51
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Yang L, Shen K, Zhang M, Zhang W, Cai H, Lin L, Long X, Xing S, Tang Y, Xiong J, Wang J, Li D, Zhou J, Xiao M. Clinical Features and MicroRNA Expression Patterns Between AML Patients With DNMT3A R882 and Frameshift Mutations. Front Oncol 2019; 9:1133. [PMID: 31709191 PMCID: PMC6821681 DOI: 10.3389/fonc.2019.01133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/10/2019] [Indexed: 01/01/2023] Open
Abstract
Background: DNA methyltransferase 3A (DNMT3A) plays a unique role in hematopoiesis and acute myeloid leukemia (AML) pathogenesis. While the influences of DNMT3A mutation subtypes are still under debate. Purpose: Exploration of the clinical and molecular differences between AML patients carrying DNMT3A R882 mutations and DNMT3A frameshift mutations. Methods: Next generation of sequencing (NGS) and clinical data of 118 AML patients in our center were analyzed and compared. NGS, mRNA and miRNA profiling and clinical data from 12 patients in TCGA database were integrative analyzed. Results: Among all patients enrolled, 113 patients were positive for the variants of interest. Overall, a total of 295 variants were discovered, among which 24 DNMT3A mutations were detected, including 1 non-sense, 20 missense, 3 frameshift mutations. And 7 DNMT3A R882 mutations (3 R882H, 2 R882C, and 2 R882P) were found. Clinical analysis from our cohort and TCGA database indicated that patients carrying DNMT3A R882 mutation exhibited significantly higher levels of peripheral blood hemoglobin and non-significantly inferior prognosis compared with patients with DNMT3A frameshift mutations. Integrative analysis indicated that miR-10b, miR-143, and miR-30a were significantly decreased in the DNMT3A R882 group. High miR-143 expression is significantly associated with better prognosis in AML patients with DNMT3A mutations. Conclusion: Different molecular and clinical characteristics existed between patients with DNMT3A variant subtypes. The distinct microRNA expression pattern for DNMT3A R882 AML patients might not only act as markers to predict disease prognosis, but also could be further investigated to develop novel therapeutic targets for patients with DNMT3A mutations.
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Affiliation(s)
- Li Yang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Ke'Feng Shen
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Mei'Lan Zhang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Zhang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Hao'Dong Cai
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Li'Man Lin
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao'Lu Long
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Shu'Gang Xing
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yang Tang
- Department of Oncology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jie Xiong
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jia'Chen Wang
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Deng'Ju Li
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Jian'Feng Zhou
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Min Xiao
- Department of Hematology, Tongji Medical College, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
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52
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Nguyen TV, Yao S, Wang Y, Rolfe A, Selvaraj A, Darman R, Ke J, Warmuth M, Smith PG, Larsen NA, Yu L, Zhu P, Fekkes P, Vaillancourt FH, Bolduc DM. The R882H DNMT3A hot spot mutation stabilizes the formation of large DNMT3A oligomers with low DNA methyltransferase activity. J Biol Chem 2019; 294:16966-16977. [PMID: 31582562 DOI: 10.1074/jbc.ra119.010126] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/27/2019] [Indexed: 01/04/2023] Open
Abstract
DNMT3A (DNA methyltransferase 3A) is a de novo DNA methyltransferase responsible for establishing CpG methylation patterns within the genome. DNMT3A activity is essential for normal development, and its dysfunction has been linked to developmental disorders and cancer. DNMT3A is frequently mutated in myeloid malignancies with the majority of mutations occurring at Arg-882, where R882H mutations are most frequent. The R882H mutation causes a reduction in DNA methyltransferase activity and hypomethylation at differentially-methylated regions within the genome, ultimately preventing hematopoietic stem cell differentiation and leading to leukemogenesis. Although the means by which the R882H DNMT3A mutation reduces enzymatic activity has been the subject of several studies, the precise mechanism by which this occurs has been elusive. Herein, we demonstrate that in the context of the full-length DNMT3A protein, the R882H mutation stabilizes the formation of large oligomeric DNMT3A species to reduce the overall DNA methyltransferase activity of the mutant protein as well as the WT-R882H complex in a dominant-negative manner. This shift in the DNMT3A oligomeric equilibrium and the resulting reduced enzymatic activity can be partially rescued in the presence of oligomer-disrupting DNMT3L, as well as DNMT3A point mutations along the oligomer-forming interface of the catalytic domain. In addition to modulating the oligomeric state of DNMT3A, the R882H mutation also leads to a DNA-binding defect, which may further reduce enzymatic activity. These findings provide a mechanistic explanation for the observed loss of DNMT3A activity associated with the R882H hot spot mutation in cancer.
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Affiliation(s)
| | - Shihua Yao
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Yahong Wang
- ChemPartner Co., Ltd., 998 Halei Road, Shanghai 201203, China
| | - Alan Rolfe
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | | | | | - Jiyuan Ke
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | | | | | | | - Lihua Yu
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Ping Zhu
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
| | - Peter Fekkes
- H3 Biomedicine Inc., Cambridge, Massachusetts 02139
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53
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Age-related clonal hematopoiesis: implications for hematopoietic stem cell transplantation. Curr Opin Hematol 2019; 25:441-445. [PMID: 30124476 DOI: 10.1097/moh.0000000000000465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Over the past decade, advances in hematopoietic stem cell transplantation (HSCT) have enabled older individuals to undergo the procedure as well as to serve as donors. Recently, aging has been linked with the development of age-related clonal hematopoiesis (ARCH), defined as the gradual clonal expansion of hematopoietic stem and progenitor cells (HSPC) carrying recurrent disruptive genetic variants in individuals without a diagnosis of hematologic malignancy. Here we will review the implications of ARCH in the context of HSCT. RECENT FINDINGS ARCH is highly prevalent in the general population and commonly involves genes that are recurrently mutated in hematologic malignancies. Nevertheless, the vast majority of individuals with ARCH will not develop overt hematologic disease in their lifetime. The presence of ARCH may increase the risk of therapy-related myeloid neoplasms (t-MN) in individuals undergoing autologous HSCT. In the setting of allogeneic HSCT, ARCH present in the donor may contribute to adverse outcomes such as unexplained cytopenias posttransplant and donor cell leukemia. SUMMARY A better understanding of the hematopoietic milieu of HSCT recipients and of the importance of ARCH in the context of the replicative pressures imposed on transplanted HSPCs is needed in order to optimize conditioning regimens, donor selection and clinical outcomes post-HSCT.
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54
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Jeong M, Park HJ, Celik H, Ostrander EL, Reyes JM, Guzman A, Rodriguez B, Lei Y, Lee Y, Ding L, Guryanova OA, Li W, Goodell MA, Challen GA. Loss of Dnmt3a Immortalizes Hematopoietic Stem Cells In Vivo. Cell Rep 2019; 23:1-10. [PMID: 29617651 PMCID: PMC5908249 DOI: 10.1016/j.celrep.2018.03.025] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 01/19/2018] [Accepted: 03/07/2018] [Indexed: 12/22/2022] Open
Abstract
Somatic mutations in DNMT3A are recurrent events across a range of blood cancers. Dnmt3a loss of function in hematopoietic stem cells (HSCs) skews divisions toward self-renewal at the expense of differentiation. Moreover, DNMT3A mutations can be detected in the blood of aging individuals, indicating that mutant cells outcompete normal HSCs over time. It is important to understand how these mutations provide a competitive advantage to HSCs. Here we show that Dnmt3a-null HSCs can regenerate over at least 12 transplant generations in mice, far exceeding the lifespan of normal HSCs. Molecular characterization reveals that this in vivo immortalization is associated with gradual and focal losses of DNA methylation at key regulatory regions associated with self-renewal genes, producing a highly stereotypical HSC phenotype in which epigenetic features are further buttressed. These findings lend insight into the preponderance of DNMT3A mutations in clonal hematopoiesis and the persistence of mutant clones after chemotherapy.
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Affiliation(s)
- Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hyun Jung Park
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hamza Celik
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Elizabeth L Ostrander
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jaime M Reyes
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anna Guzman
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin Rodriguez
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yong Lei
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yeojin Lee
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Lei Ding
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Microbiology and Immunology, Columbia University Medical Center, New York, NY 10032, USA
| | - Olga A Guryanova
- Department of Pharmacology and Therapeutics, University of Florida College of Medicine, and UF Health Cancer Center, Gainesville, FL 32610, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Grant A Challen
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA; Developmental, Regenerative and Stem Cell Biology Program, Division of Biology and Biomedical Sciences, Washington University School of Medicine, St. Louis, MO 63110, USA.
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55
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Veland N, Lu Y, Hardikar S, Gaddis S, Zeng Y, Liu B, Estecio MR, Takata Y, Lin K, Tomida MW, Shen J, Saha D, Gowher H, Zhao H, Chen T. DNMT3L facilitates DNA methylation partly by maintaining DNMT3A stability in mouse embryonic stem cells. Nucleic Acids Res 2019; 47:152-167. [PMID: 30321403 PMCID: PMC6326784 DOI: 10.1093/nar/gky947] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/05/2018] [Indexed: 12/12/2022] Open
Abstract
DNMT3L (DNMT3-like), a member of the DNMT3 family, has no DNA methyltransferase activity but regulates de novo DNA methylation. While biochemical studies show that DNMT3L is capable of interacting with both DNMT3A and DNMT3B and stimulating their enzymatic activities, genetic evidence suggests that DNMT3L is essential for DNMT3A-mediated de novo methylation in germ cells but is dispensable for de novo methylation during embryogenesis, which is mainly mediated by DNMT3B. How DNMT3L regulates DNA methylation and what determines its functional specificity are not well understood. Here we show that DNMT3L-deficient mouse embryonic stem cells (mESCs) exhibit downregulation of DNMT3A, especially DNMT3A2, the predominant DNMT3A isoform in mESCs. DNA methylation analysis of DNMT3L-deficient mESCs reveals hypomethylation at many DNMT3A target regions. These results confirm that DNMT3L is a positive regulator of DNA methylation, contrary to a previous report that, in mESCs, DNMT3L regulates DNA methylation positively or negatively, depending on genomic regions. Mechanistically, DNMT3L forms a complex with DNMT3A2 and prevents DNMT3A2 from being degraded. Restoring the DNMT3A protein level in DNMT3L-deficient mESCs partially recovers DNA methylation. Thus, our work uncovers a role for DNMT3L in maintaining DNMT3A stability, which contributes to the effect of DNMT3L on DNMT3A-dependent DNA methylation.
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Affiliation(s)
- Nicolas Veland
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Yue Lu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Sally Gaddis
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yang Zeng
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Bigang Liu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Marcos R Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Yoko Takata
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Kevin Lin
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Mary W Tomida
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
| | - Jianjun Shen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
| | - Debapriya Saha
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Humaira Gowher
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Hongbo Zhao
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Hospital and Institute of Obstetrics and Gynecology, Fudan University, Shanghai, People's Republic of China
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA.,Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, TX 77030, USA
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Chandhok NS, Prebet T. Insights into novel emerging epigenetic drugs in myeloid malignancies. Ther Adv Hematol 2019; 10:2040620719866081. [PMID: 31431820 PMCID: PMC6685116 DOI: 10.1177/2040620719866081] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 06/10/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetics has been defined as ‘a stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence’ and several epigenetic regulators are recurrently mutated in hematological malignancies. Epigenetic modifications include changes such as DNA methylation, histone modifications and RNA associated gene silencing. Transcriptional regulation, chromosome stability, DNA replication and DNA repair are all controlled by these modifications. Mutations in genes encoding epigenetic modifiers are a frequent occurrence in hematologic malignancies and important in both the initiation and progression of cancer. Epigenetic modifications are also frequently reversible, allowing excellent opportunities for therapeutic intervention. The goal of epigenetic therapies is to reverse epigenetic dysregulation, restore the epigenetic balance, and revert malignant cells to a more normal condition. The role of epigenetic therapies thus far is most established in hematologic malignancies, with several agents already approved by the US Food and Drug Administration. In this review, we discuss pharmacological agents targeting epigenetic regulators.
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Affiliation(s)
- Namrata S Chandhok
- Division of Hematology/Oncology, Smilow Cancer Center at Yale New Haven Hospital, New Haven, CT, USA
| | - Thomas Prebet
- Division of Hematology/Oncology, Smilow Cancer Center at Yale New Haven Hospital, 35 Park Street, New Haven, CT 06511, USA
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57
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Emperle M, Rajavelu A, Kunert S, Arimondo PB, Reinhardt R, Jurkowska RZ, Jeltsch A. The DNMT3A R882H mutant displays altered flanking sequence preferences. Nucleic Acids Res 2019. [PMID: 29518238 PMCID: PMC5887309 DOI: 10.1093/nar/gky168] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The DNMT3A R882H mutation is frequently observed in acute myeloid leukemia (AML). It is located in the subunit and DNA binding interface of DNMT3A and has been reported to cause a reduction in activity and dominant negative effects. We investigated the mechanistic consequences of the R882H mutation on DNMT3A showing a roughly 40% reduction in overall DNA methylation activity. Biochemical assays demonstrated that R882H does not change DNA binding affinity, protein stability or subnuclear distribution of DNMT3A. Strikingly, DNA methylation experiments revealed pronounced changes in the flanking sequence preference of the DNMT3A-R882H mutant. Based on these results, different DNA substrates with selected flanking sequences were designed to be favored or disfavored by R882H. Kinetic analyses showed that the R882H favored substrate was methylated by R882H with 45% increased rate when compared with wildtype DNMT3A, while methylation of the disfavored substrate was reduced 7-fold. Our data expand the model of the potential carcinogenic effect of the R882H mutation by showing CpG site specific activity changes. This result suggests that R882 is involved in the indirect readout of flanking sequence preferences of DNMT3A and it may explain the particular enrichment of the R882H mutation in cancer patients by revealing mutation specific effects.
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Affiliation(s)
- Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Stefan Kunert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Paola B Arimondo
- CNRS ETaC FRE3600, Bât. IBCG. 118, Route de Narbonne, 31062 Toulouse cedex 9, France
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569 Stuttgart, Germany
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58
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Yuan XQ, Chen P, Du YX, Zhu KW, Zhang DY, Yan H, Liu H, Liu YL, Cao S, Zhou G, Zeng H, Chen SP, Zhao XL, Yang J, Zeng WJ, Chen XP. Influence of DNMT3A R882 mutations on AML prognosis determined by the allele ratio in Chinese patients. J Transl Med 2019; 17:220. [PMID: 31291961 PMCID: PMC6621981 DOI: 10.1186/s12967-019-1959-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 06/21/2019] [Indexed: 01/13/2023] Open
Abstract
Background The influence of DNMT3A R882 mutations on adult acute myeloid leukemia (AML) prognosis is still controversial presently. The influence of R882 allele ratio on drug response and prognosis of AML is unknown yet. Besides, it is obscure whether anthracyclines are involved in chemoresistance resulted from R882 mutations. Methods DNMT3A R882 mutations in 870 adult AML patients receiving standard induction therapy were detected by pyrosequencing. Associations of the mutants with responses to induction therapy and disease prognosis were analyzed. Results DNMT3A R882 mutations were detected in 74 (8.51%) patients and allele ratio of the mutations ranged from 6 to 50% in the cohort. After the first and second courses of induction therapy including aclarubicin, complete remission rates were significantly lower in carriers of the DNMT3A R882 mutants as compared with R882 wildtype patients (P = 0.022 and P = 0.038, respectively). Compared with R882 wild-type patients, those with the R882 mutations showed significantly shorter overall survival (OS) and disease-free survival (DFS) (P = 1.92 × 10−4 and P = 0.004, respectively). Patients with higher allele ratio of R882 mutations showed a significantly shorter OS as compared with the lower allele ratio group (P = 0.035). Conclusion Our results indicate that the impact of DNMT3A R882 mutations on AML prognosis was determined by the mutant-allele ratio and higher allele ratio could predict a worse prognosis, which might improve AML risk stratification. In addition, DNMT3A R882 mutations were associated with an inferior response to induction therapy with aclarubicin in Chinese AML patients. Electronic supplementary material The online version of this article (10.1186/s12967-019-1959-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiao-Qing Yuan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Peng Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Yin-Xiao Du
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Ke-Wei Zhu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Dao-Yu Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Han Yan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Han Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Yan-Ling Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Shan Cao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Gan Zhou
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China
| | - Hui Zeng
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Shu-Ping Chen
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Xie-Lan Zhao
- Department of Hematology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China
| | - Jing Yang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, People's Republic of China
| | - Wen-Jing Zeng
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China.
| | - Xiao-Ping Chen
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China. .,Institute of Clinical Pharmacology, Hunan Key Laboratory of Pharmacogenetics, Central South University, Changsha, 410078, Hunan, People's Republic of China. .,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, People's Republic of China.
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59
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Gu Y, Zhou JD, Xu ZJ, Zhang TJ, Wen XM, Ma JC, Ji RB, Yuan Q, Zhang W, Chen Q, Lin J, Qian J. Promoter methylation of the candidate tumor suppressor gene TCF21 in myelodysplastic syndrome and acute myeloid leukemia. Am J Transl Res 2019; 11:3450-3460. [PMID: 31312357 PMCID: PMC6614633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 05/12/2019] [Indexed: 06/10/2023]
Abstract
Transcription factor 21 (TCF21) has been identified as a candidate tumor suppressor gene which was epigenetically inactivated in a variety of human cancers. However, TCF21 methylation pattern remains unknown in hematologic malignancies. The aim of this study was to investigate TCF21 methylation and its clinical relevance in myelodysplastic syndrome (MDS) and non-M3 acute myeloid leukemia (AML). A total cohort of 33 MDS patients, 100 non-M3 AML patients and 25 healthy donors were enrolled in the study. Targeted bisulfite sequencing assay was performed to identify the methylation pattern of CpG islands within the promoter of TCF21 gene. The bioinformatics analyses were based on The Cancer Genome Atlas (TCGA) database and Gene Expression Omnibus (GEO). The results showed that there were significant differences in the methylation levels of TCF21 between MDS, non-M3 AML and controls (P = 0.003 and < 0.001, respectively). TCF21 hypermethylation might be served as a promising biomarker which could distinguish MDS/AML from normal controls (P < 0.001 and = 0.003, respectively). There was a significant difference in cytogenetic risk categories between TCF21 hypermethylation and non-hypermethylation AML patients (P = 0.032). Notably, TCF21 hypermethylation occurred frequently in AML patients with adverse risk category, compared with those with favorable and intermediate categories, respectively (67% vs 44% and 29%). TCF21 non-hypermethylation AML patients showed a higher probability of normal karyotype than abnormal karyotype (P = 0.003). The rate of DNMT3A gene mutation was significantly higher in the non-hypermethylation AML patients than that in the hypermethylation (8/44 vs 0/34, P = 0.020). These results suggested that aberrant DNA promoter methylation of TCF21 was frequent event in MDS and non-M3 AML, and TCF21 hypermathylation was associated with adverse risk karyotype in AML.
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Affiliation(s)
- Yu Gu
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jing-Dong Zhou
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Zi-Jun Xu
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ting-Juan Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Xiang-Mei Wen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ji-Chun Ma
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Ren-Bi Ji
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
| | - Qian Yuan
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Wei Zhang
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Qin Chen
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jiang Lin
- Laboratory Center, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
| | - Jun Qian
- Department of Hematology, Affiliated People’s Hospital of Jiangsu UniversityZhenjiang, Jiangsu, People’s Republic of China
- Zhenjiang Clinical Research Center of HematologyZhenjiang, Jiangsu, People’s Republic of China
- The Key Lab of Precision Diagnosis and Treatment of Zhenjiang CityZhenjiang, Jiangsu, People’s Republic of China
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Lu R, Wang J, Ren Z, Yin J, Wang Y, Cai L, Wang GG. A Model System for Studying the DNMT3A Hotspot Mutation (DNMT3A R882) Demonstrates a Causal Relationship between Its Dominant-Negative Effect and Leukemogenesis. Cancer Res 2019; 79:3583-3594. [PMID: 31164355 DOI: 10.1158/0008-5472.can-18-3275] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 04/03/2019] [Accepted: 05/29/2019] [Indexed: 01/01/2023]
Abstract
Mutation of DNA methyltransferase 3A at arginine 882 (DNMT3AR882mut) is prevalent in hematologic cancers and disorders. Recently, DNMT3AR882mut has been shown to have hypomorphic, dominant-negative, and/or gain-of-function effects on DNA methylation under different biological contexts. However, the causal role for such a multifaceted effect of DNMT3AR882mut in leukemogenesis remains undetermined. Here, we report TF-1 leukemia cells as a robust system useful for modeling the DNMT3AR882mut-dependent transformation and for dissecting the cause-effect relationship between multifaceted activities of DNMT3AR882mut and leukemic transformation. Ectopic expression of DNMT3AR882mut and not wild-type DNMT3A promoted TF-1 cell transformation characterized by cytokine-independent growth, and induces CpG hypomethylation predominantly at enhancers. This effect was dose dependent, acted synergistically with the isocitrate dehydrogenase 1 (IDH1) mutation, and resembled what was seen in human leukemia patients carrying DNMT3AR882mut. The transformation- and hypomethylation-inducing capacities of DNMT3AR882mut relied on a motif involved in heterodimerization, whereas its various chromatin-binding domains were dispensable. Mutation of the heterodimerization motif that interferes with DNMT3AR882mut binding to endogenous wild-type DNMT proteins partially reversed the CpG hypomethylation phenotype caused by DNMT3AR882mut, thus supporting a dominant-negative mechanism in cells. In mice, bromodomain inhibition repressed gene-activation events downstream of DNMT3AR882mut-induced CpG hypomethylation, thereby suppressing leukemogenesis mediated by DNMT3AR882mut. Collectively, this study reports a model system useful for studying DNMT3AR882mut, shows a requirement of the dominant-negative effect by DNMT3AR882mut for leukemogenesis, and describes an attractive strategy for the treatment of leukemias carrying DNMT3AR882mut. SIGNIFICANCE: These findings highlight a model system to study the functional impact of a hotspot mutation of DNMT3A at R882 in leukemia.
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Affiliation(s)
- Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Zhihong Ren
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California.,Department of Chemistry, University of California, Riverside, California
| | - Ling Cai
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina. .,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
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61
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Effect of Disease-Associated Germline Mutations on Structure Function Relationship of DNA Methyltransferases. Genes (Basel) 2019; 10:genes10050369. [PMID: 31091831 PMCID: PMC6562416 DOI: 10.3390/genes10050369] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 12/21/2022] Open
Abstract
Despite a large body of evidence supporting the role of aberrant DNA methylation in etiology of several human diseases, the fundamental mechanisms that regulate the activity of mammalian DNA methyltransferases (DNMTs) are not fully understood. Recent advances in whole genome association studies have helped identify mutations and genetic alterations of DNMTs in various diseases that have a potential to affect the biological function and activity of these enzymes. Several of these mutations are germline-transmitted and associated with a number of hereditary disorders, which are potentially caused by aberrant DNA methylation patterns in the regulatory compartments of the genome. These hereditary disorders usually cause neurological dysfunction, growth defects, and inherited cancers. Biochemical and biological characterization of DNMT variants can reveal the molecular mechanism of these enzymes and give insights on their specific functions. In this review, we introduce roles and regulation of DNA methylation and DNMTs. We discuss DNMT mutations that are associated with rare diseases, the characterized effects of these mutations on enzyme activity and provide insights on their potential effects based on the known crystal structure of these proteins.
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62
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DeZern AE. Treatments targeting MDS genetics: a fool's errand? HEMATOLOGY. AMERICAN SOCIETY OF HEMATOLOGY. EDUCATION PROGRAM 2018; 2018:277-285. [PMID: 30504322 PMCID: PMC6246001 DOI: 10.1182/asheducation-2018.1.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The myelodysplastic syndromes are collectively the most common myeloid neoplasms. Clonal hematopoiesis present in these diseases results in bone marrow failure characteristically seen in patients. The heterogeneity of myelodysplastic syndrome pathobiology has historically posed a challenge to the development of newer therapies. Recent advances in molecular characterization of myelodysplastic syndromes are improving diagnostic accuracy, providing insights into pathogenesis, and refining therapeutic options for patients. With the advent of these developments, appropriately chosen therapeutics or even targeted agents may be able to improve patient outcomes in the future.
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Affiliation(s)
- Amy E DeZern
- Division of Hematologic Malignancies, John Hopkins Medicine, Baltimore, MD
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63
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Emperle M, Dukatz M, Kunert S, Holzer K, Rajavelu A, Jurkowska RZ, Jeltsch A. The DNMT3A R882H mutation does not cause dominant negative effects in purified mixed DNMT3A/R882H complexes. Sci Rep 2018; 8:13242. [PMID: 30185810 PMCID: PMC6125428 DOI: 10.1038/s41598-018-31635-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 08/23/2018] [Indexed: 12/17/2022] Open
Abstract
The DNA methyltransferase DNMT3A R882H mutation is observed in 25% of all AML patients. DNMT3A is active as tetramer and the R882H mutation is located in one of the subunit/subunit interfaces. Previous work has reported that formation of mixed wildtype/R882H complexes leads to a strong loss of catalytic activity observed in in vitro DNA methylation assays (Russler-Germain et al., 2014, Cancer Cell 25:442–454). To investigate this effect further, we have prepared mixed wildtype/R882H DNMT3A complexes by incubation of individually purified subunits of the DNMT3A catalytic domain and full-length DNMT3A2. In addition, we have used a double affinity tag approach and specifically purified mixed catalytic domain complexes formed after co-expression of R882H and wildtype subunits in E. coli cells. Afterwards, we determined the catalytic activity of the mixed complexes and compared it to that of purified complexes only consisting of one subunit type. In both settings, the expected catalytic activities of mixed R882H/wildtype complexes were observed demonstrating an absence of a dominant negative effect of the R882H mutation in purified DNMT3A enzymes. This result suggests that heterocomplex formation of DNMT3A and R882H is unlikely to cause dominant negative effects in human cells as well. The limitations of this conclusion and its implications are discussed.
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Affiliation(s)
- Max Emperle
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Michael Dukatz
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stefan Kunert
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Katharina Holzer
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Arumugam Rajavelu
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,Rajiv Gandhi Center for Biotechnology (RGCB), Trivandrum, 695014, Kerala, India
| | - Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.,BioMed X Innovation Center, Im Neuenheimer Feld 583, D-69120, Heidelberg, Germany
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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64
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Norvil AB, Petell CJ, Alabdi L, Wu L, Rossie S, Gowher H. Dnmt3b Methylates DNA by a Noncooperative Mechanism, and Its Activity Is Unaffected by Manipulations at the Predicted Dimer Interface. Biochemistry 2018; 57:4312-4324. [PMID: 27768276 PMCID: PMC5992102 DOI: 10.1021/acs.biochem.6b00964] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The catalytic domains of the de novo DNA methyltransferases Dnmt3a-C and Dnmt3b-C are highly homologous. However, their unique biochemical properties could potentially contribute to differences in the substrate preferences or biological functions of these enzymes. Dnmt3a-C forms tetramers through interactions at the dimer interface, which also promote multimerization on DNA and cooperativity. Similar to the case for processive enzymes, cooperativity allows Dnmt3a-C to methylate multiple sites on the same DNA molecule; however, it is unclear whether Dnmt3b-C methylates DNA by a cooperative or processive mechanism. The importance of the tetramer structure and cooperative mechanism is emphasized by the observation that the R882H mutation in the dimer interface of DNMT3A is highly prevalent in acute myeloid leukemia and leads to a substantial loss of its activity. Under conditions that distinguish between cooperativity and processivity, we show that in contrast to that of Dnmt3a-C, the activity of Dnmt3b-C is not cooperative and confirm the processivity of Dnmt3b-C and the full length Dnmt3b enzyme. Whereas the R878H mutation (mouse homologue of R882H) led to the loss of cooperativity of Dnmt3a-C, the activity and processivity of the analogous Dnmt3b-C R829H variant were comparable to those of the wild-type enzyme. Additionally, buffer acidification that attenuates the dimer interface interactions of Dnmt3a-C had no effect on Dnmt3b-C activity. Taken together, these results demonstrate an important mechanistic difference between Dnmt3b and Dnmt3a and suggest that interactions at the dimer interface may play a limited role in regulating Dnmt3b-C activity. These new insights have potential implications for the distinct biological roles of Dnmt3a and Dnmt3b.
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Affiliation(s)
- Allison B. Norvil
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Christopher J. Petell
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lama Alabdi
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Lanchen Wu
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Sandra Rossie
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Humaira Gowher
- Department of Biochemistry, Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
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65
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Molecular Minimal Residual Disease Testing in Acute Myeloid Leukemia: A Review for the Practicing Clinician. CLINICAL LYMPHOMA MYELOMA & LEUKEMIA 2018; 18:636-647. [PMID: 30006258 DOI: 10.1016/j.clml.2018.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 06/12/2018] [Accepted: 06/19/2018] [Indexed: 11/21/2022]
Abstract
Minimal residual disease (MRD) testing in acute myeloid leukemia is increasingly being used to assess treatment response and stratify the risk of relapse for individual patients. Molecular methods for MRD testing began with PCR-based assays for individual recurrent mutations. To date, there is robust evidence for testing NPM1, CBFB-MYH11, and RUNX1/RUNXT1 mutations using this approach, though the best timing and threshold level for each mutation varies. More recent approaches have been with PCR-based multigene panels, occasionally combined with flow cytometric techniques, and next-generation sequencing techniques. This review outlines the various techniques used in molecular approaches to MRD, the evidence behind individual mutation testing, and the novel approaches for evaluating multigene MRD so that clinicians can understand and incorporate these evaluations into their practice.
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66
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Hamidi T, Singh AK, Veland N, Vemulapalli V, Chen J, Hardikar S, Bao J, Fry CJ, Yang V, Lee KA, Guo A, Arrowsmith CH, Bedford MT, Chen T. Identification of Rpl29 as a major substrate of the lysine methyltransferase Set7/9. J Biol Chem 2018; 293:12770-12780. [PMID: 29959229 DOI: 10.1074/jbc.ra118.002890] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 06/11/2018] [Indexed: 11/06/2022] Open
Abstract
Set7/9 (also known as Set7, Set9, Setd7, and Kmt7) is a lysine methyltransferase that catalyzes the methylation of multiple substrates, including histone H3 and non-histone proteins. Although not essential for normal development and physiology, Set7/9-mediated methylation events play important roles in regulating cellular pathways involved in various human diseases, making Set7/9 a promising therapeutic target. Multiple Set7/9 inhibitors have been developed, which exhibit varying degrees of potency and selectivity in vitro However, validation of these compounds in vivo has been hampered by the lack of a reliable cellular biomarker for Set7/9 activity. Here, we report the identification of Rpl29, a ribosomal protein abundantly expressed in all cell types, as a major substrate of Set7/9. We show that Rpl29 lysine 5 (Rpl29K5) is methylated exclusively by Set7/9 and can be demethylated by Lsd1 (also known as Kdm1a). Rpl29 is not a core component of the ribosome translational machinery and plays a regulatory role in translation efficiency. Our results indicate that Rpl29 methylation has no effect on global protein synthesis but affects Rpl29 subcellular localization. Using an Rpl29 methylation-specific antibody, we demonstrate that Rpl29K5 methylation is present ubiquitously and validate that (R)-PFI-2, a Set7/9 inhibitor, efficiently reduces Rpl29K5 methylation in cell lines. Thus, Rpl29 methylation can serve as a specific cellular biomarker for measuring Set7/9 activity.
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Affiliation(s)
- Tewfik Hamidi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Anup Kumar Singh
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Nicolas Veland
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Vidyasiri Vemulapalli
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Jianji Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Swanand Hardikar
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | - Jianqiang Bao
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957
| | | | - Vicky Yang
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923
| | - Kimberly A Lee
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923
| | - Ailan Guo
- Cell Signaling Technology Inc., Danvers, Massachusetts 01923
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada; Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Mark T Bedford
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Smithville, Texas 78957; Program in Genetics and Epigenetics, The University of Texas MD Anderson Cancer Center UT Health Graduate School of Biomedical Sciences, Houston, Texas 77030.
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67
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Bräuninger A, Blau W, Kunze K, Desch AK, Brobeil A, Tur MK, Etschmann B, Günther U, Körholz D, Schliesser G, Käbisch A, Kiehl M, Rummel M, Gattenlöhner S. Targeted Next-Generation Sequencing Is a Sensitive Tool for Differential Diagnosis of Myelodysplastic Syndromes in Bone Marrow Trephines. J Mol Diagn 2018; 20:344-354. [DOI: 10.1016/j.jmoldx.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 01/09/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022] Open
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68
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Lin ME, Hou HA, Tsai CH, Wu SJ, Kuo YY, Tseng MH, Liu MC, Liu CW, Chou WC, Chen CY, Tang JL, Yao M, Li CC, Huang SY, Ko BS, Hsu SC, Lin CT, Tien HF. Dynamics of DNMT3A mutation and prognostic relevance in patients with primary myelodysplastic syndrome. Clin Epigenetics 2018; 10:42. [PMID: 29619119 PMCID: PMC5879939 DOI: 10.1186/s13148-018-0476-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 03/21/2018] [Indexed: 01/28/2023] Open
Abstract
Background DNMT3A gene mutation has been associated with poor prognosis in acute myeloid leukemia, but its clinical implications in myelodysplastic syndrome (MDS) and dynamic changes during disease progression remain controversial. Results In this study, DNMT3A mutation was identified in 7.9% of 469 de novo MDS patients. DNMT3A-mutated patients had higher platelet counts at diagnosis, and patients with ring sideroblasts had the highest incidence of DNMT3A mutations, whereas those with multilineage dysplasia had the lowest incidence. Thirty-one (83.8%) of 37 DNMT3A-mutated patients had additional molecular abnormalities at diagnosis, and DNMT3A mutation was highly associated with mutations of IDH2 and SF3B1. Patients with DNMT3A mutations had a higher risk of leukemia transformation and shorter overall survival. Further, DNMT3A mutation was an independent poor prognostic factor irrespective of age, IPSS-R, and genetic alterations. The sequential study demonstrated that the original DNMT3A mutations were retained during follow-ups unless allogeneic hematopoietic stem cell transplantation was performed, while DNMT3A mutation was rarely acquired during disease progression. Conclusions DNMT3A mutation predicts unfavorable outcomes in MDS and was stable during disease evolutions. It may thus be a potential biomarker to predict prognosis and monitor the treatment response. Electronic supplementary material The online version of this article (10.1186/s13148-018-0476-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ming-En Lin
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan.,2Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, Hsin-Chu Branch, Hsinchu City, Taiwan.,3Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Hsin-An Hou
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Cheng-Hong Tsai
- 4Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Shang-Ju Wu
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Yuan-Yeh Kuo
- 5Graduate Institute of Oncology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Mei-Hsuan Tseng
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Ming-Chih Liu
- 6Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chia-Wen Liu
- 6Departments of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Wen-Chien Chou
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan.,7Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Yuan Chen
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Jih-Luh Tang
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Ming Yao
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Chi-Cheng Li
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan.,4Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Shang-Yi Huang
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Bor-Sheng Ko
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
| | - Szu-Chun Hsu
- 7Department of Laboratory Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Ting Lin
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan.,4Tai-Cheng Stem Cell Therapy Center, National Taiwan University, Taipei, Taiwan
| | - Hwei-Fang Tien
- 1Division of Hematology, Department of Internal Medicine, National Taiwan University Hospital, No.7, Chung Shan S. Rd., Zhongzheng Dist, Taipei, 10002 Taiwan
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69
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Yang L, Liu Y, Zhang N, Ding X, Zhang W, Shen K, Huang L, Zhou J, Cui S, Zhu Z, Hu Z, Xiao M. Novel impact of the DNMT3A R882H mutation on GSH metabolism in a K562 cell model established by TALENs. Oncotarget 2018; 8:30395-30409. [PMID: 28418922 PMCID: PMC5444751 DOI: 10.18632/oncotarget.16449] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 02/20/2017] [Indexed: 01/22/2023] Open
Abstract
DNA methyltransferase 3A (DNMT3A) mutations occurred in 18%~23% of acute myeloid leukemia (AML) patients, and were considered to be an adverse prognostic factor for adult de novo AML cases. However, the relevant molecular mechanism of the mutation in AML pathogenesis remains obscure. In this study, we established K562 and SKM1 cell model carrying the DNMT3A R882H mutation via transcription activator-like effector nuclease (TALEN) and Clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) technology, and discovered that mutated DNMT3A could promote the proliferative capability of malignant cell clones. Further RNA microarray analysis revealed that some genes crucial for glutathione (GSH) synthesis, including CTH, PSPH, PSAT1 and especially SLC7A11 (the cysteine/glutamate transporter) were significantly up-regulated, which resulted in significant elevation of intracellular GSH levels. A subsequent experiment demonstrated that the mutant clones are resistant to chemotherapy as well as SLC7A11-inhibitorsBy shRNA induced SLC7A11 silencing, we discovered profoundly decreased cellular GSH and cell proliferative ability of DNMT3A mutated clones. Our results provided novel insight into the role of the DNMT3A R882H mutation in AML pathogenesis and suggested that targeting the cellular GSH synthetic pathway could enhance the current therapy for AML patients with the DNMT3A R882H mutation.
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Affiliation(s)
- Li Yang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Ya'Nan Liu
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei Province, P.R. China
| | - Na Zhang
- Department of Hematology, Xijing Hospital Affiliated by The Fourth Military Medical University (FMMU), Xi'an, Shanxi Province, P.R.China
| | - Xiao'Yi Ding
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Wei Zhang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Ke'Feng Shen
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Liang Huang
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
| | - Jian'Feng Zhou
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China.,Qinghai University, XiNing, Qinghai Province, P.R.China
| | - Sen Cui
- Department of Hematology, Qinghai University Affiliated Hospital, Qinghai University, XiNing, Qinghai Province, P.R.China
| | - Zun'Min Zhu
- Department of Hematology, Henan Provincial People's Hospital, ZhengZhou, Henan Province, P.R.China
| | - Zheng Hu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen 14 University, Guangzhou, Guangdong, China
| | - Min Xiao
- Department of Hematology, Tongji Hospital Affiliated with Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, P.R.China
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70
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Poitras JL, Heiser D, Li L, Nguyen B, Nagai K, Duffield AS, Gamper C, Small D. Dnmt3a deletion cooperates with the Flt3/ITD mutation to drive leukemogenesis in a murine model. Oncotarget 2018; 7:69124-69135. [PMID: 27636998 PMCID: PMC5342464 DOI: 10.18632/oncotarget.11986] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023] Open
Abstract
Internal tandem duplications of the juxtamembrane domain of FLT3 (FLT3/ITD) are among the most common mutations in Acute Myeloid Leukemia (AML). Resulting in constitutive activation of the kinase, FLT3/ITD portends a particularly poor prognosis, with reduced overall survival and increased rates of relapse. We previously generated a knock-in mouse, harboring an internal tandem duplication at the endogenous Flt3 locus, which develops a fatal myeloproliferative neoplasm (MPN), but fails to develop acute leukemia, suggesting additional mutations are necessary for transformation. To investigate the potential cooperativity of FLT3/ITD and mutant DNMT3A, we bred a conditional Dnmt3a knockout to a substrain of our Flt3/ITD knock-in mice, and found deletion of Dnmt3a significantly reduced median survival of Flt3ITD/+ mice in a dose dependent manner. As expected, pIpC treated Flt3ITD/+ mice solely developed MPN, while Flt3ITD/+;Dnmt3af/f and Flt3ITD/+;Dnmt3af/+ developed a spectrum of neoplasms, including MPN, T-ALL, and AML. Functionally, FLT3/ITD and DNMT3A deletion cooperate to expand LT-HSCs, which exhibit enhanced self-renewal in serial re-plating assays. These results illustrate that DNMT3A loss cooperates with FLT3/ITD to generate hematopoietic neoplasms, including AML. In combination with FLT3/ITD, homozygous Dnmt3a knock-out results in reduced time to disease onset, LT-HSC expansion, and a higher incidence of T-ALL compared with loss of just one allele. The co-occurrence of FLT3 and DNMT3A mutations in AML, as well as subsets of T-ALL, suggests the Flt3ITD/+;Dnmt3af/f model may serve as a valuable resource for delineating effective therapeutic strategies in two clinically relevant contexts.
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Affiliation(s)
- Jennifer L Poitras
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Diane Heiser
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Li Li
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Bao Nguyen
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kozo Nagai
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Amy S Duffield
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher Gamper
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Donald Small
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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71
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Structural basis for DNMT3A-mediated de novo DNA methylation. Nature 2018; 554:387-391. [PMID: 29414941 PMCID: PMC5814352 DOI: 10.1038/nature25477] [Citation(s) in RCA: 171] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 12/21/2017] [Indexed: 12/27/2022]
Abstract
DNA methylation by de novo DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B) is essential for genome regulation and development1, 2. Dysregulation of this process is implicated in various diseases, notably cancer. However, the mechanisms underlying DNMT3 substrate recognition and enzymatic specificity remain elusive. Here we report a 2.65-Å crystal structure of the DNMT3A-DNMT3L-DNA complex where two DNMT3A monomers simultaneously attack two CpG dinucleotides, with the target sites separated by fourteen base pairs within the same DNA duplex. The DNMT3A–DNA interaction involves a target recognition domain (TRD), a catalytic loop and DNMT3A homodimeric interface. A TRD residue Arg836 makes crucial contacts with CpG, ensuring DNMT3A enzymatic preference towards CpG sites in cells. Hematological cancer-associated somatic mutations of the substrate-binding residues decrease DNMT3A activity, induce CpG hypomethylation, and promote transformation of hematopoietic cells. Together, our study reveals the mechanistic basis for DNMT3A-mediated DNA methylation and establishes its etiologic link to human disease.
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72
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Deng L, Richine BM, Virts EL, Jideonwo-Auman VN, Chan RJ, Kapur R. Rapid development of myeloproliferative neoplasm in mice with Ptpn11D61Y mutation and haploinsufficient for Dnmt3a. Oncotarget 2018; 9:6055-6061. [PMID: 29464054 PMCID: PMC5814194 DOI: 10.18632/oncotarget.23680] [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] [Received: 11/02/2017] [Accepted: 12/08/2017] [Indexed: 11/25/2022] Open
Abstract
PTPN11 gain-of-function mutation is the most common mutation found in patients with juvenile myelomonocytic leukemia and DNMT3A loss occurs in over 20% of acute myeloid leukemia patients. We studied the combined effect of both Ptpn11 gain-of-function mutation (D61Y) and Dnmt3a haploinsufficiency on mouse hematopoiesis, the presence of which has been described in both juvenile myelomonocytic leukemia and acute myeloid leukemia patients. Double mutant mice rapidly become moribund relative to any of the other genotypes, which is associated with enlargement of the spleen and an increase in white blood cell counts. An increase in the mature myeloid cell compartment as reflected by the presence of Gr1+Mac1+ cells was also observed in double mutant mice relative to any other group. Consistent with these observations, a significant increase in the absolute number of granulocyte macrophage progenitors (GMPs) was seen in double mutant mice. A decrease in the lymphoid compartment including both T and B cells was noted in the double mutant mice. Another significant difference was the presence of extramedullary erythropoiesis with increased erythroid progenitors in the spleens of Dnmt3a+/−;D61Y mice relative to other groups. Taken together, our results suggest that the combined haploinsufficiency of Dnmt3a and presence of an activated Shp2 changes the composition of multiple hematopoietic lineages in mice relative to the individual heterozygosity of these genes.
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Affiliation(s)
- Lisa Deng
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Briana M Richine
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Elizabeth L Virts
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Victoria N Jideonwo-Auman
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rebecca J Chan
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA.,Gilead Sciences, Inc., Foster City, CA, USA
| | - Reuben Kapur
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
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73
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Haider M, Duncavage EJ, Afaneh KF, Bejar R, List AF. New Insight Into the Biology, Risk Stratification, and Targeted Treatment of Myelodysplastic Syndromes. Am Soc Clin Oncol Educ Book 2017; 37:480-494. [PMID: 28561687 DOI: 10.1200/edbk_175397] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In myelodysplastic syndromes (MDS), somatic mutations occur in five major categories: RNA splicing, DNA methylation, activated cell signaling, myeloid transcription factors, and chromatin modifiers. Although many MDS cases harbor more than one somatic mutation, in general, there is mutual exclusivity of mutated genes within a class. In addition to the prognostic significance of individual somatic mutations, more somatic mutations in MDS have been associated with poor prognosis. Prognostic assessment remains a critical component of the personalization of care for patient with MDS because treatment is highly risk adapted. Multiple methods for risk stratification are available with the revised International Prognostic Scoring System (IPSS-R), currently considered the gold standard. Increasing access to myeloid gene panels and greater evidence for the diagnostic and predictive value of somatic mutations will soon make sequencing part of the standard evaluation of patients with MDS. In the absence of formal guidelines for their prognostic use, well-validated mutations can still refine estimates of risk made with the IPSS-R. Not only are somatic gene mutations advantageous in understanding the biology of MDS and prognosis, they also offer potential as biomarkers and targets for the treatment of patients with MDS. Examples include deletion 5q, spliceosome complex gene mutations, and TP53 mutations.
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Affiliation(s)
- Mintallah Haider
- From the Department of Hematology and Medical Oncology, Moffitt Cancer Center and the University of South Florida, Tampa, FL; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO; Moores Cancer Center, Division of Hematology and Oncology, University of California, San Diego, CA; Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Eric J Duncavage
- From the Department of Hematology and Medical Oncology, Moffitt Cancer Center and the University of South Florida, Tampa, FL; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO; Moores Cancer Center, Division of Hematology and Oncology, University of California, San Diego, CA; Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Khalid F Afaneh
- From the Department of Hematology and Medical Oncology, Moffitt Cancer Center and the University of South Florida, Tampa, FL; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO; Moores Cancer Center, Division of Hematology and Oncology, University of California, San Diego, CA; Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Rafael Bejar
- From the Department of Hematology and Medical Oncology, Moffitt Cancer Center and the University of South Florida, Tampa, FL; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO; Moores Cancer Center, Division of Hematology and Oncology, University of California, San Diego, CA; Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
| | - Alan F List
- From the Department of Hematology and Medical Oncology, Moffitt Cancer Center and the University of South Florida, Tampa, FL; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO; Moores Cancer Center, Division of Hematology and Oncology, University of California, San Diego, CA; Department of Malignant Hematology, Moffitt Cancer Center, Tampa, FL
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74
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Lyko F. The DNA methyltransferase family: a versatile toolkit for epigenetic regulation. Nat Rev Genet 2017; 19:81-92. [PMID: 29033456 DOI: 10.1038/nrg.2017.80] [Citation(s) in RCA: 795] [Impact Index Per Article: 113.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The DNA methyltransferase (DNMT) family comprises a conserved set of DNA-modifying enzymes that have a central role in epigenetic gene regulation. Recent studies have shown that the functions of the canonical DNMT enzymes - DNMT1, DNMT3A and DNMT3B - go beyond their traditional roles of establishing and maintaining DNA methylation patterns. This Review analyses how molecular interactions and changes in gene copy numbers modulate the activity of DNMTs in diverse gene regulatory functions, including transcriptional silencing, transcriptional activation and post-transcriptional regulation by DNMT2-dependent tRNA methylation. This mechanistic diversity enables the DNMT family to function as a versatile toolkit for epigenetic regulation.
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Affiliation(s)
- Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
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75
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Balasubramanian SK, Aly M, Nagata Y, Bat T, Przychodzen BP, Hirsch CM, Adema V, Visconte V, Kuzmanovic T, Radivoyevitch T, Nazha A, Mukherjee S, Sekeres MA, Maciejewski JP. Distinct clinical and biological implications of various DNMT3A mutations in myeloid neoplasms. Leukemia 2017; 32:550-553. [PMID: 28935992 DOI: 10.1038/leu.2017.295] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- S K Balasubramanian
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - M Aly
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Y Nagata
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - T Bat
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - B P Przychodzen
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - C M Hirsch
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - V Adema
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - V Visconte
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - T Kuzmanovic
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - T Radivoyevitch
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - A Nazha
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - S Mukherjee
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA
| | - M A Sekeres
- Department of Hematology and Medical Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, OH, USA.,Department of Hematology and Medical Oncology, Leukemia Program, Cleveland Clinic, Cleveland, OH, USA
| | - J P Maciejewski
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
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76
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DNMT3A and TET2 dominate clonal hematopoiesis and demonstrate benign phenotypes and different genetic predispositions. Blood 2017; 130:753-762. [PMID: 28655780 DOI: 10.1182/blood-2017-04-777029] [Citation(s) in RCA: 250] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/21/2017] [Indexed: 12/11/2022] Open
Abstract
Age-associated clonal hematopoiesis caused by acquired mutations in myeloid cancer-associated genes is highly prevalent in the normal population. Its etiology, biological impact on hematopoiesis, and oncogenic risk is poorly defined at this time. To gain insight into this phenomenon, we analyzed a cohort of 2530 related and unrelated hematologically normal individuals (ages 55 to 101 years). We used a sensitive gene-targeted deep sequencing approach to gain precision on the exact prevalence of driver mutations and the proportions of affected genes. Mutational status was correlated with biological parameters. We report a higher overall prevalence of driver mutations (13.7%), which occurred mostly (93%) in DNMT3A or TET2 and were highly age-correlated. Mutation in these 2 genes had some distinctive effects on end points. TET2 mutations were more age-dependent, associated with a modest neutropenic effect (9%, P = .012), demonstrated familial aggregation, and associated with chronic obstructive pulmonary disease. Mutations in DNMT3A had no impact on blood counts or indices. Mutational burden of both genes correlated with X-inactivation skewing but no significant association with age-adjusted telomere length reduction was documented. The discordance between the high prevalence of mutations in these 2 genes and their limited biological impact raise the question of the potential role of dysregulated epigenetic modifiers in normal aging hematopoiesis, which may include support to failing hematopoiesis.
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77
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Abstract
In this review, Hu and Shilatifard summarize recent advances in our understanding of the role of chromatin modifiers in normal hematopoiesis and their contributions in hematopoietic transformation. Hematological malignancies comprise a diverse set of lymphoid and myeloid neoplasms in which normal hematopoiesis has gone awry and together account for ∼10% of all new cancer cases diagnosed in the United States in 2016. Recent intensive genomic sequencing of hematopoietic malignancies has identified recurrent mutations in genes that encode regulators of chromatin structure and function, highlighting the central role that aberrant epigenetic regulation plays in the pathogenesis of these neoplasms. Deciphering the molecular mechanisms for how alterations in epigenetic modifiers, specifically histone and DNA methylases and demethylases, drive hematopoietic cancer could provide new avenues for developing novel targeted epigenetic therapies for treating hematological malignancies. Just as past studies of blood cancers led to pioneering discoveries relevant to other cancers, determining the contribution of epigenetic modifiers in hematologic cancers could also have a broader impact on our understanding of the pathogenesis of solid tumors in which these factors are mutated.
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Affiliation(s)
- Deqing Hu
- Department of Biochemistry and Molecular Genetics
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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78
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Epigenetic dysregulation of hematopoietic stem cells and preleukemic state. Int J Hematol 2017; 106:34-44. [PMID: 28555413 DOI: 10.1007/s12185-017-2257-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 05/16/2017] [Indexed: 12/31/2022]
Abstract
Recent genetic analyses have revealed that premalignant somatic mutations in hematopoietic cells are common in older people without an evidence of hematologic malignancies, leading to clonal hematopoietic expansion. This phenomenon has been termed clonal hematopoiesis of indeterminate potential (CHIP). Frequency of such clonal somatic mutations increases with age: in 5-10% of people older than 70 years and around 20% of people older than 90 years. The most commonly mutated genes found in individuals with CHIP were epigenetic regulators, including DNA methyltransferase 3A (DNMT3A), Ten-eleven-translocation 2 (TET2), and Additional sex combs-like 1 (ASXL1), which are also recurrently mutated in myeloid malignancies. Recent functional studies have uncovered pleiotropic effect of mutations in DNMT3A, TET2, and ASXL1 in hematopoietic stem cell regulation and leukemic transformation. Of note, CHIP is associated with an increased risk of hematologic malignancy and all-cause mortality, albeit the annual risk of leukemic transformation was relatively low (0.5-1%). These findings suggest that clonal hematopoiesis per se may not be sufficient to engender preleukemic state. Further studies are required to decipher the exact mechanism by which preleukemic stem cells originate and transform into a full-blown leukemic state.
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79
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Conditional knockin of Dnmt3a R878H initiates acute myeloid leukemia with mTOR pathway involvement. Proc Natl Acad Sci U S A 2017; 114:5237-5242. [PMID: 28461508 DOI: 10.1073/pnas.1703476114] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
DNMT3A is frequently mutated in acute myeloid leukemia (AML). To explore the features of human AML with the hotspot DNMT3A R882H mutation, we generated Dnmt3a R878H conditional knockin mice, which developed AML with enlarged Lin-Sca1+cKit+ cell compartments. The transcriptome and DNA methylation profiling of bulk leukemic cells and the single-cell RNA sequencing of leukemic stem/progenitor cells revealed significant changes in gene expression and epigenetic regulatory patterns that cause differentiation arrest and growth advantage. Consistent with leukemic cell accumulation in G2/M phase, CDK1 was up-regulated due to mTOR activation associated with DNA hypomethylation. Overexpressed CDK1-mediated EZH2 phosphorylation resulted in an abnormal trimethylation of H3K27 profile. The mTOR inhibitor rapamycin elicited a significant therapeutic response in Dnmt3aR878H/WT mice.
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80
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Glass JL, Hassane D, Wouters BJ, Kunimoto H, Avellino R, Garrett-Bakelman FE, Guryanova OA, Bowman R, Redlich S, Intlekofer AM, Meydan C, Qin T, Fall M, Alonso A, Guzman ML, Valk PJM, Thompson CB, Levine R, Elemento O, Delwel R, Melnick A, Figueroa ME. Epigenetic Identity in AML Depends on Disruption of Nonpromoter Regulatory Elements and Is Affected by Antagonistic Effects of Mutations in Epigenetic Modifiers. Cancer Discov 2017; 7:868-883. [PMID: 28408400 DOI: 10.1158/2159-8290.cd-16-1032] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 04/07/2017] [Indexed: 11/16/2022]
Abstract
We performed cytosine methylation sequencing on genetically diverse patients with acute myeloid leukemia (AML) and found leukemic DNA methylation patterning is primarily driven by nonpromoter regulatory elements and CpG shores. Enhancers displayed stronger differential methylation than promoters, consisting predominantly of hypomethylation. AMLs with dominant hypermethylation featured greater epigenetic disruption of promoters, whereas those with dominant hypomethylation displayed greater disruption of distal and intronic regions. Mutations in IDH and DNMT3A had opposing and mutually exclusive effects on the epigenome. Notably, co-occurrence of both mutations resulted in epigenetic antagonism, with most CpGs affected by either mutation alone no longer affected in double-mutant AMLs. Importantly, this epigenetic antagonism precedes malignant transformation and can be observed in preleukemic LSK cells from Idh2R140Q or Dnmt3aR882H single-mutant and Idh2R140Q/Dnmt3aR882H double-mutant mice. Notably, IDH/DNMT3A double-mutant AMLs manifested upregulation of a RAS signaling signature and displayed unique sensitivity to MEK inhibition ex vivo as compared with AMLs with either single mutation.Significance: AML is biologically heterogeneous with subtypes characterized by specific genetic and epigenetic abnormalities. Comprehensive DNA methylation profiling revealed that differential methylation of nonpromoter regulatory elements is a driver of epigenetic identity, that gene mutations can be context-dependent, and that co-occurrence of mutations in epigenetic modifiers can result in epigenetic antagonism. Cancer Discov; 7(8); 868-83. ©2017 AACR.This article is highlighted in the In This Issue feature, p. 783.
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Affiliation(s)
- Jacob L Glass
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Duane Hassane
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Bas J Wouters
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Hiroyoshi Kunimoto
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Roberto Avellino
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Francine E Garrett-Bakelman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.,Department of Medicine, University of Virginia, Charlottesville, Virginia.,Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia
| | - Olga A Guryanova
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Robert Bowman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shira Redlich
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Andrew M Intlekofer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Cem Meydan
- Department of Medicine, University of Virginia, Charlottesville, Virginia
| | - Tingting Qin
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Mame Fall
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Alicia Alonso
- Epigenomics Core Facility, Weill Medical College of Cornell University, New York, New York
| | - Monica L Guzman
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York
| | - Peter J M Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Craig B Thompson
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ross Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York.,Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York.,Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Olivier Elemento
- Institute of Computational Biomedicine, Weill Medical College of Cornell University, New York, New York
| | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, the Netherlands.
| | - Ari Melnick
- Department of Medicine, Hematology/Oncology Division, Weill Medical College of Cornell University, New York, New York.
| | - Maria E Figueroa
- Department of Human Genetics and Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, Florida.
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81
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Dnmt3a regulates T-cell development and suppresses T-ALL transformation. Leukemia 2017; 31:2479-2490. [PMID: 28321121 PMCID: PMC5636646 DOI: 10.1038/leu.2017.89] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 03/13/2017] [Accepted: 03/16/2017] [Indexed: 12/30/2022]
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematopoietic neoplasm resulting from the malignant transformation of T-cell progenitors, and comprises approximately 15% and 25% of pediatric and adult ALL cases respectively. It is well-established that activating NOTCH1 mutations are the major genetic lesions driving T-ALL in most patients, but efforts to develop targeted therapies against this pathway have produced limited success in decreasing leukemic burden and come with significant clinical side effects. A finer detailed understanding of the genetic and molecular mechanisms underlying T-ALL is required identify patients at increased risk for treatment failure and the development of precision medicine strategies. Generation of genetic models that more accurately reflect the normal developmental history of T-ALL are necessary to identify new avenues for treatment. The DNA methyltransferase enzyme DNMT3A is also recurrently mutated in T-ALL patients, and we show here that inactivation of Dnmt3a combined with Notch1 gain-of-function leads to an aggressive T-ALL in mouse models. Moreover, conditional inactivation of Dnmt3a in mouse hematopoietic cells leads to an accumulation of immature progenitors in the thymus which are less apoptotic. These data demonstrate that Dnmt3a is required for normal T-cell development, and acts as a T-ALL tumor suppressor.
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82
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Chang YI, Kong G, Ranheim EA, Tu PS, Yu YS, Zhang J. Dnmt3a haploinsufficiency cooperates with oncogenic Kras to promote an early-onset T-cell acute lymphoblastic leukemia. Am J Transl Res 2017; 9:1326-1334. [PMID: 28386358 PMCID: PMC5376023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 02/08/2017] [Indexed: 06/07/2023]
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) are prevalent in various myeloid and lymphoid malignancies. The most common DNMT3A R882 mutations inhibit methyltransferase activity of the remaining wild-type DNMT3A proteins at a heterozygous state due to their dominant-negative activity. Reports and COSMIC database analysis reveal significantly different frequencies of R882 mutations in myeloid versus T-cell malignancies, inspiring us to investigate whether downregulation of DNMT3A regulates malignancies of different lineages in a dose-dependent manner. In a competitive transplant setting, the survival of recipients with KrasG12D/+ ; Dnmt3a+/- bone marrow (BM) cells was significantly shortened than that of recipients with KrasG12D/+ cells. Moreover, all of the recipients with KrasG12D/+ ; Dnmt3a+/- cells developed a lethal T-cell acute lymphoblastic leukemia (T-ALL) without significant myeloproliferative neoplasm (MPN) phenotypes, while ~20% of recipients with KrasG12D/+ cells developed MPN with or without T-ALL. This is in sharp contrast to the recipients with KrasG12D/+ ; Dnmt3a-/- cells, in which ~60% developed a lethal myeloid malignancy (MPN or acute myeloid leukemia [AML]). Our data suggest that in the context of oncogenic Kras, loss of Dnmt3a promotes myeloid malignancies, while Dnmt3a haploinsufficiency induces T-ALL. This dose-dependent phenotype is highly consistent with the prevalence of DNMT3A R882 mutations in AML versus T-ALL in human.
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Affiliation(s)
- Yuan-I Chang
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadison, WI 53706, USA
- Department and Institute of Physiology, National Yang-Ming UniversityTaipei 11221, Taiwan
| | - Guangyao Kong
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadison, WI 53706, USA
- National Local Joint Engineering Research Center of Biodiagnostics and Biotherapy, The Second Affiliated Hospital of Xi’an Jiaotong UniversityXi’an, P. R. China
| | - Erik A Ranheim
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, University of Wisconsin Carbone Cancer CenterMadison, WI 53792, USA
| | - Po-Shu Tu
- Department and Institute of Physiology, National Yang-Ming UniversityTaipei 11221, Taiwan
| | - Yi-Shan Yu
- Department and Institute of Physiology, National Yang-Ming UniversityTaipei 11221, Taiwan
| | - Jing Zhang
- McArdle Laboratory for Cancer Research, University of Wisconsin-MadisonMadison, WI 53706, USA
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83
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Epigenetic Guardian: A Review of the DNA Methyltransferase DNMT3A in Acute Myeloid Leukaemia and Clonal Haematopoiesis. BIOMED RESEARCH INTERNATIONAL 2017; 2017:5473197. [PMID: 28286768 PMCID: PMC5329657 DOI: 10.1155/2017/5473197] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/18/2016] [Accepted: 11/14/2016] [Indexed: 12/25/2022]
Abstract
Acute myeloid leukaemia (AML) is a haematological malignancy characterized by clonal stem cell proliferation and aberrant block in differentiation. Dysfunction of epigenetic modifiers contributes significantly to the pathogenesis of AML. One frequently mutated gene involved in epigenetic modification is DNMT3A (DNA methyltransferase-3-alpha), a DNA methyltransferase that alters gene expression by de novo methylation of cytosine bases at CpG dinucleotides. Approximately 22% of AML and 36% of cytogenetically normal AML cases carry DNMT3A mutations and around 60% of these mutations affect the R882 codon. These mutations have been associated with poor prognosis and adverse survival outcomes for AML patients. Advances in whole-exome sequencing techniques have recently identified a large number of DNMT3A mutations present in clonal cells in normal elderly individuals with no features of haematological malignancy. Categorically distinct from other preleukaemic conditions, this disorder has been termed clonal haematopoiesis of indeterminate potential (CHIP). Further insight into the mutational landscape of CHIP may illustrate the consequence of particular mutations found in DNMT3A and identify specific “founder” mutations responsible for clonal expansion that may contribute to leukaemogenesis. This review will focus on current research and understanding of DNMT3A mutations in both AML and CHIP.
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84
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Abstract
DNA methylation is an epigenetic process involved in development, aging, and cancer. Although the advent of new molecular techniques has enhanced our knowledge of how DNA methylation alters chromatin and subsequently affects gene expression, a direct link between epigenetic marks and tumorigenesis has not been established. DNMT3A is a de novo DNA methyltransferase that has recently gained relevance because of its frequent mutation in a large variety of immature and mature hematologic neoplasms. DNMT3A mutations are early events during cancer development and seem to confer poor prognosis to acute myeloid leukemia (AML) patients making this gene an attractive target for new therapies. Here, we discuss the biology of DNMT3A and its role in controlling hematopoietic stem cell fate decisions. In addition, we review how mutant DNMT3A may contribute to leukemogenesis and the clinical relevance of DNMT3A mutations in hematologic cancers.
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Affiliation(s)
- Lorenzo Brunetti
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,CREO, University of Perugia, 06123 Perugia, Italy
| | - Michael C Gundry
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas 77030
| | - Margaret A Goodell
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030.,Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, Texas 77030.,CREO, University of Perugia, 06123 Perugia, Italy.,Texas Children's Hospital, and Houston Methodist Hospital, Houston, Texas 77030
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85
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Zhang W, Xu J. DNA methyltransferases and their roles in tumorigenesis. Biomark Res 2017; 5:1. [PMID: 28127428 PMCID: PMC5251331 DOI: 10.1186/s40364-017-0081-z] [Citation(s) in RCA: 225] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Accepted: 01/03/2017] [Indexed: 01/13/2023] Open
Abstract
DNA methylation plays an important role in gene expression, chromatin stability, and genetic imprinting. In mammals, DNA methylation patterns are written and regulated by DNA methyltransferases (DNMTs), including DNMT1, DNMT3A and DNMT3B. Recent emerging evidence shows that defects in DNMTs are involved in tumor transformation and progression, thus indicating that epigenetic disruptions caused by DNMT abnormalities are associated with tumorigenesis. Herein, we review the latest findings related to DNMT alterations in cancer cells and discuss the contributions of these effects to oncogenic phenotypes.
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Affiliation(s)
- Wu Zhang
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
| | - Jie Xu
- State Key Laboratory for Medical Genomics, Shanghai Institute of Hematology, Rui-Jin Hospital affiliated to Shanghai Jiao-Tong University School of Medicine, 197 Rui Jin Er Road, 200025 Shanghai, China
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86
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Pastore F, Levine RL. Epigenetic regulators and their impact on therapy in acute myeloid leukemia. Haematologica 2017; 101:269-78. [PMID: 26928248 DOI: 10.3324/haematol.2015.140822] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Genomic studies of hematologic malignancies have identified a spectrum of recurrent somatic alterations that contribute to acute myeloid leukemia initiation and maintenance, and which confer sensitivities to molecularly targeted therapies. The majority of these genetic events are small, site-specific alterations in DNA sequence. In more than two thirds of patients with de novo acute myeloid leukemia mutations epigenetic modifiers are detected. Epigenetic modifiers encompass a large group of proteins that modify DNA at cytosine residues or cause post-translational histone modifications such as methylations or acetylations. Altered functions of these epigenetic modifiers disturb the physiological balance between gene activation and gene repression and contribute to aberrant gene expression regulation found in acute myeloid leukemia. This review provides an overview of the epigenetic modifiers mutated in acute myeloid leukemia, their clinical relevance and how a deeper understanding of their biological function has led to the discovery of new specific targets, some of which are currently tested in mechanism-based clinical trials.
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Affiliation(s)
- Friederike Pastore
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center
| | - Ross L Levine
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York City, NY, USA
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87
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DNMT3A mutations promote anthracycline resistance in acute myeloid leukemia via impaired nucleosome remodeling. Nat Med 2016; 22:1488-1495. [PMID: 27841873 PMCID: PMC5359771 DOI: 10.1038/nm.4210] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2016] [Accepted: 09/16/2016] [Indexed: 01/16/2023]
Abstract
Although the majority of patients with acute myeloid leukemia (AML) initially respond to chemotherapy, many of them subsequently relapse, and the mechanistic basis for AML persistence following chemotherapy has not been determined. Recurrent somatic mutations in DNA methyltransferase 3A (DNMT3A), most frequently at arginine 882 (DNMT3AR882), have been observed in AML and in individuals with clonal hematopoiesis in the absence of leukemic transformation. Patients with DNMT3AR882 AML have an inferior outcome when treated with standard-dose daunorubicin-based induction chemotherapy, suggesting that DNMT3AR882 cells persist and drive relapse. We found that Dnmt3a mutations induced hematopoietic stem cell expansion, cooperated with mutations in the FMS-like tyrosine kinase 3 gene (Flt3ITD) and the nucleophosmin gene (Npm1c) to induce AML in vivo, and promoted resistance to anthracycline chemotherapy. In patients with AML, the presence of DNMT3AR882 mutations predicts minimal residual disease, underscoring their role in AML chemoresistance. DNMT3AR882 cells showed impaired nucleosome eviction and chromatin remodeling in response to anthracycline treatment, which resulted from attenuated recruitment of histone chaperone SPT-16 following anthracycline exposure. This defect led to an inability to sense and repair DNA torsional stress, which resulted in increased mutagenesis. Our findings identify a crucial role for DNMT3AR882 mutations in driving AML chemoresistance and highlight the importance of chromatin remodeling in response to cytotoxic chemotherapy.
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88
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Bhatnagar B, Eisfeld AK, Nicolet D, Mrózek K, Blachly JS, Orwick S, Lucas DM, Kohlschmidt J, Blum W, Kolitz JE, Stone RM, Bloomfield CD, Byrd JC. Persistence of DNMT3A R882 mutations during remission does not adversely affect outcomes of patients with acute myeloid leukaemia. Br J Haematol 2016; 175:226-236. [PMID: 27476855 DOI: 10.1111/bjh.14254] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 06/07/2016] [Indexed: 12/30/2022]
Abstract
Somatic mutation of the DNMT3A gene at the arginine R882 site is common in acute myeloid leukaemia (AML). The prognostic significance of DNMT3A R882 mutation clearance, using traditional diagnostic next generation sequencing (NGS) methods, during complete remission (CR) in AML patients is controversial. We examined the impact of clearing DNMT3A R882 mutations at diagnosis to the detectable threshold of ˂3% during CR on outcome in 56 adult AML patients. Mutational remission, defined as clearance of pre-treatment DNMT3A R882 and all other AML-associated mutations to a variant allele frequency ˂3%, occurred in 14 patients whereas persistent DNMT3A R882 mutations were observed in 42 patients. There were no significant differences in disease-free or overall survival between patients with and without DNMT3A R882 mutation clearance. Patients with persistent DNMT3A R882 who cleared all other AML mutations and did not acquire new mutations (n = 30), trended towards longer disease-free survival (1·6 vs. 0·6 years, P = 0·06) than patients with persistence of DNMT3A R882, in addition to other mutations or acquisition of new AML-associated mutations, such as those in TET2, JAK2, ASXL1 and TP53 (n = 12). These data demonstrate that DNMT3A R882 mutations, as assessed by traditional NGS methods, persist in the majority of AML patients in CR.
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Affiliation(s)
- Bhavana Bhatnagar
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. .,The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
| | | | - Deedra Nicolet
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - Krzysztof Mrózek
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - James S Blachly
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Shelley Orwick
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - David M Lucas
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jessica Kohlschmidt
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,Alliance for Clinical Trials in Oncology Statistics and Data Center, Mayo Clinic, Rochester, MN, USA
| | - William Blum
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - Jonathan E Kolitz
- Monter Cancer Center, Hofstra North Shore-Long Island Jewish School of Medicine, Lake Success, NY, USA
| | | | - Clara D Bloomfield
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.,The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA
| | - John C Byrd
- Division of Hematology, Department of Internal Medicine, The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA. .,The Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.
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89
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Buscarlet M, Tessier A, Provost S, Mollica L, Busque L. Human blood cell levels of 5-hydroxymethylcytosine (5hmC) decline with age, partly related to acquired mutations in TET2. Exp Hematol 2016; 44:1072-1084. [PMID: 27475703 DOI: 10.1016/j.exphem.2016.07.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 07/08/2016] [Accepted: 07/14/2016] [Indexed: 12/15/2022]
Abstract
Epigenetic alteration may play a role in age-associated dysfunction of stem cells and predispose to the development of hematological cancers. We analyzed global levels of hematopoietic 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) in a cross-sectional study comprising 198 unrelated individuals from four age categories (neonates, 25-30, 70-75, and >90 years old) by liquid chromatography-electrospray ionization-tandem mass spectrometry with multiple reaction monitoring. X-chromosome inactivation (XCI) ratios and telomere length (TL) were measured in all individuals by polymerase chain reaction. Sequencing of epigenetic regulator genes (including TET2, DNMT3A, ASXL1, IDH1, IDH2, and WT1) was performed in the two older subcohorts. We found that global 5hmC levels declined with age in human blood cells (27.5% reduction from birth to old age, p < 0.0005). The levels of 5mC underwent a more modest reduction (2.4% drop) between newborns and the elderly (p < 0.0005). Low 5hmC was associated with increased skewing of XCI (age-adjusted p = 0.0304) and reduced TL (age-adjusted p = 0.0354), both surrogate markers of clonal dominance. Of the 100 individuals over the age of 70, 16 had somatic mutations in TET2, 14 in DNMT3A, and none in IDH1, IDH2, or WT1. Individuals with TET2 mutations had significantly lower 5hmC (relative to unmutated individuals), whereas DNMT3A-mutated subjects did not. However, mutations in TET2 cannot account solely for the decline in 5hmC levels observed with aging because unmutated older individuals also had lower 5hmC levels compared with younger individuals. This suggests that the age-associated decline in 5hmC is multifactorial. Larger prospective studies are needed to determine whether 5hmC reduction is a biomarker of hematological cancer development.
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Affiliation(s)
| | - Alain Tessier
- Centre for Biological Applications of Mass Spectrometry, Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Sylvie Provost
- Beaulieu-Saucier Pharmacogenomics Centre, Montreal Heart Institute Research Centre, Montreal, Canada
| | - Luigina Mollica
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada
| | - Lambert Busque
- Research Centre, Montreal, Canada; Department of Hematology, Installation Hôpital Maisonneuve-Rosemont, Montreal, Canada; Université de Montréal, Montreal, Canada.
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90
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Lu R, Wang P, Parton T, Zhou Y, Chrysovergis K, Rockowitz S, Chen WY, Abdel-Wahab O, Wade PA, Zheng D, Wang GG. Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development. Cancer Cell 2016; 30:92-107. [PMID: 27344947 PMCID: PMC4945461 DOI: 10.1016/j.ccell.2016.05.008] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Revised: 03/03/2016] [Accepted: 05/19/2016] [Indexed: 12/19/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) is frequently mutated in hematological cancers; however, the underlying oncogenic mechanism remains elusive. Here, we report that the DNMT3A mutational hotspot at Arg882 (DNMT3A(R882H)) cooperates with NRAS mutation to transform hematopoietic stem/progenitor cells and induce acute leukemia development. Mechanistically, DNMT3A(R882H) directly binds to and potentiates transactivation of stemness genes critical for leukemogenicity including Meis1, Mn1, and Hoxa gene cluster. DNMT3A(R882H) induces focal epigenetic alterations, including CpG hypomethylation and concurrent gain of active histone modifications, at cis-regulatory elements such as enhancers to facilitate gene transcription. CRISPR/Cas9-mediated ablation of a putative Meis1 enhancer carrying DNMT3A(R882H)-induced DNA hypomethylation impairs Meis1 expression. Importantly, DNMT3A(R882H)-induced gene-expression programs can be repressed through Dot1l inhibition, providing an attractive therapeutic strategy for DNMT3A-mutated leukemias.
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MESH Headings
- Animals
- Arginine/genetics
- DNA (Cytosine-5-)-Methyltransferases/genetics
- DNA Methylation
- DNA Methyltransferase 3A
- Epigenesis, Genetic
- Gene Expression Profiling
- Gene Expression Regulation, Leukemic
- Genes, ras
- Homeodomain Proteins/genetics
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/pathology
- Methyltransferases/antagonists & inhibitors
- Mice
- Mutation
- Myeloid Ecotropic Viral Integration Site 1 Protein
- Neoplasm Proteins/genetics
- Neoplasms, Experimental
- Promoter Regions, Genetic
- Stem Cells/cytology
- Stem Cells/pathology
- Tumor Cells, Cultured
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Affiliation(s)
- Rui Lu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Ping Wang
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Trevor Parton
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Yang Zhou
- Department of Pathology and Laboratory Medicine, McAllister Heart Institute, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Kaliopi Chrysovergis
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
| | - Shira Rockowitz
- Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11221, Taiwan
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
| | - Paul A Wade
- Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27709, USA
| | - Deyou Zheng
- Department of Neurology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Departments of Genetics and Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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91
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DOT1L as a therapeutic target for the treatment of DNMT3A-mutant acute myeloid leukemia. Blood 2016; 128:971-81. [PMID: 27335278 DOI: 10.1182/blood-2015-11-684225] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 06/06/2016] [Indexed: 12/22/2022] Open
Abstract
Mutations in DNA methyltransferase 3A (DNMT3A) are common in acute myeloid leukemia and portend a poor prognosis; thus, new therapeutic strategies are needed. The likely mechanism by which DNMT3A loss contributes to leukemogenesis is altered DNA methylation and the attendant gene expression changes; however, our current understanding is incomplete. We observed that murine hematopoietic stem cells (HSCs) in which Dnmt3a had been conditionally deleted markedly overexpress the histone 3 lysine 79 (H3K79) methyltransferase, Dot1l. We demonstrate that Dnmt3a(-/-) HSCs have increased H3K79 methylation relative to wild-type (WT) HSCs, with the greatest increases noted at DNA methylation canyons, which are regions highly enriched for genes dysregulated in leukemia and prone to DNA methylation loss with Dnmt3a deletion. These findings led us to explore DOT1L as a therapeutic target for the treatment of DNMT3A-mutant AML. We show that pharmacologic inhibition of DOT1L resulted in decreased expression of oncogenic canyon-associated genes and led to dose- and time-dependent inhibition of proliferation, induction of apoptosis, cell-cycle arrest, and terminal differentiation in DNMT3A-mutant cell lines in vitro. We show in vivo efficacy of the DOT1L inhibitor EPZ5676 in a nude rat xenograft model of DNMT3A-mutant AML. DOT1L inhibition was also effective against primary patient DNMT3A-mutant AML samples, reducing colony-forming capacity (CFC) and inducing terminal differentiation in vitro. These studies suggest that DOT1L may play a critical role in DNMT3A-mutant leukemia. With pharmacologic inhibitors of DOT1L already in clinical trials, DOT1L could be an immediately actionable therapeutic target for the treatment of this poor prognosis disease.
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92
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Yang L, Rodriguez B, Mayle A, Park HJ, Lin X, Luo M, Jeong M, Curry CV, Kim SB, Ruau D, Zhang X, Zhou T, Zhou M, Rebel VI, Challen GA, Gottgens B, Lee JS, Rau R, Li W, Goodell MA. DNMT3A Loss Drives Enhancer Hypomethylation in FLT3-ITD-Associated Leukemias. Cancer Cell 2016; 29:922-934. [PMID: 27300438 PMCID: PMC4908977 DOI: 10.1016/j.ccell.2016.05.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 02/29/2016] [Accepted: 05/10/2016] [Indexed: 10/21/2022]
Abstract
DNMT3A, the gene encoding the de novo DNA methyltransferase 3A, is among the most frequently mutated genes in hematologic malignancies. However, the mechanisms through which DNMT3A normally suppresses malignancy development are unknown. Here, we show that DNMT3A loss synergizes with the FLT3 internal tandem duplication in a dose-influenced fashion to generate rapid lethal lymphoid or myeloid leukemias similar to their human counterparts. Loss of DNMT3A leads to reduced DNA methylation, predominantly at hematopoietic enhancer regions in both mouse and human samples. Myeloid and lymphoid diseases arise from transformed murine hematopoietic stem cells. Broadly, our findings support a role for DNMT3A as a guardian of the epigenetic state at enhancer regions, critical for inhibition of leukemic transformation.
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Affiliation(s)
- Liubin Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin Rodriguez
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Allison Mayle
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Hyun Jung Park
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xueqiu Lin
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Bioinformatics, School of Life sciences and Technology, Tongji University, Shanghai 20092, China
| | - Min Luo
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Mira Jeong
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Choladda V. Curry
- Department of Pathology and Immunology, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Sang-Bae Kim
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - David Ruau
- Wellcome Trust/MRC Stem Cell Institute, Cambridge CB2 0XY, UK
| | - Xiaotian Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Ting Zhou
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | | | - Vivienne I. Rebel
- Greehey Children's Cancer Research Institute and Department of Cellular and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Grant A. Challen
- Division of Oncology, Washington University School of Medicine, St. Louis, Missouri 63110, USA
| | | | - Ju-Seog Lee
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Rachel Rau
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Margaret A. Goodell
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
- Stem Cells and Regenerative Medicine Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Systems Biology, Division of Cancer Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
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93
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Yuan XQ, Peng L, Zeng WJ, Jiang BY, Li GC, Chen XP. DNMT3A R882 Mutations Predict a Poor Prognosis in AML: A Meta-Analysis From 4474 Patients. Medicine (Baltimore) 2016; 95:e3519. [PMID: 27149454 PMCID: PMC4863771 DOI: 10.1097/md.0000000000003519] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
DNA (cytosine-5)-methyltransferase 3 alpha (DNMT3A) mutations were widely believed to be independently associated with inferior prognosis in acute myeloid leukemia (AML) patients. As dominant missense alterations in DNMT3A mutations, R882 mutations cause the focal hypomethylation phenotype. However, there remains debate on the influence of R882 mutations on AML prognosis. Thus, this meta-analysis aimed at further illustrating the prognostic power of DNMT3A R882 mutations in AML patients.Eligible studies were identified from 5 databases containing PubMed, Embase, Web of Science, Clinical Trials, and the Cochrane Library (up to October 25, 2015). Effects (hazard ratios [HRs] with 95% confidence interval [CI]) of relapse-free survival (RFS) and overall survival (OS) were pooled to estimate the prognostic power of mutant DNMT3A R882 in overall patients and subgroups of AML patients.Eight competent studies with 4474 AML patients including 694 with DNMT3A R882 mutations were included. AML patients with DNMT3A R882 mutations showed significant shorter RFS (HR = 1.40, 95% CI = 1.24-1.59, P < 0.001) and OS (HR = 1.47, 95% CI = 1.17-1.86, P = 0.001) in the overall population. DNMT3A R882 mutations predicted worse RFS and OS among the subgroups of patients under age 60 (RFS: HR = 1.44, 95% CI = 1.25-1.66, P < 0.001; OS: HR = 1.48, 95% CI = 1.15-1.90, P = 0.002), over age 60 (RFS: HR = 2.03, 95% CI = 1.40-2.93, P < 0.001; OS: HR = 1.85, 95% CI = 1.36-2.53, P < 0.001), cytogenetically normal (CN)-AML (RFS: HR = 1.52, 95% CI = 1.26-1.83, P < 0.001; OS: HR = 1.67, 95% CI = 1.16-2.41, P = 0.006), and non-CN-AML (RFS: HR = 1.96, 95% CI = 1.20-3.21, P = 0.006; OS: HR = 2.51, 95% CI = 1.52-4.15, P = 0.0038).DNMT3A R882 mutations possessed significant unfavorable prognostic influence on RFS and OS in AML patients.
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Affiliation(s)
- Xiao-Qing Yuan
- From the Department of Clinical Pharmacology, Xiangya Hospital; Institute of Clinical Pharmacology, Central South University; Hunan Key Laboratory of Pharmacogenetics (X-QY, W-JZ, X-PC); Cancer Research Institute, Central South University; Key Laboratory of Carcinogenesis, National Health and Family Planning Commission; Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Changsha (LP, B-YJ, G-CL); and Hunan Province Cooperation Innovation Center for Molecular Target New Drug Study, Hengyang, P.R. China (X-PC)
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94
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Guryanova OA, Lieu YK, Garrett-Bakelman FE, Spitzer B, Glass JL, Shank K, Valencia Martinez AB, Rivera SA, Durham BH, Rapaport F, Keller MD, Pandey S, Bastian L, Tovbin D, Weinstein AR, Teruya-Feldstein J, Abdel-Wahab O, Santini V, Mason CE, Melnick AM, Mukherjee S, Levine RL. Dnmt3a regulates myeloproliferation and liver-specific expansion of hematopoietic stem and progenitor cells. Leukemia 2016; 30:1133-42. [PMID: 26710888 PMCID: PMC4856586 DOI: 10.1038/leu.2015.358] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 12/22/2022]
Abstract
DNA methyltransferase 3A (DNMT3A) mutations are observed in myeloid malignancies, including myeloproliferative neoplasms (MPN), myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). Transplantation studies have elucidated an important role for Dnmt3a in stem cell self-renewal and in myeloid differentiation. Here, we investigated the impact of conditional hematopoietic Dnmt3a loss on disease phenotype in primary mice. Mx1-Cre-mediated Dnmt3a ablation led to the development of a lethal, fully penetrant MPN with myelodysplasia (MDS/MPN) characterized by peripheral cytopenias and by marked, progressive hepatomegaly. We detected expanded stem/progenitor populations in the liver of Dnmt3a-ablated mice. The MDS/MPN induced by Dnmt3a ablation was transplantable, including the marked hepatomegaly. Homing studies showed that Dnmt3a-deleted bone marrow cells preferentially migrated to the liver. Gene expression and DNA methylation analyses of progenitor cell populations identified differential regulation of hematopoietic regulatory pathways, including fetal liver hematopoiesis transcriptional programs. These data demonstrate that Dnmt3a ablation in the hematopoietic system leads to myeloid transformation in vivo, with cell-autonomous aberrant tissue tropism and marked extramedullary hematopoiesis (EMH) with liver involvement. Hence, in addition to the established role of Dnmt3a in regulating self-renewal, Dnmt3a regulates tissue tropism and limits myeloid progenitor expansion in vivo.
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Affiliation(s)
- Olga A. Guryanova
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Yen K. Lieu
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY
| | | | - Barbara Spitzer
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jacob L. Glass
- Department of Medicine, Weill Cornell Medical College, New York, NY
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kaitlyn Shank
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Sharon A. Rivera
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY
| | - Benjamin H. Durham
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Franck Rapaport
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Matthew D. Keller
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Suveg Pandey
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Lennart Bastian
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Daniel Tovbin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Abby R. Weinstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Julie Teruya-Feldstein
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Christopher E. Mason
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medical College, New York, NY
| | - Siddhartha Mukherjee
- Department of Medicine and Irving Cancer Research Center, Columbia University, New York, NY
| | - Ross L. Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY
- Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY
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95
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Haney SL, Upchurch GM, Opavska J, Klinkebiel D, Hlady RA, Suresh A, Pirruccello SJ, Shukla V, Lu R, Costinean S, Rizzino A, Karpf AR, Joshi S, Swanson P, Opavsky R. Promoter Hypomethylation and Expression Is Conserved in Mouse Chronic Lymphocytic Leukemia Induced by Decreased or Inactivated Dnmt3a. Cell Rep 2016; 15:1190-201. [PMID: 27134162 DOI: 10.1016/j.celrep.2016.04.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/18/2016] [Accepted: 03/28/2016] [Indexed: 01/06/2023] Open
Abstract
DNA methyltransferase 3a (DNMT3A) catalyzes the formation of 5-methyl-cytosine in mammalian genomic DNA, and it is frequently mutated in human hematologic malignancies. Bi-allelic loss of Dnmt3a in mice results in leukemia and lymphoma, including chronic lymphocytic leukemia (CLL). Here, we investigate whether mono-allelic loss of Dnmt3a is sufficient to induce disease. We show that, by 16 months of age, 65% of Dnmt3a(+/-) mice develop a CLL-like disease, and 15% of mice develop non-malignant myeloproliferation. Genome-wide methylation analysis reveals that reduced Dnmt3a levels induce promoter hypomethylation at similar loci in Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL, suggesting that promoters are particularly sensitive to Dnmt3a levels. Gene expression analysis identified 26 hypomethylated and overexpressed genes common to both Dnmt3a(+/-) and Dnmt3a(Δ/Δ) CLL as putative oncogenic drivers. Our data provide evidence that Dnmt3a is a haplo-insufficient tumor suppressor in CLL and highlights the importance of deregulated molecular events in disease pathogenesis.
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Affiliation(s)
- Staci L Haney
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - G Michael Upchurch
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Jana Opavska
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - David Klinkebiel
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Abhinav Suresh
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Samuel J Pirruccello
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vipul Shukla
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Runqing Lu
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Stefan Costinean
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angie Rizzino
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA; Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Adam R Karpf
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shantaram Joshi
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Patrick Swanson
- Department of Medical Microbiology and Immunology, Creighton University, Omaha, NE 68102, USA
| | - Rene Opavsky
- Department of Genetics, Cell Biology, and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA; Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA; Center for Leukemia and Lymphoma Research, University of Nebraska Medical Center, Omaha, NE 68198, USA.
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96
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DNA methylation in normal and malignant hematopoiesis. Int J Hematol 2016; 103:617-26. [PMID: 26943352 DOI: 10.1007/s12185-016-1957-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 02/08/2016] [Indexed: 01/08/2023]
Abstract
The study of DNA methylation has been a rapidly expanding field since its dawn in the 1960s. DNA methylation is an epigenetic modification that plays a crucial role in guiding the differentiation of stem cells to their destined lineage, and in maintaining tissue homeostasis. Moreover, aberrant DNA methylation has been well characterized as a significant contributing factor in the pathogenesis of a variety of cancers. Hematopoiesis is a process that is uniquely susceptible to epigenetic changes due to the small pool of actively cycling stem cells that give rise to the entire mature immune-hematopoietic system. Mutations in DNA methyltransferase enzymes have been shown to be initiating events in the development of hematological malignancies such as acute myeloid leukemia and, therefore, have become targets for improved diagnostics and therapy. The spatial and temporal regulation of DNA methylation in the hematopoietic developmental hierarchy is critical to hematopoietic homeostasis. An improved understanding of the roles that DNA methylation plays in normal and malignant hematopoiesis will have a significant impact on the future of regenerative stem cell therapy and clinical treatment of hematopoietic malignancies. This review aims to highlight current developments in the field and prioritize future research directions.
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97
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DNMT3A(R882H) mutant and Tet2 inactivation cooperate in the deregulation of DNA methylation control to induce lymphoid malignancies in mice. Leukemia 2016; 30:1388-98. [PMID: 26876596 PMCID: PMC4869893 DOI: 10.1038/leu.2016.29] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/07/2016] [Accepted: 01/18/2016] [Indexed: 12/21/2022]
Abstract
TEN-ELEVEN-TRANSLOCATION-2 (TET2) and DNA-METHYLTRANSFERASE-3A (DNMT3A), both encoding proteins involved in regulating DNA methylation, are mutated in hematological malignancies affecting both myeloid and lymphoid lineages. We previously reported an association of TET2 and DNMT3A mutations in progenitors of patients with angioimmunoblastic T-cell lymphomas (AITL). Here, we report on the cooperative effect of Tet2-inactivation and DNMT3A mutation affecting arginine 882 (DNMT3AR882H) using a murine bone marrow transplantation assay. Five out of 18 primary recipients developed hematological malignancies with one mouse developing an AITL-like disease, 2 mice presenting acute myeloid leukemia (AML)-like and 2 others T cell acute lymphoblastic leukemia (T-ALL)-like diseases within 6 months following transplantation. Serial transplantations of DNMT3AR882H Tet2−/− progenitors led to a differentiation bias toward the T-cell compartment, eventually leading to AITL-like disease in 9/12 serially transplanted recipients. Expression profiling suggested that DNMT3AR882H Tet2−/− T-ALLs resemble those of NOTCH1 mutant. Methylation analysis of DNMT3AR882H Tet2−/− T-ALLs showed a global increase in DNA methylation affecting tumor suppressor genes and local hypomethylation affecting genes involved in the Notch pathway. Our data confirm the transformation potential of DNMT3AR882H Tet2−/− progenitors and represent the first cooperative model in mice involving Tet2-inactivation driving lymphoid malignancies.
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98
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Dan J, Chen T. Genetic Studies on Mammalian DNA Methyltransferases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:123-150. [PMID: 27826837 DOI: 10.1007/978-3-319-43624-1_6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cytosine methylation at the C5-position, generating 5-methylcytosine (5mC), is a DNA modification found in many eukaryotic organisms, including fungi, plants, invertebrates, and vertebrates, albeit its levels vary greatly in different organisms. In mammals, cytosine methylation occurs predominantly in the context of CpG dinucleotides, with the majority (60-80 %) of CpG sites in their genomes being methylated. DNA methylation plays crucial roles in the regulation of chromatin structure and gene expression and is essential for mammalian development. Aberrant changes in DNA methylation levels and patterns are associated with various human diseases, including cancer and developmental disorders. DNA methylation is mediated by three active DNA methyltransferases (Dnmts), namely, Dnmt1, Dnmt3a, and Dnmt3b, in mammals. Over the last two decades, genetic manipulations of these enzymes, as well as their regulators, in mice have greatly contributed to our understanding of the biological functions of DNA methylation in mammals. In this chapter, we discuss genetic studies on mammalian Dnmts, focusing on their roles in embryogenesis, cellular differentiation, genomic imprinting, and X-chromosome inactivation.
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Affiliation(s)
- Jiameng Dan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA
| | - Taiping Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, 1808 Park Road 1C, Smithville, TX, 78957, USA.
- Graduate School of Biomedical Sciences at Houston, Houston, TX, 77030, USA.
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99
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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 2015; 126:85-98. [PMID: 26595813 DOI: 10.1172/jci82897] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Accepted: 10/14/2015] [Indexed: 12/27/2022] Open
Abstract
The DNA methyltransferases DNMT3A and DNMT3B are primarily responsible for de novo methylation of specific cytosine residues in CpG dinucleotides during mammalian development. While loss-of-function mutations in DNMT3A are highly recurrent in acute myeloid leukemia (AML), DNMT3A mutations are almost never found in AML patients with translocations that create oncogenic fusion genes such as PML-RARA, RUNX1-RUNX1T1, and MLL-AF9. Here, we explored how DNMT3A is involved in the function of these fusion genes. We used retroviral vectors to express PML-RARA, RUNX1-RUNX1T1, or MLL-AF9 in bone marrow cells derived from WT or DNMT3A-deficient mice. Additionally, we examined the phenotypes of hematopoietic cells from Ctsg-PML-RARA mice, which express PML-RARA in early hematopoietic progenitors and myeloid precursors, with or without DNMT3A. We determined that the methyltransferase activity of DNMT3A, but not DNMT3B, is required for aberrant PML-RARA-driven self-renewal ex vivo and that DNMT3A is dispensable for RUNX1-RUNX1T1- and MLL-AF9-driven self-renewal. Furthermore, both the PML-RARA-driven competitive transplantation advantage and development of acute promyelocytic leukemia (APL) required DNMT3A. Together, these findings suggest that PML-RARA requires DNMT3A to initiate APL in mice.
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100
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Kitamura T, Watanabe-Okochi N, Enomoto Y, Nakahara F, Oki T, Komeno Y, Kato N, Doki N, Uchida T, Kagiyama Y, Togami K, Kawabata KC, Nishimura K, Hayashi Y, Nagase R, Saika M, Fukushima T, Asada S, Fujino T, Izawa Y, Horikawa S, Fukuyama T, Tanaka Y, Ono R, Goyama S, Nosaka T, Kitaura J, Inoue D. Novel working hypothesis for pathogenesis of hematological malignancies: combination of mutations-induced cellular phenotypes determines the disease (cMIP-DD). J Biochem 2015; 159:17-25. [PMID: 26590301 DOI: 10.1093/jb/mvv114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 10/22/2015] [Indexed: 11/12/2022] Open
Abstract
Recent progress in high-speed sequencing technology has revealed that tumors harbor novel mutations in a variety of genes including those for molecules involved in epigenetics and splicing, some of which were not categorized to previously thought malignancy-related genes. However, despite thorough identification of mutations in solid tumors and hematological malignancies, how these mutations induce cell transformation still remains elusive. In addition, each tumor usually contains multiple mutations or sometimes consists of multiple clones, which makes functional analysis difficult. Fifteen years ago, it was proposed that combination of two types of mutations induce acute leukemia; Class I mutations induce cell growth or inhibit apoptosis while class II mutations block differentiation, co-operating in inducing acute leukemia. This notion has been proven using a variety of mouse models, however most of recently found mutations are not typical class I/II mutations. Although some novel mutations have been found to functionally work as class I or II mutation in leukemogenesis, the classical class I/II theory seems to be too simple to explain the whole story. We here overview the molecular basis of hematological malignancies based on clinical and experimental results, and propose a new working hypothesis for leukemogenesis.
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Affiliation(s)
- Toshio Kitamura
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Naoko Watanabe-Okochi
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yutaka Enomoto
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Fumio Nakahara
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Toshihiko Oki
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yukiko Komeno
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Naoko Kato
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Noriko Doki
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tomoyuki Uchida
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuki Kagiyama
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Katsuhiro Togami
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kimihito C Kawabata
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Koutarou Nishimura
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yasutaka Hayashi
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Reina Nagase
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Makoto Saika
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tsuyoshi Fukushima
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Shuhei Asada
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuto Izawa
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Sayuri Horikawa
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tomofusa Fukuyama
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yosuke Tanaka
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ryoichi Ono
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Susumu Goyama
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Tetsuya Nosaka
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Jiro Kitaura
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Daichi Inoue
- Division of Cellular Therapy/Division of Stem Cell Signaling, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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