Whole-exome sequencing in splenic marginal zone lymphoma reveals mutations in genes involved in marginal zone differentiation (original) (raw)

• Schmid C, Kirkham N, Diss T, Isaacson PG . Splenic marginal zone cell lymphoma. Am J Surg Pathol 1992; 16: 455–466.
  CAS PubMed Google Scholar
• Matutes E, Oscier D, Montalban C, Berger F, Callet-Bauchu E, Dogan A et al. Splenic marginal zone lymphoma proposals for a revision of diagnostic, staging and therapeutic criteria. Leukemia 2008; 22: 487–495.
  Article CAS PubMed Google Scholar
• Rinaldi A, Kwee I, Young KH, Zucca E, Gaidano G, Forconi F et al. Genome-wide high resolution DNA profiling of hairy cell leukaemia. Br J Haematol 2013; 162: 566–569.
  Article CAS PubMed Google Scholar
• Robledo C, Garcia JL, Benito R, Flores T, Mollejo M, Martinez-Climent JA et al. Molecular characterization of the region 7q22.1 in splenic marginal zone lymphomas. PLoS One 2011; 6: e24939.
  Article CAS PubMed PubMed Central Google Scholar
• Arribas AJ, Gomez-Abad C, Sanchez-Beato M, Martinez N, Dilisio L, Casado F et al. Splenic marginal zone lymphoma: comprehensive analysis of gene expression and miRNA profiling. Modern Pathol 2013; 26: 889–901.
  Article CAS Google Scholar
• Kiel MJ, Velusamy T, Betz BL, Zhao L, Weigelin HG, Chiang MY et al. Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma. J Exp Med 2012; 209: 1553–1565.
  Article CAS PubMed PubMed Central Google Scholar
• Rossi D, Trifonov V, Fangazio M, Bruscaggin A, Rasi S, Spina V et al. The coding genome of splenic marginal zone lymphoma: activation of NOTCH2 and other pathways regulating marginal zone development. J Exp Med 2012; 209: 1537–1551.
  Article CAS PubMed PubMed Central Google Scholar
• Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H et al. WHO Classification of Tumours of Haematopoietic and Lymphoid Tissues. IARC Press: Lyon, 2008.
  Google Scholar
• Marco-Sola S, Sammeth M, Guigo R, Ribeca P . The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods 2012; 9: 1185–1188.
  Article CAS PubMed Google Scholar
• Homer N, Merriman B, Nelson SF . BFAST: an alignment tool for large scale genome resequencing. PLoS One 2009; 4: e7767.
  Article PubMed PubMed Central Google Scholar
• Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25: 2078–2079.
  Article PubMed PubMed Central Google Scholar
• Derrien T, Estelle J, Marco Sola S, Knowles DG, Raineri E, Guigo R et al. Fast computation and applications of genome mappability. PLoS One 2012; 7: e30377.
  Article CAS PubMed PubMed Central Google Scholar
• Wang K, Li M, Hakonarson H . ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 2010; 38: e164.
  Article PubMed PubMed Central Google Scholar
• Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly 2012; 6: 80–92.
  Article CAS PubMed PubMed Central Google Scholar
• Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 2001; 29: 308–311.
  Article CAS PubMed PubMed Central Google Scholar
• Abecasis GR, Altshuler D, Auton A, Brooks LD, Durbin RM, Gibbs RA et al. A map of human genome variation from population-scale sequencing. Nature 2010; 467: 1061–1073.
  Article PubMed Google Scholar
• Hampel F, Ehrenberg S, Hojer C, Draeseke A, Marschall-Schroter G, Kuhn R et al. CD19-independent instruction of murine marginal zone B-cell development by constitutive Notch2 signaling. Blood 2011; 118: 6321–6331.
  Article CAS PubMed Google Scholar
• Kuroda K, Han H, Tani S, Tanigaki K, Tun T, Furukawa T et al. Regulation of marginal zone B cell development by MINT, a suppressor of Notch/RBP-J signaling pathway. Immunity 2003; 18: 301–312.
  Article CAS PubMed Google Scholar
• Ayoub N, Noma K, Isaac S, Kahan T, Grewal SI, Cohen A . A novel jmjC domain protein modulates heterochromatization in fission yeast. Mol Cell Biol 2003; 23: 4356–4370.
  Article CAS PubMed PubMed Central Google Scholar
• Lai A, Kennedy BK, Barbie DA, Bertos NR, Yang XJ, Theberge MC et al. RBP1 recruits the mSIN3-histone deacetylase complex to the pocket of retinoblastoma tumor suppressor family proteins found in limited discrete regions of the nucleus at growth arrest. Mol Cell Biol 2001; 21: 2918–2932.
  Article CAS PubMed PubMed Central Google Scholar
• Lin D, Ippolito GC, Zong RT, Bryant J, Koslovsky J, Tucker P . Bright/ARID3A contributes to chromatin accessibility of the immunoglobulin heavy chain enhancer. Mol Cancer 2007; 6: 23.
  Article PubMed PubMed Central Google Scholar
• Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann R, Tucker PW . The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev 1995; 9: 3067–3082.
  Article CAS PubMed Google Scholar
• Nixon JC, Rajaiya JB, Ayers N, Evetts S, Webb CF . The transcription factor, Bright, is not expressed in all human B lymphocyte subpopulations. Cell Immunol 2004; 228: 42–53.
  Article CAS PubMed Google Scholar
• Webb CF, Smith EA, Medina KL, Buchanan KL, Smithson G, Dou S . Expression of bright at two distinct stages of B lymphocyte development. J Immunol 1998; 160: 4747–4754.
  CAS PubMed Google Scholar
• Oldham AL, Miner CA, Wang HC, Webb CF . The transcription factor Bright plays a role in marginal zone B lymphocyte development and autoantibody production. Mol Immunol 2011; 49: 367–379.
  Article CAS PubMed PubMed Central Google Scholar
• Cariappa A, Tang M, Parng C, Nebelitskiy E, Carroll M, Georgopoulos K et al. The follicular versus marginal zone B lymphocyte cell fate decision is regulated by Aiolos, Btk, and CD21. Immunity 2001; 14: 603–615.
  Article CAS PubMed Google Scholar
• Nie Y, Waite J, Brewer F, Sunshine MJ, Littman DR, Zou YR . The role of CXCR4 in maintaining peripheral B cell compartments and humoral immunity. J Exp Med 2004; 200: 1145–1156.
  Article CAS PubMed PubMed Central Google Scholar
• Pasqualetto V, Vasseur F, Zavala F, Schneider E, Ezine S . Fas receptor signaling is requisite for B cell differentiation. J Leukoc Biol 2005; 78: 1106–1117.
  Article CAS PubMed Google Scholar
• Lee SY, Kumano K, Nakazaki K, Sanada M, Matsumoto A, Yamamoto G et al. Gain-of-function mutations and copy number increases of Notch2 in diffuse large B-cell lymphoma. Cancer Sci 2009; 100: 920–926.
  Article CAS PubMed Google Scholar
• Varettoni M, Arcaini L, Zibellini S, Boveri E, Rattotti S, Riboni R et al. Prevalence and clinical significance of the MYD88 (L265P) somatic mutation in Waldenstrom's macroglobulinemia and related lymphoid neoplasms. Blood 2013; 121: 2522–2528.
  Article CAS PubMed Google Scholar
• Ruiz-Ballesteros E, Mollejo M, Rodriguez A, Camacho FI, Algara P, Martinez N et al. Splenic marginal zone lymphoma: proposal of new diagnostic and prognostic markers identified after tissue and cDNA microarray analysis. Blood 2005; 106: 1831–1838.
  Article CAS PubMed Google Scholar
• Bourachot B, Yaniv M, Muchardt C . Growth inhibition by the mammalian SWI-SNF subunit Brm is regulated by acetylation. EMBO J 2003; 22: 6505–6515.
  Article CAS PubMed PubMed Central Google Scholar
• Yamamichi N, Yamamichi-Nishina M, Mizutani T, Watanabe H, Minoguchi S, Kobayashi N et al. The Brm gene suppressed at the post-transcriptional level in various human cell lines is inducible by transient HDAC inhibitor treatment, which exhibits antioncogenic potential. Oncogene 2005; 24: 5471–5481.
  Article CAS PubMed Google Scholar
• Nagarajan P, Onami TM, Rajagopalan S, Kania S, Donnell R, Venkatachalam S . Role of chromodomain helicase DNA-binding protein 2 in DNA damage response signaling and tumorigenesis. Oncogene 2009; 28: 1053–1062.
  Article CAS PubMed PubMed Central Google Scholar
• Huang WC, Ju TK, Hung MC, Chen CC . Phosphorylation of CBP by IKKalpha promotes cell growth by switching the binding preference of CBP from p53 to NF-kappaB. Mol Cell 2007; 26: 75–87.
  Article PubMed PubMed Central Google Scholar
• Green MR, Gentles AJ, Nair RV, Irish JM, Kihira S, Liu CL et al. Hierarchy in somatic mutations arising during genomic evolution and progression of follicular lymphoma. Blood 2013; 121: 1604–1611.
  Article CAS PubMed PubMed Central Google Scholar
• Love C, Sun Z, Jima D, Li G, Zhang J, Miles R et al. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet 2012; 44: 1321–1325.
  Article CAS PubMed PubMed Central Google Scholar
• Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature 2011; 476: 298–303.
  Article CAS PubMed PubMed Central Google Scholar
• Mullighan CG, Zhang J, Kasper LH, Lerach S, Payne-Turner D, Phillips LA et al. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 2011; 471: 235–239.
  Article CAS PubMed PubMed Central Google Scholar
• Grossmann V, Tiacci E, Holmes AB, Kohlmann A, Martelli MP, Kern W et al. Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood 2011; 118: 6153–6163.
  Article CAS PubMed Google Scholar
• Ghetu AF, Corcoran CM, Cerchietti L, Bardwell VJ, Melnick A, Prive GG . Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer. Mol Cell 2008; 29: 384–391.
  Article CAS PubMed PubMed Central Google Scholar
• Capparuccia L, Tamagnone L . Semaphorin signaling in cancer cells and in cells of the tumor microenvironment–two sides of a coin. J Cell Sci 2009; 122 (Pt 11): 1723–1736.
  Article CAS PubMed Google Scholar
• Casazza A, Finisguerra V, Capparuccia L, Camperi A, Swiercz JM, Rizzolio S et al. Sema3E-Plexin D1 signaling drives human cancer cell invasiveness and metastatic spreading in mice. J Clin Invest 2010; 120: 2684–2698.
  Article CAS PubMed PubMed Central Google Scholar
• Hou R, Liu L, Anees S, Hiroyasu S, Sibinga NE . The Fat1 cadherin integrates vascular smooth muscle cell growth and migration signals. J Cell Biol 2006; 173: 417–429.
  Article CAS PubMed PubMed Central Google Scholar
• Skouloudaki K, Puetz M, Simons M, Courbard JR, Boehlke C, Hartleben B et al. Scribble participates in Hippo signaling and is required for normal zebrafish pronephros development. Proc Natl Acad Sci USA 2009; 106: 8579–8584.
  Article CAS PubMed PubMed Central Google Scholar
• Morris LG, Kaufman AM, Gong Y, Ramaswami D, Walsh LA, Turcan S et al. Recurrent somatic mutation of FAT1 in multiple human cancers leads to aberrant Wnt activation. Nat Genet 2013; 2745: 253–261.
  Article Google Scholar
• Han S, Witt RM, Santos TM, Polizzano C, Sabatini BL, Ramesh V . Pam (Protein associated with Myc) functions as an E3 ubiquitin ligase and regulates TSC/mTOR signaling. Cell Signal 2008; 20: 1084–1091.
  Article CAS PubMed PubMed Central Google Scholar
• Holland S, Coste O, Zhang DD, Pierre SC, Geisslinger G, Scholich K . The ubiquitin ligase MYCBP2 regulates transient receptor potential vanilloid receptor 1 (TRPV1) internalization through inhibition of p38 MAPK signaling. J Biol Chem 2011; 286: 3671–3680.
  Article CAS PubMed Google Scholar
• Pui CH . T cell acute lymphoblastic leukemia: NOTCHing the way toward a better treatment outcome. Cancer Cell 2009; 15: 85–87.
  Article CAS PubMed Google Scholar