Variability in DNA methylation defines novel epigenetic subgroups of DLBCL associated with different clinical outcomes

Blood

Volumn 123, Issue 11, 2014, Pages 1699-1708

  Chambwe, Nyasha ^a   Kormaksson, Matthias ^a,b   Geng, Huimin ^c   De, Subhajyoti ^d,e,f   Michor, Franziska ^g,h   Johnson, Nathalie A ⁱ   Morin, Ryan D ^j,k   Scott, David W ^k   Godley, Lucy A ^l   Gascoyne, Randy D ^k,m   Melnick, Ari ⁿ   Campagne, Fabien ^a   Shaknovich, Rita ⁿ  

^a WEILL CORNELL MEDICAL CENTER   (United States)

^b IBM RESEARCH   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d UNIVERSITY OF COLORADO SCHOOL OF MEDICINE   (United States)

^e Global Health and Health Disparities   (United States)

^f UNIVERSITY OF COLORADO CANCER CENTER   (United States)

^g DANA FARBER CANCER INSTITUTE   (United States)

^h HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

ⁱ MCGILL UNIVERSITY   (Canada)

^j SIMON FRASER UNIVERSITY   (Canada)

^k BRITISH COLUMBIA CANCER AGENCY   (Canada)

^l UNIVERSITY OF CHICAGO   (United States)

^m UNIVERSITY OF BRITISH COLUMBIA   (Canada)

ⁿ WEILL CORNELL MEDICAL COLLEGE   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

EPHRIN;

APOPTOSIS; ARTICLE; B LYMPHOCYTE; CELL CYCLE REGULATION; DNA HYBRIDIZATION; DNA METHYLATION; EPIGENETICS; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GERMINAL CENTER; HUMAN; HUMAN CELL; LARGE CELL LYMPHOMA; MAJOR CLINICAL STUDY; OVERALL SURVIVAL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROGRESSION FREE SURVIVAL; PROMOTER REGION; SIGNAL TRANSDUCTION;

CASE-CONTROL STUDIES; CELLS, CULTURED; DNA METHYLATION; EPIGENESIS, GENETIC; FOLLOW-UP STUDIES; GENE EXPRESSION REGULATION, NEOPLASTIC; GENETIC VARIATION; HUMANS; LYMPHOMA, LARGE B-CELL, DIFFUSE; NEOPLASM PROTEINS; PROGNOSIS; SURVIVAL RATE;

EID: 84897498688     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2013-07-509885     Document Type: Article

References (53)

1. Alizadeh AA, Eisen MB, Davis RE, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403(6769):503-511. (Pubitemid 30082188)
2. Rosenwald A, Wright G, Leroy K, et al. Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma. J Exp Med. 2003;198(6):851-862. (Pubitemid 37152922)
3. Dunleavy K, Grant C, Wilson WH. Using biologic predictive factors to direct therapy of diffuse large B-cell lymphoma. Ther Adv Hematol. 2013;4(1):43-57.
4. Rosenwald A, Staudt LM. Gene expression profiling of diffuse large B-cell lymphoma. Leuk Lymphoma. 2003;44(Suppl 3):S41-S47. (Pubitemid 38196062)
5. Fernandez AF, Assenov Y, Martin-Subero JI, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012;22(2):407-419.
6. Kulis M, Heath S, Bibikova M, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet. 2012;44(11):1236-1242.
7. Taylor KH, Briley A, Wang Z, Cheng J, Shi H, Caldwell CW. Aberrant epigenetic gene regulation in lymphoid malignancies. Semin Hematol. 2013;50(1):38-47.
8. Klose RJ, Bird AP. Genomic DNA methylation: the mark and its mediators. Trends Biochem Sci. 2006;31(2):89-97. (Pubitemid 43221841)
9. Ubeda F, Wilkins JF. Imprinted genes and human disease: an evolutionary perspective. Adv Exp Med Biol. 2008;626:101-115.
10. Carmona FJ, Esteller M. DNA methylation in early neoplasia. Cancer Biomark. 2010;9(1-6):101-111.
11. Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003;349(21):2042-2054. (Pubitemid 37448928)
12. Xiong H-L, Liu X-Q, Sun A-H, He Y, Li J, Xia Y. Aberrant DNA methylation of P16, MGMT, hMLH1 and hMSH2 genes in combination with the MTHFR C677T genetic polymorphism in gastric cancer. Asian Pac J Cancer Prev. 2013;14(5):3139-3142.
13. Oricchio E, Nanjangud G, Wolfe AL, et al. The Eph-receptor A7 is a soluble tumor suppressor for follicular lymphoma. Cell. 2011;147(3):554-564.
14. Esteller M, Gaidano G, Goodman SN, et al. Hypermethylation of the DNA repair gene O(6)-methylguanine DNA methyltransferase and survival of patients with diffuse large B-cell lymphoma. J Natl Cancer Inst. 2002;94(1):26-32.
15. Lee SMSH, Lee EJ, Ko Y-H, Lee SH, Maeng L, Kim KM. Prognostic significance of O6-methylguanine DNA methyltransferase and p57 methylation in patients with diffuse large B-cell lymphomas. APMIS. 2009;117(2):87-94.
16. Shaknovich R, Geng H, Johnson NA, et al. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma. Blood. 2010;116(20):e81-e89.
17. Pike BL, Greiner TC, Wang X, et al. DNA methylation profiles in diffuse large B-cell lymphoma and their relationship to gene expression status. Leukemia. 2008;22(5):1035-1043. (Pubitemid 351689886)
18. Wang X-M, Greiner TC, Bibikova M, et al. Identification and functional relevance of de novo DNA methylation in cancerous B-cell populations. J Cell Biochem. 2010;109(4):818-827.
19. Hansen KD, Timp W, Bravo HC, et al. Increased methylation variation in epigenetic domains across cancer types. Nat Genet. 2011;43(8):768-775.
20. De S, Shaknovich R, Riester M, et al. Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity. PLoS Genet. 2013;9(1):e1003137.
21. Khulan B, Thompson RF, Ye K, et al. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res. 2006;16(8):1046-1055. (Pubitemid 44162264)
22. Shaknovich R, Figueroa ME, Melnick A. HELP (HpaII tiny fragment enrichment by ligation-mediated PCR) assay for DNA methylation profiling of primary normal and malignant B lymphocytes. Methods Mol Biol. 2010;632:191-201.
23. Thompson RF, Reimers M, Khulan B, et al. An analytical pipeline for genomic representations used for cytosine methylation studies. Bioinformatics. 2008;24(9):1161-1167. (Pubitemid 351594165)
24. Figueroa ME, Abdel-Wahab O, Lu C, et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553-567.
25. Martín-Subero JI, Kreuz M, Bibikova M, et al Molecular Mechanisms in Malignant Lymphomas Network Project of the Deutsche Krebshilfe. New insights into the biology and origin of mature aggressive B-cell lymphomas by combined epigenomic, genomic, and transcriptional profiling. Blood. 2009;113(11):2488- 2497.
26. Velichutina I, Shaknovich R, Geng H, et al. EZH2-mediated epigenetic silencing in germinal center B cells contributes to proliferation and lymphomagenesis. Blood. 2010;116(24):5247-5255.
27. Beroukhim R, Getz G, Nghiemphu L, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A. 2007;104(50):20007-20012.
28. Lenz G, Wright GW, Emre NCT, et al. Molecular subtypes of diffuse large B-cell lymphoma arise by distinct genetic pathways. Proc Natl Acad Sci U S A. 2008;105(36):13520-13525.
29. Motoyama M, Yamazaki S, Eto-Kimura A, Takeshige K, Muta T. Positive and negative regulation of nuclear factor-kappaB-mediated transcription by IkappaB-zeta, an inducible nuclear protein. J Biol Chem. 2005;280(9):7444-7451. (Pubitemid 40349635)
30. Turner CA Jr, Mack DH, Davis MM. Blimp-1, a novel zinc finger-containing protein that can drive the maturation of B lymphocytes into immunoglobulin- secreting cells. Cell. 1994;77(2):297-306. (Pubitemid 24138626)
31. Nitta T, Takahama Y. The lymphocyte guard-IANs: regulation of lymphocyte survival by IAN/GIMAP family proteins. Trends Immunol. 2007;28(2):58-65. (Pubitemid 46176732)
32. Béguelin W, Popovic R, Teater M, et al. EZH2 is required for germinal center formation and somatic EZH2 mutations promote lymphoid transformation. Cancer Cell. 2013;23(5):677-692.
33. Morin RD, Johnson NA, Severson TM, et al. Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet. 2010;42(2):181-185.
34. Morin RD, Mendez-Lago M, Mungall AJ, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature. 2011;476(7360):298-303.
35. Guney S, Jardin F, Bertrand P, et al. Several mechanisms lead to the inactivation of the CDKN2A (P16), P14ARF, or CDKN2B (P15) genes in the GCB and ABC molecular DLBCL subtypes. Genes Chromosomes Cancer. 2012;51(9):858-867.
36. Zainuddin N, Kanduri M, Berglund M, et al. Quantitative evaluation of p16(INK4a) promoter methylation using pyrosequencing in de novo diffuse large B-cell lymphoma. Leuk Res. 2011;35(4):438-443.
37. Uccella S, Cerutti R, Placidi C, et al. MGMT methylation in diffuse large B-cell lymphoma: validation of quantitative methylation-specific PCR and comparison with MGMT protein expression. J Clin Pathol. 2009;62(8):715-723.
38. Lee G-W, Kang J-H, Kim I-S, et al. Is inactivation of O6-methylguanine DNA methyltransferase still a favorable prognostic factor of patients with diffuse large B-cell lymphoma in the era of R-CHOP chemotherapy? Leuk Lymphoma. 2009;50(12):1992-1998.
39. Lai AY, Fatemi M, Dhasarathy A, et al. DNA methylation prevents CTCF-mediated silencing of the oncogene BCL6 in B cell lymphomas. J Exp Med. 2010;207(9):1939-1950.
40. Figueroa ME, Lugthart S, Li Y, et al. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010;17(1):13-27.
41. Lugthart S, Figueroa ME, Bindels E, et al. Aberrant DNA hypermethylation signature in acute myeloid leukemia directed by EVI1. Blood. 2011;117(1):234-241.
42. Lu C, Ward PS, Kapoor GS, et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature. 2012;483(7390):474-478.
43. Ley TJ, Ding L, Walter MJ, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424-2433.
44. Yan X-J, Xu J, Gu Z-H, et al. Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia. Nat Genet. 2011;43(4):309-315.
45. Delhommeau F, Dupont S, Della Valle V, et al. Mutation in TET2 in myeloid cancers. N Engl J Med. 2009;360(22):2289-2301.
46. Amara K, Ziadi S, Hachana M, Soltani N, Korbi S, Trimeche M. DNA methyltransferase DNMT3b protein overexpression as a prognostic factor in patients with diffuse large B-cell lymphomas. Cancer Sci. 2010;101(7):1722-1730.
47. Ranuncolo SM, Polo JM, Dierov J, et al. Bcl-6 mediates the germinal center B cell phenotype and lymphomagenesis through transcriptional repression of the DNA-damage sensor ATR. Nat Immunol. 2007;8(7):705-714. (Pubitemid 46965346)
48. Bea S, Zettl A, Wright G, et al Lymphoma/Leukemia Molecular Profiling Project. Diffuse large B-cell lymphoma subgroups have distinct genetic profiles that influence tumor biology and improve gene-expression-based survival prediction. Blood. 2005;106(9):3183-3190. (Pubitemid 41565917)
49. Gelsi-Boyer V, Brecqueville M, Devillier R, Murati A, Mozziconacci M-J, Birnbaum D. Mutations in ASXL1 are associated with poor prognosis across the spectrum of malignant myeloid diseases. J Hematol Oncol. 2012;5(1):12.
50. Baur AS, Shaw P, Burri N, Delacrétaz F, Bosman FT, Chaubert P. Frequent methylation silencing of p15(INK4b) (MTS2) and p16(INK4a) (MTS1) in B-cell and T-cell lymphomas. Blood. 1999;94(5):1773-1781. (Pubitemid 29411328)
51. Guney S, Bertrand P, Jardin F, et al. Molecular characterization of 9p21 deletions shows a minimal common deleted region removing CDKN2A exon 1 and CDKN2B exon 2 in diffuse large B-cell lymphomas. Genes Chromosomes Cancer. 2011;50(9):715-725.
52. Sánchez-Beato M, Sáez AI, Martínez-Montero JC, et al. Cyclin-dependent kinase inhibitor p27KIP1 in lymphoid tissue: p27KIP1 expression is inversely proportional to the proliferative index. Am J Pathol. 1997;151(1):151-160.
53. Go JH. Expressions of the CIP/KIP family of CDK inhibitor proteins in primary intestinal large B-cell lymphomas: correlation with clinical outcomes. Pathol Res Pract. 2002;198(11):741-746. (Pubitemid 36032883)