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Published in: Journal of Hematology & Oncology 1/2017

Open Access 01-12-2017 | Review

Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia

Authors: Yan Li, Qingyu Xu, Na Lv, Lili Wang, Hongmei Zhao, Xiuli Wang, Jing Guo, Chongjian Chen, Yonghui Li, Li Yu

Published in: Journal of Hematology & Oncology | Issue 1/2017

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Abstract

Acute myeloid leukemia (AML) is the most common type of acute leukemia in adults. AML is a heterogeneous malignancy characterized by distinct genetic and epigenetic abnormalities. Recent genome-wide DNA methylation studies have highlighted an important role of dysregulated methylation signature in AML from biological and clinical standpoint. In this review, we will outline the recent advances in the methylome study of AML and overview the impacts of DNA methylation on AML diagnosis, treatment, and prognosis.
Literature
1.
go back to reference Dohner H, Weisdorf DJ, Bloomfield CD. Acute myeloid leukemia. N Engl J Med. 2015;373(12):1136–52.CrossRefPubMed Dohner H, Weisdorf DJ, Bloomfield CD. Acute myeloid leukemia. N Engl J Med. 2015;373(12):1136–52.CrossRefPubMed
2.
3.
go back to reference Grimwade D, Hills RK, Moorman AV, Walker H, Chatters S, Goldstone AH, Wheatley K, Harrison CJ, Burnett AK, National Cancer Research Institute Adult Leukaemia Working G. Refinement of cytogenetic classification in acute myeloid leukemia: determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the United Kingdom Medical Research Council Trials. Blood. 2010;116(3):354–65.CrossRefPubMed Grimwade D, Hills RK, Moorman AV, Walker H, Chatters S, Goldstone AH, Wheatley K, Harrison CJ, Burnett AK, National Cancer Research Institute Adult Leukaemia Working G. Refinement of cytogenetic classification in acute myeloid leukemia: determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the United Kingdom Medical Research Council Trials. Blood. 2010;116(3):354–65.CrossRefPubMed
4.
go back to reference Dohner H, Estey EH, Amadori S, Appelbaum FR, Buchner T, Burnett AK, Dombret H, Fenaux P, Grimwade D, Larson RA, Lo-Coco F, Naoe T, Niederwieser D, Ossenkoppele GJ, Sanz MA, Sierra J, Tallman MS, Lowenberg B, Bloomfield CD, European L. 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):453–74.CrossRefPubMed Dohner H, Estey EH, Amadori S, Appelbaum FR, Buchner T, Burnett AK, Dombret H, Fenaux P, Grimwade D, Larson RA, Lo-Coco F, Naoe T, Niederwieser D, Ossenkoppele GJ, Sanz MA, Sierra J, Tallman MS, Lowenberg B, Bloomfield CD, European L. 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):453–74.CrossRefPubMed
5.
go back to reference Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Dohner K, Schlenk RF, Dohner H, Campbell PJ. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016;374(23):2209–21.CrossRefPubMedPubMedCentral Papaemmanuil E, Gerstung M, Bullinger L, Gaidzik VI, Paschka P, Roberts ND, Potter NE, Heuser M, Thol F, Bolli N, Gundem G, Van Loo P, Martincorena I, Ganly P, Mudie L, McLaren S, O'Meara S, Raine K, Jones DR, Teague JW, Butler AP, Greaves MF, Ganser A, Dohner K, Schlenk RF, Dohner H, Campbell PJ. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016;374(23):2209–21.CrossRefPubMedPubMedCentral
6.
go back to reference Testa JR, Mintz U, Rowley JD, Vardiman JW, Golomb HM. Evolution of karyotypes in acute nonlymphocytic leukemia. Cancer Res. 1979;39(9):3619–27.PubMed Testa JR, Mintz U, Rowley JD, Vardiman JW, Golomb HM. Evolution of karyotypes in acute nonlymphocytic leukemia. Cancer Res. 1979;39(9):3619–27.PubMed
7.
go back to reference Cancer Genome Atlas Research N. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059–74.CrossRef Cancer Genome Atlas Research N. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059–74.CrossRef
8.
go back to reference Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, et al. The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012;150(2):264–78.CrossRefPubMedPubMedCentral Welch JS, Ley TJ, Link DC, Miller CA, Larson DE, Koboldt DC, Wartman LD, Lamprecht TL, Liu F, Xia J, Kandoth C, Fulton RS, McLellan MD, Dooling DJ, Wallis JW, Chen K, Harris CC, Schmidt HK, Kalicki-Veizer JM, Lu C, Zhang Q, Lin L, O'Laughlin MD, McMichael JF, Delehaunty KD, Fulton LA, Magrini VJ, McGrath SD, Demeter RT, Vickery TL, et al. The origin and evolution of mutations in acute myeloid leukemia. Cell. 2012;150(2):264–78.CrossRefPubMedPubMedCentral
9.
go back to reference Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Lowenberg B, Dohner H, Dohner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, et al. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nat Med. 2016;22(7):792–9.CrossRefPubMedPubMedCentral Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Lowenberg B, Dohner H, Dohner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, et al. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nat Med. 2016;22(7):792–9.CrossRefPubMedPubMedCentral
10.
go back to reference Bullinger L, Kronke J, Schon C, Radtke I, Urlbauer K, Botzenhardt U, Gaidzik V, Cario A, Senger C, Schlenk RF, Downing JR, Holzmann K, Dohner K, Dohner H. Identification of acquired copy number alterations and uniparental disomies in cytogenetically normal acute myeloid leukemia using high-resolution single-nucleotide polymorphism analysis. Leukemia. 2010;24(2):438–49.CrossRefPubMed Bullinger L, Kronke J, Schon C, Radtke I, Urlbauer K, Botzenhardt U, Gaidzik V, Cario A, Senger C, Schlenk RF, Downing JR, Holzmann K, Dohner K, Dohner H. Identification of acquired copy number alterations and uniparental disomies in cytogenetically normal acute myeloid leukemia using high-resolution single-nucleotide polymorphism analysis. Leukemia. 2010;24(2):438–49.CrossRefPubMed
11.
go back to reference Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361(11):1058–66.CrossRefPubMedPubMedCentral Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, Koboldt DC, Fulton RS, Delehaunty KD, McGrath SD, Fulton LA, Locke DP, Magrini VJ, Abbott RM, Vickery TL, Reed JS, Robinson JS, Wylie T, Smith SM, Carmichael L, Eldred JM, Harris CC, Walker J, Peck JB, Du F, Dukes AF, Sanderson GE, Brummett AM, Clark E, McMichael JF, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361(11):1058–66.CrossRefPubMedPubMedCentral
12.
go back to reference Shen Y, Zhu YM, Fan X, Shi JY, Wang QR, Yan XJ, Gu ZH, Wang YY, Chen B, Jiang CL, Yan H, Chen FF, Chen HM, Chen Z, Jin J, Chen SJ. Gene mutation patterns and their prognostic impact in a cohort of 1185 patients with acute myeloid leukemia. Blood. 2011;118(20):5593–603.CrossRefPubMed Shen Y, Zhu YM, Fan X, Shi JY, Wang QR, Yan XJ, Gu ZH, Wang YY, Chen B, Jiang CL, Yan H, Chen FF, Chen HM, Chen Z, Jin J, Chen SJ. Gene mutation patterns and their prognostic impact in a cohort of 1185 patients with acute myeloid leukemia. Blood. 2011;118(20):5593–603.CrossRefPubMed
13.
14.
go back to reference Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics. 2010;11:137.CrossRefPubMedPubMedCentral Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G. Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC Genomics. 2010;11:137.CrossRefPubMedPubMedCentral
15.
16.
go back to reference Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Lowenberg B, Licht JD, Godley LA, Delwel R, Valk PJ, Thompson CB, Levine RL, Melnick A. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553–67.CrossRefPubMedPubMedCentral Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, Li Y, Bhagwat N, Vasanthakumar A, Fernandez HF, Tallman MS, Sun Z, Wolniak K, Peeters JK, Liu W, Choe SE, Fantin VR, Paietta E, Lowenberg B, Licht JD, Godley LA, Delwel R, Valk PJ, Thompson CB, Levine RL, Melnick A. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18(6):553–67.CrossRefPubMedPubMedCentral
17.
go back to reference Schoofs T, Berdel WE, Muller-Tidow C. Origins of aberrant DNA methylation in acute myeloid leukemia. Leukemia. 2014;28(1):1–14.CrossRefPubMed Schoofs T, Berdel WE, Muller-Tidow C. Origins of aberrant DNA methylation in acute myeloid leukemia. Leukemia. 2014;28(1):1–14.CrossRefPubMed
19.
go back to reference Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288–95.CrossRefPubMed Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R. High density DNA methylation array with single CpG site resolution. Genomics. 2011;98(4):288–95.CrossRefPubMed
20.
go back to reference Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450 K technology. Epigenomics. 2011;3(6):771–84.CrossRefPubMed Dedeurwaerder S, Defrance M, Calonne E, Denis H, Sotiriou C, Fuks F. Evaluation of the Infinium Methylation 450 K technology. Epigenomics. 2011;3(6):771–84.CrossRefPubMed
21.
go back to reference Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016;8(3):389–99.CrossRefPubMed Moran S, Arribas C, Esteller M. Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences. Epigenomics. 2016;8(3):389–99.CrossRefPubMed
22.
go back to reference Keating GM. Azacitidine: a review of its use in the management of myelodysplastic syndromes/acute myeloid leukaemia. Drugs. 2012;72(8):1111–36.CrossRefPubMed Keating GM. Azacitidine: a review of its use in the management of myelodysplastic syndromes/acute myeloid leukaemia. Drugs. 2012;72(8):1111–36.CrossRefPubMed
23.
go back to reference Gao F, Wang J, Ji G, Liu S, Yao Y, Wang T, Wu H, Xia Y, Gong D, Jiang H, Yang H, Zhang X. Clustering of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach. Technol Cancer Res Treat. 2015;14(4):383–94.CrossRefPubMed Gao F, Wang J, Ji G, Liu S, Yao Y, Wang T, Wu H, Xia Y, Gong D, Jiang H, Yang H, Zhang X. Clustering of cancer cell lines using a promoter-targeted liquid hybridization capture-based bisulfite sequencing approach. Technol Cancer Res Treat. 2015;14(4):383–94.CrossRefPubMed
24.
go back to reference Allum F, Shao X, Guenard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman AK, Kwan T, Ge B, Multiple Tissue Human Expression Resource Consurtium, Ronnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun. 2015;6:7211.CrossRefPubMedPubMedCentral Allum F, Shao X, Guenard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman AK, Kwan T, Ge B, Multiple Tissue Human Expression Resource Consurtium, Ronnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun. 2015;6:7211.CrossRefPubMedPubMedCentral
25.
go back to reference Stirzaker C, Taberlay PC, Statham AL, Clark SJ. Mining cancer methylomes: prospects and challenges. Trends Genet. 2014;30(2):75–84.CrossRefPubMed Stirzaker C, Taberlay PC, Statham AL, Clark SJ. Mining cancer methylomes: prospects and challenges. Trends Genet. 2014;30(2):75–84.CrossRefPubMed
26.
go back to reference consortium B. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol. 2016;34(7):726–37.CrossRef consortium B. Quantitative comparison of DNA methylation assays for biomarker development and clinical applications. Nat Biotechnol. 2016;34(7):726–37.CrossRef
27.
go back to reference Meldi K, Qin T, Buchi F, Droin N, Sotzen J, Micol JB, Selimoglu-Buet D, Masala E, Allione B, Gioia D, Poloni A, Lunghi M, Solary E, Abdel-Wahab O, Santini V, Figueroa ME. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia. J Clin Invest. 2015;125(5):1857–72.CrossRefPubMedPubMedCentral Meldi K, Qin T, Buchi F, Droin N, Sotzen J, Micol JB, Selimoglu-Buet D, Masala E, Allione B, Gioia D, Poloni A, Lunghi M, Solary E, Abdel-Wahab O, Santini V, Figueroa ME. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia. J Clin Invest. 2015;125(5):1857–72.CrossRefPubMedPubMedCentral
28.
go back to reference Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Saturation analysis for whole-genome bisulfite sequencing data. Nat Biotechnol. 2016. doi:10.1038/nbt.3524. Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Herrero J, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Saturation analysis for whole-genome bisulfite sequencing data. Nat Biotechnol. 2016. doi:10.​1038/​nbt.​3524.
29.
go back to reference Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Information recovery from low coverage whole-genome bisulfite sequencing. Nat Commun. 2016;7:11306.CrossRefPubMedPubMedCentral Libertini E, Heath SC, Hamoudi RA, Gut M, Ziller MJ, Czyz A, Ruotti V, Stunnenberg HG, Frontini M, Ouwehand WH, Meissner A, Gut IG, Beck S. Information recovery from low coverage whole-genome bisulfite sequencing. Nat Commun. 2016;7:11306.CrossRefPubMedPubMedCentral
30.
go back to reference Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Lowenberg B, Delwel R, Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010;17(1):13–27.CrossRefPubMedPubMedCentral Figueroa ME, Lugthart S, Li Y, Erpelinck-Verschueren C, Deng X, Christos PJ, Schifano E, Booth J, van Putten W, Skrabanek L, Campagne F, Mazumdar M, Greally JM, Valk PJ, Lowenberg B, Delwel R, Melnick A. DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell. 2010;17(1):13–27.CrossRefPubMedPubMedCentral
31.
go back to reference Deneberg S, Grovdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A, Gaidzik V, Dohner K, Paul C, Ekstrom TJ, Hellstrom-Lindberg E, Lehmann S. Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia. 2010;24(5):932–41.CrossRefPubMed Deneberg S, Grovdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A, Gaidzik V, Dohner K, Paul C, Ekstrom TJ, Hellstrom-Lindberg E, Lehmann S. Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia. Leukemia. 2010;24(5):932–41.CrossRefPubMed
32.
go back to reference Yalcin A, Kreutz C, Pfeifer D, Abdelkarim M, Klaus G, Timmer J, Lubbert M, Hackanson B. MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells. Leuk Res. 2013;37(1):102–11.CrossRefPubMed Yalcin A, Kreutz C, Pfeifer D, Abdelkarim M, Klaus G, Timmer J, Lubbert M, Hackanson B. MeDIP coupled with a promoter tiling array as a platform to investigate global DNA methylation patterns in AML cells. Leuk Res. 2013;37(1):102–11.CrossRefPubMed
33.
go back to reference Bullinger L, Ehrich M, Dohner K, Schlenk RF, Dohner H, Nelson MR, van den Boom D. Quantitative DNA methylation predicts survival in adult acute myeloid leukemia. Blood. 2010;115(3):636–42.CrossRefPubMed Bullinger L, Ehrich M, Dohner K, Schlenk RF, Dohner H, Nelson MR, van den Boom D. Quantitative DNA methylation predicts survival in adult acute myeloid leukemia. Blood. 2010;115(3):636–42.CrossRefPubMed
34.
go back to reference Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, Blanchet O, Karimi M, Bengtzen S, Nahi H, Uggla B, Tidefelt U, Hoglund M, Paul C, Ekwall K, Dohner K, Lehmann S. Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks. Blood. 2011;118(20):5573–82.CrossRefPubMed Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, Blanchet O, Karimi M, Bengtzen S, Nahi H, Uggla B, Tidefelt U, Hoglund M, Paul C, Ekwall K, Dohner K, Lehmann S. Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks. Blood. 2011;118(20):5573–82.CrossRefPubMed
35.
go back to reference Luskin MR, Gimotty PA, Smith C, Loren AW, Figueroa ME, Harrison J, Sun Z, Tallman MS, Paietta EM, Litzow MR, Melnick AM, Levine RL, Fernandez HF, Luger SM, Carroll M, Master SR, Wertheim GB. A clinical measure of DNA methylation predicts outcome in de novo acute myeloid leukemia. JCI insight. 2016;1(9):e87323. Luskin MR, Gimotty PA, Smith C, Loren AW, Figueroa ME, Harrison J, Sun Z, Tallman MS, Paietta EM, Litzow MR, Melnick AM, Levine RL, Fernandez HF, Luger SM, Carroll M, Master SR, Wertheim GB. A clinical measure of DNA methylation predicts outcome in de novo acute myeloid leukemia. JCI insight. 2016;1(9):e87323.
36.
go back to reference Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–92.CrossRefPubMed Jones PA. Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nat Rev Genet. 2012;13(7):484–92.CrossRefPubMed
37.
go back to reference Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14(3):204–20.CrossRefPubMed Smith ZD, Meissner A. DNA methylation: roles in mammalian development. Nat Rev Genet. 2013;14(3):204–20.CrossRefPubMed
38.
go back to reference Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30.CrossRefPubMedCentral Roadmap Epigenomics Consortium, Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, et al. Integrative analysis of 111 reference human epigenomes. Nature. 2015;518(7539):317–30.CrossRefPubMedCentral
39.
go back to reference Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Lowenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781.CrossRefPubMedPubMedCentral Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Lowenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME. Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet. 2012;8(6):e1002781.CrossRefPubMedPubMedCentral
40.
go back to reference Arber DA, Attilio O, Robert H, J¨urgen T, Borowitz MJ, Le Beau MM, Bloomfield CD, Mario C, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391–405.CrossRefPubMed Arber DA, Attilio O, Robert H, J¨urgen T, Borowitz MJ, Le Beau MM, Bloomfield CD, Mario C, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391–405.CrossRefPubMed
41.
go back to reference Qu Y, Lennartsson A, Gaidzik VI, Deneberg S, Karimi M, Bengtzen S, Hoglund M, Bullinger L, Dohner K, Lehmann S. Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes. Epigenetics. 2014;9(8):1108–19.CrossRefPubMedPubMedCentral Qu Y, Lennartsson A, Gaidzik VI, Deneberg S, Karimi M, Bengtzen S, Hoglund M, Bullinger L, Dohner K, Lehmann S. Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes. Epigenetics. 2014;9(8):1108–19.CrossRefPubMedPubMedCentral
42.
go back to reference Hajkova H, Fritz MH, Haskovec C, Schwarz J, Salek C, Markova J, Krejcik Z, Dostalova Merkerova M, Kostecka A, Vostry M, Fuchs O, Michalova K, Cetkovsky P, Benes V. CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia. J Hematol Oncol. 2014;7:66.CrossRefPubMedPubMedCentral Hajkova H, Fritz MH, Haskovec C, Schwarz J, Salek C, Markova J, Krejcik Z, Dostalova Merkerova M, Kostecka A, Vostry M, Fuchs O, Michalova K, Cetkovsky P, Benes V. CBFB-MYH11 hypomethylation signature and PBX3 differential methylation revealed by targeted bisulfite sequencing in patients with acute myeloid leukemia. J Hematol Oncol. 2014;7:66.CrossRefPubMedPubMedCentral
43.
go back to reference Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, Fuks F, Lo Coco F, Kouzarides T, Nervi C, Minucci S, Pelicci PG. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science. 2002;295(5557):1079–82.CrossRefPubMed Di Croce L, Raker VA, Corsaro M, Fazi F, Fanelli M, Faretta M, Fuks F, Lo Coco F, Kouzarides T, Nervi C, Minucci S, Pelicci PG. Methyltransferase recruitment and DNA hypermethylation of target promoters by an oncogenic transcription factor. Science. 2002;295(5557):1079–82.CrossRefPubMed
44.
go back to reference Liu S, Shen T, Huynh L, Klisovic MI, Rush LJ, Ford JL, Yu J, Becknell B, Li Y, Liu C, Vukosavljevic T, Whitman SP, Chang KS, Byrd JC, Perrotti D, Plass C, Marcucci G. Interplay of RUNX1/MTG8 and DNA methyltransferase 1 in acute myeloid leukemia. Cancer Res. 2005;65(4):1277–84.CrossRefPubMed Liu S, Shen T, Huynh L, Klisovic MI, Rush LJ, Ford JL, Yu J, Becknell B, Li Y, Liu C, Vukosavljevic T, Whitman SP, Chang KS, Byrd JC, Perrotti D, Plass C, Marcucci G. Interplay of RUNX1/MTG8 and DNA methyltransferase 1 in acute myeloid leukemia. Cancer Res. 2005;65(4):1277–84.CrossRefPubMed
45.
go back to reference Cole CB, Verdoni AM, Ketkar S, Leight ER, Russler-Germain DA, Lamprecht TL, Demeter RT, Magrini V, Ley TJ. PML-RARA requires DNA methyltransferase 3A to initiate acute promyelocytic leukemia. J Clin Invest. 2016;126(1):85–98.CrossRefPubMed Cole CB, Verdoni AM, Ketkar S, Leight ER, Russler-Germain DA, Lamprecht TL, Demeter RT, Magrini V, Ley TJ. PML-RARA requires DNA methyltransferase 3A to initiate acute promyelocytic leukemia. J Clin Invest. 2016;126(1):85–98.CrossRefPubMed
46.
go back to reference Schoofs T, Rohde C, Hebestreit K, Klein HU, Gollner S, Schulze I, Lerdrup M, Dietrich N, Agrawal-Singh S, Witten A, Stoll M, Lengfelder E, Hofmann WK, Schlenke P, Buchner T, Hansen K, Berdel WE, Rosenbauer F, Dugas M, Muller-Tidow C. DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Blood. 2013;121(1):178–87.CrossRefPubMed Schoofs T, Rohde C, Hebestreit K, Klein HU, Gollner S, Schulze I, Lerdrup M, Dietrich N, Agrawal-Singh S, Witten A, Stoll M, Lengfelder E, Hofmann WK, Schlenke P, Buchner T, Hansen K, Berdel WE, Rosenbauer F, Dugas M, Muller-Tidow C. DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding. Blood. 2013;121(1):178–87.CrossRefPubMed
47.
go back to reference Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG. PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia. Cancer Cell. 2010;17(2):173–85.CrossRefPubMed Martens JH, Brinkman AB, Simmer F, Francoijs KJ, Nebbioso A, Ferrara F, Altucci L, Stunnenberg HG. PML-RARalpha/RXR alters the epigenetic landscape in acute promyelocytic leukemia. Cancer Cell. 2010;17(2):173–85.CrossRefPubMed
48.
go back to reference Saeed S, Logie C, Stunnenberg HG, Martens JH. Genome-wide functions of PML-RARalpha in acute promyelocytic leukaemia. Br J Cancer. 2011;104(4):554–8.CrossRefPubMedPubMedCentral Saeed S, Logie C, Stunnenberg HG, Martens JH. Genome-wide functions of PML-RARalpha in acute promyelocytic leukaemia. Br J Cancer. 2011;104(4):554–8.CrossRefPubMedPubMedCentral
49.
go back to reference Ng HY, Wan TS, So CC, Chim CS. Epigenetic inactivation of DAPK1, p14ARF, mir-34a and -34b/c in acute promyelocytic leukaemia. J Clin Pathol. 2014;67(7):626–31.CrossRefPubMed Ng HY, Wan TS, So CC, Chim CS. Epigenetic inactivation of DAPK1, p14ARF, mir-34a and -34b/c in acute promyelocytic leukaemia. J Clin Pathol. 2014;67(7):626–31.CrossRefPubMed
50.
go back to reference Marcucci G, Yan P, Maharry K, Frankhouser D, Nicolet D, Metzeler KH, Kohlschmidt J, Mrozek K, Wu YZ, Bucci D, Curfman JP, Whitman SP, Eisfeld AK, Mendler JH, Schwind S, Becker H, Bar C, Carroll AJ, Baer MR, Wetzler M, Carter TH, Powell BL, Kolitz JE, Byrd JC, Plass C, Garzon R, Caligiuri MA, Stone RM, Volinia S, Bundschuh R, et al. Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score. J Clin Oncol Off J Am Soc Clin Oncol. 2014;32(6):548–56.CrossRef Marcucci G, Yan P, Maharry K, Frankhouser D, Nicolet D, Metzeler KH, Kohlschmidt J, Mrozek K, Wu YZ, Bucci D, Curfman JP, Whitman SP, Eisfeld AK, Mendler JH, Schwind S, Becker H, Bar C, Carroll AJ, Baer MR, Wetzler M, Carter TH, Powell BL, Kolitz JE, Byrd JC, Plass C, Garzon R, Caligiuri MA, Stone RM, Volinia S, Bundschuh R, et al. Epigenetics meets genetics in acute myeloid leukemia: clinical impact of a novel seven-gene score. J Clin Oncol Off J Am Soc Clin Oncol. 2014;32(6):548–56.CrossRef
51.
go back to reference Li KK, Luo LF, Shen Y, Xu J, Chen Z, Chen SJ. DNA methyltransferases in hematologic malignancies. Semin Hematol. 2013;50(1):48–60.CrossRefPubMed Li KK, Luo LF, Shen Y, Xu J, Chen Z, Chen SJ. DNA methyltransferases in hematologic malignancies. Semin Hematol. 2013;50(1):48–60.CrossRefPubMed
52.
go back to reference Liu X, Jia X, Yuan H, Ma K, Chen Y, Jin Y, Deng M, Pan W, Chen S, Chen Z, de The H, Zon LI, Zhou Y, Zhou J, Zhu J. DNA methyltransferase 1 functions through C/ebpa to maintain hematopoietic stem and progenitor cells in zebrafish. J Hematol Oncol. 2015;8:15.CrossRefPubMedPubMedCentral Liu X, Jia X, Yuan H, Ma K, Chen Y, Jin Y, Deng M, Pan W, Chen S, Chen Z, de The H, Zon LI, Zhou Y, Zhou J, Zhu J. DNA methyltransferase 1 functions through C/ebpa to maintain hematopoietic stem and progenitor cells in zebrafish. J Hematol Oncol. 2015;8:15.CrossRefPubMedPubMedCentral
53.
go back to reference Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2012;44(1):23–31.CrossRef Challen GA, Sun D, Jeong M, Luo M, Jelinek J, Berg JS, Bock C, Vasanthakumar A, Gu H, Xi Y, Liang S, Lu Y, Darlington GJ, Meissner A, Issa JP, Godley LA, Li W, Goodell MA. Dnmt3a is essential for hematopoietic stem cell differentiation. Nat Genet. 2012;44(1):23–31.CrossRef
54.
go back to reference Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424–33.CrossRefPubMedPubMedCentral Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363(25):2424–33.CrossRefPubMedPubMedCentral
55.
go back to reference Mizuno S, Chijiwa T, Okamura T, Akashi K, Fukumaki Y, Niho Y, Sasaki H. Expression of DNA methyltransferases DNMT1, 3A, and 3B in normal hematopoiesis and in acute and chronic myelogenous leukemia. Blood. 2001;97(5):1172–9.CrossRefPubMed Mizuno S, Chijiwa T, Okamura T, Akashi K, Fukumaki Y, Niho Y, Sasaki H. Expression of DNA methyltransferases DNMT1, 3A, and 3B in normal hematopoiesis and in acute and chronic myelogenous leukemia. Blood. 2001;97(5):1172–9.CrossRefPubMed
56.
go back to reference Deveau AP, Forrester AM, Coombs AJ, Wagner GS, Grabher C, Chute IC, Leger D, Mingay M, Alexe G, Rajan V, Liwski R, Hirst M, Steigmaier K, Lewis SM, Look AT, Berman JN. Epigenetic therapy restores normal hematopoiesis in a zebrafish model of NUP98-HOXA9-induced myeloid disease. Leukemia. 2015;29(10):2086–97.CrossRefPubMed Deveau AP, Forrester AM, Coombs AJ, Wagner GS, Grabher C, Chute IC, Leger D, Mingay M, Alexe G, Rajan V, Liwski R, Hirst M, Steigmaier K, Lewis SM, Look AT, Berman JN. Epigenetic therapy restores normal hematopoiesis in a zebrafish model of NUP98-HOXA9-induced myeloid disease. Leukemia. 2015;29(10):2086–97.CrossRefPubMed
57.
go back to reference Shlush LI, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, Kennedy JA, Schimmer AD, Schuh AC, Yee KW, McLeod JL, Doedens M, Medeiros JJ, Marke R, Kim HJ, Lee K, McPherson JD, Hudson TJ, Consortium HP-LGP, Brown AM, Yousif F, Trinh QM, Stein LD, Minden MD, Wang JC, Dick JE. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014;506(7488):328–33.CrossRefPubMedPubMedCentral Shlush LI, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, Kennedy JA, Schimmer AD, Schuh AC, Yee KW, McLeod JL, Doedens M, Medeiros JJ, Marke R, Kim HJ, Lee K, McPherson JD, Hudson TJ, Consortium HP-LGP, Brown AM, Yousif F, Trinh QM, Stein LD, Minden MD, Wang JC, Dick JE. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014;506(7488):328–33.CrossRefPubMedPubMedCentral
58.
go back to reference Jiang D, Hong Q, Shen Y, Xu Y, Zhu H, Li Y, Xu C, Ouyang G, Duan S. The diagnostic value of DNA methylation in leukemia: a systematic review and meta-analysis. PLoS One. 2014;9(5):e96822.CrossRefPubMedPubMedCentral Jiang D, Hong Q, Shen Y, Xu Y, Zhu H, Li Y, Xu C, Ouyang G, Duan S. The diagnostic value of DNA methylation in leukemia: a systematic review and meta-analysis. PLoS One. 2014;9(5):e96822.CrossRefPubMedPubMedCentral
59.
go back to reference Gao XN, Yan F, Lin J, Gao L, Lu XL, Wei SC, Shen N, Pang JX, Ning QY, Komeno Y, Deng AL, Xu YH, Shi JL, Li YH, Zhang DE, Nervi C, Liu SJ, Yu L. AML1/ETO cooperates with HIF1alpha to promote leukemogenesis through DNMT3a transactivation. Leukemia. 2015;29(8):1730–40.CrossRefPubMed Gao XN, Yan F, Lin J, Gao L, Lu XL, Wei SC, Shen N, Pang JX, Ning QY, Komeno Y, Deng AL, Xu YH, Shi JL, Li YH, Zhang DE, Nervi C, Liu SJ, Yu L. AML1/ETO cooperates with HIF1alpha to promote leukemogenesis through DNMT3a transactivation. Leukemia. 2015;29(8):1730–40.CrossRefPubMed
60.
go back to reference Wertheim GB, Smith C, Figueroa ME, Kalos M, Bagg A, Carroll M, Master SR. Microsphere-based multiplex analysis of DNA methylation in acute myeloid leukemia. J Mol Diagn. 2014;16(2):207–15.CrossRefPubMedPubMedCentral Wertheim GB, Smith C, Figueroa ME, Kalos M, Bagg A, Carroll M, Master SR. Microsphere-based multiplex analysis of DNA methylation in acute myeloid leukemia. J Mol Diagn. 2014;16(2):207–15.CrossRefPubMedPubMedCentral
61.
go back to reference Wertheim GB, Smith C, Luskin M, Rager A, Figueroa ME, Carroll M, Master SR. Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP. Clin Chem. 2015;61(1):249–58.CrossRefPubMed Wertheim GB, Smith C, Luskin M, Rager A, Figueroa ME, Carroll M, Master SR. Validation of DNA methylation to predict outcome in acute myeloid leukemia by use of xMELP. Clin Chem. 2015;61(1):249–58.CrossRefPubMed
62.
go back to reference DiNardo CD, Luskin MR, Carroll M, Smith C, Harrison J, Pierce S, Kornblau S, Konopleva M, Kadia T, Kantarjian H, Wertheim GB, Master SR. Validation of a clinical assay of multi-locus DNA methylation for prognosis of newly diagnosed AML. Am J Hematol. 2017;92(2):E14-5. DiNardo CD, Luskin MR, Carroll M, Smith C, Harrison J, Pierce S, Kornblau S, Konopleva M, Kadia T, Kantarjian H, Wertheim GB, Master SR. Validation of a clinical assay of multi-locus DNA methylation for prognosis of newly diagnosed AML. Am J Hematol. 2017;92(2):E14-5.
63.
go back to reference Raj K, John A, Ho A, Chronis C, Khan S, Samuel J, Pomplun S, Thomas NS, Mufti GJ. CDKN2B methylation status and isolated chromosome 7 abnormalities predict responses to treatment with 5-azacytidine. Leukemia. 2007;21(9):1937–44.CrossRefPubMed Raj K, John A, Ho A, Chronis C, Khan S, Samuel J, Pomplun S, Thomas NS, Mufti GJ. CDKN2B methylation status and isolated chromosome 7 abnormalities predict responses to treatment with 5-azacytidine. Leukemia. 2007;21(9):1937–44.CrossRefPubMed
64.
go back to reference Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM, Carraway H, Licht JD, Gore SD, Melnick A. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. Blood. 2009;114(16):3448–58.CrossRefPubMedPubMedCentral Figueroa ME, Skrabanek L, Li Y, Jiemjit A, Fandy TE, Paietta E, Fernandez H, Tallman MS, Greally JM, Carraway H, Licht JD, Gore SD, Melnick A. MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. Blood. 2009;114(16):3448–58.CrossRefPubMedPubMedCentral
65.
go back to reference Zhang LY, Yuan YQ, Zhou DM, Wang ZY, Ju SG, Sun Y, Li J, Fu JX. Impact of global and gene-specific DNA methylation in de novo or relapsed acute myeloid leukemia patients treated with decitabine. Asian Pac J Cancer Prev. 2016;17(1):431–7.CrossRefPubMed Zhang LY, Yuan YQ, Zhou DM, Wang ZY, Ju SG, Sun Y, Li J, Fu JX. Impact of global and gene-specific DNA methylation in de novo or relapsed acute myeloid leukemia patients treated with decitabine. Asian Pac J Cancer Prev. 2016;17(1):431–7.CrossRefPubMed
66.
go back to reference Grovdal M, Khan R, Aggerholm A, Antunovic P, Astermark J, Bernell P, Engstrom LM, Kjeldsen L, Linder O, Nilsson L, Olsson A, Wallvik J, Tangen JM, Oberg G, Jacobsen SE, Hokland P, Porwit A, Hellstrom-Lindberg E. Negative effect of DNA hypermethylation on the outcome of intensive chemotherapy in older patients with high-risk myelodysplastic syndromes and acute myeloid leukemia following myelodysplastic syndrome. Clin Cancer Res. 2007;13(23):7107–12.CrossRefPubMed Grovdal M, Khan R, Aggerholm A, Antunovic P, Astermark J, Bernell P, Engstrom LM, Kjeldsen L, Linder O, Nilsson L, Olsson A, Wallvik J, Tangen JM, Oberg G, Jacobsen SE, Hokland P, Porwit A, Hellstrom-Lindberg E. Negative effect of DNA hypermethylation on the outcome of intensive chemotherapy in older patients with high-risk myelodysplastic syndromes and acute myeloid leukemia following myelodysplastic syndrome. Clin Cancer Res. 2007;13(23):7107–12.CrossRefPubMed
67.
go back to reference Ribeiro AF, Pratcorona M, Erpelinck-Verschueren C, Rockova V, Sanders M, Abbas S, Figueroa ME, Zeilemaker A, Melnick A, Lowenberg B, Valk PJ, Delwel R. Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia. Blood. 2012;119(24):5824–31.CrossRefPubMed Ribeiro AF, Pratcorona M, Erpelinck-Verschueren C, Rockova V, Sanders M, Abbas S, Figueroa ME, Zeilemaker A, Melnick A, Lowenberg B, Valk PJ, Delwel R. Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia. Blood. 2012;119(24):5824–31.CrossRefPubMed
68.
go back to reference Abbas S, Lugthart S, Kavelaars FG, Schelen A, Koenders JE, Zeilemaker A, van Putten WJ, Rijneveld AW, Lowenberg B, Valk PJ. Acquired mutations in the genes encoding IDH1 and IDH2 both are recurrent aberrations in acute myeloid leukemia: prevalence and prognostic value. Blood. 2010;116(12):2122–6.CrossRefPubMed Abbas S, Lugthart S, Kavelaars FG, Schelen A, Koenders JE, Zeilemaker A, van Putten WJ, Rijneveld AW, Lowenberg B, Valk PJ. Acquired mutations in the genes encoding IDH1 and IDH2 both are recurrent aberrations in acute myeloid leukemia: prevalence and prognostic value. Blood. 2010;116(12):2122–6.CrossRefPubMed
69.
go back to reference Gaidzik VI, Paschka P, Spath D, Habdank M, Kohne CH, Germing U, von Lilienfeld-Toal M, Held G, Horst HA, Haase D, Bentz M, Gotze K, Dohner H, Schlenk RF, Bullinger L, Dohner K. TET2 mutations in acute myeloid leukemia (AML): results from a comprehensive genetic and clinical analysis of the AML study group. J Clin Oncol Off J Am Soc Clin Oncol. 2012;30(12):1350–7.CrossRef Gaidzik VI, Paschka P, Spath D, Habdank M, Kohne CH, Germing U, von Lilienfeld-Toal M, Held G, Horst HA, Haase D, Bentz M, Gotze K, Dohner H, Schlenk RF, Bullinger L, Dohner K. TET2 mutations in acute myeloid leukemia (AML): results from a comprehensive genetic and clinical analysis of the AML study group. J Clin Oncol Off J Am Soc Clin Oncol. 2012;30(12):1350–7.CrossRef
70.
go back to reference Wouters BJ, Delwel R. Epigenetics and approaches to targeted epigenetic therapy in acute myeloid leukemia. Blood. 2016;127(1):42–52.CrossRefPubMed Wouters BJ, Delwel R. Epigenetics and approaches to targeted epigenetic therapy in acute myeloid leukemia. Blood. 2016;127(1):42–52.CrossRefPubMed
72.
go back to reference Chau D, Ng K, Chan TS, Cheng YY, Fong B, Tam S, Kwong YL, Tse E. Azacytidine sensitizes acute myeloid leukemia cells to arsenic trioxide by up-regulating the arsenic transporter aquaglyceroporin 9. J Hematol Oncol. 2015;8:46.CrossRefPubMedPubMedCentral Chau D, Ng K, Chan TS, Cheng YY, Fong B, Tam S, Kwong YL, Tse E. Azacytidine sensitizes acute myeloid leukemia cells to arsenic trioxide by up-regulating the arsenic transporter aquaglyceroporin 9. J Hematol Oncol. 2015;8:46.CrossRefPubMedPubMedCentral
73.
go back to reference Tibes R, Al-Kali A, Oliver GR, Delman DH, Hansen N, Bhagavatula K, Mohan J, Rakhshan F, Wood T, Foran JM, Mesa RA, Bogenberger JM. The Hedgehog pathway as targetable vulnerability with 5-azacytidine in myelodysplastic syndrome and acute myeloid leukemia. J Hematol Oncol. 2015;8:114.CrossRefPubMedPubMedCentral Tibes R, Al-Kali A, Oliver GR, Delman DH, Hansen N, Bhagavatula K, Mohan J, Rakhshan F, Wood T, Foran JM, Mesa RA, Bogenberger JM. The Hedgehog pathway as targetable vulnerability with 5-azacytidine in myelodysplastic syndrome and acute myeloid leukemia. J Hematol Oncol. 2015;8:114.CrossRefPubMedPubMedCentral
74.
go back to reference Nieto M, Demolis P, Behanzin E, Moreau A, Hudson I, Flores B, Stemplewski H, Salmonson T, Gisselbrecht C, Bowen D, Pignatti F. The European Medicines Agency Review of Decitabine (Dacogen) for the treatment of adult patients with acute myeloid leukemia: summary of the scientific assessment of the committee for medicinal products for human use. Oncologist. 2016;21(6):692–700.CrossRefPubMed Nieto M, Demolis P, Behanzin E, Moreau A, Hudson I, Flores B, Stemplewski H, Salmonson T, Gisselbrecht C, Bowen D, Pignatti F. The European Medicines Agency Review of Decitabine (Dacogen) for the treatment of adult patients with acute myeloid leukemia: summary of the scientific assessment of the committee for medicinal products for human use. Oncologist. 2016;21(6):692–700.CrossRefPubMed
75.
go back to reference Dombret H, Seymour JF, Butrym A, Wierzbowska A, Selleslag D, Jang JH, Kumar R, Cavenagh J, Schuh AC, Candoni A, Recher C, Sandhu I, Bernal del Castillo T, Al-Ali HK, Martinelli G, Falantes J, Noppeney R, Stone RM, Minden MD, McIntyre H, Songer S, Lucy LM, Beach CL, Dohner H. International phase 3 study of azacitidine vs conventional care regimens in older patients with newly diagnosed AML with >30% blasts. Blood. 2015;126(3):291–9.CrossRefPubMedPubMedCentral Dombret H, Seymour JF, Butrym A, Wierzbowska A, Selleslag D, Jang JH, Kumar R, Cavenagh J, Schuh AC, Candoni A, Recher C, Sandhu I, Bernal del Castillo T, Al-Ali HK, Martinelli G, Falantes J, Noppeney R, Stone RM, Minden MD, McIntyre H, Songer S, Lucy LM, Beach CL, Dohner H. International phase 3 study of azacitidine vs conventional care regimens in older patients with newly diagnosed AML with >30% blasts. Blood. 2015;126(3):291–9.CrossRefPubMedPubMedCentral
76.
go back to reference Han S, Kim YJ, Lee J, Jeon S, Hong T, Park GJ, Yoon JH, Yahng SA, Shin SH, Lee SE, Eom KS, Kim HJ, Min CK, Lee S, Yim DS. Model-based adaptive phase I trial design of post-transplant decitabine maintenance in myelodysplastic syndrome. J Hematol Oncol. 2015;8:118.CrossRefPubMedPubMedCentral Han S, Kim YJ, Lee J, Jeon S, Hong T, Park GJ, Yoon JH, Yahng SA, Shin SH, Lee SE, Eom KS, Kim HJ, Min CK, Lee S, Yim DS. Model-based adaptive phase I trial design of post-transplant decitabine maintenance in myelodysplastic syndrome. J Hematol Oncol. 2015;8:118.CrossRefPubMedPubMedCentral
77.
go back to reference Traina F, Visconte V, Elson P, Tabarroki A, Jankowska AM, Hasrouni E, Sugimoto Y, Szpurka H, Makishima H, O'Keefe CL, Sekeres MA, Advani AS, Kalaycio M, Copelan EA, Saunthararajah Y, Olalla Saad ST, Maciejewski JP, Tiu RV. Impact of molecular mutations on treatment response to DNMT inhibitors in myelodysplasia and related neoplasms. Leukemia. 2014;28(1):78–87.CrossRefPubMed Traina F, Visconte V, Elson P, Tabarroki A, Jankowska AM, Hasrouni E, Sugimoto Y, Szpurka H, Makishima H, O'Keefe CL, Sekeres MA, Advani AS, Kalaycio M, Copelan EA, Saunthararajah Y, Olalla Saad ST, Maciejewski JP, Tiu RV. Impact of molecular mutations on treatment response to DNMT inhibitors in myelodysplasia and related neoplasms. Leukemia. 2014;28(1):78–87.CrossRefPubMed
78.
go back to reference Emadi A, Faramand R, Carter-Cooper B, Tolu S, Ford LA, Lapidus RG, Wetzler M, Wang ES, Etemadi A, Griffiths EA. Presence of isocitrate dehydrogenase mutations may predict clinical response to hypomethylating agents in patients with acute myeloid leukemia. Am J Hematol. 2015;90(5):E77–9.CrossRefPubMed Emadi A, Faramand R, Carter-Cooper B, Tolu S, Ford LA, Lapidus RG, Wetzler M, Wang ES, Etemadi A, Griffiths EA. Presence of isocitrate dehydrogenase mutations may predict clinical response to hypomethylating agents in patients with acute myeloid leukemia. Am J Hematol. 2015;90(5):E77–9.CrossRefPubMed
80.
go back to reference Stein EM. Molecular pathways: IDH2 mutations-co-opting cellular metabolism for malignant transformation. Clin Cancer Res. 2016;22(1):16–9.CrossRefPubMed Stein EM. Molecular pathways: IDH2 mutations-co-opting cellular metabolism for malignant transformation. Clin Cancer Res. 2016;22(1):16–9.CrossRefPubMed
82.
go back to reference Hansen E, Quivoron C, Straley K, Lemieux RM, Popovici-Muller J, Sadrzadeh H, Fathi AT, Gliser C, David M, Saada V, Micol JB, Bernard O, Dorsch M, Yang H, Su M, Agresta S, de Botton S, Lacronique VP, Yen K. AG-120, an oral, selective, first-in-Class, potent inhibitor of mutant IDH1, reduces intracellular 2HG and induces cellular differentiation in TF-1 R132H cells and primary human IDH1 mutant AML patient samples treated ex vivo. Blood. 2014;124(21):3734. Hansen E, Quivoron C, Straley K, Lemieux RM, Popovici-Muller J, Sadrzadeh H, Fathi AT, Gliser C, David M, Saada V, Micol JB, Bernard O, Dorsch M, Yang H, Su M, Agresta S, de Botton S, Lacronique VP, Yen K. AG-120, an oral, selective, first-in-Class, potent inhibitor of mutant IDH1, reduces intracellular 2HG and induces cellular differentiation in TF-1 R132H cells and primary human IDH1 mutant AML patient samples treated ex vivo. Blood. 2014;124(21):3734.
83.
go back to reference DiNardo CD, Schimmer A, Yee KWL, Hochhaus A, Kraemer A, Carvajal RD, Janku F, Bedard P, Carpio C, Wick A, Schwartz GK, Schöffski P, Wen P, van den Bent MJ, Rosenthal M, O'Keeffe J, Chen X, Pagliarini R, Schuck V, Myers A, Wei A. A phase I study of IDH305 in patients with advanced malignancies including relapsed/refractory AML and MDS that harbor IDH1R132 mutations. Blood. 2016;128(22):1073. DiNardo CD, Schimmer A, Yee KWL, Hochhaus A, Kraemer A, Carvajal RD, Janku F, Bedard P, Carpio C, Wick A, Schwartz GK, Schöffski P, Wen P, van den Bent MJ, Rosenthal M, O'Keeffe J, Chen X, Pagliarini R, Schuck V, Myers A, Wei A. A phase I study of IDH305 in patients with advanced malignancies including relapsed/refractory AML and MDS that harbor IDH1R132 mutations. Blood. 2016;128(22):1073.
84.
go back to reference DiNardo CD, de Botton S, Stein EM, Roboz GJ, Swords RT, Pollyea DA, Fathi AT, Collins R, Altman JK, Flinn IW, Mannis GN, Mims AS, Foran JM, Pigneux A, Prince GT, Uy GL, Tallman MS, Kantarjian HM, Liu H, Attar EC, Sacolick J, Yen K, Hurov JB, Choe S, Wu B, Stone RM. Determination of IDH1 mutational burden and clearance via next-generation sequencing in patients with IDH1 mutation-positive hematologic malignancies receiving AG-120, a first-in-class inhibitor of mutant IDH1. Blood. 2016;128(22):1070. DiNardo CD, de Botton S, Stein EM, Roboz GJ, Swords RT, Pollyea DA, Fathi AT, Collins R, Altman JK, Flinn IW, Mannis GN, Mims AS, Foran JM, Pigneux A, Prince GT, Uy GL, Tallman MS, Kantarjian HM, Liu H, Attar EC, Sacolick J, Yen K, Hurov JB, Choe S, Wu B, Stone RM. Determination of IDH1 mutational burden and clearance via next-generation sequencing in patients with IDH1 mutation-positive hematologic malignancies receiving AG-120, a first-in-class inhibitor of mutant IDH1. Blood. 2016;128(22):1070.
85.
go back to reference Stein EM, Fathi AT, DiNardo CD, Pollyea DA, Swords RT, Roboz GJ, Collins R, Sekeres MA, Stone RM, Attar EC, Tosolini A, Xu Q, Amatangelo M, Gupta I, Knight RD, De Botton S, Tallman MS, Kantarjian HM. Enasidenib (AG-221), a potent oral inhibitor of mutant isocitrate dehydrogenase 2 (IDH2) enzyme, induces hematologic responses in patients with myelodysplastic syndromes (MDS). Blood. 2016;128(22):343. Stein EM, Fathi AT, DiNardo CD, Pollyea DA, Swords RT, Roboz GJ, Collins R, Sekeres MA, Stone RM, Attar EC, Tosolini A, Xu Q, Amatangelo M, Gupta I, Knight RD, De Botton S, Tallman MS, Kantarjian HM. Enasidenib (AG-221), a potent oral inhibitor of mutant isocitrate dehydrogenase 2 (IDH2) enzyme, induces hematologic responses in patients with myelodysplastic syndromes (MDS). Blood. 2016;128(22):343.
86.
go back to reference Stein EM, DiNardo CD, Altman JK, Collins R, DeAngelo DJ, Kantarjian HM, Sekeres MA, Fathi AT, Flinn LW, Frankel AE, Levine RL, Medeiros BC, Patel MR, Pollyea DA, Roboz GJ, Stone RM, Swords RT, Tallman MS, Yen K, Attar EC, Xu Q, Tosolini A, Mei JM, Thakurta A, Knight RD, De Botton S. Safety and efficacy of AG-221, a potent inhibitor of mutant IDH2 that promotes differentiation of myeloid cells in patients with advanced hematologic malignancies: results of a phase 1/2 trial. Blood. 2015;126(23):323. Stein EM, DiNardo CD, Altman JK, Collins R, DeAngelo DJ, Kantarjian HM, Sekeres MA, Fathi AT, Flinn LW, Frankel AE, Levine RL, Medeiros BC, Patel MR, Pollyea DA, Roboz GJ, Stone RM, Swords RT, Tallman MS, Yen K, Attar EC, Xu Q, Tosolini A, Mei JM, Thakurta A, Knight RD, De Botton S. Safety and efficacy of AG-221, a potent inhibitor of mutant IDH2 that promotes differentiation of myeloid cells in patients with advanced hematologic malignancies: results of a phase 1/2 trial. Blood. 2015;126(23):323.
87.
go back to reference Taskesen E, Babaei S, Reinders MM, de Ridder J. Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia. BMC Bioinf. 2015;16 Suppl 4:S5.CrossRef Taskesen E, Babaei S, Reinders MM, de Ridder J. Integration of gene expression and DNA-methylation profiles improves molecular subtype classification in acute myeloid leukemia. BMC Bioinf. 2015;16 Suppl 4:S5.CrossRef
88.
go back to reference Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL. Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. Cancer Cell. 2015;27(4):502–15.CrossRefPubMedPubMedCentral Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL. Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. Cancer Cell. 2015;27(4):502–15.CrossRefPubMedPubMedCentral
89.
go back to reference Ohgami RS, Arber DA. The diagnostic and clinical impact of genetics and epigenetics in acute myeloid leukemia. Int J Lab Hematol. 2015;37 Suppl 1:122–32.CrossRefPubMed Ohgami RS, Arber DA. The diagnostic and clinical impact of genetics and epigenetics in acute myeloid leukemia. Int J Lab Hematol. 2015;37 Suppl 1:122–32.CrossRefPubMed
90.
go back to reference Bujold D, Morais DA, Gauthier C, Cote C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PE, Bourque G. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496–9. e492.CrossRefPubMed Bujold D, Morais DA, Gauthier C, Cote C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PE, Bourque G. The International Human Epigenome Consortium Data Portal. Cell Syst. 2016;3(5):496–9. e492.CrossRefPubMed
91.
go back to reference Fernandez JM, de la Torre V, Richardson D, Royo R, Puiggros M, Moncunill V, Fragkogianni S, Clarke L, Consortium B, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. The BLUEPRINT Data Analysis Portal. Cell Syst. 2016;3(5):491–5. e495.CrossRefPubMed Fernandez JM, de la Torre V, Richardson D, Royo R, Puiggros M, Moncunill V, Fragkogianni S, Clarke L, Consortium B, Flicek P, Rico D, Torrents D, Carrillo de Santa Pau E, Valencia A. The BLUEPRINT Data Analysis Portal. Cell Syst. 2016;3(5):491–5. e495.CrossRefPubMed
92.
go back to reference Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PE, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. eFORGE: a tool for identifying cell type-specific signal in epigenomic data. Cell Rep. 2016;17(8):2137–50.CrossRefPubMedPubMedCentral Breeze CE, Paul DS, van Dongen J, Butcher LM, Ambrose JC, Barrett JE, Lowe R, Rakyan VK, Iotchkova V, Frontini M, Downes K, Ouwehand WH, Laperle J, Jacques PE, Bourque G, Bergmann AK, Siebert R, Vellenga E, Saeed S, Matarese F, Martens JH, Stunnenberg HG, Teschendorff AE, Herrero J, Birney E, Dunham I, Beck S. eFORGE: a tool for identifying cell type-specific signal in epigenomic data. Cell Rep. 2016;17(8):2137–50.CrossRefPubMedPubMedCentral
Metadata
Title
Clinical implications of genome-wide DNA methylation studies in acute myeloid leukemia
Authors
Yan Li
Qingyu Xu
Na Lv
Lili Wang
Hongmei Zhao
Xiuli Wang
Jing Guo
Chongjian Chen
Yonghui Li
Li Yu
Publication date
01-12-2017
Publisher
BioMed Central
Published in
Journal of Hematology & Oncology / Issue 1/2017
Electronic ISSN: 1756-8722
DOI
https://doi.org/10.1186/s13045-017-0409-z

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