Sense-Antisense lncRNA Pair Encoded by Locus 6p22.3 Determines Neuroblastoma Susceptibility via the USP36-CHD7-SOX9 Regulatory Axis.

Trait-associated loci often map to genomic regions encoding long noncoding RNAs (lncRNAs), but the role of these lncRNAs in disease etiology is largely unexplored. We show that a pair of sense/antisense lncRNA (6p22lncRNAs) encoded by CASC15 and NBAT1 located at the neuroblastoma (NB) risk-associated 6p22.3 locus are tumor suppressors and show reduced expression in high-risk NBs. Loss of functional synergy between 6p22lncRNAs results in an undifferentiated state that is maintained by a gene-regulatory network, including SOX9 located on 17q, a region frequently gained in NB. 6p22lncRNAs regulate SOX9 expression by controlling CHD7 stability via modulating the cellular localization of USP36, encoded by another 17q gene. This regulatory nexus between 6p22.3 and 17q regions may lead to potential NB treatment strategies.

[1]  Simon C Watkins,et al.  Telomerase activation by genomic rearrangements in high-risk neuroblastoma , 2015, Nature.

[2]  Gudrun Schleiermacher,et al.  Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations , 2015, Nature Genetics.

[3]  A. Chinnaiyan,et al.  The emergence of lncRNAs in cancer biology. , 2011, Cancer discovery.

[4]  Nazneen Rahman,et al.  Integrative genomics identifies LMO1 as a neuroblastoma oncogene , 2011, Nature.

[5]  J. Rinn,et al.  lincRNAs act in the circuitry controlling pluripotency and differentiation , 2011, Nature.

[6]  S. Dhanasekaran,et al.  The landscape of long noncoding RNAs in the human transcriptome , 2015, Nature Genetics.

[7]  S. Jason,et al.  Neuroblastoma , 2018 .

[8]  Steven J. M. Jones,et al.  The genetic landscape of high-risk neuroblastoma , 2013, Nature Genetics.

[9]  C. Kanduri,et al.  Global DNA methylation profiling reveals new insights into epigenetically deregulated protein coding and long noncoding RNAs in CLL , 2016, Clinical Epigenetics.

[10]  C. Liang,et al.  In vitro scratch assay: a convenient and inexpensive method for analysis of cell migration in vitro , 2007, Nature Protocols.

[11]  Cheng Li,et al.  Adjusting batch effects in microarray expression data using empirical Bayes methods. , 2007, Biostatistics.

[12]  Gordon K Smyth,et al.  Statistical Applications in Genetics and Molecular Biology Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments , 2011 .

[13]  Chandrasekhar Kanduri,et al.  GeneSCF: a real-time based functional enrichment tool with support for multiple organisms , 2016, BMC Bioinformatics.

[14]  John M. Maris,et al.  Identification of ALK as a major familial neuroblastoma predisposition gene , 2008, Nature.

[15]  May D. Wang,et al.  Comparison of RNA-seq and microarray-based models for clinical endpoint prediction , 2015, Genome Biology.

[16]  Staffan Nilsson,et al.  High-risk neuroblastoma tumors with 11q-deletion display a poor prognostic, chromosome instability phenotype with later onset , 2010, Proceedings of the National Academy of Sciences.

[17]  J. Rinn,et al.  Scaffold function of long non-coding RNA HOTAIR in protein ubiquitination , 2013, Nature Communications.

[18]  D. Black,et al.  Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions , 2012, Cell.

[19]  Achim Zeileis,et al.  Generalized Maximally Selected Statistics , 2008, Biometrics.

[20]  B. Conklin,et al.  Generating trunk neural crest from human pluripotent stem cells , 2016, Scientific Reports.

[21]  Nazneen Rahman,et al.  Chromosome 6p22 locus associated with clinically aggressive neuroblastoma. , 2008, The New England journal of medicine.

[22]  A. Califano,et al.  HAUSP deubiquitinated and stabilizes N-Myc in neuroblastoma , 2016, Nature Medicine.

[23]  Xiao-xin Sun,et al.  The nucleolar ubiquitin-specific protease USP36 deubiquitinates and stabilizes c-Myc , 2015, Proceedings of the National Academy of Sciences.

[24]  G. Basso,et al.  The lncRNA CASC15 regulates SOX4 expression in RUNX1-rearranged acute leukemia , 2017, Molecular Cancer.

[25]  Gaurav Kumar Pandey,et al.  The risk-associated long noncoding RNA NBAT-1 controls neuroblastoma progression by regulating cell proliferation and neuronal differentiation. , 2014, Cancer cell.

[26]  G. Mills,et al.  Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. , 2015, Cancer cell.

[27]  S. Beck,et al.  Genome-wide methylation profiling identifies novel methylated genes in neuroblastoma tumors , 2016, Epigenetics.

[28]  K. Cole,et al.  CASC15-S Is a Tumor Suppressor lncRNA at the 6p22 Neuroblastoma Susceptibility Locus. , 2015, Cancer research.

[29]  D. M. Martin,et al.  Inappropriate p53 Activation During Development Induces Features of CHARGE Syndrome , 2014, Nature.

[30]  R. Winn,et al.  The soft agar colony formation assay. , 2014, Journal of visualized experiments : JoVE.

[31]  G. Brodeur.  Neuroblastoma: biological insights into a clinical enigma , 2003, Nature Reviews Cancer.

[32]  Jindan Yu,et al.  LncRNA HOTAIR Enhances the Androgen-Receptor-Mediated Transcriptional Program and Drives Castration-Resistant Prostate Cancer , 2015, Cell reports.

[33]  Stephen P. Jackson,et al.  Deubiquitylating enzymes and drug discovery: emerging opportunities , 2017, Nature Reviews Drug Discovery.

[34]  Howard Y. Chang,et al.  Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. , 2011, Molecular cell.

[35]  Dorota H. Sendorek,et al.  Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer , 2016, Nature Genetics.

[36]  Jordan A. Ramilowski,et al.  An atlas of human long non-coding RNAs with accurate 5′ ends , 2017, Nature.

[37]  M. Komada,et al.  Nucleophosmin/B23 Regulates Ubiquitin Dynamics in Nucleoli by Recruiting Deubiquitylating Enzyme USP36* , 2009, The Journal of Biological Chemistry.

[38]  Rasna R. Walia,et al.  RNABindRPlus: A Predictor that Combines Machine Learning and Sequence Homology-Based Methods to Improve the Reliability of Predicted RNA-Binding Residues in Proteins , 2014, PloS one.

[39]  David R. Kelley,et al.  Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre , 2014, Nature Structural &Molecular Biology.

[40]  D. Zwijnenburg,et al.  Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes , 2012, Nature.

[41]  Steven J. M. Jones,et al.  MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA–DNA triplex structures , 2015, Nature Communications.

[42]  J. Helms,et al.  CHD7 cooperates with PBAF to control multipotent neural crest formation , 2010, Nature.

[43]  J. Claverie,et al.  The significance of digital gene expression profiles. , 1997, Genome research.

[44]  S. Dalton,et al.  Directed differentiation of human pluripotent cells to neural crest stem cells , 2013, Nature Protocols.

[45]  Norman E. Davey,et al.  Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins , 2012, Cell.

[46]  Giovanni Parmigiani,et al.  Integrated genomic analyses identify ARID1A and ARID1B alterations in the childhood cancer neuroblastoma , 2012, Nature Genetics.

[47]  Gudrun Schleiermacher,et al.  Advances in Risk Classification and Treatment Strategies for Neuroblastoma. , 2015, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[48]  David T. W. Jones,et al.  Chd7 is indispensable for mammalian brain development through activation of a neuronal differentiation programme , 2017, Nature Communications.

[49]  H. Hakonarson,et al.  Common variation at 6q16 within HACE1 and LIN28B influences susceptibility to neuroblastoma , 2012, Nature Genetics.

[50]  Jeannie T. Lee,et al.  New and Xisting regulatory mechanisms of X chromosome inactivation. , 2012, Current opinion in genetics & development.

[51]  Andrew E. Teschendorff,et al.  ChAMP: 450k Chip Analysis Methylation Pipeline , 2014, Bioinform..