Exploring the genetic landscape in chronic lymphocytic leukemia using high-resolution technologies

Leukemia and Lymphoma

Volumn 54, Issue 8, 2013, Pages 1583-1590

  Gunnarsson, Rebeqa ^a   Mansouri, Larry ^a   Rosenquist, Richard ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

CLL; Genomic aberrations; Microarray; Next generation sequencing

Indexed keywords

ATM PROTEIN; FLUDARABINE; IMMUNOGLOBULIN HEAVY CHAIN; MICRORNA 15A; MICRORNA 16; MYELOID DIFFERENTIATION FACTOR 88; NOTCH1 RECEPTOR; PROTEIN P53; TRANSCRIPTOME;

CANCER CHEMOTHERAPY; CANCER GENETICS; CANCER PATIENT; CANCER PROGNOSIS; CANCER SURVIVAL; CHROMOSOME ABERRATION; CHRONIC LYMPHATIC LEUKEMIA; CLONAL EVOLUTION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; HUMAN; MICROARRAY ANALYSIS; NEXT GENERATION SEQUENCING; NONHUMAN; OVERALL SURVIVAL; PRIORITY JOURNAL; REVIEW; RNA SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM;

CHROMOSOME ABERRATIONS; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, LYMPHOCYTIC, CHRONIC, B-CELL;

EID: 84880262505     PISSN: 10428194     EISSN: 10292403     Source Type: Journal    
DOI: 10.3109/10428194.2012.751530     Document Type: Review

References (71)

1. Dohner H, Stilgenbauer S, Benner A, et a l. Genomic aberrations and survival in chronic lymphocytic leukemia. NEngl J Med 2000 ; 343 : 1910-1916
2. Gunnarsson R, Mansouri L, Isaksson A, et a l. Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia. Haematologica 2011; 96: 1161-1169
3. Pinkel D, Segraves R, Sudar D, et a l. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 1998 ; 20 : 207-211
4. Solinas-Toldo S, Lampel S, Stilgenbauer S, et a l. Matrix-based comparative genomic hybridization: Biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997 ; 20 : 399-407
5. Coe BP, Ylstra B, Carvalho B, et al. Resolving the resolution of array CGH. Genomics 2007 ; 89 : 647-653
6. Gaasenbeek M, Howarth K, Rowan AJ, et al. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex changes and multiple forms of chromosomal instability in colorectal cancers. Cancer Res 2006; 66: 3471-3479
7. Greshock J, Feng B, Nogueira C, et a l. Acomparison of DNA copy number profi ling platforms. Cancer Res 2007; 67: 10173-10180
8. Gunnarsson R, Staaf J, Jansson M, 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
9. Hagenkord JM, Monzon FA, Kash SF, et al. Array-based karyotyping for prognostic assessment in chronic lymphocytic leukemia: Performance comparison of Aff ymetrix 10K2.0, 250K Nsp, and SNP6.0 arrays. JMol Diagn 2010; 12: 184-196
10. Hehir-Kwa J Y, Egmont-Petersen M, Janssen I M, et a l. Genomewide copy number profi ling on high-density bacterial artifi cial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: A platform comparison based on statistical power analysis. DNA Res 2007; 14: 1-11
11. Kloth JN, Oosting J, van Wezel T, et al. Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer. BMC Genomics 2007; 8: 53
12. Wicker N, Carles A, Mills I G, et a l. Anew look towards BAC-based array CGH througha comprehensive comparison with oligo-based array CGH. BMC Genomics 2007; 8 : 84
13. Patel A, Kang S H, Lennon P A, et a l. Validation of a targeted DNA microarray for the clinical evaluation of recurrent abnormalities in chronic lymphocytic leukemia. Am J Hematol 2008; 83: 540-546
14. Schwaenen C, Nessling M, Wessendorf S, et a l. Automated array-based genomic profi ling in chronic lymphocytic leukemia: Development of a clinical tool and discovery of recurrent genomic alterations. Proc Natl Acad Sci USA 2004 ; 101 : 1039-1044
15. Mosca L, Fabris S, Lionetti M, et al. Integrative genomics analyses reveal molecularly distinct subgroups of B-cell chronic lymphocytic leukemia patients with 13q14 deletion. Clin Cancer Res 2010 ; 16 : 5641 -5653
16. Ouillette P, Erba H, Kujawski L, et al. Integrated genomic profi ling of chronic lymphocytic leukemia identifi es subtypes of deletion 13q14. Cancer Res 2008; 68: 1012-1021
17. Calin GA, Dumitru CD, Shimizu M, et al. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 2002 ; 99 : 15524-15529
18. Cimmino A, Calin GA, Fabbri M, et al. miR-15 and miR-16 induce apoptosis by targeting BCL2. Proc Natl Acad Sci USA 2005 ; 102 : 13944-13949
19. Kitada S, Andersen J, Akar S, et al. Expression of apoptosisregulating proteins in chronic lymphocytic leukemia: Correlations with in vitro and in vivo chemoresponses. Blood 1998 ; 91 : 3379-3389
20. Klein U, Lia M, Crespo M, et al. The DLEU2/miR-15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 2010; 17: 28-40
21. Lia M, Carette A, Tang H, et al. Functional dissection of the chromosome 13q14 tumor-suppressor locus using transgenic mouse lines. Blood 2012 ; 119 : 2981-2990
22. Mian M, Rinaldi A, Mensaha A, et a l. Del(13q14.3) length matters: An integrated analysis of genomic, fluorescence in situ hybridization and clinical data in 169 chronic lymphocytic leukaemia patients with 13q deletion alone or a normal karyotype. Hematol Oncol 2012 ; 30 : 46-49
23. Parker H, Rose-Zerilli MJ, Parker A, et al. 13q deletion anatomy and disease progression in patients with chronic lymphocytic leukemia. Leukemia 2011; 25: 489-497
24. Gunnarsson R, Isaksson A, Mansouri M, et al. Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: A high-resolution genomic screening of newly diagnosed patients. Leukemia 2010; 24: 211-215
25. Lehmann S, Ogawa S, Raynaud S D, et a l. Molecular allelokaryotyping of early-stage, untreated chronic lymphocytic leukemia. Cancer 2008 ; 112 : 1296-1305
26. Pfeifer D, Pantic M, Skatulla I, et al. Genome-wide analysis of DNA copy number changes and LOH in CLL using high-density SNP arrays. Blood 2007 ; 109 : 1202-1210
27. Chapiro E, Leporrier N, Radford-Weiss I, et al. Gain of the short arm of chromosome 2 (2p) is a frequent recurring chromosome aberration in untreated chronic lymphocytic leukemia (CLL) at advanced stages. Leuk Res 2010; 34: 63-68
28. Grubor V, Krasnitz A, Troge JE, et al. Novel genomic alterations and clonal evolution in chronic lymphocytic leukemia revealed by representational oligonucleotide microarray analysis (ROMA). Blood 2009 ; 113 : 1294-1303
29. Deambrogi C, De Paoli L, Fangazio M, et al. Analysis of the REL, BCL11A, and MYCN proto-oncogenes belonging to the 2p amplicon in chronic lymphocytic leukemia. Am J Hematol 2010; 85: 541-544
30. Brown JR, Hanna M, Tesar B, et al. Integrative genomic analysis implicates gain of PIK3CA at 3q26 and MYC at 8q24 in chronic lymphocytic leukemia. Clin Cancer Res 2012; 18: 3791-3802
31. Edelmann J, Holzmann K, Miller F, et a l. High-resolution genomic profi ling of chronic lymphocytic leukemia reveals new recurrent genomic alterations. Blood 2012 Oct 9. [Epub ahed of print]
32. Kujawski L, Ouillette P, Erba H, et a l. Genomic complexity identifi es patients withaggressive chronic lymphocytic leukemia. Blood 2008 ; 112 : 1993-2003
33. Stephens PJ, Greenman CD, Fu B, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell 2011; 144: 27-40
34. Berkova A, Zemanova Z, Trneny M, et a l. Clonal evolution in chronic lymphocytic leukemia studied by interphase fluorescence insitu hybridization. Neoplasma 2009 ; 56 : 455-458
35. Finn W G, Kay N E, Kroft S H, et a l. Secondary abnormalities of chromosome 6q in B-cell chronic lymphocytic leukemia: A sequential study of karyotypic instability in 51 patients. Am J Hematol 1998 ; 59 : 223-229
36. Juliusson G, Friberg K, Gahrton G. Consistency of chromosomal aberrations in chronic B-lymphocytic leukemia. Alongitudinal cytogenetic study of 41 patients. Cancer 1988 ; 62 : 500-506
37. Juliusson G, Friberg K, Gahrton G. Chromosomal aberrations in progressive and indolent chronic B-lymphocytic leukaemia. A longitudinal study. Acta Oncol 1988; 27: 473-477
38. Nowell PC, Moreau L, Growney P, et al. Karyotypic stability in chronic B-cell leukemia. Cancer Genet Cytogenet 1988 ; 33 : 155-160
39. Oscier D, Fitchett M, Herbert T, et a l. Karyotypic evolution in B-cell chronic lymphocytic leukaemia. Genes Chromosomes Cancer 1991 ; 3 : 16-20
40. Shanafelt TD, Witzig TE, Fink SR, et al. Prospective evaluation of clonal evolution during long-Term follow-up of patients withuntreated early-stage chronic lymphocytic leukemia. J Clin Oncol 2006 ; 24 : 4634-4641
41. Stilgenbauer S, Sander S, Bullinger L, et al. Clonal evolution in chronic lymphocytic leukemia: Acquisition of high-risk genomic aberrations associated withunmutated VH, resistance to therapy, and short survival. Haematologica 2007; 92: 1242-1245
42. Dicker F, Herholz H, Schnittger S, et al. The detection of TP53 mutations in chronic lymphocytic leukemia independently predicts rapid disease progression and is highly correlated witha complex aberrant karyotype. Leukemia 2009; 23: 117-124
43. Malcikova J, Smardova J, Rocnova L, et al. Monoallelic and biallelic inactivation of TP53 gene in chronic lymphocytic leukemia: Selection, impact on survival, and response to DNA damage. Blood 2009 ; 114 : 5307-5314
44. Rossi D, Cerri M, Deambrogi C, et al. The prognostic value of TP53 mutations in chronic lymphocytic leukemia is independent of del17p13: Implications for overall survival and chemorefractoriness. Clin Cancer Res 2009 ; 15 : 995-1004
45. Zenz T, Krober A, Scherer K, et a l. Monoallelic TP53 inactivation is associated with poor prognosis in chronic lymphocytic leukemia: Results from a detailed genetic characterization with long-Term followup. Blood 2008 ; 112 : 3322-3329
46. Zainuddin N, Murray F, Kanduri M, et al. TP53 mutations are infrequent in newly diagnosed chronic lymphocytic leukemia. Leuk Res 2011; 35: 272-274
47. Zenz T, Habe S, Denzel T, et al. Detailed analysis of p53 pathway defects in fl udarabine-refractory chronic lymphocytic leukemia (CLL): Dissecting the contribution of 17p deletion, TP53 mutation, p53-p21 dysfunction, and miR34a in a prospective clinical trial. Blood 2009 ; 114 : 2589-2597
48. Zenz T, Vollmer D, Trbusek M, et a l. T P53 mutation profi le in chronic lymphocytic leukemia: Evidence for a disease specific profi le from a comprehensive analysis of 268 mutations. Leukemia 2010 ; 24 : 2072-2079
49. Gonzalez D, Martinez P, Wade R, et al. Mutational status of the TP53 gene as a predictor of response and survival in patients with chronic lymphocytic leukemia: Results from the LRF CLL4 trial. J Clin Oncol 2011 ; 29 : 2223-2229
50. Zenz T, Eichhorst B, Busch R, et al. TP53 mutation and survival in chronic lymphocytic leukemia. J Clin Oncol 2010 ; 28 : 4473-4479
51. Pospisilova S, Gonzalez D, Malcikova J, et al. ERIC recommendations on TP53 mutation analysis in chronic lymphocytic leukemia. Leukemia 2012; 26: 1458-1461
52. Rossi D, Fangazio M, Rasi S, et al. Disruption of BIRC3 associates with fl udarabine chemorefractoriness in TP53 wild-Type chronic lymphocytic leukemia. Blood 2012; 119: 2854-2862
53. Fabbri G, Rasi S, Rossi D, et a l. Analysis of the chronic lymphocytic leukemia coding genome: Role of NOTCH1 mutational activation. JExp Med 2011 ; 208 : 1389-1401
54. Puente XS, Pinyol M, Quesada V, et al. Whole-genome sequencing identifi es recurrent mutations in chronic lymphocytic leukaemia. Nature 2011 ; 475 : 101-105
55. Quesada V, Conde L, Villamor N, et a l. Exome sequencing identifi es recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet 2012; 44: 47-52
56. Di Ianni M, Baldoni S, Rosati E, et al. Anew genetic lesion in B-CLL: A NOTCH1 PEST domain mutation. Br J Haematol 2009 ; 146 : 689-691
57. Wang L, Lawrence MS, Wan Y, et al. SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. NEngl J Med 2011; 365: 2497-2506
58. Rosati E, Sabatini R, Rampino G, et al. Constitutively activated Notch signaling is involved in survival and apoptosis resistance of B-CLL cells. Blood 2009 ; 113 : 856-865
59. Balatti V, Bottoni A, Palamarchuk A, et al. NOTCH1 mutations in CLL associated with trisomy 12. Blood 2012 ; 119 : 329-331
60. Del Giudice I, Rossi D, Chiaretti S, et al. NOTCH1 mutations in 12 chronic lymphocytic leukemia (CLL) confer an unfavorable prognosis, induce a distinctive transcriptional profiling and refine the intermediate prognosis of 12 CLL. Haematologica 2012 ; 97 : 437-441
61. Rossi D, Rasi S, Fabbri G, et a l. Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood 2012 ; 119 : 521-529
62. Lopez C, Delgado J, Costa D, et al. Different distribution of NOTCH1 mutations in chronic lymphocytic leukemia with isolated trisomy 12 or associated with other chromosomal alterations. Genes Chromosomes Cancer 2012 ; 51 : 881-889
63. Wahl MC, Will CL, Luhrmann R. The spliceosome: Design principles of a dynamic RNP machine. Cell 2009 ; 136 : 701-718
64. Kotake Y, Sagane K, Owa T, et al. Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol 2007 ; 3 : 570-575
65. Rossi D, Bruscaggin A, Spina V, et a l. Mutations of the SF3B1 splicing factor in chronic lymphocytic leukemia: Association with progression and fl udarabine-refractoriness. Blood 2011 ; 118 : 6904-6908
66. Mansouri L, Cahill N, Gunnarsson R, et al. NOTCH1 and SF3B1 mutations can be added to the hierarchical prognostic classifi cation in chronic lymphocytic leukemia. Leukemia 2012 Nov 6. [Epub ahead of print]
67. Coste I, Le Corf K, Kfoury A, et a l. Dual function of MyD88 in RAS signaling and inflammation, leading to mouse and human cell transformation. J Clin Invest 2010 ; 120 : 3663-3667
68. Ngo V N, Young R M, Schmitz R, et a l. Oncogenically active MYD88 mutations in human lymphoma. Nature 2011 ; 470 : 115-119
69. Domenech E, Gomez-Lopez G, Gzlez-Pena D, et al. New mutations in chronic lymphocytic leukemia identifi ed by target enrichment and deep sequencing. PLoS One 2012; 7: E38158
70. Mansouri L, Gunnarsson R, Sutton LA, et al. Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia. Am J Hematol 2012 ; 87 : 737-740
71. Kharas MG, Lengner CJ, Al-Shahrour F, et al. Musashi-2 regulates normal hematopoiesis and promotes aggressive myeloid leukemia. Nat Med 2010 ; 16 : 903-908