Mutational spectrum of myeloid malignancies with inv(3)/t(3;3) reveals a predominant involvement of RAS/RTK signaling pathways

Blood

Volumn 125, Issue 1, 2015, Pages 133-139

  Gröschel, Stefan ^a,b,c   Sanders, Mathijs A ^a   Hoogenboezem, Remco ^a   Zeilemaker, Annelieke ^a   Havermans, Marije ^a   Erpelinck, Claudia ^a   Bindels, Eric M J ^a   Beverloo, H Berna ^a,d   Döhner, Hartmut ^c   Löwenberg, Bob ^a   Döhner, Konstanze ^c   Delwel, Ruud ^a   Valk, Peter J M ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^c UNIVERSITY HOSPITAL ULM   (Germany)

^d Dutch Working Group on Hemato Oncologic Genome Diagnostics   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHATIDYLINOSITOL 3 KINASE; PROTEIN TYROSINE KINASE; RAS PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR RUNX1; TRANSCRIPTION FACTOR SF3B1; UNCLASSIFIED DRUG;

ACUTE GRANULOCYTIC LEUKEMIA; ALLELE; ARTICLE; BONE MARROW; CANCER SURVIVAL; CHROMOSOME ABERRATION; CHRONIC MYELOID LEUKEMIA; CLONAL EVOLUTION; CLONAL VARIATION; CYTOGENETICS; DNA METHYLATION; EPIGENETICS; EVENT FREE SURVIVAL; GENE EXPRESSION; GENE MUTATION; HUMAN; HUMAN CELL; LEUKEMIA REMISSION; MYELOBLAST; MYELODYSPLASTIC SYNDROME; NEXT GENERATION SEQUENCING; OVERALL SURVIVAL; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR GENE; ACUTE MYELOBLASTIC LEUKEMIA; CHROMOSOME 3; CHROMOSOME BANDING PATTERN; CHROMOSOME INVERSION; DNA SEQUENCE; EXOME; GENE EXPRESSION PROFILING; GENE TRANSLOCATION; GENETIC EPIGENESIS; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; SEQUENCE ANALYSIS;

ALLELES; CHROMOSOME BANDING; CHROMOSOME INVERSION; CHROMOSOMES, HUMAN, PAIR 3; DNA MUTATIONAL ANALYSIS; EPIGENESIS, GENETIC; EXOME; GENE EXPRESSION PROFILING; HUMANS; LEUKEMIA, MYELOID, ACUTE; MYELODYSPLASTIC SYNDROMES; RAS PROTEINS; RECEPTOR PROTEIN-TYROSINE KINASES; SEQUENCE ANALYSIS, DNA; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; TRANSLOCATION, GENETIC;

EID: 84920596795     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2014-07-591461     Document Type: Article

References (53)

1. Vardiman JW, Thiele J, Arber DA, et al. The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes. Blood. 2009;114(5):937-951.
2. Grigg AP, Gascoyne RD, Phillips GL, Horsman DE. Clinical, haematological and cytogenetic features in 24 patients with structural rearrangements of the Q arm of chromosome 3. Br J Haematol. 1993;83(1): 158-165.
3. Lugthart S, Gröschel S, Beverloo HB, et al. Clinical, molecular, and prognostic significance of WHO type inv(3)(q21q26.2)/t(3;3)(q21;q26.2) and various other 3q abnormalities in acute myeloid leukemia. J Clin Oncol. 2010;28(24):3890-3898.
4. Testoni N, Borsaru G, Martinelli G, et al. 3q21 and 3q26 cytogenetic abnormalities in acute myeloblastic leukemia: biological and clinical features. Haematologica. 1999;84(8):690-694.
5. Cui W, Sun J, Cotta CV, Medeiros LJ, Lin P. Myelodysplastic syndrome with inv(3)(q21q26.2) or t(3;3)(q21;q26.2) has a high risk for progression to acute myeloid leukemia. Am J Clin Pathol. 2011;136(2):282-288.
6. Haferlach C, Bacher U, Haferlach T, et al. The inv(3)(q21q26)/t(3;3)(q21;q26) is frequently accompanied by alterations of the RUNX1, KRAS and NRAS and NF1 genes and mediates adverse prognosis both in MDS and in AML: a study in 39 cases of MDS or AML. Leukemia. 2011;25(5): 874-877.
7. Johansson B, Fioretos T, Mitelman F. Cytogenetic and molecular genetic evolution of chronic myeloid leukemia. Acta Haematol. 2002;107(2): 76-94.
8. Cattaneo F, Nucifora G. EVI1 recruits the histone methyltransferase SUV39H1 for transcription repression. J Cell Biochem. 2008;105(2):344-352.
9. Goyama S, Yamamoto G, Shimabe M, et al. Evi-1 is a critical regulator for hematopoietic stem cells and transformed leukemic cells. Cell Stem Cell. 2008;3(2):207-220.
10. Perkins AS, Fishel R, Jenkins NA, Copeland NG. Evi-1, a murine zinc finger proto-oncogene, encodes a sequence-specific DNA-binding protein. Mol Cell Biol. 1991;11(5):2665-2674.
11. Gröschel S, Lugthart S, Schlenk RF, et al. High EVI1 expression predicts outcome in younger adult patients with acute myeloid leukemia and is associated with distinct cytogenetic abnormalities. J Clin Oncol. 2010;28(12):2101-2107.
12. Gröschel S, Sanders MA, Hoogenboezem R, et al. A single oncogenic enhancer rearrangement causes concomitant EVI1 and GATA2 deregulation in leukemia. Cell. 2014;157(2): 369-381.
13. Yamazaki H, Suzuki M, Otsuki A, et al. A remote GATA2 hematopoietic enhancer drives leukemogenesis in inv(3)(q21;q26) by activating EVI1 expression. Cancer Cell. 2014;25(4): 415-427.
14. Hsu AP, Johnson KD, Falcone EL, et al. GATA2 haploinsufficiency caused by mutations in a conserved intronic element leads to MonoMAC syndrome. Blood. 2013;121(19):3830-3837, S3831-S3837.
15. Lim KC, Hosoya T, Brandt W, et al. Conditional Gata2 inactivation results in HSC loss and lymphatic mispatterning. J Clin Invest. 2012; 122(10):3705-3717.
16. Ling KW, Ottersbach K, van Hamburg JP, et al. GATA-2 plays two functionally distinct roles during the ontogeny of hematopoietic stem cells. J Exp Med. 2004;200(7):871-882.
17. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009;25(14):1754-1760.
18. Chen K, Wallis JW, McLellan MD, et al. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation. Nat Methods. 2009;6(9):677-681.
19. Li H, Handsaker B, Wysoker A, et al; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079.
20. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res. 2008;18(5):821-829.
21. Kent WJ. BLAT-the BLAST-like alignment tool. Genome Res. 2002;12(4):656-664.
22. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013; 14(4):R36.
23. Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-Seq data with DESeq2. bioRxiv. 2014.
24. McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9): 1297-1303.
25. Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31(3):213-219.
26. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
27. Kandoth C, McLellan MD, Vandin F, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013;502(7471): 333-339.
28. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059-2074.
29. Ladroue C. phenotypicForest 0.2. http://chrisladroue.com/phorest/. Accessed October, 13, 2014.
30. Kassambara A. Statistical tools for high-throughput data analysis. http://www.sthda.com/english/articles/3-easyggplot2/. Accessed October, 13, 2014.
31. Streubel B, Vinatzer U, Lamprecht A, Raderer M, Chott A. T(3;14)(p14.1;q32) involving IGH and FOXP1 is a novel recurrent chromosomal aberration in MALT lymphoma. Leukemia. 2005; 19(4):652-658.
32. Breems DA, Van Putten WL, De Greef GE, et al. Monosomal karyotype in acute myeloid leukemia: a better indicator of poor prognosis than a complex karyotype. J Clin Oncol. 2008;26(29): 4791-4797.
33. Rücker FG, Schlenk RF, Bullinger L, et al. TP53 alterations in acute myeloid leukemia with complex karyotype correlate with specific copy number alterations, monosomal karyotype, and dismal outcome. Blood. 2012;119(9):2114-2121.
34. Wong CC, Martincorena I, Rust AG, et al; Chronic Myeloid Disorders Working Group of the International Cancer Genome Consortium. Inactivating CUX1 mutations promote tumorigenesis. Nat Genet. 2014;46(1):33-38.
35. McNerney ME, Brown CD, Wang X, et al. CUX1 is a haploinsufficient tumor suppressor gene on chromosome 7 frequently inactivated in acute myeloid leukemia. Blood. 2013;121(6):975-983.
36. Grass JA, Jing H, Kim SI, et al. Distinct functions of dispersed GATA factor complexes at an endogenous gene locus. Mol Cell Biol. 2006; 26(19):7056-7067.
37. Koche RP, Armstrong SA. Genomic dark matter sheds light on EVI1-driven leukemia. Cancer Cell. 2014;25(4):407-408.
38. Döhner H, Estey EH, Amadori S, et al; European LeukemiaNet. Diagnosis and management of acute myeloid leukemia in adults: recommendations from an international expert panel, on behalf of the European LeukemiaNet. Blood. 2010;115(3):453-474.
39. Renneville A, Roumier C, Biggio V, et al. Cooperating gene mutations in acute myeloid leukemia: a review of the literature. Leukemia. 2008;22(5):915-931.
40. Tsurumi S, Nakamura Y, Maki K, et al. N-ras and p53 gene mutations in Japanese patients with myeloproliferative disorders. Am J Hematol. 2002; 71(2):131-133.
41. de Pater E, Kaimakis P, Vink CS, et al. Gata2 is required for HSC generation and survival. J Exp Med. 2013;210(13):2843-2850.
42. Hahn CN, Chong CE, Carmichael CL, et al. Heritable GATA2 mutations associated with familial myelodysplastic syndrome and acute myeloid leukemia. Nat Genet. 2011;43(10): 1012-1017.
43. Nishimoto N, Arai S, Ichikawa M, et al. Loss of AML1/Runx1 accelerates the development of MLL-ENL leukemia through down-regulation of p19ARF. Blood. 2011;118(9):2541-2550.
44. Mardis ER, Ding L, Dooling DJ, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361(11): 1058-1066.
45. Watanabe-Okochi N, Kitaura J, Ono R, et al. AML1 mutations induced MDS and MDS/AML in a mouse BMT model. Blood. 2008;111(8): 4297-4308.
46. Green CL, Tawana K, Hills RK, et al. GATA2 mutations in sporadic and familial acute myeloid leukaemia patients with CEBPA mutations. Br J Haematol. 2013;161(5):701-705.
47. Greif PA, Dufour A, Konstandin NP, et al. GATA2 zinc finger 1 mutations associated with biallelic CEBPA mutations define a unique genetic entity of acute myeloid leukemia. Blood. 2012;120(2): 395-403.
48. Radich JP. The Biology of CML blast crisis. Hematology (Am Soc Hematol Educ Program). 2007;384-391.
49. Calabretta B, Perrotti D. The biology of CML blast crisis. Blood. 2004;103(11):4010-4022.
50. Sawyers CL, McLaughlin J, Witte ON. Genetic requirement for Ras in the transformation of fibroblasts and hematopoietic cells by the Bcr-Abl oncogene. J Exp Med. 1995;181(1):307-313.
51. Hsu AP, Sampaio EP, Khan J, et al. Mutations in GATA2 are associated with the autosomal dominant and sporadic monocytopenia and mycobacterial infection (MonoMAC) syndrome. Blood. 2011;118(10):2653-2655.
52. Rodrigues NP, Janzen V, Forkert R, et al. Haploinsufficiency of GATA-2 perturbs adult hematopoietic stem-cell homeostasis. Blood. 2005;106(2):477-484.
53. Park S, Chapuis N, Tamburini J, et al. Role of the PI3K/AKT and mTOR signaling pathways in acute myeloid leukemia. Haematologica. 2010;95(5): 819-828.