtypes with unique molecular profiles and clinical behavior. Increased expression of the miR-183~96~182 cluster of microRNAs has been noted in several subgroups, including the most clinically aggressive subgroup associated with genetic amplification of MYC. To understand the contribution of miR-183~96~182 to the pathogenesis of this aggressive subtype of medulloblastoma, we analyzed global gene expression and proteomic changes that occur upon modulation of miRNAs in this cluster individually and as a group in MYC-amplified medulloblastoma cells. Knockdown of the full miR-183~96~182 cluster results in enrichment of genes associated with apoptosis and dysregulation of the PI3K/AKT/mTOR signaling axis. Conversely, there is a relative enrichment of pathways associated with migration, metastasis and epithelial to mesenchymal transition, as well as pathways associated with dysfunction of DNA repair in cells with preserved miR-183 cluster expression. Immunocytochemistry and FACS analysis confirm induction of apoptosis upon knockdown of the miR-183 cluster. Importantly, cell-based migration and invasion assays verify the positive regulation of cell motility/migration by the miR-183 cluster, which is largely mediated by miR-182. We show that the effects on cell migration induced by the miR-183 cluster are coupled to the PI3K/AKT/mTOR pathway through differential regulation of AKT1 and AKT2 isoforms. Furthermore, we show that rapamycin inhibits cell motility/migration in medulloblastoma cells and phenocopies miR-183 cluster knockdown. Thus, the miR-183 cluster regulates multiple biological programs that converge to support the maintenance and metastatic potential of medulloblastoma.

    View details for DOI 10.1007/s00401-012-0969-5

    View details for Web of Science ID 000301849000008

    View details for PubMedID 22402744

  • Molecular subgroups of medulloblastoma: the current consensus ACTA NEUROPATHOLOGICA Taylor, M. D., Northcott, P. A., Korshunov, A., Remke, M., Cho, Y., Clifford, S. C., Eberhart, C. G., Parsons, D. W., Rutkowski, S., Gajjar, A., Ellison, D. W., Lichter, P., Gilbertson, R. J., Pomeroy, S. L., Kool, M., Pfister, S. M. 2012; 123 (4): 465-472

    Abstract

    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 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.

    View details for DOI 10.1007/s00401-011-0922-z

    View details for Web of Science ID 000301849000002

    View details for PubMedID 22134537

  • Biological and clinical heterogeneity of MYCN-amplified medulloblastoma ACTA NEUROPATHOLOGICA Korshunov, A., Remke, M., Kool, M., Hielscher, T., Northcott, P. A., Williamson, D., Pfaff, E., Witt, H., Jones, D. T., Ryzhova, M., Cho, Y., Wittmann, A., Benner, A., Weiss, W. A., von Deimling, A., Scheurlen, W., Kulozik, A. E., Clifford, S. C., Collins, V. P., Westermann, F., Taylor, M. D., Lichter, P., Pfister, S. M. 2012; 123 (4): 515-527

    Abstract

    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 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.

    View details for DOI 10.1007/s00401-011-0918-8

    View details for Web of Science ID 000301849000006

    View details for PubMedID 22160402

  • Clonal selection drives genetic divergence of metastatic medulloblastoma NATURE Wu, X., Northcott, P. A., Dubuc, A., Dupuy, A. J., Shih, D. J., Witt, H., Croul, S., Bouffet, E., Fults, D. W., Eberhart, C. G., Garzia, L., Van Meter, T., Zagzag, D., Jabado, N., Schwartzentruber, J., Majewski, J., Scheetz, T. E., Pfister, S. M., Korshunov, A., Li, X., Scherer, S. W., Cho, Y., Akagi, K., MacDonald, T. J., Koster, J., McCabe, M. G., Sarver, A. L., Collins, V. P., Weiss, W. A., Largaespada, D. A., Collier, L. S., Taylor, M. D. 2012; 482 (7386): 529-U254

    Abstract

    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 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.

    View details for DOI 10.1038/nature10825

    View details for Web of Science ID 000300770500051

    View details for PubMedID 22343890

  • An Animal Model of MYC-Driven Medulloblastoma CANCER CELL Pei, Y., Moore, C. E., Wang, J., Tewari, A. K., Eroshkin, A., Cho, Y., Witt, H., Korshunov, A., Read, T., Sun, J. L., Schmitt, E. M., Miller, C. R., Buckley, A. F., McLendon, R. E., Westbrook, T. F., Northcott, P. A., Taylor, M. D., Pfister, S. M., Febbo, P. G., Wechsler-Reya, R. J. 2012; 21 (2): 155-167

    Abstract

    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 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.

    View details for DOI 10.1016/j.ccr.2011.12.021

    View details for Web of Science ID 000300476000008

    View details for PubMedID 22340590

  • Expression of FoxM1 is required for the proliferation of medulloblastoma cells and indicates worse survival of patients. Clinical cancer research Priller, M., Pöschl, J., Abrão, L., von Bueren, A. O., Cho, Y., Rutkowski, S., Kretzschmar, H. A., Schüller, U. 2011; 17 (21): 6791-6801

    Abstract

    The transcription factor Forkhead box M1 (FoxM1) is a key regulator of cell-cycle progression. It is involved in the development of multiple organs, and we have previously reported on its important role for the mitotic entry of cerebellar granule neuron precursors. Constitutive expression of FoxM1 is required for the growth of multiple cancer types. This study aimed to determine its role in medulloblastoma, the most frequent malignant brain tumor in childhood that can derive from cerebellar granule neuron precursors.We evaluated the expression of FoxM1 together with its prognostic value in two independent series of human medulloblastoma samples using immunohistochemistry (n = 43) and gene expression arrays (n = 193). The functional impact of FoxM1 expression was characterized by knockdown experiments in four human medulloblastoma cell lines, and the thiazole antibiotic siomycin A was tested to downregulate FoxM1 and inhibit tumor cell growth.FoxM1 was highly expressed in all subtypes of medulloblastoma. Importantly, expression levels of FoxM1 significantly correlated with unfavorable clinical outcome in univariate analysis (P = 0.0005), and FoxM1 was identified as an independent prognostic marker by multivariate analysis (P = 0.037). Knockdown of FoxM1 in medulloblastoma cell lines resulted in a significant decrease of cell viability which was caused by a failure in mitotic spindle formation and caspase-dependent mitotic catastrophe. Siomycin A significantly inhibited the expression of FoxM1 and the growth of medulloblastoma cells.FoxM1 may be used as an additional prognostic marker and may represent a potential novel target to treat patients suffering from medulloblastoma.

    View details for DOI 10.1158/1078-0432.CCR-11-1214

    View details for PubMedID 21918172

  • Delineation of Two Clinically and Molecularly Distinct Subgroups of Posterior Fossa Ependymoma CANCER CELL Witt, H., Mack, S. C., Ryzhova, M., Bender, S., Sill, M., Isserlin, R., Benner, A., Hielscher, T., Milde, T., Remke, M., Jones, D. T., Northcott, P. A., Garzia, L., Bertrand, K. C., Wittmann, A., Yao, Y., Roberts, S. S., Massimi, L., Van Meter, T., Weiss, W. A., Gupta, N., Grajkowska, W., Lach, B., Cho, Y., von Deimling, A., Kulozik, A. E., Witt, O., Bader, G. D., Hawkins, C. E., Tabori, U., Guha, A., Rutka, J. T., Lichter, P., Korshunov, A., Taylor, M. D., Pfister, S. M. 2011; 20 (2): 143-157

    Abstract

    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.

    View details for DOI 10.1016/j.ccr.2011.07.007

    View details for Web of Science ID 000294099700005

    View details for PubMedID 21840481

  • Predicting Relapse in Patients With Medulloblastoma by Integrating Evidence From Clinical and Genomic Features JOURNAL OF CLINICAL ONCOLOGY Tamayo, P., Cho, Y., Tsherniak, A., Greulich, H., Ambrogio, L., Schouten-van Meeteren, N., Zhou, T., Buxton, A., Kool, M., Meyerson, M., Pomeroy, S. L., Mesirov, J. P. 2011; 29 (11): 1415-1423

    Abstract

    Despite significant progress in the molecular understanding of medulloblastoma, stratification of risk in patients remains a challenge. Focus has shifted from clinical parameters to molecular markers, such as expression of specific genes and selected genomic abnormalities, to improve accuracy of treatment outcome prediction. Here, we show how integration of high-level clinical and genomic features or risk factors, including disease subtype, can yield more comprehensive, accurate, and biologically interpretable prediction models for relapse versus no-relapse classification. We also introduce a novel Bayesian nomogram indicating the amount of evidence that each feature contributes on a patient-by-patient basis.A Bayesian cumulative log-odds model of outcome was developed from a training cohort of 96 children treated for medulloblastoma, starting with the evidence provided by clinical features of metastasis and histology (model A) and incrementally adding the evidence from gene-expression-derived features representing disease subtype-independent (model B) and disease subtype-dependent (model C) pathways, and finally high-level copy-number genomic abnormalities (model D). The models were validated on an independent test cohort (n = 78).On an independent multi-institutional test data set, models A to D attain an area under receiver operating characteristic (au-ROC) curve of 0.73 (95% CI, 0.60 to 0.84), 0.75 (95% CI, 0.64 to 0.86), 0.80 (95% CI, 0.70 to 0.90), and 0.78 (95% CI, 0.68 to 0.88), respectively, for predicting relapse versus no relapse.The proposed models C and D outperform the current clinical classification schema (au-ROC, 0.68), our previously published eight-gene outcome signature (au-ROC, 0.71), and several new schemas recently proposed in the literature for medulloblastoma risk stratification.

    View details for DOI 10.1200/JCO.2010.28.1675

    View details for Web of Science ID 000289276900021

    View details for PubMedID 21357789

  • Molecular fingerprints of medulloblastoma and their application to clinical practice FUTURE ONCOLOGY Pomeroy, S. L., Cho, Y. 2011; 7 (3): 327-329

    View details for DOI 10.2217/FON.11.15

    View details for Web of Science ID 000289594400002

    View details for PubMedID 21417897

  • miR-34a confers chemosensitivity through modulation of MAGE-A and p53 in medulloblastoma NEURO-ONCOLOGY Weeraratne, S. D., Amani, V., Neiss, A., Teider, N., Scott, D. K., Pomeroy, S. L., Cho, Y. 2011; 13 (2): 165-175

    Abstract

    Recent studies have established miR-34a as a key effector of the p53 signaling pathway and have implicated its role in multiple cancer types. Here, we establish that miR-34a induces apoptosis, G2 arrest, and senescence in medulloblastoma and renders these cells more sensitive to chemotherapeutic agents. These effects are mediated in part by the direct post-transcriptional repression of the oncogenic MAGE-A gene family. We demonstrate that miR-34a directly targets the 3' untranslated regions of MAGE-A genes and decreases MAGE-A protein levels. This decrease in MAGE-A results in a concomitant increase in p53 and its associated transcriptional targets, p21/WAF1/CIP1 and, importantly, miR-34a. This establishes a positive feedback mechanism where miR-34a is not only induced by p53 but increases p53 mRNA and protein levels through the modulation of MAGE-A genes. Additionally, the forced expression of miR-34a or the knockdown of MAGE-A genes by small interfering RNA similarly sensitizes medulloblastoma cells to several classes of chemotherapeutic agents, including mitomycin C and cisplatin. Finally, the analysis of mRNA and micro-RNA transcriptional profiles of a series of primary medulloblastomas identifies a subset of tumors with low miR-34a expression and correspondingly high MAGE-A expression, suggesting the coordinate regulation of these genes. Our work establishes a role for miR-34a in modulating responsiveness to chemotherapy in medulloblastoma and presents a novel positive feedback mechanism involving miR-34a and p53, via direct targeting of MAGE-A.

    View details for DOI 10.1093/neuonc/noq179

    View details for Web of Science ID 000287002700002

    View details for PubMedID 21177782

  • Tumour microvesicles contain retrotransposon elements and amplified oncogene sequences NATURE COMMUNICATIONS Balaj, L., Lessard, R., Dai, L., Cho, Y., Pomeroy, S. L., Breakefield, X. O., Skog, J. 2011; 2

    Abstract

    Tumour cells release an abundance of microvesicles containing a selected set of proteins and RNAs. Here, we show that tumour microvesicles also carry DNA, which reflects the genetic status of the tumour, including amplification of the oncogene c-Myc. We also find amplified c-Myc in serum microvesicles from tumour-bearing mice. Further, we find remarkably high levels of retrotransposon RNA transcripts, especially for some human endogenous retroviruses, such as LINE-1 and Alu retrotransposon elements, in tumour microvesicles and these transposable elements could be transferred to normal cells. These findings expand the nucleic acid content of tumour microvesicles to include: elevated levels of specific coding and non-coding RNA and DNA, mutated and amplified oncogene sequences and transposable elements. Thus, tumour microvesicles contain a repertoire of genetic information available for horizontal gene transfer and potential use as blood biomarkers for cancer.

    View details for DOI 10.1038/ncomms1180

    View details for Web of Science ID 000288225900009

    View details for PubMedID 21285958

  • Loss of the tumor suppressor Snf5 leads to aberrant activation of the Hedgehog-Gli pathway NATURE MEDICINE Jagani, Z., Mora-Blanco, E. L., Sansam, C. G., McKenna, E. S., Wilson, B., Chen, D., Klekota, J., Tamayo, P., Nguyen, P. T., Tolstorukov, M., Park, P. J., Cho, Y., Hsiao, K., Buonamici, S., Pomeroy, S. L., Mesirov, J. P., Ruffner, H., Bouwmeester, T., Luchansky, S. J., Murtie, J., Kelleher, J. F., Warmuth, M., Sellers, W. R., Roberts, C. W., Dorsch, M. 2010; 16 (12): 1429-U112

    Abstract

    Aberrant activation of the Hedgehog (Hh) pathway can drive tumorigenesis. To investigate the mechanism by which glioma-associated oncogene family zinc finger-1 (GLI1), a crucial effector of Hh signaling, regulates Hh pathway activation, we searched for GLI1-interacting proteins. We report that the chromatin remodeling protein SNF5 (encoded by SMARCB1, hereafter called SNF5), which is inactivated in human malignant rhabdoid tumors (MRTs), interacts with GLI1. We show that Snf5 localizes to Gli1-regulated promoters and that loss of Snf5 leads to activation of the Hh-Gli pathway. Conversely, re-expression of SNF5 in MRT cells represses GLI1. Consistent with this, we show the presence of a Hh-Gli-activated gene expression profile in primary MRTs and show that GLI1 drives the growth of SNF5-deficient MRT cells in vitro and in vivo. Therefore, our studies reveal that SNF5 is a key mediator of Hh signaling and that aberrant activation of GLI1 is a previously undescribed targetable mechanism contributing to the growth of MRT cells.

    View details for DOI 10.1038/nm.2251

    View details for Web of Science ID 000285048900037

    View details for PubMedID 21076395

  • Neuralized1 causes apoptosis and downregulates Notch target genes in medulloblastoma NEURO-ONCOLOGY Teider, N., Scott, D. K., Neiss, A., Weeraratne, S. D., Amani, V. M., Wang, Y., Marquez, V. E., Cho, Y., Pomeroy, S. L. 2010; 12 (12): 1244-?

    Abstract

    Neuralized (Neurl) is a highly conserved E3 ubiquitin ligase, which in Drosophila acts upon Notch ligands to regulate Notch pathway signaling. Human Neuralized1 (NEURL1) was investigated as a potential tumor suppressor in medulloblastoma (MB). The gene is located at 10q25.1, a region demonstrating frequent loss of heterozygosity in tumors. In addition, prior publications have shown that the Notch pathway is functional in a proportion of MB tumors and that Neurl1 is only expressed in differentiated cells in the developing cerebellum. In this study, NEURL1 expression was downregulated in MB compared with normal cerebellar tissue, with the lowest levels of expression in hedgehog-activated tumors. Control of gene expression by histone modification was implicated mechanistically; loss of 10q, sequence mutation, and promoter hypermethylation did not play major roles. NEURL1-transfected MB cell lines demonstrated decreased population growth, colony-forming ability, tumor sphere formation, and xenograft growth compared with controls, and a significant increase in apoptosis was seen on cell cycle and cell death analysis. Notch pathway inhibition occurred on the exogenous expression of NEURL1, as shown by decreased expression of the Notch ligand, Jagged1, and the target genes, HES1 and HEY1. From these studies, we conclude that NEURL1 is a candidate tumor suppressor in MB, at least in part through its effects on the Notch pathway.

    View details for DOI 10.1093/neuonc/noq091

    View details for Web of Science ID 000284429000002

    View details for PubMedID 20847082

  • Epigenetic Antagonism between Polycomb and SWI/SNF Complexes during Oncogenic Transformation CANCER CELL Wilson, B. G., Wang, X., Shen, X., McKenna, E. S., Lemieux, M. E., Cho, Y., Koellhoffer, E. C., Pomeroy, S. L., Orkin, S. H., Roberts, C. W. 2010; 18 (4): 316-328

    Abstract

    Epigenetic alterations have been increasingly implicated in oncogenesis. Analysis of Drosophila mutants suggests that Polycomb and SWI/SNF complexes can serve antagonistic developmental roles. However, the relevance of this relationship to human disease is unclear. Here, we have investigated functional relationships between these epigenetic regulators in oncogenic transformation. Mechanistically, we show that loss of the SNF5 tumor suppressor leads to elevated expression of the Polycomb gene EZH2 and that Polycomb targets are broadly H3K27-trimethylated and repressed in SNF5-deficient fibroblasts and cancers. Further, we show antagonism between SNF5 and EZH2 in the regulation of stem cell-associated programs and that Snf5 loss activates those programs. Finally, using conditional mouse models, we show that inactivation of Ezh2 blocks tumor formation driven by Snf5 loss.

    View details for DOI 10.1016/j.ccr.2010.09.006

    View details for Web of Science ID 000283697200006

    View details for PubMedID 20951942

  • The landscape of somatic copy-number alteration across human cancers NATURE Beroukhim, R., Mermel, C. H., Porter, D., Wei, G., Raychaudhuri, S., Donovan, J., Barretina, J., Boehm, J. S., Dobson, J., Urashima, M., Mc Henry, K. T., Pinchback, R. M., Ligon, A. H., Cho, Y., Haery, L., Greulich, H., Reich, M., Winckler, W., Lawrence, M. S., Weir, B. A., Tanaka, K. E., Chiang, D. Y., Bass, A. J., Loo, A., Hoffman, C., Prensner, J., Liefeld, T., Gao, Q., Yecies, D., Signoretti, S., Maher, E., Kaye, F. J., Sasaki, H., Tepper, J. E., Fletcher, J. A., Tabernero, J., Baselga, J., Tsao, M., Demichelis, F., Rubin, M. A., Janne, P. A., Daly, M. J., Nucera, C., Levine, R. L., Ebert, B. L., Gabriel, S., Rustgi, A. K., Antonescu, C. R., Ladanyi, M., Letai, A., Garraway, L. A., Loda, M., Beer, D. G., True, L. D., Okamoto, A., Pomeroy, S. L., Singer, S., Golub, T. R., Lander, E. S., Getz, G., Sellers, W. R., Meyerson, M. 2010; 463 (7283): 899-905

    Abstract

    A powerful way to discover key genes with causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here we present high-resolution analyses of somatic copy-number alterations (SCNAs) from 3,131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across several cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-kappaBeta pathway. We show that cancer cells containing amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend on the expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in several cancer types.

    View details for DOI 10.1038/nature08822

    View details for Web of Science ID 000274582700036

    View details for PubMedID 20164920

  • MELATONIN DEFICIENCY AND DISRUPTED CIRCADIAN RHYTHMS IN PEDIATRIC SURVIVORS OF CRANIOPHARYNGIOMA NEUROLOGY Lipton, J., Megerian, J. T., Kothare, S. V., Cho, Y., Shanahan, T., Chart, H., Ferber, R., Adler-Golden, L., Cohen, L. E., Czeisler, C. A., Pomeroy, S. L. 2009; 73 (4): 323-325

    View details for DOI 10.1212/WNL.0b013e3181af78a5

    View details for Web of Science ID 000268356500013

    View details for PubMedID 19636054

  • Loss of the epigenetic tumor suppressor SNF5 leads to cancer without genomic instability MOLECULAR AND CELLULAR BIOLOGY McKenna, E. S., Sansam, C. G., Cho, Y., Greulich, H., Evans, J. A., Thom, C. S., Moreau, L. A., Biegel, J. A., Pomeroy, S. L., Roberts, C. W. 2008; 28 (20): 6223-6233

    Abstract

    There is a growing appreciation of the role that epigenetic alterations can play in oncogenesis. However, given the large number of genetic anomalies present in most cancers, it has been difficult to evaluate the extent to which epigenetic changes contribute to cancer. SNF5 (INI1/SMARCB1/BAF47) is a tumor suppressor that regulates the epigenome as a core member of the SWI/SNF chromatin remodeling complex. While the SWI/SNF complex displays potent tumor suppressor activity, it is unknown whether this activity is exerted genetically via maintenance of genome integrity or epigenetically via transcriptional regulation. Here we show that Snf5-deficient primary cells do not show altered sensitivity to DNA damaging agents, defects in gamma-H2AX induction, or an abrogated DNA damage checkpoint. Further, the aggressive malignancies that arise following SNF5 loss are diploid and genomically stable. Remarkably, we demonstrate that most human SNF5-deficient cancers lack genomic amplifications/deletions and, aside from SNF5 loss, are indistinguishable from normal cells on single-nucleotide polymorphism arrays. Finally, we show that epigenetically based changes in transcription that occur following SNF5 loss correlate with the tumor phenotype. Collectively, our results provide novel insight into the mechanisms of oncogenesis by demonstrating that disruption of a chromatin remodeling complex can largely, if not completely, substitute for genomic instability in the genesis of aggressive cancer.

    View details for DOI 10.1128/MCB.00658-08

    View details for Web of Science ID 000259634800007

    View details for PubMedID 18710953

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