p53-dependent non-coding RNA networks in chronic lymphocytic leukemia (original) (raw)

• Vogelstein B, Lane D, Levine AJ . Surfing the p53 network. Nature 2000; 408: 307–310.
  Article CAS Google Scholar
• Riley T, Sontag E, Chen P, Levine A . Transcriptional control of human p53-regulated genes. Nat Rev Mol Cell Biol 2008; 9: 402–412.
  Article CAS Google Scholar
• Wade M, Li YC, Wahl GM . MDM2, MDMX and p53 in oncogenesis and cancer therapy. Nat Rev Cancer 2013; 13: 83–96.
  Article CAS Google Scholar
• Te Raa GD, Malcikova J, Mraz M, Trbusek M, Le Garff-Tavernier M, Merle-Beral H et al. Assessment of TP53 functionality in chronic lymphocytic leukaemia by different assays; an ERIC-wide approach. Br J Haematol 2014; 167: 565–569.
  Article Google Scholar
• te Raa GD, Malcikova J, Pospisilova S, Trbusek M, Mraz M, Garff-Tavernier ML et al. Overview of available p53 function tests in relation to TP53 and ATM gene alterations and chemoresistance in chronic lymphocytic leukemia. Leuk Lymphoma 2013; 54: 1849–1853.
  Article CAS Google Scholar
• Zenz T, Mertens D, Kuppers R, Dohner H, Stilgenbauer S . From pathogenesis to treatment of chronic lymphocytic leukaemia. Nat Rev Cancer 2010; 10: 37–50.
  Article CAS Google Scholar
• Malcikova J, Smardova J, Rocnova L, Tichy B, Kuglik P, Vranova V et al. Monoallelic and biallelic inactivation of TP53 gene in chronic lymphocytic leukemia: selection, impact on survival, and response to DNA damage. Blood 2009; 114: 5307–5314.
  Article CAS Google Scholar
• Zenz T, Krober A, Scherer K, Habe S, Buhler A, Benner A et al. Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: results from a detailed genetic characterization with long-term follow-up. Blood 2008; 112: 3322–3329.
  Article CAS Google Scholar
• Rossi D, Cerri M, Deambrogi C, Sozzi E, Cresta S, Rasi S et al. The prognostic value of TP53 mutations in chronic lymphocytic leukemia is independent of Del17p13: implications for overall survival and chemorefractoriness. Clin Cancer Res 2009; 15: 995–1004.
  Article CAS Google Scholar
• Friedman RC, Farh KK, Burge CB, Bartel DP . Most mammalian mRNAs are conserved targets of microRNAs. Genome Res 2009; 19: 92–105.
  Article CAS Google Scholar
• Tarasov V, Jung P, Verdoodt B, Lodygin D, Epanchintsev A, Menssen A et al. Differential regulation of microRNAs by p53 revealed by massively parallel sequencing. Cell Cycle 2007; 6: 1586–1593.
  Article CAS Google Scholar
• Chang TC, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH et al. Transactivation of miR-34a by p53 broadly influences gene expression and promotes apoptosis. Mol Cell 2007; 26: 745–752.
  Article CAS Google Scholar
• Raver-Shapira N, Marciano E, Meiri E, Spector Y, Rosenfeld N, Moskovits N et al. Transcriptional activation of miR-34a contributes to p53-mediated apoptosis. Mol Cell 2007; 26: 731–743.
  Article CAS Google Scholar
• He L, He X, Lim LP, de Stanchina E, Xuan Z, Liang Y et al. A microRNA component of the p53 tumour suppressor network. Nature 2007; 447: 1130–1134.
  Article CAS Google Scholar
• Sun F, Fu H, Liu Q, Tie Y, Zhu J, Xing R et al. Downregulation of CCND1 and CDK6 by miR-34a induces cell cycle arrest. FEBS Lett 2008; 582: 1564–1568.
  Article CAS Google Scholar
• Tazawa H, Tsuchiya N, Izumiya M, Nakagama H . Tumor-suppressive miR-34a induces senescence-like growth arrest through modulation of the E2F pathway in human colon cancer cells. Proc Natl Acad Sci USA 2007; 104: 15472–15477.
  Article CAS Google Scholar
• Bommer GT, Gerin I, Feng Y, Kaczorowski AJ, Kuick R, Love RE et al. p53-mediated activation of miRNA34 candidate tumor-suppressor genes. Curr Biol 2007; 17: 1298–1307.
  Article CAS Google Scholar
• Zenz T, Mohr J, Eldering E, Kater AP, Buhler A, Kienle D et al. miR-34a as part of the resistance network in chronic lymphocytic leukemia. Blood 2009; 113: 3801–3808.
  Article CAS Google Scholar
• Mraz M, Malinova K, Kotaskova J, Pavlova S, Tichy B, Malcikova J et al. miR-34a, miR-29c and miR-17-5p are downregulated in CLL patients with TP53 abnormalities. Leukemia 2009; 23: 1159–1163.
  Article CAS Google Scholar
• Dufour A, Palermo G, Zellmeier E, Mellert G, Duchateau-Nguyen G, Schneider S et al. Inactivation of TP53 correlates with disease progression and low miR-34a expression in previously treated chronic lymphocytic leukemia patients. Blood 2013; 121: 3650–3657.
  Article CAS Google Scholar
• Visone R, Rassenti LZ, Veronese A, Taccioli C, Costinean S, Aguda BD et al. Karyotype-specific microRNAsignature in chronic lymphocytic leukemia. Blood 2009; 114: 3872–3879.
  Article CAS Google Scholar
• Fabbri M, Bottoni A, Shimizu M, Spizzo R, Nicoloso MS, Rossi S et al. Association of a microRNA/TP53 feedback circuitry with pathogenesis and outcome of B-cell chronic lymphocytic leukemia. JAMA 2011; 305: 59–67.
  Article CAS Google Scholar
• Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 2009; 458: 223–227.
  Article CAS Google Scholar
• Kung JT, Colognori D, Lee JT . Long noncoding RNAs: past, present, and future. Genetics 2013; 193: 651–669.
  Article CAS Google Scholar
• Gutschner T, Diederichs S . The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 2012; 9: 703–719.
  Article CAS Google Scholar
• Huarte M, Guttman M, Feldser D, Garber M, Koziol MJ, Kenzelmann-Broz D et al. A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 2010; 142: 409–419.
  Article CAS Google Scholar
• Hung T, Wang Y, Lin MF, Koegel AK, Kotake Y, Grant GD et al. Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 2011; 43: 621–629.
  Article CAS Google Scholar
• Sanchez Y, Segura V, Marin-Bejar O, Athie A, Marchese FP, Gonzalez J et al. Genome-wide analysis of the human p53 transcriptional network unveils a lncRNA tumour suppressor signature. Nat Commun 2014; 5: 5812.
  Article CAS Google Scholar
• Hullein J, Jethwa A, Stolz T, Blume C, Sellner L, Sill M et al. Next-generation sequencing of cancer consensus genes in lymphoma. Leuk Lymphoma 2013; 54: 1831–1835.
  Article Google Scholar
• Castro F, Dirks WG, Fahnrich S, Hotz-Wagenblatt A, Pawlita M, Schmitt M . High-throughput SNP-based authentication of human cell lines. Int J Cancer 2013; 132: 308–314.
  Article CAS Google Scholar
• Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelsen TS et al. Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 2014; 343: 84–87.
  Article CAS Google Scholar
• Jethwa A, Hullein J, Stolz T, Blume C, Sellner L, Jauch A et al. Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia. Br J Haematol 2013; 163: 496–500.
  Article CAS Google Scholar
• Rosenkranz D, Zischler H . proTRAC—a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics 2012; 13: 5.
  Article Google Scholar
• Ernst P, Glatting KH, Suhai S . A task framework for the web interface W2H. Bioinformatics 2003; 19: 278–282.
  Article CAS Google Scholar
• Anders S, Huber W . Differential expression analysis for sequence count data. Genome Biol 2010; 11: R106.
  Article CAS Google Scholar
• McCarthy DJ, Chen Y, Smyth GK . Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation. Nucleic Acids Res 2012; 40: 4288–4297.
  Article CAS Google Scholar
• Volinia S, Calin GA, Liu CG, Ambs S, Cimmino A, Petrocca F et al. A microRNA expression signature of human solid tumors defines cancer gene targets. Proc Natl Acad Sci USA 2006; 103: 2257–2261.
  Article CAS Google Scholar
• Jima DD, Zhang J, Jacobs C, Richards KL, Dunphy CH, Choi WW et al. Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs. Blood 2010; 116: e118–e127.
  Article CAS Google Scholar
• Mraz M, Chen L, Rassenti LZ, Ghia EM, Li H, Jepsen K et al. MicroRNA-150 contributes to the proficiency of B-cell receptor signaling in chronic lymphocytic leukemia by regulating expression of GAB1 and FOXP1 genes. Blood 2014; 124: 84–95.
  Article CAS Google Scholar
• Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A et al. A mammalian microRNA expression atlas based on small RNA library sequencing. Cell 2007; 129: 1401–1414.
  Article CAS Google Scholar
• Yoon JH, Abdelmohsen K, Srikantan S, Yang X, Martindale JL, De S et al. LincRNA-p21 suppresses target mRNA translation. Mol Cell 2012; 47: 648–655.
  Article CAS Google Scholar
• Clemson CM, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A et al. An architectural role for a nuclear noncoding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 2009; 33: 717–726.
  Article CAS Google Scholar
• Zenz T, Habe S, Denzel T, Mohr J, Winkler D, Buhler A et al. Detailed analysis of p53 pathway defects in fludarabine-refractory chronic lymphocytic leukemia (CLL): dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial. Blood 2009; 114: 2589–2597.
  Article CAS Google Scholar
• Rossi S, Shimizu M, Barbarotto E, Nicoloso MS, Dimitri F, Sampath D et al. microRNA fingerprinting of CLL patients with chromosome 17p deletion identify a miR-21 score that stratifies early survival. Blood 2010; 116: 945–952.
  Article CAS Google Scholar
• Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE et al. A MicroRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 2005; 353: 1793–1801.
  Article CAS Google Scholar
• Xu X, Wu J, Li S, Hu Z, Xu X, Zhu Y et al. Downregulation of microRNA-182-5p contributes to renal cell carcinoma proliferation via activating the AKT/FOXO3a signaling pathway. Mol Cancer 2014; 13: 109.
  Article Google Scholar
• Botcheva K, McCorkle SR, McCombie WR, Dunn JJ, Anderson CW . Distinct p53 genomic binding patterns in normal and cancer-derived human cells. Cell Cycle 2011; 10: 4237–4249.
  Article CAS Google Scholar
• Zhang N, Li X, Wu CW, Dong Y, Cai M, Mok MT et al. microRNA-7 is a novel inhibitor of YY1 contributing to colorectal tumorigenesis. Oncogene 2013; 32: 5078–5088.
  Article CAS Google Scholar
• Wahlestedt C . Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 2013; 12: 433–446.
  Article CAS Google Scholar
• Schlereth K, Heyl C, Krampitz AM, Mernberger M, Finkernagel F, Scharfe M et al. Characterization of the p53 cistrome—DNA binding cooperativity dissects p53's tumor suppressor functions. PLoS Genet 2013; 9: e1003726.
  Article CAS Google Scholar
• Allen MA, Andrysik Z, Dengler VL, Mellert HS, Guarnieri A, Freeman JA et al. Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms. eLife 2014; 3: e02200.
  Article Google Scholar
• Wei CL, Wu Q, Vega VB, Chiu KP, Ng P, Zhang T et al. A global map of p53 transcription-factor binding sites in the human genome. Cell 2006; 124: 207–219.
  Article CAS Google Scholar
• Wang B, Niu D, Lam TH, Xiao Z, Ren EC . Mapping the p53 transcriptome universe using p53 natural polymorphs. Cell Death Differ 2014; 21: 521–532.
  Article CAS Google Scholar
• Naganuma T, Nakagawa S, Tanigawa A, Sasaki YF, Goshima N, Hirose T . Alternative 3'-end processing of long noncoding RNA initiates construction of nuclear paraspeckles. EMBO J 2012; 31: 4020–4034.
  Article CAS Google Scholar
• Fox AH, Lamond AI . Paraspeckles. Cold Spring Harb Perspect Biol 2010; 2: a000687.
  PubMed PubMed Central Google Scholar
• Salton M, Lerenthal Y, Wang SY, Chen DJ, Shiloh Y . Involvement of Matrin 3 and SFPQ/NONO in the DNA damage response. Cell Cycle 2010; 9: 1568–1576.
  Article CAS Google Scholar
• Rajesh C, Baker DK, Pierce AJ, Pittman DL . The splicing-factor related protein SFPQ/PSF interacts with RAD51D and is necessary for homology-directed repair and sister chromatid cohesion. Nucleic Acids Res 2011; 39: 132–145.
  Article CAS Google Scholar
• Mastrocola AS, Kim SH, Trinh AT, Rodenkirch LA, Tibbetts RS . The RNA-binding protein fused in sarcoma (FUS) functions downstream of poly(ADP-ribose) polymerase (PARP) in response to DNA damage. J Biol Chem 2013; 288: 24731–24741.
  Article CAS Google Scholar
• Yuan M, Eberhart CG, Kai M . RNA binding protein RBM14 promotes radio-resistance in glioblastoma by regulating DNA repair and cell differentiation. Oncotarget 2014; 5: 2820–2826.
  Article Google Scholar
• Chakravarty D, Sboner A, Nair SS, Giannopoulou E, Li R, Hennig S et al. The oestrogen receptor alpha-regulated lncRNA NEAT1 is a critical modulator of prostate cancer. Nat Commun 2014; 5: 5383.
  Article CAS Google Scholar