Recurrent targets of aberrant somatic hypermutation in lymphoma

Oncotarget

Volumn 3, Issue 11, 2012, Pages 1308-1319

  Khodabakhshi, Alireza Hadj ^a   Morin, Ryan D ^a   Fejes, Anthony P ^a   Mungall, Andrew J ^a   Mungall, Karen L ^a   Bolger Munro, Madison ^a   Johnson, Nathalie A ^b   Connors, Joseph M ^b   Gascoyne, Randy D ^b,c   Marra, Marco A ^a,c   Birol, Inanc ^a   Jones, Steven J M ^a,c,d  

^a CANADA'S MICHAEL SMITH GENOME SCIENCES CENTRE   (Canada)

^b BRITISH COLUMBIA CANCER AGENCY   (Canada)

^c UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^d SIMON FRASER UNIVERSITY   (Canada)

Author keywords

Aberrant somatic hypermutation; Diffuse large B cell lymphoma; Genome wide study; Genomic rearrangements

Indexed keywords

CD38 ANTIGEN; CD74 ANTIGEN; IMMUNOGLOBULIN; INTERFERON REGULATORY FACTOR 4; MESSENGER RNA; SERUM AND GLUCOCORTICOID REGULATED KINASE 1; SUPPRESSOR OF CYTOKINE SIGNALING 1; TRANSCRIPTOME;

ABERRANT SOMATIC HYPERMUTATION; ARTICLE; BCL7A GENE; BTG1 GENE; BTG2 GENE; CD38 GENE; CD74 GENE; CHROMOSOME TRANSLOCATION; CIITA GENE; CLINICAL ARTICLE; CONTROLLED STUDY; CR607557 GENE; GENE LOCUS; GENE REARRANGEMENT; GENE TARGETING; GENETIC IDENTIFICATION; GENETIC SCREENING; GENOMICS; HIST1H2AC GENE; HUMAN; IRF4 GENE; LARGE CELL LYMPHOMA; LTB GENE; MUTATION RATE; PROTO ONCOGENE; RHOH GENE; SGK1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SOCS1 GENE; SOMATIC HYPERMUTATION; TMSB4X GENE; TRANSCRIPTOMICS; ZFP36L1 GENE;

EID: 84872779378     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.653     Document Type: Article

References (47)

1. Muschen M, Re D, Jungnickel B, Diehl V, Rajewsky K, Kuppers R. Somatic mutation of the CD95 gene in human B cells as a side-effect of the germinal center reaction. J. Exp. Med. 2000; 192:1833-1840.
2. Pasqualucci L, Migliazza A, Fracchiolla N, William C, Neri A, Baldini L, Chaganti RS, Klein U, Kuppers R, Rajewsky K, Dalla-Favera R. BCL-6 mutations in normal germinal center B cells: evidence of somatic hypermutation acting outside Ig loci. Proc. Natl. Acad. Sci. U.S.A. 1998; 95:11816-11821.
3. Di Noia JM, Neuberger MS. Molecular mechanisms of antibody somatic hypermutation. Annu. Rev. Biochem. 2007; 76:1-22.
4. Neuberger MS, Harris RS, Di Noia J, Petersen-Mahrt SK. Immunity through DNA deamination. Trends Biochem. Sci. 2003; 28:305-312.
5. Odegard VH, Schatz DG. Targeting of somatic hypermutation. Nat. Rev. Immunol. 2006; 6:573-583.
6. Storb U, Peters A, Klotz E, Kim N, Shen HM, Hackett J, Rogerson B, Martin TE. Cis-acting sequences that affect somatic hypermutation of Ig genes. Immunol. Rev. 1998; 162:153-160.
7. Rada C, Milstein C. The intrinsic hypermutability of antibody heavy and light chain genes decays exponentially. EMBO J. 2001; 20:4570-4576.
8. Rossi D, Cerri M, Capello D, Deambrogi C, Berra E, Franceschetti S, Alabiso O, Gloghini A, Paulli M, Carbone A, Pileri SA, Pasqualucci L, Gaidano G. Aberrant somatic hypermutation in primary mediastinal large B-cell lymphoma. Leukemia. 2005; 19:2363-2366.
9. Rogozin IB, Diaz M. Cutting edge: DGYW/WRCH is a better predictor of mutability at G:C bases in Ig hypermutation than the widely accepted RGYW/WRCY motif and probably reflects a two-step activation-induced cytidine deaminase-triggered process. J. Immunol. 2004; 172:3382-3384.
10. Unniraman S, Schatz DG. Strand-biased spreading of mutations during somatic hypermutation. Science. 2007; 317:1227-1230.
11. Liso A, Capello D, Marafioti T, Tiacci E, Cerri M, Distler V, Paulli M, Carbone A, Delsol G, Campo E, Pileri S, Pasqualucci L, Gaidano G, Falini B. Aberrant somatic hypermutation in tumor cells of nodular-lymphocyte-predominant and classic Hodgkin lymphoma. Blood. 2006; 108:1013-1020.
12. Pasqualucci L, Neumeister P, Goossens T, Nanjangud G, Chaganti RS, Kuppers R, Dalla-Favera R. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature. 2001; 412:341-346.
13. Lenz G, Staudt LM. Aggressive lymphomas. N. Engl. J. Med., 362:1417-1429, Apr 2010.
14. Liu M, Duke JL, Richter DJ, Vinuesa CG, Goodnow CC, Kleinstein SH, Schatz DG. Two levels of protection for the B cell genome during somatic hypermutation. Nature. 2008; 451:841-845.
15. Kuppers R, Dalla-Favera R. Mechanisms of chromosomal translocations in B cell lymphomas. Oncogene. 2001; 20:5580-5594.
16. Goossens T, Klein U, Kuppers R. Frequent occurrence of deletions and duplications during somatic hypermutation: implications for oncogene translocations and heavy chain disease. Proc. Natl. Acad. Sci. U.S.A. 1998; 95:2463-2468.
17. Pasqualucci L, Guglielmino R, Malek SN, et al. Aberrant somatic hypermutation targets an extensive set of genes in diffuse large B-cell lymphoma. Blood (ASH Annual Meeting Abstracts). 2004; 104:1528.
18. Saito M, Novak U, Piovan E, Basso K, Sumazin P, Schneider C, Crespo M, Shen Q, Bhagat G, Califano A, Chadburn A, Pasqualucci L, Dalla-Favera R. BCL6 suppression of BCL2 via Miz1 and its disruption in diffuse large B cell lymphoma. Proc. Natl. Acad. Sci. U.S.A. 2009; 106:11294-11299.
19. Mottok A, Renne C, Seifert M, Oppermann E, Bechstein W, Hansmann ML, Kuppers R, Brauninger A. Inactivating SOCS1 mutations are caused by aberrant somatic hypermutation and restricted to a subset of B-cell lymphoma entities. Blood. 2009; 114:4503-4506.
20. Hsu F, Kent WJ, Clawson H, Kuhn RM, Diekhans M, Haussler D. The UCSC Known Genes. Bioinformatics. 2006; 22:1036-1046.
21. Auer RL, Starczynski J, McElwaine S, Bertoni F, Newland AC, Fegan CD, Cotter FE. Identification of a potential role for POU2AF1 and BTG4 in the deletion of 11q23 in chronic lymphocytic leukemia. Genes Chromosomes Cancer; 2005. 43(1):1-10.
22. Turkmen S, Riehn M, Klopocki E, Molkentin M, Reinhardt R, Burmeister T. A BACH2-BCL2L1 fusion gene resulting from a t(6;20)(q15;q11.2) chromosomal translocation in the lymphoma cell line BLUE-1. Genes Chromosomes Cancer. 2011; 50:389-396.
23. Kobayashi S, Taki T, Chinen Y, Tsutsumi Y, Ohshiro M, Kobayashi T, Matsumoto Y, Kuroda J, Horiike S, Nishida K, Taniwaki M. Identification of IGHCI-BACH2 fusion transcripts resulting from cryptic chromosomal rearrangements of 14q32 with 6q15 in aggressive B-cell lymphoma/leukemia. Genes Chromosomes Cancer. 2011; 50:207-216.
24. Bachl J, Carlson C, Gray-Schopfer V, Dessing M, Olsson C. Increased transcription levels induce higher mutation rates in a hypermutating cell line. J. Immunol. 2001; 166:5051-5057.
25. Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, et al. De novo assembly and analysis of RNA-seq data. Nat. Methods. 2010; 7:909-912.
26. Lo Coco F, Ye BH, Lista F, Corradini P, Offit K, Knowles DM, Chaganti RS, Dalla-Favera R. Rearrangements of the BCL6 gene in diffuse large cell non-Hodgkin's lymphoma. Blood. 1994; 83:1757-1759.
27. Willis TG, Dyer MJ. The role of immunoglobulin translocations in the pathogenesis of B-cell malignancies. Blood. 2000; 96:808-822.
28. Higgins ME, Claremont M, Major JE, Sander C, Lash AE. CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res., 35:D721-726, Jan 2007.
29. Futreal PA, Coin L, Marshall M, Down T, Hubbard T, Wooster R, Rahman N, Stratton MR. A census of human cancer genes. Nat. Rev. Cancer. 2004; 4:177-183.
30. Nummela P, Yin M, Kielosto M, Leaner V, Birrer MJ, Holtta E. Thymosin beta4 is a determinant of the transformed phenotype and invasiveness of S-adenosylmethionine decarboxylase-transfected fibroblasts. Cancer Res. 2006; 66:701-712.
31. Frazer JK, Jackson DG, Gaillard JP, Lutter M, Liu YJ, Banchereau J, Capra JD, Pascual V. Identification of centerin: a novel human germinal center B cell-restricted serpin. Eur. J. Immunol. 2000; 30:3039-3048.
32. Warzocha K, Renard N, Charlot C, Bienvenu J, Coiffier B, Salles G. Identification of two lymphotoxin beta isoforms expressed in human lymphoid cell lines and non-Hodgkin's lymphomas. Biochem. Biophys. Res. Commun. 1997; 238:273-276.
33. Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, Jia M, Shepherd R, Leung K, Menzies A, Teague JW, Campbell PJ, Stratton MR, Futreal PA. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011; 39:D945-950.
34. Morin RD, Mendez-Lago M, Mungall AJ, Goya R, Mungall KL, Corbett RD, Johnson NA, Severson TM, Chiu R, Field M, Jackman S, Krzywinski M, Scott DW, Trinh DL, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011; 476:298-303.
35. Compagno M, Lim WK, Grunn A, Nandula SV, Brahmachary M, Shen Q, Bertoni F, Ponzoni M, Scandurra M, Califano A, Bhagat G, Chadburn A, Dalla-Favera R, Pasqualucci L. Mutations of multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 2009; 459:717-721.
36. Du MQ, Peng H, Liu H, Hamoudi RA, Diss TC, Willis TG, Ye H, Dogan A, Wotherspoon AC, Dyer MJ, Isaacson PG. BCL10 gene mutation in lymphoma. Blood. 2000; 95:3885-3890.
37. Eis PS, Tam W, Sun L, Chadburn A, Li Z, Gomez MF, Lund E, Dahlberg JE. Accumulation of miR-155 and BIC RNA in human B cell lymphomas. Proc. Natl. Acad. Sci. U.S.A. 2005; 102:3627-3632.
38. Huang W., Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensiveanalysis of large gene lists. Nucleic Acids Res. 2009; 37:1-13.
39. Lenz G, Wright GW, Emre NC, Kohlhammer H, Dave SS, Davis RE, Carty S, Lam LT, Shaffer AL, Xiao W, Powell J, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, et al. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc. Natl. Acad. Sci. U.S.A. 2008; 105:13520-13525.
40. Mottok A, Renne C, Willenbrock K, Hansmann ML, Brauninger A. Somatic hypermutation of SOCS1 in lymphocyte-predominant Hodgkin lymphoma is accompanied by high JAK2 expression and activation of STAT6. Blood. 2007; 110:3387-3390.
41. Pasqualucci L, Trifonov V, Fabbri G, Ma J, Rossi D, Chiarenza A, Wells VA, Grunn A, Messina M, Elliot O, Chan J, Bhagat G, Chadburn A, Gaidano G, Mullighan CG, Rabadan R, Dalla-Favera R. Analysis of the coding genome of diffuse large B-cell lymphoma. Nat. Genet. 2011; 43:830-837.
42. Pasqualucci L, Compagno M, Houldsworth J, Monti S, Grunn A, Nandula SV, Aster JC, Murty VV, Shipp MA, Dalla-Favera R. Inactivation of the PRDM1/BLIMP1 gene in diffuse large B cell lymphoma. J. Exp. Med. 2006; 203:311-317.
43. Rui L, Schmitz R, Ceribelli M, Staudt LM. Malignant pirates of the immune system. Nat. Immunol. 2011; 12:933-940.
44. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26:589-595.
45. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25:2078-2079.
46. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Methods. 2008; 5:621-628.
47. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA. Circos: an information aesthetic for comparative genomics. Genome Res. 2009; 19:1639-1645.