Andrey Korshunov

Medulloblastoma Comprises Four Distinct Molecular Variants

PURPOSEnRecent genomic approaches have suggested the existence of multiple distinct subtypes of medulloblastoma. We studied a large cohort of medulloblastomas to determine how many subgroups of the disease exist, how they differ, and the extent of overlap between subgroups.nnnMETHODSnWe determined gene expression profiles and DNA copy number aberrations for 103 primary medulloblastomas. Bioinformatic tools were used for class discovery of medulloblastoma subgroups based on the most informative genes in the data set. Immunohistochemistry for subgroup-specific signature genes was used to determine subgroup affiliation for 294 nonoverlapping medulloblastomas on two independent tissue microarrays.nnnRESULTSnMultiple unsupervised analyses of transcriptional profiles identified the following four distinct, nonoverlapping molecular variants: WNT, SHH, group C, and group D. Supervised analysis of these four subgroups revealed significant subgroup-specific demographics, histology, metastatic status, and DNA copy number aberrations. Immunohistochemistry for DKK1 (WNT), SFRP1 (SHH), NPR3 (group C), and KCNA1 (group D) could reliably and uniquely classify formalin-fixed medulloblastomas in approximately 98% of patients. Group C patients (NPR3-positive tumors) exhibited a significantly diminished progression-free and overall survival irrespective of their metastatic status.nnnCONCLUSIONnOur integrative genomics approach to a large cohort of medulloblastomas has identified four disparate subgroups with distinct demographics, clinical presentation, transcriptional profiles, genetic abnormalities, and clinical outcome. Medulloblastomas can be reliably assigned to subgroups through immunohistochemistry, thereby making medulloblastoma subclassification widely available. Future research on medulloblastoma and the development of clinical trials should take into consideration these four distinct types of medulloblastoma.

International Society of Neuropathology‐Haarlem Consensus Guidelines for Nervous System Tumor Classification and Grading

Major discoveries in the biology of nervous system tumors have raised the question of how non‐histological data such as molecular information can be incorporated into the next World Health Organization (WHO) classification of central nervous system tumors. To address this question, a meeting of neuropathologists with expertise in molecular diagnosis was held in Haarlem, the Netherlands, under the sponsorship of the International Society of Neuropathology (ISN). Prior to the meeting, participants solicited input from clinical colleagues in diverse neuro‐oncological specialties. The present “white paper” catalogs the recommendations of the meeting, at which a consensus was reached that incorporation of molecular information into the next WHO classification should follow a set of provided “ISN‐Haarlem” guidelines. Salient recommendations include that (i) diagnostic entities should be defined as narrowly as possible to optimize interobserver reproducibility, clinicopathological predictions and therapeutic planning; (ii) diagnoses should be “layered” with histologic classification, WHO grade and molecular information listed below an “integrated diagnosis”; (iii) determinations should be made for each tumor entity as to whether molecular information is required, suggested or not needed for its definition; (iv) some pediatric entities should be separated from their adult counterparts; (v) input for guiding decisions regarding tumor classification should be solicited from experts in complementary disciplines of neuro‐oncology; and (iv) entity‐specific molecular testing and reporting formats should be followed in diagnostic reports. It is hoped that these guidelines will facilitate the forthcoming update of the fourth edition of the WHO classification of central nervous system tumors.

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

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.

WNT activation by lithium abrogates TP53 mutation associated radiation resistance in medulloblastoma

TP53 mutations confer subgroup specific poor survival for children with medulloblastoma. We hypothesized that WNT activation which is associated with improved survival for such children abrogates TP53 related radioresistance and can be used to sensitize TP53 mutant tumors for radiation. We examined the subgroup-specific role of TP53 mutations in a cohort of 314 patients treated with radiation. TP53 wild-type or mutant human medulloblastoma cell-lines and normal neural stem cells were used to test radioresistance of TP53 mutations and the radiosensitizing effect of WNT activation on tumors and the developing brain. Children with WNT/TP53 mutant medulloblastoma had higher 5-year survival than those with SHH/TP53 mutant tumours (100% and 36.6%u2009±u20098.7%, respectively (pu2009<u20090.001)). Introduction of TP53 mutation into medulloblastoma cells induced radioresistance (survival fractions at 2Gy (SF2) of 89%u2009±u20092% vs. 57.4%u2009±u20091.8% (pu2009<u20090.01)). In contrast, β-catenin mutation sensitized TP53 mutant cells to radiation (pu2009<u20090.05). Lithium, an activator of the WNT pathway, sensitized TP53 mutant medulloblastoma to radiation (SF2 of 43.5%u2009±u20091.5% in lithium treated cells vs. 56.6u2009±u20093% (pu2009<u20090.01)) accompanied by increased number of γH2AX foci. Normal neural stem cells were protected from lithium induced radiation damage (SF2 of 33%u2009±u20098% for lithium treated cells vs. 27%u2009±u20093% for untreated controls (pu2009=u20090.05). Poor survival of patients with TP53 mutant medulloblastoma may be related to radiation resistance. Since constitutive activation of the WNT pathway by lithium sensitizes TP53 mutant medulloblastoma cells and protect normal neural stem cells from radiation, this oral drug may represent an attractive novel therapy for high-risk medulloblastomas.

Papillary Tumor of the Pineal Region: A Distinct Molecular Entity

Papillary tumor of the pineal region (PTPR) is a neuroepithelial brain tumor, which might pose diagnostic difficulties and recurs often. Little is known about underlying molecular alterations. We therefore investigated chromosomal copy number alterations, DNA methylation patterns and mRNA expression profiles in a series of 24 PTPRs. Losses of chromosome 10 were identified in all 13 PTPRs examined. Losses of chromosomes 3 and 22q (54%) as well as gains of chromosomes 8p (62%) and 12 (46%) were also common. DNA methylation profiling using Illumina 450k arrays reliably distinguished PTPR from ependymomas and pineal parenchymal tumors of intermediate differentiation. PTPR could be divided into two subgroups based on methylation pattern, PTPR group 2 showing higher global methylation and a tendency toward shorter progression‐free survival (Pu2009=u20090.06). Genes overexpressed in PTPR as compared with ependymal tumors included SPDEF, known to be expressed in the rodent subcommissural organ. Notable SPDEF protein expression was encountered in 15/19 PTPRs as compared with only 2/36 ependymal tumors, 2/19 choroid plexus tumors and 0/23 samples of other central nervous system (CNS) tumor entities. In conclusion, PTPRs show typical chromosomal alterations as well as distinct DNA methylation and expression profiles, which might serve as useful diagnostic tools.

A comprehensive multicenter comparison of whole genome sequencing pipelines using a uniform tumor-normal sample pair

As next-generation sequencing becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Through the International Cancer Genome Consortium (ICGC), we compared sequencing pipelines at five independent centers (CNAG, DKFZ, OICR, RIKEN and WTSI) using a single tumor-blood DNA pair. Analyses by each center and with one standardized algorithm revealed significant discrepancies. Although most pipelines performed well for coding mutations, library preparation methods and sequencing coverage metrics clearly influenced downstream results. PCR-free methods showed reduced GC-bias and more even coverage. Increasing sequencing depth to ∼100x (two- to three-fold higher than current standards) showed a benefit, as long as the tumor:control coverage ratio remained balanced. To become part of routine clinical care, high-throughput sequencing must be globally compatible and comparable. This benchmarking exercise has highlighted several fundamental parameters to consider in this regard, which will allow for better optimization and planning of both basic and translational studies.

Abstract 3687: An integrative genomics approach identifies distinct molecular and epigenetic subgroups of pediatric glioblastoma

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, ILnnPediatric glioblastoma (GBM) belongs to the comparably small group of childhood malignancies for which cure is still an exception. Histologically indistinguishable from their adult counterparts, they carry a similar dismal prognosis. Whereas genetic and epigenetic properties have been extensively studied in adult tumors, little is known about the molecular characteristics of pediatric GBM, although some reports indicate that it is likely a different entity in terms of tumor biology and molecular genetics. Thus, this study aimed to elucidate disease-defining molecular lesions by determining genomic, transcriptomic and epigenetic alteration profiles. Using an integrative genomics approach combining multiple screening strategies, we investigated primary tumor samples from 55 childhood GBM for copy-number aberrations (CNA), transcriptomic and epigenetic changes, complemented by sequencing analysis of TP53, IDH1/2 and further candidate genes. Methylome analysis revealed the existence of five separate clusters of childhood GBM with distinct molecular and clinico-pathological features. Methylation patterns correlated with novel recurrent, subgroup-specific driver mutations unique to the pediatric population, and with clearly distinguishable transcriptomic profiles. Integration of methylation and gene expression data suggested that different tumor subgroups are derived from at least two distinct precursor-cell populations, one of them without any signs of neural lineage commitment. Furthermore, distinct clusters were highly associated with the presence of balanced (13%) or aneuploid (33%) genomic profiles or with cases displaying highly-rearranged genomes (11%), or various high-level focal amplifications (43%) of known and novel oncogenes. Similar to adults, CNA frequently targeted GBM core signaling pathways such as RTK/PI3K, p53 and RB signaling. TP53 loss-of-function mutations were present in 46% of pediatric GBM. IDH1 mutations were detected in only six patients (11%), but these tumors displayed concerted hypermethylation at a large number of loci, resembling a CpG island methylator phenotype (CIMP). Relevant findings are being validated by immunohistochemistry or FISH analysis in an independent, large-scale cohort representing 130 uniformly-treated pediatric GBM. This study, one of the largest cohorts of pediatric GBM investigated for molecular alterations to date, describes frequent genetic and epigenetic features of this devastating disease and further emphasizes and differences between adult and pediatric GBM. The identification of distinct molecular subgroups and commonly altered pathways will help to characterize molecular biomarkers for improved prognostic assessment and risk-adapted treatment stratification, and may facilitate the development of suitable in vitro and in vivo models for defining novel therapeutic strategies.nnCitation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3687. doi:1538-7445.AM2012-3687

A mouse model for embryonal tumors with multilayered rosettes uncovers the therapeutic potential of Sonic-hedgehog inhibitors

Embryonal tumors with multilayered rosettes (ETMRs) have recently been described as a new entity of rare pediatric brain tumors with a fatal outcome. We show here that ETMRs are characterized by a parallel activation of Shh and Wnt signaling. Co-activation of these pathways in mouse neural precursors is sufficient to induce ETMR-like tumors in vivo that resemble their human counterparts on the basis of histology and global gene-expression analyses, and that point to apical radial glia cells as the possible tumor cell of origin. Overexpression of LIN28A, which is a hallmark of human ETMRs, augments Sonic-hedgehog (Shh) and Wnt signaling in these precursor cells through the downregulation of let7-miRNA, and LIN28A/let7a interaction with the Shh pathway was detected at the level of Gli mRNA. Finally, human ETMR cells that were transplanted into immunocompromised host mice were responsive to the SHH inhibitor arsenic trioxide (ATO). Our work provides a novel mouse model in which to study this tumor type, demonstrates the driving role of Wnt and Shh activation in the growth of ETMRs and proposes downstream inhibition of Shh signaling as a therapeutic option for patients with ETMRs.

Myxoid glioneuronal tumor of the septum pellucidum and lateral ventricle is defined by a recurrent PDGFRA p.K385 mutation and DNT-like methylation profile

David A. Solomon1,2 · Andrey Korshunov3,4 · Martin Sill5,6,7 · David T. W. Jones5,6 · Marcel Kool5,6 · Stefan M. Pfister5,6,7 · Xuemo Fan8 · Serguei Bannykh8 · Jethro Hu9 · Moise Danielpour10 · Rong Li11 · James Johnston12 · Elaine Cham13 · Tabitha Cooney14 · Peter P. Sun15 · Nancy Ann Oberheim Bush16 · Michael McDermott17 · Jessica Van Ziffle1,2 · Courtney Onodera1,2 · James P. Grenert1,2 · Boris C. Bastian1,2 · Javier E. Villanueva‐Meyer18 · Melike Pekmezci1 · Andrew W. Bollen1 · Arie Perry1,17

Abstract PR02: Somatic CRISPR/Cas9-mediated tumor suppressor disruption enables versatile brain tumor modeling

Modeling cancer in mice through engineering of candidate genes in the germline has long been the gold standard for the validation of putative oncogenes or tumor suppressor genes (TSGs). For TSGs, whereby loss-of-function (LOF) mutations act as a driver for malignant transformation, this has traditionally been accomplished using constitutive or cell type-specific knockout strategies mediated by homologous recombination in embryonic stem cells. While this allows evaluation of cell type-specific susceptibility to malignant transformation, generation of genetically engineered mouse models (GEMMs) is a time consuming process. For in vivo investigation of a large number of molecular alterations, such as the many new candidates currently emerging from large-scale tumor genome sequencing efforts, a faster and more flexible method is required. We therefore sought to adapt the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9-guided endonuclease technique for the somatic disruption of candidate TSGs and thereby complement aforementioned already existing models like GEMM. To provide a flexible and effective method for investigating somatic LOF alterations and their influence on tumorigenesis in vivo, we established in vivo somatic gene transfer of CRISPR/Cas9-encoding vectors using polyethylenimine or in utero electroporation, respectively, allowing for in vivo targeting of TSGs in the developing murine brain. We demonstrate the utility of this approach by deleting the tumor suppressor Ptch1, which resulted in the development of cerebellar tumors resembling sonic hedgehog (SHH) subgroup medulloblastoma both at the histopathological as well as the molecular level. Furthermore, we show that multiple genes can be disrupted with this approach, using in utero electroporation of guide RNAs (gRNAs) targeting Trp53, Pten and Nf1 into the forebrain of mice. This resulted in induction of glioblastoma with 100% penetrance. Using whole genome sequencing (WGS) we characterized the MB-driving Ptch1 deletions in detail and show that no off-targets were detected in these tumors. Taken together, these approaches provide a fast and convenient way for validating the emerging wealth of novel candidate TSGs and the generation of faithful animal models of human cancer. Citation Format: Marc Zuckermann, Volker Hovestadt, Christiane B. Knobbe-Thomsen, Marc Zapatka, Paul A. Northcott, Kathrin Schramm, Jelena Belic, David T.W. Jones, Barbara Tschida, Branden Moriarity, David Largaespada, Martine F. Roussel, Andrey Korshunov, Guido Reifenberger, Stefan M. Pfister, Peter Lichter, Daisuke Kawauchi, Jan Gronych. Somatic CRISPR/Cas9-mediated tumor suppressor disruption enables versatile brain tumor modeling. [abstract]. In: Proceedings of the AACR Special Conference: Advances in Brain Cancer Research; May 27-30, 2015; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2015;75(23 Suppl):Abstract nr PR02.