Sonic hedgehog medulloblastoma encompasses a clinically and molecularly diverse group of cancers of the developing central nervous system. Here, we use unbiased sequencing of the transcriptome across a large cohort of 250 tumors to reveal differences among molecular subtypes of the disease, and demonstrate the previously unappreciated importance of non-coding RNA transcripts. We identify alterations within the cAMP dependent pathway (GNAS, PRKAR1A) which converge on GLI2 activity and show that 18% of tumors have a genetic event that directly targets the abundance and/or stability of MYCN. Furthermore, we discover an extensive network of fusions in focally amplified regions encompassing GLI2, and several loss-of-function fusions in tumor suppressor genes PTCH1, SUFU and NCOR1. Molecular convergence on a subset of genes by nucleotide variants, copy number aberrations, and gene fusions highlight the key roles of specific pathways in the pathogenesis of Sonic hedgehog medulloblastoma and open up opportunities for therapeutic intervention.

2nd Department of Pediatrics Semmelweis University Budapest Hungary

Adaptive Oncology Ontario Institute for Cancer Research Toronto ON Canada

Alberta Children's Hospital Research Institute Calgary AB Canada

Canada's Michael Smith Genome Sciences Centre BC Cancer Agency Vancouver BC Canada

Cancer Research Program Research Institute of the McGill University Health Centre Montreal QC Canada

Charbonneau Cancer Institute University of Calgary Calgary AB Canada

Clinical Research Division Fred Hutchinson Cancer Research Center Seattle WA United States

Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada

Department of Anatomical and Cellular Pathology The Chinese University of Hong Kong Shatin New Territories Hong Kong

Department of Biochemistry and Molecular Biology Cumming School of Medicine University of Calgary Calgary AB Canada

Department of Cell and Systems Biology University of Toronto Toronto ON Canada

Department of Cellular and Molecular Pharmacology University of California San Francisco San Francisco CA United States

Department of Hematology and Medical Oncology School of Medicine and Winship Cancer Institute Emory University Atlanta GA United States

Department of Human Genetics McGill University Montreal QC Canada

Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada

Department of Laboratory Medicine and Pathology Mayo Clinic Rochester MN United States

Department of Medical Biophysics University of Toronto Toronto ON Canada

Department of Medical Genetics University of British Columbia Vancouver BC Canada

Department of Molecular Biology and Biochemistry Simon Fraser University Burnaby BC Canada

Department of Molecular Genetics University of Toronto Toronto ON Canada

Department of Neurological Surgery University of California San Francisco San Francisco CA United States

Department of Neurological Surgery University of Pittsburgh School of Medicine Pittsburgh PA United States

Department of Neurological Surgery Vanderbilt Medical Center Nashville TN United States

Department of Neurology Erasmus University Medical Center Rotterdam Netherlands

Department of Neurology University of California San Francisco San Francisco CA United States

Department of Neurology Vanderbilt Medical Center Nashville TN United States

Department of Neurosurgery Chonnam National University Research Institute of Medical Sciences Chonnam National University Hwasun Hospital and Medical School Hwasun gun Jeollanam do South Korea

Department of Neurosurgery David Geffen School of Medicine at UCLA Los Angeles California United States

Department of Neurosurgery Division of Pediatric Neurosurgery Seoul National University Children's Hospital Seoul South Korea

Department of Neurosurgery Duke University Durham NC United States

Department of Neurosurgery Kitasato University School of Medicine Sagamihara Kanagawa Japan

Department of Neurosurgery University of Alabama at Birmingham Birmingham AL United States

Department of Neurosurgery University of Debrecen Medical and Health Science Centre Debrecen Hungary

Department of Neurosurgery University of Ulsan Asan Medical Center Seoul South Korea

Department of Pathology and Laboratory Medicine Hamilton General Hospital Hamilton ON Canada

Department of Pathology and Molecular Medicine Division of Anatomical Pathology McMaster University Hamilton ON Canada

Department of Pathology and Neurosurgery NYU Grossman School of Medicine and NYU Langone Health New York NY United States

Department of Pathology Duke University Durham NC United States

Department of Pathology Erasmus University Medical Center Rotterdam Netherlands

Department of Pathology The Children's Memorial Health Institute Warsaw Poland

Department of Pathology University of California San Francisco San Francisco CA United States

Department of Pathology University of Pittsburgh School of Medicine Pittsburgh PA United States

Department of Pediatric Oncology Masaryk University School of Medicine Brno Czech Republic

Department of Pediatrics University of California San Francisco San Francisco CA United States

Department of Pediatrics University of Colorado Denver Aurora CO United States

Department of Surgery and Anatomy Faculty of Medicine of Ribeirão Preto University of Sao Paulo São Paulo Brazil

Department of Surgery Division of Thoracic and Upper Gastrointestinal Surgery Faculty of Medicine McGill University Montreal QC Canada

Department of Surgery The Chinese University of Hong Kong Shatin New Territories Hong Kong

Department of Surgery University of Toronto Toronto ON Canada

Departments of Neuroscience Washington University School of Medicine in St Louis St Louis MO United States

Departments of Pathology Ophthalmology and Oncology John Hopkins University School of Medicine Baltimore MD United States

Developmental and Stem Cell Biology Program The Hospital for Sick Children Toronto ON Canada

Developmental Tumor Biology Laboratory Hospital Sant Joan de Déu Esplugues de Llobregat Barcelona Spain

Division of Experimental Medicine McGill University Montreal QC Canada

Division of Haematology Oncology Department of Pediatrics The Hospital for Sick Children Toronto ON Canada

Division of Neurosurgery Centro Hospitalar Lisboa Norte Hospital de Santa Maria Lisbon Portugal

Division of Neurosurgery The Hospital for Sick Children Toronto ON Canada

Division of Neurosurgery Toronto Western Hospital University Health Network Toronto ON Canada

Division of Pediatric Hematology Oncology Hospital Pediatría Centro Médico Nacional century XXI Mexico City Mexico

Division of Pediatric Hematology Oncology Mayo Clinic Rochester MN United States

Division of Stem Cell Research Institute for Clinical Research Osaka National Hospital Osaka Japan

Hospices Civils de Lyon Institute of Pathology University Lyon 1 Department of Cancer Cell Plasticity INSERM U1052 Cancer Research Center of Lyon Lyon France

INSERM U 830 Institut Curie Paris France

Institute of Medical Science University of Toronto Toronto ON Canada

Institute of Neuropathology University Medical Center Hamburg Eppendorf Germany

Instituto de Medicina Molecular João Lobo Antunes Faculdade de Medicina Universidade de Lisboa Lisbon Portugal

MacFeeters Hamilton Center for Neuro Oncology Research Princess Margaret Cancer Centre University Health Network Toronto ON Canada

McGill University Genome Centre McGill University Montreal QC Canada

Pediatric Hematology and Oncology University Medical Center Hamburg Eppendorf Germany

PSL Research University Université Paris Sud Université Paris Saclay CNRS UMR 3347 INSERM U1021 Institut Curie Paris France

Research Institute Children's Cancer Center Hamburg Germany

SIREDO Center Institut Curie University of Paris Paris France

The Arthur and Sonia Labatt Brain Tumour Research Centre The Hospital for Sick Children Toronto ON Canada

The Donnelly Centre University of Toronto Toronto ON Canada

U O Neurochirurgia Istituto Giannina Gaslini Genova Italy

Unit of Somatic Genetics Institut Curie Paris France

Zobrazit více v PubMed

Stucklin ASG, Ramaswamy V, Daniels C, Taylor MD. Review of molecular classification and treatment implications of pediatric brain tumors. Curr. Opin. Pediatr. 2018;30:3–9. doi: 10.1097/MOP.0000000000000562. PubMed DOI

Taylor MD, et al. Molecular subgroups of medulloblastoma: the current consensus. Acta Neuropathol. 2012;123:465–472. doi: 10.1007/s00401-011-0922-z. PubMed DOI PMC

Cavalli FMG, et al. Intertumoral heterogeneity within medulloblastoma subgroups. Cancer Cell. 2017;31:737–754.e6. doi: 10.1016/j.ccell.2017.05.005. PubMed DOI PMC

Suzuki H, et al. Recurrent noncoding U1 snRNA mutations drive cryptic splicing in SHH medulloblastoma. Nature. 2019;574:707–711. doi: 10.1038/s41586-019-1650-0. PubMed DOI PMC

He X, et al. The G protein α subunit Gαs is a tumor suppressor in Sonic hedgehog−driven medulloblastoma. Nat. Med. 2014;20:1035–1042. doi: 10.1038/nm.3666. PubMed DOI PMC

Rhayem Y, et al. Functional characterization of PRKAR1A mutations reveals a unique molecular mechanism causing acrodysostosis but multiple mechanisms causing carney complex. J. Biol. Chem. 2015;290:27816–27828. doi: 10.1074/jbc.M115.656553. PubMed DOI PMC

Sasaki H, Nishizaki Y, Hui C, Nakafuku M, Kondoh H. Regulation of Gli2 and Gli3 activities by an amino-terminal repression domain: implication of Gli2 and Gli3 as primary mediators of Shh signaling. Development. 1999;126:3915–3924. PubMed

Niewiadomski P, et al. Gli protein activity is controlled by multisite phosphorylation in vertebrate Hedgehog signaling. Cell Rep. 2014;6:168–181. doi: 10.1016/j.celrep.2013.12.003. PubMed DOI PMC

Oghabi Bakhshaiesh T, Majidzadeh-A K, Esmaeili R. Wip1: a candidate phosphatase for cancer diagnosis and treatment. DNA Repair. 2017;54:63–66. doi: 10.1016/j.dnarep.2017.03.004. PubMed DOI

Kleiblova P, et al. Gain-of-function mutations of PPM1D/Wip1 impair the p53-dependent G1 checkpoint. J. Cell Biol. 2013;201:511–521. doi: 10.1083/jcb.201210031. PubMed DOI PMC

Zajkowicz A, et al. Truncating mutations of PPM1D are found in blood DNA samples of lung cancer patients. Br. J. Cancer. 2015;112:1114–1120. doi: 10.1038/bjc.2015.79. PubMed DOI PMC

Zhang L, et al. Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. Nat. Genet. 2014;46:726–730. doi: 10.1038/ng.2995. PubMed DOI PMC

Welcker M, et al. The Fbw7 tumor suppressor regulates glycogen synthase kinase 3 phosphorylation-dependent c-Myc protein degradation. Proc. Natl Acad. Sci. USA. 2004;101:9085–9090. doi: 10.1073/pnas.0402770101. PubMed DOI PMC

Richards MW, et al. Structural basis of N-Myc binding by Aurora-A and its destabilization by kinase inhibitors. Proc. Natl Acad. Sci. USA. 2016;113:13726–13731. doi: 10.1073/pnas.1610626113. PubMed DOI PMC

Adhikary S, Eilers M. Transcriptional regulation and transformation by Myc proteins. Nat. Rev. Mol. Cell Biol. 2005;6:635–645. doi: 10.1038/nrm1703. PubMed DOI

Farrell AS, Sears RC. MYC degradation. Cold Spring Harb. Perspect. Med. 2014;4:1–15. doi: 10.1101/cshperspect.a014365. PubMed DOI PMC

Welcker M, Clurman BE. FBW7 ubiquitin ligase: a tumour suppressor at the crossroads of cell division, growth and differentiation. Nat. Rev. Cancer. 2008;8:83–93. doi: 10.1038/nrc2290. PubMed DOI

Thompson BJ, et al. The SCF FBW7 ubiquitin ligase complex as a tumor suppressor in T cell leukemia. J. Exp. Med. 2007;204:1825–1835. doi: 10.1084/jem.20070872. PubMed DOI PMC

O’Neil J, et al. FBW7 mutations in leukemic cells mediate NOTCH pathway activation and resistance to γ-secretase inhibitors. J. Exp. Med. 2007;204:1813–1824. doi: 10.1084/jem.20070876. PubMed DOI PMC

Close V, et al. FBXW7 mutations reduce binding of NOTCH1, leading to cleaved NOTCH1 accumulation and target gene activation in CLL. Blood. 2019;133:830–839. doi: 10.1182/blood-2018-09-874529. PubMed DOI

Gadd S, et al. A Children’s Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nat. Genet. 2017;49:1487–1494. doi: 10.1038/ng.3940. PubMed DOI PMC

Northcott PA, et al. Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature. 2012;488:49–56. doi: 10.1038/nature11327. PubMed DOI PMC

Haas BJ, et al. Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods. Genome Biol. 2019;20:1–16. doi: 10.1186/s13059-019-1842-9. PubMed DOI PMC

Robertson G, et al. De novo assembly and analysis of RNA-seq data. Nat. Methods. 2010;7:909–912. doi: 10.1038/nmeth.1517. PubMed DOI

Okonechnikov K, et al. InFusion: advancing discovery of fusion genes and chimeric transcripts from deep RNA-sequencing data. PLoS ONE. 2016;11:e0167417. doi: 10.1371/journal.pone.0167417. PubMed DOI PMC

Rausch T, et al. Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with TP53 mutations. Cell. 2012;148:59–71. doi: 10.1016/j.cell.2011.12.013. PubMed DOI PMC

Ratnaparkhe M, et al. Defective DNA damage repair leads to frequent catastrophic genomic events in murine and human tumors. Nat. Commun. 2018;9:4760. doi: 10.1038/s41467-018-06925-4. PubMed DOI PMC

Jepsen K, et al. Combinatorial roles of the nuclear receptor corepressor in transcription and development. Cell. 2000;102:753–763. doi: 10.1016/S0092-8674(00)00064-7. PubMed DOI

Hermanson O, Jepsen K, Rosenfeld MG. N-CoR controls differentiation of neural stem cells into astrocytes. Nature. 2002;419:934–939. doi: 10.1038/nature01156. PubMed DOI

Huang M, et al. Engineering genetic predisposition in human neuroepithelial stem cells recapitulates Medulloblastoma Tumorigenesis. Cell Stem Cell. 2019;25:433–446.e7. doi: 10.1016/j.stem.2019.05.013. PubMed DOI PMC

Merk DJ, et al. Opposing effects of CREBBP mutations govern the phenotype of Rubinstein-Taybi syndrome and adult SHH Medulloblastoma. Dev. Cell. 2018;44:709–724.e6. doi: 10.1016/j.devcel.2018.02.012. PubMed DOI

Cedoz PL, Prunello M, Brennan K, Gevaert O. MethylMix 2.0: An R package for identifying DNA methylation genes. Bioinformatics. 2018;34:3044–3046. doi: 10.1093/bioinformatics/bty156. PubMed DOI PMC

Canisius S, Martens JWM, Wessels LFA. A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence. Genome Biol. 2016;17:1–17. doi: 10.1186/s13059-016-1114-x. PubMed DOI PMC

Remke M, et al. TERT promoter mutations are highly recurrent in SHH subgroup medulloblastoma. Acta Neuropathol. 2013;126:917–929. doi: 10.1007/s00401-013-1198-2. PubMed DOI PMC

Lonsdale J, et al. The Genotype-Tissue Expression (GTEx) project. Nat. Genet. 2013;45:580–585. doi: 10.1038/ng.2653. PubMed DOI PMC

Morrissy AS, et al. Divergent clonal selection dominates medulloblastoma at recurrence. Nature. 2016;529:351–357. doi: 10.1038/nature16478. PubMed DOI PMC

Wang B, et al. Similarity network fusion for aggregating data types on a genomic scale. Nat. Methods. 2014;11:333–337. doi: 10.1038/nmeth.2810. PubMed DOI

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

Auwera GA, et al. From FastQ data to high‐confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinforma. 2013;43:11.10.1–11.10.33. doi: 10.1002/0471250953.bi1110s43. PubMed DOI PMC

Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164–e164. doi: 10.1093/nar/gkq603. PubMed DOI PMC

Ramaswami G, Li JB. RADAR: a rigorously annotated database of A-to-I RNA editing. Nucleic Acids Res. 2014;42:D109–D113. doi: 10.1093/nar/gkt996. PubMed DOI PMC

Li YI, et al. Annotation-free quantification of RNA splicing using LeafCutter. Nat. Genet. 2018;50:151–158. doi: 10.1038/s41588-017-0004-9. PubMed DOI PMC

Schwarz JM, Cooper DN, Schuelke M, Seelow D. Mutationtaster2: mutation prediction for the deep-sequencing age. Nat. Methods. 2014;11:361–362. doi: 10.1038/nmeth.2890. PubMed DOI

Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 2011;39:37–43. doi: 10.1093/nar/gkr407. PubMed DOI PMC

Shiraishi Y, et al. An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data. Nucleic Acids Res. 2013;41:e89–e89. doi: 10.1093/nar/gkt126. PubMed DOI PMC

Lawrence MS, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214–218. doi: 10.1038/nature12213. PubMed DOI PMC

Wang K, et al. PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–1674. doi: 10.1101/gr.6861907. PubMed DOI PMC

Loo PVan, et al. Allele-specific copy number analysis of tumors. Proc. Natl Acad. Sci. USA. 2010;107:16910–16915. doi: 10.1073/pnas.1009843107. PubMed DOI PMC

Mermel CH, et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 2011;12:R41. doi: 10.1186/gb-2011-12-4-r41. PubMed DOI PMC

Quinlan AR, Hall IM. BEDTools: A flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–842. doi: 10.1093/bioinformatics/btq033. PubMed DOI PMC

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat. Methods. 2012;9:357–359. doi: 10.1038/nmeth.1923. PubMed DOI PMC

Wu Z, Wu H. Visualizing Genomic Data Using Gviz and Bioconductor. Methods Mol. Biol. 2016;1418:335–351. doi: 10.1007/978-1-4939-3578-9_16. PubMed DOI

Tischler G, Leonard S. biobambam: tools for read pair collation based algorithms on BAM files. Source Code Biol. Med. 2014;9:13. doi: 10.1186/1751-0473-9-13. DOI

Kataoka, K. et al. Aberrant PD-L1 expression through 3′-UTR disruption in multiple cancers. Nature534, 402–406 (2016). PubMed

Rausch T, et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333–i339. doi: 10.1093/bioinformatics/bts378. PubMed DOI PMC

Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18:821–829. doi: 10.1101/gr.074492.107. PubMed DOI PMC

Yang J, Zhang Y. I-TASSER server: New development for protein structure and function predictions. Nucleic Acids Res. 2015;43:W174–W181. doi: 10.1093/nar/gkv342. PubMed DOI PMC

Zhang C, Freddolino PL, Zhang Y. COFACTOR: Improved protein function prediction by combining structure, sequence and protein-protein interaction information. Nucleic Acids Res. 2017;45:W291–W299. doi: 10.1093/nar/gkx366. PubMed DOI PMC

Pettersen EF, et al. UCSF Chimera - a visualization system for exploratory research and analysis. J. Comput. Chem. 2004;25:1605–1612. doi: 10.1002/jcc.20084. PubMed DOI

Reimand J, et al. g:Profiler-a web server for functional interpretation of gene lists (2016 update) Nucleic Acids Res. 2016;44:W83–W89. doi: 10.1093/nar/gkw199. PubMed DOI PMC

Subramanian A, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci. USA. 2005;102:15545–15550. doi: 10.1073/pnas.0506580102. PubMed DOI PMC

Merico D, Isserlin R, Stueker O, Emili A, Bader GD. Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE. 2010;5:e13984. doi: 10.1371/journal.pone.0013984. PubMed DOI PMC

Paul Shannon 1, et al. Cytoscape: a software environment for integrated models of biomolecular interaction. Netw. Genome Res. 2003;13:6. PubMed PMC

Sturm D, et al. Hotspot mutations in H3F3A and IDH1 define distinct epigenetic and biological subgroups of glioblastoma. Cancer Cell. 2012;22:425–437. doi: 10.1016/j.ccr.2012.08.024. PubMed DOI

Hovestadt V, et al. Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays. Acta Neuropathol. 2013;125:913–916. doi: 10.1007/s00401-013-1126-5. PubMed DOI PMC

Zhou W, Laird PW, Shen H. Comprehensive characterization, annotation and innovative use of Infinium DNA methylation BeadChip probes. Nucleic Acids Res. 2017;45:e22. PubMed PMC

Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847–2849. doi: 10.1093/bioinformatics/btw313. PubMed DOI

Zhou X, et al. Exploring genomic alteration in pediatric cancer using ProteinPaint. Nat. Genet. 2015;48:4–6. doi: 10.1038/ng.3466. PubMed DOI PMC

Connors J, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–1645. doi: 10.1101/gr.092759.109. PubMed DOI PMC

Comparative analysis of pediatric SHH medulloblastoma DAOY spheres and adherent monolayers: implications for medulloblastoma research

Failure of human rhombic lip differentiation underlies medulloblastoma formation