Genome-wide analysis uncovers novel recurrent alterations in primary central nervous system lymphomas

Clinical Cancer Research

Volumn 21, Issue 17, 2015, Pages 3986-3994

  Braggio, Esteban ^a   Van Wier, Scott ^a   Ojha, Juhi ^a   McPhail, Ellen ^b   Asmann, Yan W ^c   Egan, Jan ^a   Da Silva, Jackline Ayres ^d   Schiff, David ^e   Lopes, M Beatriz ^e   Decker, Paul A ^b   Valdez, Riccardo ^a   Tibes, Raoul ^a   Eckloff, Bruce ^b   Witzig, Thomas E ^b   Stewart, A Keith ^a   Fonseca, Rafael ^a   O'Neill, Brian Patrick ^b  

^a MAYO CLINIC   (United States)

^b MAYO CLINIC   (United States)

^c MAYO CLINIC   (United States)

^d National Institute of Cancer   (Brazil)

^e UNIVERSITY OF VIRGINIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

B LYMPHOCYTE INDUCED MATURATION PROTEIN 1; BETA 2 MICROGLOBULIN; CD79B ANTIGEN; CYCLIN DEPENDENT KINASE INHIBITOR 2A; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; LYMPHOCYTE FUNCTION ASSOCIATED ANTIGEN 3; MYELOID DIFFERENTIATION FACTOR 88; PROTEIN KINASE C DELTA;

APOPTOSIS; ARTICLE; B2M GENE; CARD11 GENE; CD58 GENE; CD79B GENE; CDKN2A GENE; CELL PROLIFERATION; CLINICAL ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; CONTROLLED STUDY; GENE; GENE FUNCTION; GENE INACTIVATION; GENE LOSS; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENOME WIDE ANALYSIS; GNA13 GENE; HISTOPATHOLOGY; HUMAN; HUMAN TISSUE; IGH BCL6 GENE; IMMUNE RESPONSE; KARYOTYPE; LARGE CELL LYMPHOMA; MUTATIONAL ANALYSIS; MYD88 GENE; PATHOGENESIS; PRDM1 GENE; PREVALENCE; PRIMARY CENTRAL NERVOUS SYSTEM LYMPHOMA; PRIORITY JOURNAL; PRKCD GENE; SIGNAL TRANSDUCTION; TBL1XR1 GENE; TMEM30A GENE; TNFAIP3 GENE; TOX GENE; WHOLE EXOME SEQUENCING; CENTRAL NERVOUS SYSTEM TUMOR; CHROMOSOME 6; CHROMOSOME ABERRATION; COPY NUMBER VARIATION; EXOME; GENETIC VARIATION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; HIGH THROUGHPUT SEQUENCING; METABOLISM; MORTALITY; MUTATION; NONHODGKIN LYMPHOMA; PROGNOSIS;

CENTRAL NERVOUS SYSTEM NEOPLASMS; CHROMOSOME ABERRATIONS; CHROMOSOMES, HUMAN, PAIR 6; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; EXOME; GENETIC VARIATION; GENOME-WIDE ASSOCIATION STUDY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; KARYOTYPE; LYMPHOMA, NON-HODGKIN; MUTATION; PROGNOSIS;

EID: 84939563989     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-14-2116     Document Type: Article

References (49)

1. Swerdlow SH, Campo E, Harris NL, Jaffe ES, Pileri SA, Stein H, et al. WHO classification of tumours of haematopoietic and lymphoid tissues. 4th ed. Lyon, France: IARC Press; 2008.
2. Richter J, Ammerpohl O, Martin-Subero JI, Montesinos-Rongen M, Bibikova M, Wickham-Garcia E, et al. Array-based DNA methylation profiling of primary lymphomas of the central nervous system. BMC Cancer 2009;9:455.
3. Schwindt H, Vater I, Kreuz M, Montesinos-Rongen M, Brunn A, Richter J, et al. Chromosomal imbalances and partial uniparental disomies in primary central nervous system lymphoma. Leukemia 2009;23:1875-84.
4. Braggio E, McPhail ER, Macon W, Lopes MB, Schiff D, Law M, et al. Primary central nervous system lymphomas: a validation study of array-based comparative genomic hybridization in formalin-fixed paraffin-embedded tumor specimens. Clin Cancer Res 2011;17:4245-53.
5. Gonzalez-Aguilar A, Idbaih A, Boisselier B, Habbita N, Rossetto M, Laurenge A, et al. Recurrent mutations of MYD88 and TBL1XR1 in primary central nervous system lymphomas. Clin Cancer Res 2012;18:5203-11.
6. Courts C, Montesinos-Rongen M, Brunn A, Bug S, Siemer D, Hans V, et al. Recurrent inactivation of the PRDM1 gene in primary central nervous system lymphoma. J Neuropathol Exp Neurol 2008;67:720-7.
7. Montesinos-Rongen M, Schmitz R, Brunn A, Gesk S, Richter J, Hong K, et al. Mutations of CARD11 but not TNFAIP3 may activate the NF-kappaB pathway in primary CNS lymphoma. Acta Neuropathol 2010;120:529-35.
8. Montesinos-Rongen M, Zuhlke-Jenisch R, Gesk S, Martin-Subero JI, Schaller C, Van Roost D, et al. Interphase cytogenetic analysis of lymphoma-associated chromosomal breakpoints in primary diffuse large B-cell lymphomas of the central nervous system. J Neuropathol Exp Neurol 2002;61:926-33.
9. Booman M, Szuhai K, Rosenwald A, Hartmann E, Kluin-Nelemans H, de Jong D, et al. Genomic alterations and gene expression in primary diffuse large B-cell lymphomas of immune-privileged sites: the importance of apoptosis and immunomodulatory pathways. J Pathol 2008;216:209-17.
10. Sung CO, Kim SC, Karnan S, Karube K, Shin HJ, Nam DH, et al. Genomic profiling combined with gene expression profiling in primary central nervous system lymphoma. Blood 2011;117:1291-300.
11. Montesinos-Rongen M, Brunn A, Bentink S, Basso K, Lim WK, Klapper W, et al. Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell. Leukemia 2008;22:400-5.
12. Rubenstein JL, Fridlyand J, Shen A, Aldape K, Ginzinger D, Batchelor T, et al. Gene expression and angiotropism in primary CNS lymphoma. Blood 2006;107:3716-23.
13. Tun HW, Personett D, Baskerville KA, Menke DM, Jaeckle KA, Kreinest P, et al. Pathway analysis of primary central nervous system lymphoma. Blood 2008;111:3200-10.
14. Ferreri AJ. How I treat primary CNS lymphoma. Blood 2011;118:510-22.
15. Braggio E, Keats JJ, Leleu X, Van Wier S, Jimenez-Zepeda VH, Valdez R, et al. Identification of copy numberabnormalitiesand inactivating mutations in two negative regulators of nuclear factor-kappaB signaling pathways in Waldenstrom's macroglobulinemia. Cancer Res 2009;69:3579-88.
16. Kay NE, Eckel-Passow JE, Braggio E, Vanwier S, Shanafelt TD, Van Dyke DL, et al. Progressive but previously untreated CLL patients with greater array CGH complexity exhibitalessdurable responsetochemoimmunotherapy. Cancer Genet Cytogenet 2011;203:161-8.
17. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20: 1297-303.
18. Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 2012;28:311-7.
19. Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods 2010;7:248-9.
20. Pek JW, Kai T. DEAD-box RNA helicase Belle/DDX3 and the RNA interference pathway promote mitotic chromosome segregation. Proc Natl Acad Sci U S A 2011;108:12007-12.
21. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, et al. Integrative genomics viewer. Nat Biotechnol 2011;29:24-6.
22. Rothberg JM, Hinz W, Rearick TM, Schultz J, Mileski W, Davey M, et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011;475:348-52.
23. Cataldo KA, Jalal SM, Law ME, Ansell SM, Inwards DJ, Fine M, et al. Detection of t(2;5) in anaplastic large cell lymphoma: comparison of immunohistochemical studies, FISH, and RT-PCR in paraffin-embedded tissue. Am J Surg Pathol 1999;23:1386-92.
24. Remstein ED, Dogan A, Einerson RR, Paternoster SF, Fink SR, Law M, et al. The incidence and anatomic site specificity of chromosomal translocations in primary extranodal marginal zone B-cell lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) in North America. Am J Surg Pathol 2006;30:1546-53.
25. Montesinos-Rongen M, Godlewska E, Brunn A, Wiestler OD, Siebert R, Deckert M. Activating L265P mutations of the MYD88 gene are common in primary central nervous system lymphoma. Acta Neuropathol 2011;122: 791-2.
26. Cady FM, O'Neill BP, Law ME, Decker PA, Kurtz DM, Giannini C, et al. Del (6)(q22) and BCL6 rearrangements in primary CNS lymphoma are indicators of an aggressive clinical course. J Clin Oncol 2008;26:4814-9.
27. Montesinos-Rongen M, Schafer E, Siebert R, Deckert M. Genes regulating the B cell receptor pathway are recurrently mutated in primary central nervous system lymphoma. Acta Neuropathol 2012;124:905-6.
28. Mischak H, Goodnight JA, Kolch W, Martiny-Baron G, Schaechtle C, Kazanietz MG, et al. Overexpression of protein kinase C-delta and -epsilon in NIH 3T3 cells induces opposite effects on growth, morphology, anchorage dependence, and tumorigenicity. J Biol Chem 1993;268: 6090-6.
29. Pessino A, Passalacqua M, Sparatore B, Patrone M, Melloni E, Pontremoli S. Antisense oligodeoxynucleotide inhibition of delta protein kinase C expression accelerates induced differentiation of murine erythroleukaemia cells. Biochem J 1995;312 (Pt 2):549-54.
30. Ghayur T, Hugunin M, Talanian RV, Ratnofsky S, Quinlan C, Emoto Y, et al. Proteolytic activation of protein kinase C delta byanICE/CED 3-like protease induces characteristics of apoptosis. J Exp Med 1996;184:2399-404.
31. Lu Z, Hornia A, Jiang YW, Zang Q, Ohno S, Foster DA. Tumor promotion by depleting cells of protein kinase C delta. Mol Cell Biol 1997; 17:3418-28.
32. Kuehn HS, Niemela JE, Rangel-Santos A, Zhang M, Pittaluga S, Stoddard JL, et al. Loss-of-function of the protein kinase C delta (PKCdelta) causes a B-cell lymphoproliferative syndrome in humans. Blood 2013;121: 3117-25.
33. Belot A, Kasher PR, Trotter EW, Foray AP, Debaud AL, Rice GI, et al. Protein kinase cdelta deficiency causes mendelian systemic lupus erythematosus with B cell-defective apoptosis and hyperproliferation. Arthritis Rheum 2013;65:2161-71.
34. Miyamoto A, Nakayama K, Imaki H, Hirose S, Jiang Y, Abe M, et al. Increased proliferation of B cells and auto-immunity in mice lacking protein kinase Cdelta. Nature 2002;416:865-9.
35. Limnander A, Depeille P, Freedman TS, Liou J, Leitges M, Kurosaki T, et al. STIM1, PKC-delta and RasGRP set a threshold for proapoptotic Erk signaling during B cell development. Nat Immunol 2011;12:425-33.
36. Ke G, Liang L, Yang JM, Huang X, Han D, Huang S, et al. MiR-181a confers resistance of cervical cancer to radiation therapy through targeting the proapoptotic PRKCD gene. Oncogene 2013;32:3019-27.
37. Aliahmad P, O'Flaherty E, Han P, Goularte OD, Wilkinson B, Satake M, et al. TOX provides a link between calcineurin activation and CD8 lineage commitment. J Exp Med 2004;199:1089-99.
38. Wilkinson B, Chen JY, Han P, Rufner KM, Goularte OD, Kaye J. TOX: an HMG box protein implicated in the regulation of thymocyte selection. Nat Immunol 2002;3:272-80.
39. Aliahmad P, Kaye J. Development of all CD4 T lineages requires nuclear factor TOX. J Exp Med 2008;205:245-56.
40. Aliahmad P, de la Torre B, Kaye J. Shared dependence on the DNA-binding factor TOX for the development of lymphoid tissue-inducer cell and NK cell lineages. Nat Immunol 2010;11:945-52.
41. Descatoire M, Weller S, Irtan S, Sarnacki S, Feuillard J, Storck S, et al. Identification of a human splenic marginal zone B cell precursor with NOTCH2-dependent differentiation properties. J Exp Med 2014;211: 987-1000.
42. Ngo VN, Young RM, Schmitz R, Jhavar S, Xiao W, Lim KH, et al. Oncogenically active MYD88 mutations in human lymphoma. Nature 2011; 470:115-9.
43. Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, Villamor N, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011;475:101-5.
44. Quesada V, Conde L, Villamor N, Ordonez GR, Jares P, Bassaganyas L, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 2012;44:47-52.
45. Wang L, Lawrence MS, Wan Y, Stojanov P, Sougnez C, Stevenson K, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med 2011;365:2497-506.
46. Treon SP, Xu L, Yang G, Zhou Y, Liu X, Cao Y, et al. MYD88 L265P somatic mutation in Waldenstrom's macroglobulinemia. N Engl J Med 2012;367: 826-33.
47. 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;121:2522-8.
48. Xu L, Hunter ZR, Yang G, Zhou Y, Cao Y, Liu X, et al. MYD88 L265P in Waldenstrom macroglobulinemia, immunoglobulin M monoclonal gammopathy, and other B-cell lymphoproliferative disorders using conventional and quantitative allele-specific polymerase chain reaction. Blood 2013;121:2051-8.
49. Kraan W, Horlings HM, van Keimpema M, Schilder-Tol EJ, Oud ME, Scheepstra C, et al. High prevalence of oncogenic MYD88 and CD79B mutations in diffuse large B-cell lymphomas presenting at immune-privileged sites. Blood Cancer J 2013;3:e139.