CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia

Journal of Hematology and Oncology

Volumn 7, Issue 1, 2014, Pages

  Hájková, Hana ^a   Fritz, Markus Hsi Yang ^b   Haškovec, Cedrik ^a   Schwarz, Jiří ^a   Šálek, Cyril ^a   Marková, Jana ^a   Krejčík, Zdeněk ^a   Dostálová Merkerová, Michaela ^a   Kostečka, Arnošt ^a   Vostrý, Martin ^a   Fuchs, Ota ^a   Michalová, Kyra ^c   Cetkovský, Petr ^a   Beneš, Vladimír ^b  

^a INSTITUTE OF HEMATOLOGY AND BLOOD TRANSFUSION   (Czech Republic)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^c CHARLES UNIVERSITY   (Czech Republic)

Author keywords

Acute myeloid leukemia; CBFB MYH11; DNA methylation; PBX3; Targeted bisulfite sequencing

Indexed keywords

BISULFITE; CD34 ANTIGEN; CBFBETA-MYH11 FUSION PROTEIN; HOMEODOMAIN PROTEIN; ONCOPROTEIN; PROTO-ONCOGENE PROTEIN PBX3; TRANSCRIPTOME; TUMOR MARKER;

ACUTE GRANULOCYTIC LEUKEMIA; ADULT; ARTICLE; B CELL LEUKEMIA; BINDING SITE; BREAST CANCER; CANCER PROGNOSIS; CPG ISLAND; DNA CONTAMINATION; DNA METHYLATION; FEMALE; FILTRATION; GENE EXPRESSION; GENE EXPRESSION ASSAY; GENE EXPRESSION PROFILING; HOX GENE; HUMAN; HUMAN GENOME; LEUKEMOGENESIS; MAJOR CLINICAL STUDY; MALE; MYELODYSPLASTIC SYNDROME; MYELOID LEUKEMIA; OVERALL SURVIVAL; PROMOTER REGION; PYROSEQUENCING; RECURRENCE FREE SURVIVAL; TRANSCRIPTION INITIATION SITE; UPREGULATION; ACUTE MYELOBLASTIC LEUKEMIA; CLUSTER ANALYSIS; GENE EXPRESSION REGULATION; GENETICS; KAPLAN MEIER METHOD; MORTALITY; PROGNOSIS; PROPORTIONAL HAZARDS MODEL; REAL TIME POLYMERASE CHAIN REACTION;

BIOMARKERS, TUMOR; CLUSTER ANALYSIS; DNA METHYLATION; FEMALE; GENE EXPRESSION REGULATION, LEUKEMIC; HOMEODOMAIN PROTEINS; HUMANS; KAPLAN-MEIER ESTIMATE; LEUKEMIA, MYELOID, ACUTE; MALE; ONCOGENE PROTEINS, FUSION; PROGNOSIS; PROPORTIONAL HAZARDS MODELS; PROTO-ONCOGENE PROTEINS; REAL-TIME POLYMERASE CHAIN REACTION; TRANSCRIPTOME;

EID: 84907920569     PISSN: None     EISSN: 17568722     Source Type: Journal    
DOI: 10.1186/s13045-014-0066-4     Document Type: Article

References (33)

1. Early aberrant DNA methylation events in a mouse model of acute myeloid leukemia. M Sonnet, R Claus, N Becker, M Zucknick, J Petersen, DB Lipka, CC Oakes, M Andrulis, A Lier, MD Milsom, T Witte, L Gu, S Kim-Wanner, P Schirmacher, M Wulfert, N Gattermann, M Luebbert, F Rosenbauer, M Rehli, L Bullinger, D Weichenhan, C Plass, Genome Med 2014 6 34 10.1186/gm551 24944583
2. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. ME Figueroa, S Lugthart, Y Li, C Erpelinck-Verschueren, X Deng, PJ Christos, E Schifano, J Booth, W van Putten, L Skrabanek, F Campagne, M Mazumdar, JM Greally, PJM Valk, B Lowenberg, R Delwel, A Melnick, Cancer Cell 2010 17 1 13 27 10.1016/j.ccr.2009.11.020 20060365
3. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med 2013 368 22 2059 2074 10.1056/NEJMoa1301689
4. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. A Akalin, FE Garrett-Bakelman, M Kormaksson, J Busuttil, L Zhang, I Khrebtukova, TA Milne, Y Huang, D Biswas, JL Hess, CD Allis, RG Roeder, PJM Valk, B Lowenberg, R Delwel, HF Fernandez, E Paietta, MS Tallman, GP Schroth, CE Mason, A Melnick, ME Figueroa, PLoS Genet 2012 8 6 1002781 10.1371/journal.pgen.1002781 22737091
5. Functions of DNA methylation: islands, start sites, gene bodies and beyond. PA Jones, Nat Rev Genet 2012 13 7 484 492 10.1038/nrg3230 22641018
6. In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes. M Ivanov, M Kals, M Kacevska, A Metspalu, M Ingelman-Sundberg, L Milani, Nucleic Acids Res 2013 41 6 72 10.1093/nar/gks1467 23325842
7. Tissue of origin determines cancer-associated CpG island promoter hypermethylation patterns. D Sproul, RR Kitchen, CE Nestor, JM Dixon, AH Sims, DJ Harrison, BH Ramsahoye, RR Meehan, Genome Biol 2012 13 10 84 10.1186/gb-2012-13-10-r84 23034185
8. Prognostically useful gene-expression profiles in acute myeloid leukemia. P Valk, R Verhaak, M Beijen, C Erpelinck, S van Doorn-Khosrovani, J Boer, H Beverloo, M Moorhouse, P van der Spek, B Lowenberg, R Delwel, N Engl J Med 2004 350 16 1617 1628 10.1056/NEJMoa040465 15084694
9. PBX3 is an important cofactor of HOXA9 in leukemogenesis. Z Li, Z Zhang, Y Li, S Arnovitz, P Chen, H Huang, X Jiang, G Hong, RB Kunjamma, H Ren, C He, C Wang, AG Elkahloun, PJM Valk, K Doehner, MB Neilly, L Bullinger, R Delwel, B Lowenberg, PP Liu, R Morgan, JD Rowley, C Yuan, J Chen, Blood 2013 121 8 1422 1431 10.1182/blood-2012-07-442004 23264595
10. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. R Suzuki, H Shimodaira, Bioinformatics 2006 22 12 1540 1542 10.1093/bioinformatics/btl117 16595560
11. GREAT improves functional interpretation of cis-regulatory regions. CY McLean, D Bristor, M Hiller, SL Clarke, BT Schaar, CB Lowe, AM Wenger, G Bejerano, Nat Biotechnol 2010 28 5 495 U155 10.1038/nbt.1630 20436461
12. HOXA/PBX3 knockdown impairs growth and sensitizes cytogenetically normal acute myeloid leukemia cells to chemotherapy. GJ Dickson, FG Liberante, LM Kettyle, KA O'Hagan, DPJ Finnegan, L Bullinger, D Geerts, MF McMullin, TRJ Lappin, KI Mills, A Thompson, Haematologica 2013 98 8 1216 1225 10.3324/haematol.2012.079012 23539541
13. Routine use of microarray-based gene expression profiling to identify patients with low cytogenetic risk acute myeloid leukemia: accurate results can be obtained even with suboptimal samples. DR de la Bletiere, O Blanchet, P Cornillet-Lefebvre, A Coutolleau, L Baranger, F Genevieve, I Luquet, M Hunault-Berger, A Beucher, A Schmidt-Tanguy, M Zandecki, Y Delneste, N Ifrah, P Guardiola, BMC Med Genet 2012 5 6
14. CBFB-MYH11/RUNX1 together with a compendium of hematopoietic regulators, chromatin modifiers and basal transcription factors occupies self-renewal genes in inv(16) acute myeloid leukemia. A Mandoli, AA Singh, PWTC Jansen, ATJ Wierenga, H Riahi, G Franci, K Prange, S Saeed, E Vellenga, M Vermeulen, HG Stunnenberg, JHA Martens, Leukemia 2014 28 4 770 778 10.1038/leu.2013.257 24002588
15. High meningioma 1 (MN1) expression as a predictor for poor outcome in acute myeloid leukemia with normal cytogenetics. M Heuser, G Beutel, J Krauter, K Doehner, N von Neuhoff, B Schlegelberger, A Ganser, Blood 2006 108 12 3898 3905 10.1182/blood-2006-04-014845 16912223
16. Prognostic importance of MN1 transcript levels, and biologic insights from MN1-associated gene and MicroRNA expression signatures in cytogenetically normal acute myeloid leukemia: a cancer and leukemia group B study. C Langer, G Marcucci, KB Holland, MD Radmacher, K Maharry, P Paschka, SP Whitman, K Mrozek, CD Baldus, R Vij, BL Powell, AJ Carroll, JE Kolitz, MA Caligiuri, RA Larson, CD Bloomfield, J Clin Oncol 2009 27 19 3198 3204 10.1200/JCO.2008.20.6110 19451432
17. The importance of diagnostic cytogenetics on outcome in AML: analysis of 1,612 patients entered into the MRC AML 10 trial. D Grimwade, H Walker, F Oliver, K Wheatley, C Harrison, G Harrison, J Rees, I Hann, R Stevens, A Burnett, A Goldstone, Blood 1998 92 7 2322 2333 9746770
18. Clinical significance of the most common chromosome translocations in adult acute myeloid leukemia. K Mrózek, CD Bloomfield, JNCI Monogr 2008 2008 39 52 57 10.1093/jncimonographs/lgn003
19. MN1 overexpression is an important step in the development of inv(16) AML. C Carella, J Bonten, S Sirma, TA Kranenburg, S Terranova, R Klein-Geltink, S Shurtleff, JR Downing, EC Zwarthoff, PP Liu, GC Grosveld, Leukemia 2007 21 8 1679 1690 10.1038/sj.leu.2404778 17525718
20. Pbx modulation of Hox homeodomain amino-terminal arms establishes different DNA-binding specificities across the Hox locus. C Chang, L Brocchieri, W Shen, C Largman, M Cleary, Mol Cell Biol 1996 16 4 1734 1745 8657149
21. Expression of myeloperoxidase in acute myeloid leukemia blasts mirrors the distinct DNA methylation pattern involving the downregulation of DNA methyltransferase DNMT3B. H Itonaga, D Imanishi, Y Wong, S Sato, K Ando, Y Sawayama, D Sasaki, K Tsuruda, H Hasegawa, Y Imaizumi, J Taguchi, H Tsushima, S Yoshida, T Fukushima, T Hata, Y Moriuchi, K Yanagihara, Y Miyazaki, Leukemia 2014 28 7 1459 1466 10.1038/leu.2014.15 24457336
22. The PRDX2 gene is transcriptionally silenced and de novo methylated in Hodgkin and Reed-Sternberg cells of classical Hodgkin lymphoma. M Schneider, M Szaumkessel, J Richter, O Ammerpohl, ML Hansmann, R Küppers, R Siebert, M Giefing, Blood 2014 123 23 3672 3674 10.1182/blood-2014-02-553263 24904103
23. The diagnostic value of DNA methylation in leukemia: a systematic review and meta-analysis. D Jiang, Q Hong, Y Shen, Y Xu, H Zhu, Y Li, C Xu, G Ouyang, S Duan, PLoS One 2014 9 5 96822 10.1371/journal.pone.0096822 24810788
24. Monitoring of minimal residual disease in patients with core binding factor acute myeloid leukemia and the impact of C-KIT, FLT3, and JAK2 mutations on clinical outcome. J Markova, Z Trnkova, P Michkova, J Maaloufova, J Stary, P Cetkovsky, J Schwarz, Leuk Lymphoma 2009 50 9 1448 1460 10.1080/10428190903085951 19603346
25. A new type of NPM1 gene mutation in AML leading to a C-terminal truncated protein. AS Pitiot, I Santamaria, O Garcia-Suarez, I Centeno, A Astudillo, C Rayon, M Balbin, Leukemia 2007 21 7 1564 1566 10.1038/sj.leu.2404679 17410190
26. CEBPA polymorphisms and mutations in patients with acute myeloid leukemia, myelodysplastic syndrome, multiple myeloma and non-Hodgkin's lymphoma. O Fuchs, D Provamikova, M Kocova, A Kostecka, P Cvekova, R Neuwirtova, P Kobylka, J Cermak, J Brozinova, J Schwarz, J Markova, P Salaj, H Klamova, J Maaloufova, P Lemez, L Novakova, K Benesova, Blood Cells Mol Dis 2008 40 3 401 405 10.1016/j.bcmd.2007.11.005 18182175
27. Prognostic impact of DNMT3A mutations in patients with intermediate cytogenetic risk profile acute myeloid leukemia. J Markova, P Michkova, K Burckova, J Brezinova, K Michalova, A Dohnalova, JS Maaloufova, P Soukup, A Vitek, P Cetkovsky, J Schwarz, Eur J Haematol 2012 88 2 128 135 10.1111/j.1600-0609.2011.01716.x 21967546
28. Partial tandem duplication of ALL1 as a recurrent molecular defect in acute myeloid leukemia with trisomy 11. M Caligiuri, M Strout, S Schichman, K Mrozek, D Arthur, G Herzig, M Baer, C Schiffer, K Heinonen, S Knuutila, T Nousiainen, T Ruutu, A Block, P Schulman, J PedersenBjergaard, C Croce, C Bloomfield, Cancer Res 1996 56 6 1418 1425 8640834
29. Clinical and biological implications of partial tandem duplication of the MLL gene in acute myeloid leukemia without chromosomal abnormalities at 11q23. H Shiah, Y Kuo, J Tang, S Huang, M Yao, W Tsay, Y Chen, C Wang, M Shen, D Lin, K Lin, H Tien, Leukemia 2002 16 2 196 202 10.1038/sj.leu.2402352 11840285
30. DNA methylome analysis using short bisulfite sequencing data. F Krueger, B Kreck, A Franke, SR Andrews, Nat Methods 2012 9 2 145 151 10.1038/nmeth.1828 22290186
31. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. M Lohse, AM Bolger, A Nagel, AR Fernie, JE Lunn, M Stitt, B Usadel, Nucleic Acids Res 2012 40 W1 622 W627 10.1093/nar/gks540 22684630
32. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. F Krueger, SR Andrews, Bioinformatics 2011 27 11 1571 1572 10.1093/bioinformatics/btr167 21493656
33. BISMA-Fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. C Rohde, Y Zhang, R Reinhardt, A Jeltsch, BMC Bioinformatics 2010 11 230 10.1186/1471-2105-11-230 20459626