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Epigenetic regulation in hematopoiesis and its implications in the targeted therapy of hematologic malignancies. Signal Transduct Target Ther 2023; 8:71. [PMID: 36797244 PMCID: PMC9935927 DOI: 10.1038/s41392-023-01342-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 01/03/2023] [Accepted: 01/19/2023] [Indexed: 02/18/2023] Open
Abstract
Hematologic malignancies are one of the most common cancers, and the incidence has been rising in recent decades. The clinical and molecular features of hematologic malignancies are highly heterogenous, and some hematologic malignancies are incurable, challenging the treatment, and prognosis of the patients. However, hematopoiesis and oncogenesis of hematologic malignancies are profoundly affected by epigenetic regulation. Studies have found that methylation-related mutations, abnormal methylation profiles of DNA, and abnormal histone deacetylase expression are recurrent in leukemia and lymphoma. Furthermore, the hypomethylating agents and histone deacetylase inhibitors are effective to treat acute myeloid leukemia and T-cell lymphomas, indicating that epigenetic regulation is indispensable to hematologic oncogenesis. Epigenetic regulation mainly includes DNA modifications, histone modifications, and noncoding RNA-mediated targeting, and regulates various DNA-based processes. This review presents the role of writers, readers, and erasers of DNA methylation and histone methylation, and acetylation in hematologic malignancies. In addition, this review provides the influence of microRNAs and long noncoding RNAs on hematologic malignancies. Furthermore, the implication of epigenetic regulation in targeted treatment is discussed. This review comprehensively presents the change and function of each epigenetic regulator in normal and oncogenic hematopoiesis and provides innovative epigenetic-targeted treatment in clinical practice.
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Identification of three novel DNMT3A mutations with compromising methylation capacity in human acute myeloid leukaemia. Mol Biol Rep 2022; 49:11685-11693. [PMID: 36175738 DOI: 10.1007/s11033-022-07977-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 09/21/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Acute myeloid leukaemia (AML) is a complex and heterogeneous hematopoietic stem and progenitor cell malignancy characterised by the accumulation of immature blast cells in the bone marrow, blood, and other organs linked to environmental, genetic, and epigenetic factors. Somatic mutations in the gene DNA (cytosine-5)-methyltransferase 3A (DNMT3A; NM_022552.4) are common in AML patients. METHODS In this study, we used Sanger sequencing to detect the mutations in the DNMT3A gene in 61 Iraqi AML patients, Hence, the protein function and stability within alterations were identified and analyzed using a variety of computational tools with the goal of determining how these changes affect total protein stability, and then the capacity of methylation was analyzed by methylation specific PCR MSP status at CpG islands. RESULTS Three novel mutations in exon 23 of DNMT3A were identified in 14 patients (22.9%; V877I, N879delA, and L888Q). The V877I and L888Q substitutions are caused by heterozygous C2629G > A and C2663T > A mutations, respectively, while frameshift mutation C2635delA caused protein truncation with stop codon N879T*. Methylation was detected in the DNMT3A promoter region in 9 patients carrying DNMT3A mutations (64.28%) by MSP, and we found significant correlations between DNMT3A mutations and promoter methylation (p = 8.52 × 105). In addition, we found a significant overrepresentation of DNMT3A methylation status in patients ≥ 50 years old (p = 0.025). CONCLUSION Our findings highlight the importance of studying the effects of DNMT3A methylation alteration in Iraqi populations beyond R882 substitutions in the leukemogenic pathway so that patient treatment can be tailored to prevent therapeutic resistance and relapse.
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Study of DNA methyl transferase 3A mutation in acute myeloid leukemic patients. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2018. [DOI: 10.1016/j.ejmhg.2018.05.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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Yang X, Shi J, Zhang X, Zhang G, Zhang J, Yang S, Wang J, Ke X, Fu L. Biological and clinical influences of NPM1 in acute myeloid leukemia patients with DNMT3A mutations. Cancer Manag Res 2018; 10:2489-2497. [PMID: 30122998 PMCID: PMC6086113 DOI: 10.2147/cmar.s166714] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Purpose DNMT3A and NPM1 mutations are known to impact the prognosis of acute myeloid leukemia (AML). DNMT3A mutations are negative prognostic factors, while NPM1 mutations are low-risk factors and inclined to concurrently appear with DNMT3A mutations. In this study, we aimed to find out how NPM1 mutations affect patients’ outcomes in the background of DNMT3A mutations. Patients and methods We screened The Cancer Genome Atlas (TCGA) database and found 51 AML patients with DNMT3A mutations. Of them, 28 patients had a combination of NPM1 mutations. Results In all, NPM1 had the highest mutation frequency (n=28, 54.9%). DNMT3Amut/NPM1mut patients had higher bone marrow (BM) blasts (P=0.015), higher FLT3-ITD/TKD rate (P=0.004), and lower IDH2 mutation rate (P=0.014) than the DNMT3Amut/NPM1wild patients, while their prognoses were the same as the DNMT3Amut/NPM1wild patients (P>0.1). All 51 patients benefited from hematopoietic stem cell transplantation (HSCT) treatment (P=0.005 and 0.001 for event-free survival [EFS] and overall survival [OS], respectively). In the 23 patients with DNMT3Amut/NPM1wild, those who received HSCT had prolonged EFS and OS (P=0.043 and 0.008, respectively), while HSCT treatment did not produce a positive impact on EFS and OS in the remaining 28 patients with DNMT3Amut/NPM1mut (P=0.056 and 0.053, respectively). Conclusion Our study found that NPM1 mutations influenced BM blasts’ percentage, FLT3-ITD/TKD rate, and IDH2 mutation rate in AML patients with DNMT3A mutations but made little difference to the overall prognosis. While HSCT treatments benefited all DNMT3Amut patients, it was better for DNMT3Amut/NPM1wild patients to extend their EFS and OS.
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Affiliation(s)
- Xinrui Yang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jinlong Shi
- Department of Biomedical Engineering, Chinese PLA General Hospital, Beijing 100853, China
| | - Xinpei Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Gaoqi Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jilei Zhang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Siyuan Yang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Jing Wang
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Xiaoyan Ke
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
| | - Lin Fu
- Department of Hematology and Lymphoma Research Center, Peking University, Third Hospital, Beijing 100191, China,
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Martín I, Navarro B, Villamón E, Solano C, Serrano A, Calabuig M, Amat P, Domingo F, Abellán R, García F, Olivares MD, Chaves FJ, Tormo M, Hernández-Boluda JC. Therapy-related acute myeloid leukemia developing 14 years after allogeneic hematopoietic stem cell transplantation, from a persistent R882H- DNMT3A mutated clone of patient origin. Exp Mol Pathol 2018; 105:139-143. [DOI: 10.1016/j.yexmp.2018.07.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Revised: 06/24/2018] [Accepted: 07/07/2018] [Indexed: 10/28/2022]
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Lei B, Chen Y, He A, Luo J, Zhang P, Zhou F, Liu J, Meng X, Wang J, Zhang W. C59T mutation in exon 2 of monocytic leukemia-associated antigen-34 gene indicates a high risk of recurrence of acute myeloid leukemia. Oncol Lett 2017; 14:55-62. [PMID: 28693135 PMCID: PMC5494830 DOI: 10.3892/ol.2017.6110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 02/13/2017] [Indexed: 12/02/2022] Open
Abstract
Monocytic leukemia-associated antigen-34 (MLAA-34) is a novel monocytic leukemia-associated antigen and a candidate oncogene. The aim of the present study was to investigate the involvement of the MLAA-34 gene in acute myeloid leukemia (AML). MLAA-34 expression level, chromosome location, gene copy number and single nucleotide polymorphisms (SNPs) of 40 patients with AML and 5 healthy volunteers were analyzed by reverse transcription-polymerase chain reaction, fluorescence in situ hybridization and DNA sequencing. The effects of MLAA-34 mutation on overall survival (OS) and progression-free survival (PFS) of patients with AML were also analyzed. MLAA-34 was significantly upregulated in patients with AML when compared with volunteer controls, and this upregulation was associated with a C59T SNP site located in the second exon of MLAA-34. MLAA-34 was mapped to 13q14.2 and no translocation was observed in patients with AML. In addition, this SNP site is affinitive to the well-known molecular markers of AML, including Fms-like tyrosine kinase 3 and DNA methyltransferase 3A, as well as extramedullary lesions, periphery leukocyte numbers, remission and cytogenetic abnormalities of patients with AML. Patients with AML with MLAA-34 C59T mutations had significantly shorter OS and PFS times compared with that of patients without C59T mutations. The present findings indicated that the MLAA-34 C59T mutation was a high-risk factor for recurrence of AML, and may be a candidate target for AML therapy.
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Gaidzik VI, Weber D, Paschka P, Kaumanns A, Krieger S, Corbacioglu A, Krönke J, Kapp-Schwoerer S, Krämer D, Horst HA, Schmidt-Wolf I, Held G, Kündgen A, Ringhoffer M, Götze K, Kindler T, Fiedler W, Wattad M, Schlenk RF, Bullinger L, Teleanu V, Schlegelberger B, Thol F, Heuser M, Ganser A, Döhner H, Döhner K. DNMT3A mutant transcript levels persist in remission and do not predict outcome in patients with acute myeloid leukemia. Leukemia 2017. [PMID: 28643785 DOI: 10.1038/leu.2017.200] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We investigated the prognostic impact of minimal residual disease (MRD) monitoring in acute myeloid leukemia patients harboring DNA methyltransferase 3A-R882H/-R882C mutations (DNMT3Amut). MRD was determined by real-time quantitative PCR (RQ-PCR) in 1494 samples of 181 DNMT3Amut patients. At the time of diagnosis, DNMT3Amut transcript levels did not correlate with presenting clinical characteristics and concurrent gene mutations as well as the survival end points. In Cox regression analyses, bone marrow (BM) DNMT3Amut transcript levels (log10-transformed continuous variable) were not associated with the rate of relapse or death. DNMT3Amut transcript levels were significantly higher in BM than in blood after induction I (P=0.01), induction II (P=0.05), consolidation I (P=0.004) and consolidation II (P=0.008). With regard to the clinically relevant MRD time points, after two cycles of induction and at the end of therapy, DNMT3Amut transcript levels had no impact on the end point remission duration and overall survival. Of note, only a minority of the patients achieved RQ-PCR negativity, whereas most had constantly high DNMT3Amut transcript levels, a finding which is consistent with the persistence of clonal hematopoiesis in hematological remission.
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Affiliation(s)
| | - D Weber
- Universitätsklinikum Ulm, Ulm, Germany
| | - P Paschka
- Universitätsklinikum Ulm, Ulm, Germany
| | | | - S Krieger
- Universitätsklinikum Ulm, Ulm, Germany
| | | | - J Krönke
- Universitätsklinikum Ulm, Ulm, Germany
| | | | - D Krämer
- Klinikum Oldenburg, Oldenburg, Germany
| | - H-A Horst
- Universitätsklinikum Schleswig-Holstein Campus Kiel, Kiel, Germany
| | | | - G Held
- Universitätsklinikum des Saarlandes, Homburg, Germany
| | - A Kündgen
- Universitätsklinikum Düsseldorf, Düsseldorf, Germany
| | - M Ringhoffer
- Städtisches Klinikum Karlsruhe GmbH, Karlsruhe, Germany
| | - K Götze
- Klinikum rechts der Isar der Technischen Universität München, München, Germany
| | - T Kindler
- Universitätsmedizin Mainz, Mainz, Germany
| | - W Fiedler
- Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - M Wattad
- Kliniken Essen Süd, Ev. Krankenhaus Essen-Werden gGmbH, Essen, Germany
| | | | | | - V Teleanu
- Universitätsklinikum Ulm, Ulm, Germany
| | | | - F Thol
- Medizinische Hochschule Hannover, Hannover, Germany
| | - M Heuser
- Medizinische Hochschule Hannover, Hannover, Germany
| | - A Ganser
- Medizinische Hochschule Hannover, Hannover, Germany
| | - H Döhner
- Universitätsklinikum Ulm, Ulm, Germany
| | - K Döhner
- Universitätsklinikum Ulm, Ulm, Germany
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Hyun K, Jeon J, Park K, Kim J. Writing, erasing and reading histone lysine methylations. Exp Mol Med 2017; 49:e324. [PMID: 28450737 PMCID: PMC6130214 DOI: 10.1038/emm.2017.11] [Citation(s) in RCA: 700] [Impact Index Per Article: 100.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/20/2016] [Indexed: 02/08/2023] Open
Abstract
Histone modifications are key epigenetic regulatory features that have important roles in many cellular events. Lysine methylations mark various sites on the tail and globular domains of histones and their levels are precisely balanced by the action of methyltransferases ('writers') and demethylases ('erasers'). In addition, distinct effector proteins ('readers') recognize specific methyl-lysines in a manner that depends on the neighboring amino-acid sequence and methylation state. Misregulation of histone lysine methylation has been implicated in several cancers and developmental defects. Therefore, histone lysine methylation has been considered a potential therapeutic target, and clinical trials of several inhibitors of this process have shown promising results. A more detailed understanding of histone lysine methylation is necessary for elucidating complex biological processes and, ultimately, for developing and improving disease treatments. This review summarizes enzymes responsible for histone lysine methylation and demethylation and how histone lysine methylation contributes to various biological processes.
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Affiliation(s)
- Kwangbeom Hyun
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jongcheol Jeon
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kihyun Park
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Jaehoon Kim
- Laboratory of Eukaryotic Transcription, Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
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Peterson LE, Kovyrshina T. Progression inference for somatic mutations in cancer. Heliyon 2017; 3:e00277. [PMID: 28492066 PMCID: PMC5415494 DOI: 10.1016/j.heliyon.2017.e00277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 03/08/2017] [Accepted: 03/23/2017] [Indexed: 01/05/2023] Open
Abstract
Computational methods were employed to determine progression inference of genomic alterations in commonly occurring cancers. Using cross-sectional TCGA data, we computed evolutionary trajectories involving selectivity relationships among pairs of gene-specific genomic alterations such as somatic mutations, deletions, amplifications, downregulation, and upregulation among the top 20 driver genes associated with each cancer. Results indicate that the majority of hierarchies involved TP53, PIK3CA, ERBB2, APC, KRAS, EGFR, IDH1, VHL, etc. Research into the order and accumulation of genomic alterations among cancer driver genes will ever-increase as the costs of nextgen sequencing subside, and personalized/precision medicine incorporates whole-genome scans into the diagnosis and treatment of cancer.
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Affiliation(s)
- Leif E. Peterson
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Healthcare Policy and Research, Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
- Dept. of Biostatistics, School of Public Health, University of Texas – Health Science Center, Houston, TX 77030, USA
- Dept. of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
- Dept. of Neuroscience and Experimental Therapeutics, Texas A&M University Health Science Center, College Station, TX 77843, USA
| | - Tatiana Kovyrshina
- Center for Biostatistics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Dept. of Mathematics and Statistics, University of Houston – Downtown, Houston, TX 77002, USA
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Berenstein R. Class III Receptor Tyrosine Kinases in Acute Leukemia - Biological Functions and Modern Laboratory Analysis. Biomark Insights 2015; 10:1-14. [PMID: 26309392 PMCID: PMC4527365 DOI: 10.4137/bmi.s22433] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Revised: 07/02/2015] [Accepted: 07/04/2015] [Indexed: 12/12/2022] Open
Abstract
Acute myeloid leukemia (AML) is a complex disease caused by deregulation of multiple signaling pathways. Mutations in class III receptor tyrosine kinases (RTKs) have been implicated in alteration of cell signals concerning the growth and differentiation of leukemic cells. Point mutations, insertions, or deletions of RTKs as well as chromosomal translocations induce constitutive activation of the receptor, leading to uncontrolled proliferation of undifferentiated myeloid blasts. Aberrations can occur in all domains of RTKs causing either the ligand-independent activation or mimicking the activated conformation. The World Health Organization recommended including RTK mutations in the AML classification since their detection in routine laboratory diagnostics is a major factor for prognostic stratification of patients. Polymerase chain reaction (PCR)-based methods are well-validated for the detection of fms-related tyrosine kinase 3 (FLT3) mutations and can easily be applied for other RTKs. However, when methodological limitations are reached, accessory techniques can be applied. For a higher resolution and more quantitative approach compared to agarose gel electrophoresis, PCR fragments can be separated by capillary electrophoresis. Furthermore, high-resolution melting and denaturing high-pressure liquid chromatography are reliable presequencing screening methods that reduce the sample amount for Sanger sequencing. Because traditional DNA sequencing is time-consuming, next-generation sequencing (NGS) is an innovative modern possibility to analyze a high amount of samples simultaneously in a short period of time. At present, standardized procedures for NGS are not established, but when this barrier is resolved, it will provide a new platform for rapid and reliable laboratory diagnostic of RTK mutations in patients with AML. In this article, the biological and physiological role of RTK mutations in AML as well as possible laboratory methods for their detection will be reviewed.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Berlin, Germany
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