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1.  Cytogenetic Prognostication Within Medulloblastoma Subgroups 
Shih, David J.H. | Northcott, Paul A. | Remke, Marc | Korshunov, Andrey | Ramaswamy, Vijay | Kool, Marcel | Luu, Betty | Yao, Yuan | Wang, Xin | Dubuc, Adrian M. | Garzia, Livia | Peacock, John | Mack, Stephen C. | Wu, Xiaochong | Rolider, Adi | Morrissy, A. Sorana | Cavalli, Florence M.G. | Jones, David T.W. | Zitterbart, Karel | Faria, Claudia C. | Schüller, Ulrich | Kren, Leos | Kumabe, Toshihiro | Tominaga, Teiji | Shin Ra, Young | Garami, Miklós | Hauser, Peter | Chan, Jennifer A. | Robinson, Shenandoah | Bognár, László | Klekner, Almos | Saad, Ali G. | Liau, Linda M. | Albrecht, Steffen | Fontebasso, Adam | Cinalli, Giuseppe | De Antonellis, Pasqualino | Zollo, Massimo | Cooper, Michael K. | Thompson, Reid C. | Bailey, Simon | Lindsey, Janet C. | Di Rocco, Concezio | Massimi, Luca | Michiels, Erna M.C. | Scherer, Stephen W. | Phillips, Joanna J. | Gupta, Nalin | Fan, Xing | Muraszko, Karin M. | Vibhakar, Rajeev | Eberhart, Charles G. | Fouladi, Maryam | Lach, Boleslaw | Jung, Shin | Wechsler-Reya, Robert J. | Fèvre-Montange, Michelle | Jouvet, Anne | Jabado, Nada | Pollack, Ian F. | Weiss, William A. | Lee, Ji-Yeoun | Cho, Byung-Kyu | Kim, Seung-Ki | Wang, Kyu-Chang | Leonard, Jeffrey R. | Rubin, Joshua B. | de Torres, Carmen | Lavarino, Cinzia | Mora, Jaume | Cho, Yoon-Jae | Tabori, Uri | Olson, James M. | Gajjar, Amar | Packer, Roger J. | Rutkowski, Stefan | Pomeroy, Scott L. | French, Pim J. | Kloosterhof, Nanne K. | Kros, Johan M. | Van Meir, Erwin G. | Clifford, Steven C. | Bourdeaut, Franck | Delattre, Olivier | Doz, François F. | Hawkins, Cynthia E. | Malkin, David | Grajkowska, Wieslawa A. | Perek-Polnik, Marta | Bouffet, Eric | Rutka, James T. | Pfister, Stefan M. | Taylor, Michael D.
Journal of Clinical Oncology  2014;32(9):886-896.
Purpose
Medulloblastoma comprises four distinct molecular subgroups: WNT, SHH, Group 3, and Group 4. Current medulloblastoma protocols stratify patients based on clinical features: patient age, metastatic stage, extent of resection, and histologic variant. Stark prognostic and genetic differences among the four subgroups suggest that subgroup-specific molecular biomarkers could improve patient prognostication.
Patients and Methods
Molecular biomarkers were identified from a discovery set of 673 medulloblastomas from 43 cities around the world. Combined risk stratification models were designed based on clinical and cytogenetic biomarkers identified by multivariable Cox proportional hazards analyses. Identified biomarkers were tested using fluorescent in situ hybridization (FISH) on a nonoverlapping medulloblastoma tissue microarray (n = 453), with subsequent validation of the risk stratification models.
Results
Subgroup information improves the predictive accuracy of a multivariable survival model compared with clinical biomarkers alone. Most previously published cytogenetic biomarkers are only prognostic within a single medulloblastoma subgroup. Profiling six FISH biomarkers (GLI2, MYC, chromosome 11 [chr11], chr14, 17p, and 17q) on formalin-fixed paraffin-embedded tissues, we can reliably and reproducibly identify very low-risk and very high-risk patients within SHH, Group 3, and Group 4 medulloblastomas.
Conclusion
Combining subgroup and cytogenetic biomarkers with established clinical biomarkers substantially improves patient prognostication, even in the context of heterogeneous clinical therapies. The prognostic significance of most molecular biomarkers is restricted to a specific subgroup. We have identified a small panel of cytogenetic biomarkers that reliably identifies very high-risk and very low-risk groups of patients, making it an excellent tool for selecting patients for therapy intensification and therapy de-escalation in future clinical trials.
doi:10.1200/JCO.2013.50.9539
PMCID: PMC3948094  PMID: 24493713
2.  A microRNA-1280/JAG2 network comprises a novel biological target in high-risk medulloblastoma 
Oncotarget  2014;6(5):2709-2724.
Over-expression of PDGF receptors (PDGFRs) has been previously implicated in high-risk medulloblastoma (MB) pathogenesis. However, the exact biological functions of PDGFRα and PDGFRβ signaling in MB biology remain poorly understood. Here, we report the subgroup specific expression of PDGFRα and PDGFRβ and their associated biological pathways in MB tumors. c-MYC, a downstream target of PDGFRβ but not PDGFRα, is involved in PDGFRβ signaling associated with cell proliferation, cell death, and invasion. Concurrent inhibition of PDGFRβ and c-MYC blocks MB cell proliferation and migration synergistically. Integrated analysis of miRNA and miRNA targets regulated by both PDGFRβ and c-MYC reveals that increased expression of JAG2, a target of miR-1280, is associated with high metastatic dissemination at diagnosis and a poor outcome in MB patients. Our study may resolve the controversy on the role of PDGFRs in MB and unveils JAG2 as a key downstream effector of a PDGFRβ-driven signaling cascade and a potential therapeutic target.
PMCID: PMC4413612  PMID: 25576913
PDGFR; c-MYC; JAG2; miR-1280; medulloblastoma
3.  Recurrence patterns across medulloblastoma subgroups: an integrated clinical and molecular analysis 
The lancet oncology  2013;14(12):1200-1207.
Background
Recurrent medulloblastoma is a daunting therapeutic challenge as it is almost universally fatal. Recent studies confirmed that medulloblastoma comprises four distinct subgroups. We sought to delineate subgroup specific differences in medulloblastoma recurrence patterns.
Methods
We retrospectively identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children between 1994-2012, and performed molecular subgrouping on FFPE tissues using a nanoString-based assay. The anatomical site of recurrence (local tumour bed or leptomeningeal metastasis), time to recurrence and survival post-recurrence were determined in a subgroup specific fashion. Subgroup specific recurrence patterns were confirmed in two independent, non-overlapping FFPE validation cohorts. Where possible molecular subgrouping was performed on tissue obtained from both the initial surgery and at recurrence.
Results
A screening cohort of 30 recurrent medulloblastomas was assembled; nine with local recurrences, and 21 metastatic. When re-analysed in a subgroup specific manner, local recurrences were more frequent in SHH tumours (8/9, 88%) and metastatic recurrences were more common in Group 3 and 4 (17/20 [85%] with one WNT, p=0.0014, local vs metastatic recurrence, SHH vs Group 3 vs Group 4). The subgroup specific location of recurrence was confirmed in a multicenter validation cohort (p=0·0013 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=77), and a second independent validation cohort comprising 96 recurrences (p<0·0001 for local vs metastatic recurrence SHH vs Group 3 vs Group 4, n=96). Treatment with craniospinal irradiation at diagnosis was not significantly associated with the anatomical pattern of recurrence. Survival post recurrence was significantly longer in Group 4 patients (p=0·013) as confirmed in a multicenter validation cohort (p=0·0075). Strikingly, subgroup affiliation remained stable at recurrence in all 34 cases with available matched primary and recurrent pairs.
Conclusions
Medulloblastoma does not switch subgroup at the time of recurrence further highlighting the stability of the four principle medulloblastoma subgroups. Significant differences in the location and timing of recurrence across medulloblastoma subgroups were observed which have potential treatment ramifications. Specifically, intensified local (posterior fossa) therapy should be tested in the initial treatment of SHH patients. Refinement of therapy for Groups 3 and 4 should focus on the metastatic compartment, as it is the near universal cause of patient deaths.
doi:10.1016/S1470-2045(13)70449-2
PMCID: PMC3953419  PMID: 24140199
4.  Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma 
Northcott, Paul A | Lee, Catherine | Zichner, Thomas | Stütz, Adrian M | Erkek, Serap | Kawauchi, Daisuke | Shih, David JH | Hovestadt, Volker | Zapatka, Marc | Sturm, Dominik | Jones, David TW | Kool, Marcel | Remke, Marc | Cavalli, Florence | Zuyderduyn, Scott | Bader, Gary | VandenBerg, Scott | Esparza, Lourdes Adriana | Ryzhova, Marina | Wang, Wei | Wittmann, Andrea | Stark, Sebastian | Sieber, Laura | Seker-Cin, Huriye | Linke, Linda | Kratochwil, Fabian | Jäger, Natalie | Buchhalter, Ivo | Imbusch, Charles D | Zipprich, Gideon | Raeder, Benjamin | Schmidt, Sabine | Diessl, Nicolle | Wolf, Stephan | Wiemann, Stefan | Brors, Benedikt | Lawerenz, Chris | Eils, Jürgen | Warnatz, Hans-Jörg | Risch, Thomas | Yaspo, Marie-Laure | Weber, Ursula D | Bartholomae, Cynthia C | von Kalle, Christof | Turányi, Eszter | Hauser, Peter | Sanden, Emma | Darabi, Anna | Siesjö, Peter | Sterba, Jaroslav | Zitterbart, Karel | Sumerauer, David | van Sluis, Peter | Versteeg, Rogier | Volckmann, Richard | Koster, Jan | Schuhmann, Martin U | Ebinger, Martin | Grimes, H. Leighton | Robinson, Giles W | Gajjar, Amar | Mynarek, Martin | von Hoff, Katja | Rutkowski, Stefan | Pietsch, Torsten | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Kulozik, Andreas E | von Deimlmg, Andreas | Witt, Olaf | Eils, Roland | Gilbertson, Richard J | Korshunov, Andrey | Taylor, Michael D | Lichter, Peter | Korbel, Jan O | Wechsler-Reya, Robert J | Pfister, Stefan M
Nature  2014;511(7510):428-434.
Summary Paragraph
Medulloblastoma is a highly malignant paediatric brain tumour currently treated with a combination of surgery, radiation, and chemotherapy, posing a considerable burden of toxicity to the developing child. Genomics has illuminated the extensive intertumoural heterogeneity of medulloblastoma, identifying four distinct molecular subgroups. Group 3 and Group 4 subgroup medulloblastomas account for the majority of paediatric cases; yet, oncogenic drivers for these subtypes remain largely unidentified. Here we describe a series of prevalent, highly disparate genomic structural variants, restricted to Groups 3 and 4, resulting in specific and mutually exclusive activation of the growth factor independent 1 family protooncogenes, GFI1 and GFI1B. Somatic structural variants juxtapose GFI1/GFI1B coding sequences proximal to active enhancer elements, including super-enhancers, instigating oncogenic activity. Our results, supported by evidence from mouse models, identify GFI1 and GFI1B as prominent medulloblastoma oncogenes and implicate ‘enhancer hijacking’ as an efficient mechanism driving oncogene activation in a childhood cancer.
doi:10.1038/nature13379
PMCID: PMC4201514  PMID: 25043047
5.  Molecular diagnostics of CNS embryonal tumors 
Acta neuropathologica  2010;120(5):553-566.
Tremendous progress has recently been made in both molecular subgrouping, and the establishment of prognostic biomarkers for embryonal brain tumors, particularly medulloblastoma. Several prognostic biomarkers that were initially identified in retrospective cohorts of medulloblastoma, including MYC and MYCN amplification, nuclear β-catenin accumulation, and chromosome 17 aberrations have now been validated in clinical trials. Moreover, molecular subgroups based on distinct transcriptome profiles have been consistently reported from various groups on different platforms demonstrating that the concept of distinct medulloblastoma subgroups is very robust. Well-described subgroups of medulloblastomas include tumors showing wingless signaling pathway (Wnt) activation, and another characterized by sonic hedgehog pathway activity. Two or more additional subgroups were consistently reported to contain the vast majority of high-risk tumors, including most tumors with metastatic disease at diagnosis and/or large cell/anaplastic histology. Several years ago, atypical teratoid rhabdoid tumor (AT/RT) was recognized as a separate entity based on its distinct biology and particularly aggressive clinical behavior. These tumors may occur supra or infratentorially and are usually found to have genetic alterations of SMARCB1 (INI1/hSNF5), a tumor suppressor gene located on chromosome 22q. Subsequent loss of SMARCB1 protein expression comprises a relatively specific and sensitive diagnostic marker for AT/RT. For CNS primitive neuroectodermal tumors (CNS PNETs), a consistent finding has been that they are molecularly distinct from medulloblastoma. Furthermore, a distinct fraction of CNS PNETs with particularly poor prognosis only occurring in young children was delineated, which was previously labeled ependymoblastoma or embryonal tumor with abundant neuropil and true rosettes (ETANTR) and which is morphologically characterized by the presence of multilayered “ependymoblastic” rosettes. This group of tumors shows a unique cytogenetic abnormality not seen in other brain tumors: focal amplification of a micro-RNA cluster at chromosome 19q13.42, which has never been found to be amplified in other CNS PNETs, medulloblastoma or AT/RT. In summary, these consistent findings have significantly contributed to our ability to sub-classify embryonal brain tumors into clinically and biologically meaningful strata and, for some of the subgroups, have led to the identification of specific targets for future development of molecularly targeted therapies.
doi:10.1007/s00401-010-0751-5
PMCID: PMC4512653  PMID: 20882288
Embryonal brain tumors; Medulloblastoma; AT/RT; ETANTR; ETMR; Molecular marker; Prognostic marker; Diagnostic marker
6.  Quiescent Sox2+ Cells Drive Hierarchical Growth and Relapse in Sonic Hedgehog Subgroup Medulloblastoma 
Cancer cell  2014;26(1):33-47.
SUMMARY
Functional heterogeneity within tumors presents a significant therapeutic challenge. Here we show that quiescent, therapy-resistant Sox2+ cells propagate sonic hedgehog subgroup medulloblastoma by a mechanism that mirrors a neurogenic program. Rare Sox2+ cells produce rapidly cycling doublecortin+ progenitors that, together with their postmitotic progeny expressing NeuN, comprise tumor bulk. Sox2+ cells are enriched following anti-mitotic chemotherapy and Smoothened inhibition, creating a reservoir for tumor regrowth. Lineage traces from Sox2+ cells increase following treatment, suggesting that this population is responsible for relapse. Targeting Sox2+ cells with the antineoplastic mithramycin abrogated tumor growth. Addressing functional heterogeneity and eliminating Sox2+ cells presents a promising therapeutic paradigm for treatment of sonic hedgehog subgroup medulloblastoma.
doi:10.1016/j.ccr.2014.05.005
PMCID: PMC4441014  PMID: 24954133
7.  Genome Sequencing of SHH Medulloblastoma Predicts Genotype-Related Response to Smoothened Inhibition 
Kool, Marcel | Jones, David T.W. | Jäger, Natalie | Northcott, Paul A. | Pugh, Trevor J. | Hovestadt, Volker | Piro, Rosario M. | Esparza, L. Adriana | Markant, Shirley L. | Remke, Marc | Milde, Till | Bourdeaut, Franck | Ryzhova, Marina | Sturm, Dominik | Pfaff, Elke | Stark, Sebastian | Hutter, Sonja | Şeker-Cin, Huriye | Johann, Pascal | Bender, Sebastian | Schmidt, Christin | Rausch, Tobias | Shih, David | Reimand, Jüri | Sieber, Laura | Wittmann, Andrea | Linke, Linda | Witt, Hendrik | Weber, Ursula D. | Zapatka, Marc | König, Rainer | Beroukhim, Rameen | Bergthold, Guillaume | van Sluis, Peter | Volckmann, Richard | Koster, Jan | Versteeg, Rogier | Schmidt, Sabine | Wolf, Stephan | Lawerenz, Chris | Bartholomae, Cynthia C. | von Kalle, Christof | Unterberg, Andreas | Herold-Mende, Christel | Hofer, Silvia | Kulozik, Andreas E. | von Deimling, Andreas | Scheurlen, Wolfram | Felsberg, Jörg | Reifenberger, Guido | Hasselblatt, Martin | Crawford, John R. | Grant, Gerald A. | Jabado, Nada | Perry, Arie | Cowdrey, Cynthia | Croul, Sydney | Zadeh, Gelareh | Korbel, Jan O. | Doz, Francois | Delattre, Olivier | Bader, Gary D. | McCabe, Martin G. | Collins, V. Peter | Kieran, Mark W. | Cho, Yoon-Jae | Pomeroy, Scott L. | Witt, Olaf | Brors, Benedikt | Taylor, Michael D. | Schüller, Ulrich | Korshunov, Andrey | Eils, Roland | Wechsler-Reya, Robert J. | Lichter, Peter | Pfister, Stefan M.
Cancer cell  2014;25(3):393-405.
Summary
Smoothened (SMO) inhibitors recently entered clinical trials for sonic-hedgehog-driven medulloblastoma (SHH-MB). Clinical response is highly variable. To understand the mechanism(s) of primary resistance and identify pathways cooperating with aberrant SHH signaling, we sequenced and profiled a large cohort of SHH-MBs (n = 133). SHH pathway mutations involved PTCH1 (across all age groups), SUFU (infants, including germline), and SMO (adults). Children >3 years old harbored an excess of downstream MYCN and GLI2 amplifications and frequent TP53 mutations, often in the germline, all of which were rare in infants and adults. Functional assays in different SHH-MB xenograft models demonstrated that SHH-MBs harboring a PTCH1 mutation were responsive to SMO inhibition, whereas tumors harboring an SUFU mutation or MYCN amplification were primarily resistant.
doi:10.1016/j.ccr.2014.02.004
PMCID: PMC4493053  PMID: 24651015
8.  EPIGENOME ALTERATIONS DEFINE LETHAL CIMP POSITIVE EPENDYMOMAS OF INFANCY 
Neuro-Oncology  2014;16(Suppl 3):iii16.
BACKGROUND: Ependymomas are common childhood brain tumors that occur throughout the nervous system, but are most common in the pediatric hindbrain. Current standard therapy comprises surgery and radiation, but not cytotoxic chemotherapy as it does not further increase survival. METHODS: We undertook genetic, and epigenetic studies of a series of childhood posterior fossa ependymomas. RESULTS: Whole-genome and whole-exome sequencing of 47 hindbrain ependymomas reveals an extremely low mutation rate, and zero significant recurrent somatic SNVs. While devoid of recurrent SNVs and focal copy number aberrations, poor prognosis hindbrain ependymomas exhibit a CpG island methylator phenotype (CIMP). Transcriptional silencing driven by CpG methylation converges exclusively on targets of the polycomb repressor complex 2 (PRC2) that represses expression of differentiation genes through tri-methylation of H3K27. CIMP-positive (CIMP+) hindbrain ependymomas are responsive to clinical drugs that target either DNA or H3K27 methylation both in vitro and in vivo. CONCLUSIONS: We conclude that epigenetic modifiers are the first rational therapeutic candidates for this deadly malignancy, which is epigenetically de-regulated but genetically bland. SECONDARY CATEGORY: n/a.
doi:10.1093/neuonc/nou206.58
PMCID: PMC4144526
9.  METASTASIS AND TUMOR RECURRENCE FROM RARE SOX9-POSITIVE CELLS IN MYCN-DRIVEN MEDULLOBLASTOMA 
Neuro-Oncology  2014;16(Suppl 3):iii28.
BACKGROUND: Tumor recurrence is the main cause of death for children with medulloblastoma, the most common malignant childhood brain tumor. The MYCN oncogene is a poor prognosis marker and is amplified in the molecularly defined SHH and Group 4 subgroups but rarely in WNT and Group 3 subgroups of human medulloblastoma. Recent findings on childhood brain tumor relapse mechanisms suggest spatiotemporal differences within these four subgroups. SOX9 is a transcription factor that is important for glial fate determination in the brain but has also been found to promote tumor metastasization. We previously showed how expression of SOX9 correlates well with human SHH tumors but only few scattered SOX9-positive cells are found in SHH-independent Group 3 and Group 4 human medulloblastoma. METHODS: In order to study recurrence processes experimentally, we used a previously described transgenic Tet-OFF (Glt1-tTA) inducible model of MYCN-driven SHH-independent medulloblastoma (GTML mouse). To recreate metastatic recurrence we further used a Tet-ON (SOX9-rtTA) model that drives MYCN expression from the SOX9 promoter upon doxycycline treatment. RESULTS: By crossing the GTML Tet-OFF model with a Tet-ON transgene we managed to study rare SOX9-positive tumor cells after SOX9-negative tumor cells were first depleted using doxycycline. SOX9-positive GTML cells were tumorigenic and reinitiated distant recurrences over time. The SOX9-positive cells further showed an increased resistance to MYCN-targeted therapies. Relapses showed similar histopathology but presented generally higher levels SOX9 as compared to primary GTML tumors. A similar correlation was found in Group 3 and Group 4 medulloblastoma patients where isolated metastases had consistently higher SOX9 levels as compared to corresponding primary tumors. Finally, we overexpressed SOX9 in normal cerebellar stem cells transduced with mutationally stabilized MYCN-T58A and injected them back into the cerebellum of adult mice. Surprisingly, SOX9-positive MYCN-T58A brain tumors migrated and developed in the forebrain in contrast to the cerebellar stem cells transduced with MYCN-T58A only. CONCLUSIONS: Our findings suggest that increased levels of SOX9 drives migration in MYCN-driven medulloblastoma. Rare SOX9-positive tumor cells show an increased therapy resistance and are alone capable of reinitiating childhood brain tumors. Further characterization of SOX9-positive cells in Group 3 and Group 4 tumors could help us understand what drives metastatic medulloblastoma relapse and could lead to new therapies directed against these particularly serious cell types. SECONDARY CATEGORY: Tumor Biology.
doi:10.1093/neuonc/nou208.20
PMCID: PMC4144565
10.  FORETINIB IS EFFECTIVE THERAPY FOR METASTATIC SONIC HEDGEHOG MEDULLOBLASTOMA 
Neuro-Oncology  2014;16(Suppl 3):iii35.
BACKGROUND: (blind field). METHODS: Expression profiling, molecular subgrouping and analysis of somatic copy number alterations were conducted on multiple independent cohorts of patient tumour samples to examine intermediates of the MET signaling pathway in medulloblastoma. To examine the in vitro and in vivo effects of foretinib treatment; MET signalling biochemical analysis; migration and invasion assays; and foretinib pharmacokinetic studies were performed. Medulloblastoma xenografts and transgenic mouse models were used to evaluate foretinib treatment in vivo. RESULTS: We analyzed three large non-overlapping cohorts of medulloblastoma patients (discovery cohort, n = 199; validation cohort 1, n = 439; validation cohort 2, n = 285) and demonstrated that cMET, known to be involved in tumor progression and dissemination, is a marker of sonic hedgehog (SHH) medulloblastoma. Importantly, immunohistochemical analysis of activated cMET (phosphorylated cMET) in another independent patient cohort (n = 385) revealed that cMET activation correlates with increased tumor relapse and a poor survival in pediatric patients with SHH medulloblastomas, thus defining a subset of patients that may benefit from cMET targeted therapy. We show that foretinib, an FDA approved inhibitor of cMET, suppresses cMET activation, decreases proliferation and induces apoptosis, both in medulloblastoma cell lines and in SHH medulloblastoma xenografts. Furthermore foretinib penetrates the blood-brain barrier and is effective both in the primary and in the metastatic compartments. Treatment of mouse xenografts and of an aggressive transgenic model of metastatic SHH medulloblastoma with foretinib reduced primary medulloblastoma growth, decreased the incidence of metastases by 36% and increased survival by 45%. CONCLUSIONS: Our results provide strong rationale for advancing foretinib into clinical trials for SHH-driven medulloblastomas. SECONDARY CATEGORY: Tumor Biology.
doi:10.1093/neuonc/nou208.47
PMCID: PMC4144594
11.  PROGNOSTIC SIGNIFICANCE OF CLINICAL, HISTOPATHOLOGICAL, AND MOLECULAR CHARACTERISTICS OF MEDULLOBLASTOMAS IN THE PROSPECTIVE HIT2000 MULTICENTER CLINICAL TRIAL COHORT 
Neuro-Oncology  2014;16(Suppl 3):iii24-iii25.
BACKGROUND: This study aimed to prospectively evaluate clinical, histopathological and molecular variables for outcome prediction in medulloblastoma patients. METHODS: Patients from the HIT2000 cooperative clinical trial were prospectively enrolled based on the availability of sufficient tumor material and complete clinical information. This revealed a cohort of 184 patients (median age 7.6 years), which was randomly split at a 2:1 ratio into a training (n = 127), and a validation (n = 57) dataset. All samples were subjected to thorough histopathological investigation, CTNNB1 mutation analysis, quantitative PCR, MLPA and FISH analyses for cytogenetic variables, and methylome analysis. RESULTS: By univariable analysis, clinical factors (M-stage), histopathological variables (large cell component, endothelial proliferation, synaptophysin pattern), and molecular features (chromosome 6q status, MYC amplification, TOP2A copy-number, subgrouping) were found to be prognostic. Molecular consensus subgrouping (WNT, SHH, Group 3, Group 4) was validated as an independent feature to stratify patients into different risk groups. When comparing methods for the identification of WNT-driven medulloblastoma, this study identified CTNNB1 sequencing and methylation profiling to most reliably identify these patients. After removing patients with particularly favorable (CTNNB1 mutation, extensive nodularity) or unfavorable (MYC amplification) markers, a risk score for the remaining “intermediate molecular risk” population dependent on age, M-stage, pattern of synaptophysin expression, and MYCN copy-number status was identified and validated, with speckled synaptophysin expression indicating worse outcome. CONCLUSIONS: Methylation subgrouping and CTNNB1 mutation status represent robust tools for the risk-stratification of medulloblastoma. A simple clinico-pathological risk score for “intermediate molecular risk” patients was identified, which deserves further validation. SECONDARY CATEGORY: Pediatrics.
doi:10.1093/neuonc/nou208.7
PMCID: PMC4144619
12.  Multiple recurrent genetic events converge on control of histone lysine methylation in medulloblastoma 
Nature genetics  2009;41(4):465-472.
We used high-resolution SNP genotyping to identify regions of genomic gain and loss in the genomes of 212 medulloblastomas, malignant pediatric brain tumors. We found focal amplifications of 15 known oncogenes and focal deletions of 20 known tumor suppressor genes (TSG), most not previously implicated in medulloblastoma. Notably, we identified previously unknown amplifications and homozygous deletions, including recurrent, mutually exclusive, highly focal genetic events in genes targeting histone lysine methylation, particularly that of histone 3, lysine 9 (H3K9). Post-translational modification of histone proteins is critical for regulation of gene expression, can participate in determination of stem cell fates and has been implicated in carcinogenesis. Consistent with our genetic data, restoration of expression of genes controlling H3K9 methylation greatly diminishes proliferation of medulloblastoma in vitro. Copy number aberrations of genes with critical roles in writing, reading, removing and blocking the state of histone lysine methylation, particularly at H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma.
doi:10.1038/ng.336
PMCID: PMC4454371  PMID: 19270706
13.  Update on a Pharmacokinetic-Centric Alternative Tier II Program for MMT—Part II: Physiologically Based Pharmacokinetic Modeling and Manganese Risk Assessment 
Journal of Toxicology  2012;2012:791431.
Recently, a variety of physiologically based pharmacokinetic (PBPK) models have been developed for the essential element manganese. This paper reviews the development of PBPK models (e.g., adult, pregnant, lactating, and neonatal rats, nonhuman primates, and adult, pregnant, lactating, and neonatal humans) and relevant risk assessment applications. Each PBPK model incorporates critical features including dose-dependent saturable tissue capacities and asymmetrical diffusional flux of manganese into brain and other tissues. Varied influx and efflux diffusion rate and binding constants for different brain regions account for the differential increases in regional brain manganese concentrations observed experimentally. We also present novel PBPK simulations to predict manganese tissue concentrations in fetal, neonatal, pregnant, or aged individuals, as well as individuals with liver disease or chronic manganese inhalation. The results of these simulations could help guide risk assessors in the application of uncertainty factors as they establish exposure guidelines for the general public or workers.
doi:10.1155/2012/791431
PMCID: PMC3356703  PMID: 22645610
14.  The eEF2 Kinase Confers Resistance to Nutrient Deprivation by Blocking Translation Elongation 
Cell  2013;153(5):1064-1079.
SUMMARY
Metabolic adaptation is essential for cell survival during nutrient deprivation. We report that eukaryotic elongation factor 2 kinase (eEF2K), which is activated by AMP-kinase (AMPK), confers cell survival under acute nutrient depletion by blocking translation elongation. Tumor cells exploit this pathway to adapt to nutrient deprivation by reactivating the AMPK-eEF2K axis. Adaptation of transformed cells to nutrient withdrawal is severely compromised in cells lacking eEF2K. Moreover, eEF2K knockdown restored sensitivity to acute nutrient deprivation in highly resistant human tumor cell lines. In vivo, overexpression of eEF2K rendered murine tumors remarkably resistant to caloric restriction. Expression of eEF2K strongly correlated with overall survival in human medulloblastoma and glioblastoma multiforme. Finally, C. elegans strains deficient in efk-1, the eEF2K ortholog, were severely compromised in their response to nutrient depletion. Our data highlight a conserved role for eEF2K in protecting cells from nutrient deprivation and in conferring tumor cell adaptation to metabolic stress.
doi:10.1016/j.cell.2013.04.055
PMCID: PMC4395874  PMID: 23706743
15.  ATM regulates 3-Methylpurine-DNA glycosylase and promotes therapeutic resistance to alkylating agents 
Cancer discovery  2014;4(10):1198-1213.
Alkylating agents are a frontline therapy for the treatment of several aggressive cancers including pediatric glioblastoma, a lethal tumor in children. Unfortunately, many tumors are resistant to this therapy. We sought to identify ways of sensitizing tumor cells to alkylating agents while leaving normal cells unharmed; increasing therapeutic response while minimizing toxicity. Using a siRNA screen targeting over 240 DNA damage response genes, we identified novel sensitizers to alkylating agents. In particular the base excision repair (BER) pathway, including 3-methylpurine-DNA glycosylase (MPG), as well as ataxia telangiectasia mutated (ATM) were identified in our screen. Interestingly, we identified MPG as a direct novel substrate of ATM. ATM-mediated phosphorylation of MPG was required for enhanced MPG function. Importantly, combined inhibition or loss of MPG and ATM resulted in increased alkylating agent-induced cytotoxicity in vitro and prolonged survival in vivo. The discovery of the ATM-MPG axis will lead to improved treatment of alkylating agent-resistant tumors.
doi:10.1158/2159-8290.CD-14-0157
PMCID: PMC4184920  PMID: 25100205
16.  Measuring the optical characteristics of medulloblastoma with optical coherence tomography 
Biomedical Optics Express  2015;6(4):1487-1501.
Medulloblastoma is the most common malignant pediatric brain tumor. Standard treatment consists of surgical resection, followed by radiation and high-dose chemotherapy. Despite these efforts, recurrence is common, leading to reduced patient survival. Even with successful treatment, there are often severe long-term neurologic impacts on the developing nervous system. We present two quantitative techniques that use a high-resolution optical imaging modality: optical coherence tomography (OCT) to measure refractive index, and the optical attenuation coefficient. To the best of our knowledge, this study is the first to demonstrate OCT analysis of medulloblastoma. Refractive index and optical attenuation coefficient were able to differentiate between normal brain tissue and medulloblastoma in mouse models. More specifically, optical attenuation coefficient imaging of normal cerebellum displayed layers of grey matter and white matter, which were indistinguishable in the structural OCT image. The morphology of the tumor was distinct in the optical attenuation coefficient imaging. These inherent properties may be useful during neurosurgical intervention to better delineate tumor boundaries and minimize resection of normal tissue.
doi:10.1364/BOE.6.001487
PMCID: PMC4399685  PMID: 25909030
(110.4500) Optical coherence tomography; (170.6935) Tissue characterization; (100.2960) Image analysis; (290.1350) Backscattering
17.  Eplerenone for early cardiomyopathy in Duchenne muscular dystrophy: a randomised, double-blind, placebo-controlled trial 
The Lancet. Neurology  2014;14(2):153-161.
Summary
Background
Cardiomyopathy is a leading cause of death in patients with Duchenne muscular dystrophy and myocardial damage precedes decline in left ventricular systolic function. We tested the efficacy of eplerenone on top of background therapy in patients with Duchenne muscular dystrophy with early myocardial disease.
Methods
In this randomised, double-blind, placebo-controlled trial, boys from three centres in the USA aged 7 years or older with Duchenne muscular dystrophy, myocardial damage by late gadolinium enhancement cardiac MRI and preserved ejection fraction received either eplerenone 25 mg or placebo orally, every other day for the first month and once daily thereafter, in addition to background clinician-directed therapy with either angiotensin-converting enzyme inhibitors (ACEI) or angiotensin receptor blockers (ARB). Computer-generated randomisation was done centrally using block sizes of four and six, and only the study statistician and the investigational pharmacy had the preset randomisation assignments. The primary outcome was change in left ventricular circumferential strain (Ecc) at 12 months, a measure of contractile dysfunction. Safety was established through serial serum potassium levels and measurement of cystatin C, a non-creatinine measure of kidney function. This trial is registered with ClinicalTrials.gov, number NCT01521546.
Findings
Between Jan 26, 2012, and July 3, 2013, 188 boys were screened and 42 were enrolled. 20 were randomly assigned to receive eplerenone and 22 to receive placebo, of whom 20 in the eplerenone group and 20 in the placebo group completed baseline, 6-month, and 12-month visits. After 12 months, decline in left ventricular circumferential strain was less in those who received eplerenone than in those who received placebo (median ΔEcc 1.0 [IQR 0.3–2.2]vs2.2 [1.3–3.1]; p=0.020). Cystatin C concentrations remained normal in both groups, and all non-haemolysed blood samples showed normal potassium concentrations. One 23-year-old patient in the placebo group died of fat embolism, and another patient in the placebo group withdrew from the trial to address long-standing digestive issues. All other adverse events were mild: short-lived headaches coincident with seasonal allergies occurred in one patient given eplerenone, flushing occurred in one patient given placebo, and anxiety occurred in another patient given placebo.
Interpretation
In boys with Duchenne muscular dystrophy and preserved ejection fraction, addition of eplerenone to background ACEI or ARB therapy attenuates the progressive decline in left ventricular systolic function. Early use of available drugs warrants consideration in this population at high risk of cardiac death, but further studies are needed to determine the effect of combination cardioprotective therapy on event-free survival in Duchenne muscular dystrophy.
Funding
BallouSkies, Parent Project for Muscular Dystrophy, US National Center for Advancing Translational Sciences, and US National Institutes of Health.
doi:10.1016/S1474-4422(14)70318-7
PMCID: PMC4361281  PMID: 25554404
18.  The G-protein Alpha Subunit Gsα Is A Tumor Suppressor In Sonic Hedgehog-driven Medulloblastoma 
Nature medicine  2014;20(9):1035-1042.
Medulloblastoma, the most common malignant childhood brain tumor, exhibits distinct molecular subtypes and cellular origins. Genetic alterations driving medulloblastoma initiation and progression remain poorly understood. Herein, we identify GNAS, encoding the G-protein Gsα, as a potent tumor suppressor gene that defines a subset of aggressive Sonic Hedgehog (Shh)-driven human medulloblastomas. Ablation of the single Gnas gene in anatomically-distinct progenitors is sufficient to induce Shh-associated medulloblastomas, which recapitulate their human counterparts. Gsα is highly enriched at the primary cilium of granule neuron precursors and suppresses Shh-signaling by regulating both the cAMP-dependent pathway and ciliary trafficking of Hedgehog pathway components. Elevation of a Gsα effector, cAMP, effectively inhibits tumor cell proliferation and progression in Gnas mutants. Thus, our gain- and loss-of-function studies identify a previously unrecognized tumor suppressor function for Gsα that acts as a molecular link across Shh-group medulloblastomas of disparate cellular and anatomical origins, illuminating G-protein modulation as a potential therapeutic avenue.
doi:10.1038/nm.3666
PMCID: PMC4334261  PMID: 25150496
medulloblastoma; G-protein; cAMP; GPCR; cell lineage; sonic hedgehog signaling; cilia; cellular origins
19.  Molecular subgroups of medulloblastoma 
Recent efforts at stratifying medulloblastomas based on their molecular features have revolutionized our understanding of this morbidity. Collective efforts by multiple independent groups have subdivided medulloblastoma from a single disease into four distinct molecular subgroups characterized by disparate transcriptional signatures, mutational spectra, copy number profiles and, most importantly, clinical features. We present a summary of recent studies that have contributed to our understanding of the core medulloblastoma subgroups, focusing largely on clinically relevant discoveries that have already, and will continue to, shape research.
doi:10.1586/ern.12.66
PMCID: PMC4334443  PMID: 22853794
chromatin; genomics; medulloblastoma; molecular classification; pediatric brain tumors; subgroups
20.  SnapShot: Medulloblastoma 
Cancer cell  2014;26(6):940-940.e1.
Medulloblastoma (MB) is the most common malignant brain tumor in children. Current treatment includes surgery, craniospinal radiation, and high-dose cytotoxic chemotherapy. Despite these aggressive therapies, one-third of patients still succumb to their disease, and survivors suffer devastating side effects, including cognitive deficits, endocrine disorders, and increased incidence of secondary cancers later in life. More effective and less toxic therapies are desperately needed for MB.
doi:10.1016/j.ccell.2014.11.015
PMCID: PMC4324613  PMID: 25490452
22.  DNA methylation profiling of medulloblastoma allows robust sub-classification and improved outcome prediction using formalin-fixed biopsies 
Acta neuropathologica  2013;125(3):359-371.
Molecular sub-classification is rapidly informing the clinical management of medulloblastoma. However, the disease remains associated with poor outcomes and therapy-associated late-effects, and the majority of patients are not characterized by a validated prognostic biomarker. Here, we investigated the potential of epigenetic DNA methylation for disease sub-classification, particularly in formalin-fixed biopsies, and to identify biomarkers for improved therapeutic individualization. Tumor DNA methylation profiles were assessed, alongside molecular and clinical disease features, in 230 patients primarily from the SIOP-UKCCSG PNET3 clinical trial. We demonstrate by cross-validation in frozen training and formalin-fixed test sets that medulloblastoma comprises four robust DNA methylation subgroups (termed WNT, SHH, G3 and G4), highly related to their transcriptomic counterparts, and which display distinct molecular, clinical and pathological disease characteristics. WNT patients displayed an expected favorable prognosis, while outcomes for SHH, G3 and G4 were equivalent in our cohort. MXI1 and IL8 methylation were identified as novel independent high-risk biomarkers in cross-validated survival models of non-WNT patients, and were validated using non-array methods. Incorporation of MXI1 and IL8 into current survival models significantly improved the assignment of disease-risk; 46% of patients could be classified as ‘favorable-risk’ (>90% survival) compared to 13% using current models, while the high-risk group was reduced to 16% from 30%. DNA methylation profiling enables the robust sub-classification of four disease sub-groups in frozen and routinely-collected/archival formalin-fixed biopsy material, and the incorporation of DNA methylation biomarkers can significantly improve disease-risk stratification. These findings have important implications for future risk-adapted clinical disease management.
doi:10.1007/s00401-012-1077-2
PMCID: PMC4313078  PMID: 23291781
Subgroups; medulloblastoma; methylation; prognosis; biomarkers
23.  Mechanism of action and therapeutic efficacy of Aurora kinase B inhibition in MYC overexpressing medulloblastoma 
Oncotarget  2014;6(5):3359-3374.
Medulloblastoma comprises four molecular subgroups of which Group 3 medulloblastoma is characterized by MYC amplification and MYC overexpression. Lymphoma cells expressing high levels of MYC are susceptible to apoptosis following treatment with inhibitors of mitosis. One of the key regulatory kinases involved in multiple stages of mitosis is Aurora kinase B. We hypothesized that medulloblastoma cells that overexpress MYC would be uniquely sensitized to the apoptotic effects of Aurora B inhibition. The specific inhibition of Aurora kinase B was achieved in MYC-overexpressing medulloblastoma cells with AZD1152-HQPA. MYC overexpression sensitized medulloblastoma cells to cell death upon Aurora B inhibition. This process was found to be independent of endoreplication. Using both flank and intracranial cerebellar xenografts we demonstrate that tumors formed from MYC-overexpressing medulloblastoma cells show a response to Aurora B inhibition including growth impairment and apoptosis induction. Lastly, we show the distribution of AZD1152-HQPA within the mouse brain and the ability to inhibit intracranial tumor growth and prolong survival in mice bearing tumors formed from MYC-overexpressing medulloblastoma cells. Our results suggest the potential for therapeutic application of Aurora kinase B inhibitors in the treatment of Group 3 medulloblastoma.
PMCID: PMC4413659  PMID: 25739120
Aurora kinase; medulloblastoma; tumor biology; molecular therapy; cell-cycle
24.  Pulsatile arterial wall-blood flow interaction with wall pre-stress computed using an inverse algorithm 
BioMedical Engineering OnLine  2015;14(Suppl 1):S18.
Background
The computation of arterial wall deformation and stresses under physiologic conditions requires a coupled compliant arterial wall-blood flow interaction model. The in-vivo arterial wall motion is constrained by tethering from the surrounding tissues. This tethering, together with the average in-vivo pressure, results in wall pre-stress. For an accurate simulation of the physiologic conditions, it is important to incorporate the wall pre-stress in the computational model. The computation of wall pre-stress is complex, as the un-loaded and un-tethered arterial shape with residual stress is unknown. In this study, the arterial wall deformation and stresses in a canine femoral artery under pulsatile pressure was computed after incorporating the wall pre-stresses. A nonlinear least square optimization based inverse algorithm was developed to compute the in-vivo wall pre-stress.
Methods
First, the proposed inverse algorithm was used to obtain the un-loaded and un-tethered arterial geometry from the unstressed in-vivo geometry. Then, the un-loaded, and un-tethered arterial geometry was pre-stressed by applying a mean in-vivo pressure of 104.5 mmHg and an axial stretch of 48% from the un-tethered length. Finally, the physiologic pressure pulse was applied at the inlet and the outlet of the pre-stressed configuration to calculate the in-vivo deformation and stresses. The wall material properties were modeled with an incompressible, Mooney-Rivlin model derived from previously published experimental stress-strain data (Attinger et al., 1968).
Results
The un-loaded and un-tethered artery geometry computed by the inverse algorithm had a length, inner diameter and thickness of 35.14 mm, 3.10 mm and 0.435 mm, respectively. The pre-stressed arterial wall geometry was obtained by applying the in-vivo axial-stretch and average in-vivo pressure to the un-loaded and un-tethered geometry. The length of the pre-stressed artery, 51.99 mm, was within 0.01 mm (0.019%) of the in-vivo length of 52.0 mm; the inner diameter of 3.603 mm was within 0.003 mm (0.08%) of the corresponding in-vivo diameter of 3.6 mm, and the thickness of 0.269 mm was within 0.0015 mm (0.55%) of the in-vivo thickness of 0.27 mm. Under physiologic pulsatile pressure applied to the pre-stressed artery, the time averaged longitudinal stress was found to be 42.5% higher than the circumferential stresses. The results of this study are similar to the results reported by Zhang et al., (2005) for the left anterior descending coronary artery.
Conclusions
An inverse method was adopted to compute physiologic pre-stress in the arterial wall before conducting pulsatile hemodynamic calculations. The wall stresses were higher in magnitude in the longitudinal direction, under physiologic pressure after incorporating the effect of in-vivo axial stretch and pressure loading.
doi:10.1186/1475-925X-14-S1-S18
PMCID: PMC4306109  PMID: 25603022
25.  Right ventricle-pulmonary circulation dysfunction: a review of energy-based approach 
BioMedical Engineering OnLine  2015;14(Suppl 1):S8.
Patients with repaired or palliated right heart congenital heart disease (CHD) are often left with residual lesions that progress and can result in significant morbidity. However, right ventricular-pulmonary arterial evaluation and the timing of reintvervention is still subjective. Currently, it relies on symptomology, or RV imaging-based metrics from echocardiography or MR derived parameters including right ventricular (RV) ejection fraction (EF), end-systolic pressure (ESP), and end-diastolic volume (EDV). However, the RV is coupled to the pulmonary vasculature, and they are not typically evaluated together. For example, the dysfunctional right ventricular-pulmonary circulation (RV-PC) adversely affects the RV myocardial performance resulting in decreased efficiency. Therefore, comprehensive hemodynamic assessment should incorporate changes in RV-PC and energy efficiency for CHD patients.
The ventricular pressure-volume relationship (PVR) and other energy-based endpoints derived from PVR, such as stroke work (SW) and ventricular elastance (Ees), can provide a measure of RV performance. However, a detailed explanation of the relationship between RV performance and pulmonary arterial hemodynamics is lacking. More importantly, PVR is impractical for routine longitudinal evaluation in a clinical setting, because it requires invasive catheterization. As an alternative, analytical methods and computational fluid dynamics (CFD) have been used to compute energy endpoints, such as power loss or energy dissipation, in abnormal physiologies.
In this review, we review the causes of RV-PA failure and the limitation of current clinical parameters to quantify RV-PC dysfunction. Then, we describe the advantage of currently available energy-based endpoints and emerging energy endpoints, such as energy loss in the Pas or kinetic energy, obtained from a new non-invasive imaging technique, i.e. 4D phase contrast MRI.
doi:10.1186/1475-925X-14-S1-S8
PMCID: PMC4306123  PMID: 25602641

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