450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments

Leukemia

Volumn 27, Issue 1, 2013, Pages 150-158

  Cahill, N ^a,b   Bergh, A C ^c   Kanduri, M ^a,d   Goransson Kultima H ^a   Mansouri, L ^a   Isaksson, A ^d   Ryan, F ^b   Smedby, K E ^e   Juliusson, G ^f   Sundstrom C ^a   Rosen A ^c   Rosenquist, R ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b DUBLIN INSTITUTE OF TECHNOLOGY   (Ireland)

^c Department of Clinical and Experimental Medicine ^*  (Sweden)

^d SAHLGRENSKA UNIVERSITY HOSPITAL   (Sweden)

^e KAROLINSKA INSTITUTE   (Sweden)

^f LUND UNIVERSITY   (Sweden)

Author keywords

450K array; chronic lymphocytic leukemia; compartments; DNA methylation; prognostic subgroups

Indexed keywords

HISTONE DEACETYLASE 4; HISTONE DEACETYLASE 9; HYDROLASE; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSFORMING GROWTH FACTOR BETA; UNCLASSIFIED DRUG;

ADULT; AGED; ARTICLE; CELL SELECTION; CHRONIC LYMPHATIC LEUKEMIA; CLINICAL ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA METHYLATION; FEMALE; FOLLOW UP; GENE MUTATION; GENETIC ASSOCIATION; HUMAN; IMMUNOPHENOTYPING; LEUKEMIA CELL; MALE; MICROARRAY ANALYSIS; PRIORITY JOURNAL; PYROSEQUENCING; REGULATOR GENE;

AGED; B-LYMPHOCYTES; CASE-CONTROL STUDIES; CELL PROLIFERATION; COHORT STUDIES; CPG ISLANDS; DISEASE PROGRESSION; DNA METHYLATION; DNA, NEOPLASM; FEMALE; GENE EXPRESSION PROFILING; GENOME-WIDE ASSOCIATION STUDY; HUMANS; IMMUNOGLOBULIN HEAVY CHAINS; IMMUNOGLOBULIN VARIABLE REGION; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL; MALE; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROGNOSIS; TUMOR MARKERS, BIOLOGICAL;

EID: 84873570131     PISSN: 08876924     EISSN: 14765551     Source Type: Journal    
DOI: 10.1038/leu.2012.245     Document Type: Article

References (50)

1. Herman JG. Hypermethylation of tumor suppressor genes in cancer. Semin Cancer Biol 1999; 9: 359-367.
2. Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003; 349: 2042-2054.
3. Raval A, Tanner SM, Byrd JC, Angerman EB, Perko JD, Chen SS et al. Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia. Cell 2007; 129: 879-890.
4. Corcoran M, Parker A, Orchard J, Davis Z, Wirtz M, Schmitz OJ et al. ZAP-70 methylation status is associated with ZAP-70 expression status in chronic lymphocytic leukemia. Haematologica 2005; 90: 1078-1088.
5. Raval A, Lucas DM, Matkovic JJ, Bennett KL, Liyanarachchi S, Young DC et al. TWIST2 demonstrates differential methylation in immunoglobulin variable heavy chain mutated and unmutated chronic lymphocytic leukemia. J Clin Oncol 2005; 23: 3877-3885.
6. Strathdee G, Sim A, Parker A, Oscier D, Brown R. Promoter hypermethylation silences expression of the HoxA4 gene and correlates with IgVh mutational status in CLL. Leukemia 2006; 20: 1326-1329.
7. Liu TH, Raval A, Chen SS, Matkovic JJ, Byrd JC, Plass C. CpG island methylation and expression of the secreted frizzled-related protein gene family in chronic lymphocytic leukemia. Cancer Res 2006; 66: 653-658.
8. Chen SS, Claus R, Lucas DM, Yu L, Qian J, Ruppert AS et al. Silencing of the inhibitor of DNA binding protein 4 (ID4) contributes to the pathogenesis of mouse and human CLL. Blood 2011; 117: 862-871.
9. Rush LJ, Raval A, Funchain P, Johnson AJ, Smith L, Lucas DM et al. Epigenetic profiling in chronic lymphocytic leukemia reveals novel methylation targets. Cancer Res 2004; 64: 2424-2433.
10. Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH et al. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics 2009; 1: 39-61.
11. Kanduri M, Cahill N, Goransson H, Enstrom C, Ryan F, Isaksson A et al. Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia. Blood 2010; 115: 296-305.
12. Tong WG, Wierda WG, Lin E, Kuang SQ, Bekele BN, Estrov Z et al. Genome-wide DNA methylation profiling of chronic lymphocytic leukemia allows identification of epigenetically repressed molecular pathways with clinical impact. Epigenetics 2010; 5: 499-508.
13. Matsuda S, Yokozaki S, Yoshida H, Kitagishi Y, Shirafuji N, Okumura N. Insulin receptor substrate protein 53 (IRSp53) as a binding partner of antimetastasis molecule NESH, a member of Abelson interactor protein family. Ann Oncol 2008; 19: 1356-1357.
14. Kleer CG, Zhang Y, Pan Q, van Golen KL, Wu ZF, Livant D et al. WISP3 is a novel tumor suppressor gene of inflammatory breast cancer. Oncogene 2002; 21: 3172-3180.
15. Burger JA, Ghia P, Rosenwald A, Caligaris-Cappio F. The microenvironment in mature B-cell malignancies: a target for new treatment strategies. Blood 2009; 114: 3367-3375.
16. Messmer BT, Messmer D, Allen SL, Kolitz JE, Kudalkar P, Cesar D et al. In vivo measurements document the dynamic cellular kinetics of chronic lymphocytic leukemia B cells. J Clin Invest 2005; 115: 755-764.
17. Herishanu Y, Perez-Galan P, Liu D, Biancotto A, Pittaluga S, Vire B et al. The lymph node microenvironment promotes B-cell receptor signaling, NF-kappaB activation, and tumor proliferation in chronic lymphocytic leukemia. Blood 2011; 117: 563-574.
18. Smedby KE, Hjalgrim H, Melbye M, Torrang A, Rostgaard K, Munksgaard L et al. Ultraviolet radiation exposure and risk of malignant lymphomas. J Natl Cancer Inst 2005; 97: 199-209.
19. Hallek M, Cheson BD, Catovsky D, Caligaris-Cappio F, Dighiero G, Dohner H et al. Guidelines for the diagnosis and treatment of chronic lymphocytic leukemia: a report from the International Workshop on Chronic Lymphocytic Leukemia updating the National Cancer Institute-Working Group 1996 guidelines. Blood 2008; 111: 5446-5456.
20. Benjamini Y, Drai D, Elmer G, Kafkafi N, Golani I. Controlling the false discovery rate in behavior genetics research. Behav Brain Res 2001; 125: 279-284.
21. Wiestner A, Rosenwald A, Barry TS, Wright G, Davis RE, Henrickson SE et al. ZAP-70 expression identifies a chronic lymphocytic leukemia subtype with unmutated immunoglobulin genes, inferior clinical outcome, and distinct gene expression profile. Blood 2003; 101: 4944-4951.
22. Mansouri M, Sevov M, Fahlgren E, Tobin G, Jondal M, Osorio L et al. Lipoprotein lipase is differentially expressed in prognostic subsets of chronic lymphocytic leukemia but displays invariably low catalytical activity. Leuk Res 2010; 34: 301-306.
23. Buhl AM, Jurlander J, Geisler CH, Pedersen LB, Andersen MK, Josefsson P et al. CLLU1 expression levels predict time to initiation of therapy and overall survival in chronic lymphocytic leukemia. Eur J Haematol 2006; 76: 455-464.
24. Puente XS, Pinyol M, Quesada V, Conde L, Ordonez GR, Villamor N et al. Wholegenome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011; 475: 101-105.
25. Fabbri G, Rasi S, Rossi D, Trifonov V, Khiabanian H, Ma J et al. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. J Exp Med 2011; 208: 1389-1401.
26. Gutierrez Jr A, Tschumper RC, Wu X, Shanafelt TD, Eckel-Passow J, Huddleston 3rd PM et al. LEF-1 is a prosurvival factor in chronic lymphocytic leukemia and is expressed in the preleukemic state of monoclonal B-cell lymphocytosis. Blood 2010; 116: 2975-2983.
27. Saborit-Villarroya I, Vaisitti T, Rossi D, D'Arena G, Gaidano G, Malavasi F et al. E2A is a transcriptional regulator of CD38 expression in chronic lymphocytic leukemia. Leukemia 2011; 25: 479-488.
28. Liu W, Quinto I, Chen X, Palmieri C, Rabin RL, Schwartz OM et al. Direct inhibition of Bruton's tyrosine kinase by IBtk, a Btk-binding protein. Nat Immunol 2001; 2: 939-946.
29. Witt O, Deubzer HE, Milde T, Oehme I. HDAC family: What are the cancer relevant targets? Cancer Lett 2009; 277: 8-21.
30. Wang JC, Kafeel MI, Avezbakiyev B, Chen C, Sun Y, Rathnasabapathy C et al. Histone deacetylase in chronic lymphocytic leukemia. Oncology 2011; 81: 325-329.
31. Kn H, Bassal S, Tikellis C, El-Osta A. Expression analysis of the epigenetic methyltransferases and methyl-CpG binding protein families in the normal B-cell and B-cell chronic lymphocytic leukemia (CLL). Cancer Biol Ther 2004; 3: 989-994.
32. Chaperot L, Plumas J, Jacob MC, Bost F, Molens JP, Sotto JJ et al. Functional expression of CD80 and CD86 allows immunogenicity of malignant B cells from non-Hodgkin's lymphomas. Exp Hematol 1999; 27: 479-488.
33. Kaderi MA, Kanduri M, Buhl AM, Sevov M, Cahill N, Gunnarsson R et al. LPL is the strongest prognostic factor in a comparative analysis of RNA-based markers in early chronic lymphocytic leukemia. Haematologica 2011; 96: 1153-1160.
34. Fabris S, Bollati V, Agnelli L, Morabito F, Motta V, Cutrona G et al. Biological and clinical relevance of quantitative global methylation of repetitive DNA sequences in chronic lymphocytic leukemia. Epigenetics 2011; 6: 188-194.
35. Pei L, Choi JH, Liu J, Lee EJ, McCarthy B, Wilson JM et al. Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics 2012; 7: 567-578.
36. Jones PA, Baylin SB. The fundamental role of epigenetic events in cancer. Nat Rev Genet 2002; 3: 415-428.
37. Irizarry RA, Ladd-Acosta C, Wen B, Wu Z, Montano C, Onyango P et al. The human colon cancer methylome shows similar hypo-and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet 2009; 41: 178-186.
38. Chantepie SP, Vaur D, Grunau C, Salaun V, Briand M, Parienti JJ et al. ZAP-70 intron1 DNA methylation status: determination by pyrosequencing in B chronic lymphocytic leukemia. Leuk Res 2010; 34: 800-808.
39. Herman SE, Gordon AL, Hertlein E, Ramanunni A, Zhang X, Jaglowski S et al. Bruton tyrosine kinase represents a promising therapeutic target for treatment of chronic lymphocytic leukemia and is effectively targeted by PCI-32765. Blood 2011; 117: 6287-6296.
40. Moreno DA, Scrideli CA, Cortez MA, de Paula Queiroz R, Valera ET, da Silva Silveira V et al. Differential expression of HDAC3, HDAC7 and HDAC9 is associated with prognosis and survival in childhood acute lymphoblastic leukaemia. Br J Haematol 2010; 150: 665-673.
41. Cordingley FT, Bianchi A, Hoffbrand AV, Reittie JE, Heslop HE, Vyakarnam A et al. Tumour necrosis factor as an autocrine tumour growth factor for chronic B-cell malignancies. Lancet 1988; 1: 969-971.
42. Ferrajoli A, Keating MJ, Manshouri T, Giles FJ, Dey A, Estrov Z et al. The clinical significance of tumor necrosis factor-alpha plasma level in patients having chronic lymphocytic leukemia. Blood 2002; 100: 1215-1219.
43. Shanafelt TD, Witzig TE, Fink SR, Jenkins RB, Paternoster SF, Smoley SA et al. Prospective evaluation of clonal evolution during long-term follow-up of patients with untreated early-stage chronic lymphocytic leukemia. J Clin Oncol 2006; 24: 4634-4641.
44. Stilgenbauer S, Sander S, Bullinger L, Benner A, Leupolt E, Winkler D et al. Clonal evolution in chronic lymphocytic leukemia: acquisition of high-risk genomic aberrations associated with unmutated VH, resistance to therapy, and short survival. Haematologica 2007; 92: 1242-1245.
45. Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Goransson H, Liljedahl U et al. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-a comparative study of four differently designed, high resolution microarray platforms. Genes Chromosomes Cancer 2008; 47: 697-711.
46. Lenschow DJ, Sperling AI, Cooke MP, Freeman G, Rhee L, Decker DC et al. Differential up-regulation of the B7-1 and B7-2 costimulatory molecules after Ig receptor engagement by antigen. J Immunol 1994; 153: 1990-1997.
47. Nagy B, Lundan T, Larramendy ML, Aalto Y, Zhu Y, Niini T et al. Abnormal expression of apoptosis-related genes in haematological malignancies: overexpression of MYC is poor prognostic sign in mantle cell lymphoma. Br J Haematol 2003; 120: 434-441.
48. Ban EM, LeBoeuf RD. Suppressin: an endogenous negative regulator of immune cell activation. Immunol Res 1994; 13: 1-9.
49. Osorio LM, Aguilar-Santelises M. Apoptosis in B-chronic lymphocytic leukaemia. Med Oncol 1998; 15: 234-240.
50. Vargova K, Curik N, Burda P, Basova P, Kulvait V, Pospisil V et al. MYB transcriptionally regulates the miR-155 host gene in chronic lymphocytic leukemia. Blood 2011; 117: 3816-3825.