Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR

Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.

[1]  F. Cetani,et al.  The microRNA cluster C19MC is deregulated in parathyroid tumours. , 2012, Journal of molecular endocrinology.

[2]  V. P. Collins,et al.  Frequent amplification of a chr19q13.41 microRNA polycistron in aggressive primitive neuroectodermal brain tumors. , 2009, Cancer cell.

[3]  M. Wigler,et al.  Circular binary segmentation for the analysis of array-based DNA copy number data. , 2004, Biostatistics.

[4]  J. Bullerdiek,et al.  The dark side of a success story: microRNAs of the C19MC cluster in human tumours , 2012, The Journal of pathology.

[5]  Hideo Nakamura,et al.  Markers of survival and metastatic potential in childhood CNS primitive neuro-ectodermal brain tumours: an integrative genomic analysis. , 2012, The Lancet. Oncology.

[6]  Wing H Wong,et al.  An Oct4-Sall4-Nanog network controls developmental progression in the pre-implantation mouse embryo , 2013, Molecular systems biology.

[7]  Lung-Ji Chang,et al.  De novo DNA methyltransferases Dnmt3a and Dnmt3b primarily mediate the cytotoxic effect of 5-aza-2′-deoxycytidine , 2005, Oncogene.

[8]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[9]  D. Altshuler,et al.  A map of human genome variation from population-scale sequencing , 2010, Nature.

[10]  B. Scheithauer,et al.  Focal genomic amplification at 19q13.42 comprises a powerful diagnostic marker for embryonal tumors with ependymoblastic rosettes , 2010, Acta Neuropathologica.

[11]  David T. W. Jones,et al.  Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma , 2012, Nature.

[12]  Lior Pachter,et al.  Identification and correction of systematic error in high-throughput sequence data , 2011 .

[13]  M. Zavolan,et al.  MicroRNAs control de novo DNA methylation through regulation of transcriptional repressors in mouse embryonic stem cells , 2008, Nature Structural &Molecular Biology.

[14]  D. Watanabe,et al.  Transition of mouse de novo methyltransferases expression from Dnmt3b to Dnmt3a during neural progenitor cell development , 2006, Neuroscience.

[15]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[16]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[17]  Jacek Majewski,et al.  FishingCNV: a graphical software package for detecting rare copy number variations in exome-sequencing data , 2013, Bioinform..

[18]  Peter A. Jones,et al.  Cancer genetics and epigenetics: two sides of the same coin? , 2012, Cancer cell.

[19]  Q. Tao,et al.  DNA methyltransferase 3 B ( DNMT 3 B ) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development , neurogenesis and immune function , 2008 .

[20]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[21]  Atsuko Mizuno,et al.  A Novel Human Cl- Channel Family Related to Drosophila flightless Locus* , 2004, Journal of Biological Chemistry.

[22]  David T. W. Jones,et al.  LIN28A immunoreactivity is a potent diagnostic marker of embryonal tumor with multilayered rosettes (ETMR) , 2012, Acta Neuropathologica.

[23]  G. Salles,et al.  High DNA Methyltransferase DNMT3B Levels: A Poor Prognostic Marker in Acute Myeloid Leukemia , 2012, PloS one.

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  Aaron R. Quinlan,et al.  BIOINFORMATICS APPLICATIONS NOTE , 2022 .

[26]  M. Muckenthaler,et al.  Novel genomic amplification targeting the microRNA cluster at 19q13.42 in a pediatric embryonal tumor with abundant neuropil and true rosettes , 2008, Acta Neuropathologica.

[27]  B. Scheithauer,et al.  Embryonal Tumors With Abundant Neuropil and True Rosettes: A Distinctive CNS Primitive Neuroectodermal Tumor , 2009, The American journal of surgical pathology.

[28]  R. Aharonov,et al.  Identification of hundreds of conserved and nonconserved human microRNAs , 2005, Nature Genetics.

[29]  Jack A. M. Leunissen,et al.  Turning CFCs into salt. , 1996, Nucleic Acids Res..

[30]  Bert Vogelstein,et al.  DNMT1 and DNMT3b cooperate to silence genes in human cancer cells , 2002, Nature.

[31]  Xiaowei Wang,et al.  Sequence analysis Prediction of both conserved and nonconserved microRNA targets in animals , 2007 .

[32]  Wing H Wong,et al.  An Oct 4-Sall 4-Nanog network controls developmental progression in the preimplantation mouse embryo , 2013 .

[33]  Qian Tao,et al.  DNA methyltransferase 3B (DNMT3B) mutations in ICF syndrome lead to altered epigenetic modifications and aberrant expression of genes regulating development, neurogenesis and immune function. , 2008, Human molecular genetics.

[34]  T. Mikkelsen,et al.  The NIH Roadmap Epigenomics Mapping Consortium , 2010, Nature Biotechnology.

[35]  G. Hannon,et al.  A mammalian microRNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases , 2008, Nature Structural &Molecular Biology.

[36]  M. L. Beau,et al.  Cancer cells express aberrant DNMT3B transcripts encoding truncated proteins , 2007, Oncogene.

[37]  David Haussler,et al.  ENCODE Data in the UCSC Genome Browser: year 5 update , 2012, Nucleic Acids Res..

[38]  K. Maruyama,et al.  The human DNA methyltransferases DNMT3A and DNMT3B have two types of promoters with different CpG contents. , 2002, Biochimica et biophysica acta.

[39]  Massimo Negrini,et al.  In hepatocellular carcinoma miR‐519d is up‐regulated by p53 and DNA hypomethylation and targets CDKN1A/p21, PTEN, AKT3 and TIMP2 , 2012, The Journal of pathology.

[40]  Mark Stitt,et al.  RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics , 2012, Nucleic Acids Res..

[41]  U. Markert,et al.  Pregnancy-associated miRNA-clusters. , 2013, Journal of reproductive immunology.

[42]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[43]  C. Burge,et al.  Conserved Seed Pairing, Often Flanked by Adenosines, Indicates that Thousands of Human Genes are MicroRNA Targets , 2005, Cell.

[44]  D. Haber,et al.  DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.

[45]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[46]  Norbert Gretz,et al.  miRWalk - Database: Prediction of possible miRNA binding sites by "walking" the genes of three genomes , 2011, J. Biomed. Informatics.

[47]  D. Schroeder,et al.  Role of DNMT3B in the regulation of early neural and neural crest specifiers , 2012, Epigenetics.

[48]  A. Oshlack,et al.  SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips , 2012, Genome Biology.